Breeding period in the mangrove crab Goniopsis cruentata (Decapoda: Grapsidae) in Northeast Brazil.

PubMed

de Lira, José Jonathas Pereira Rodrigues; Calado, Tereza Cristina dos Santos; de Araújo, Marina de Sá Leitão Câmara

2013-03-01

The brachyuran crabs are iteroparous species which present a high diversification of reproduction patterns, which may have evolved as a species-specific response to environmental conditions. Tropical species commonly present a year-round reproduction due to stable environment conditions. Goniopsis cruentata is a crab species widely distributed along the Western Atlantic, inhabiting practically every microhabitat in the mangrove ecosystem. The aim of the present study is to determine the breeding period of the crab Goniopsis cruentata in Northeastern Brazil and also to evaluate the influence of water salinity, rainfall and air and water temperature on it. A total of 71 ovigerous females, captured from August-2007 to July-2008, were used to assess the breeding period of this species. It was analyzed by the monthly proportion of ovigerous females. A correlation was applied to verify the influence of the abiotic factors on the breeding period. The present population bred seasonal-continuously with peaks in the dry period, which was not associated with monthly variations of salinity, rainfall and air and water temperatures. Therefore, according to statistical analyses, our hypothesis was refuted. However, breeding was intensified in the dry period, when salinity and temperatures were higher and rainfall was lower. We conclude that, even though breeding is not related to monthly variation of environmental factors, it occurs in periods of higher salinity and temperatures and lower rainfall.

Family living sets the stage for cooperative breeding and ecological resilience in birds

PubMed Central

Drobniak, Szymon M.; Nakagawa, Shinichi; Botero, Carlos A.

2017-01-01

Cooperative breeding is an extreme form of cooperation that evolved in a range of lineages, including arthropods, fish, birds, and mammals. Although cooperative breeding in birds is widespread and well-studied, the conditions that favored its evolution are still unclear. Based on phylogenetic comparative analyses on 3,005 bird species, we demonstrate here that family living acted as an essential stepping stone in the evolution of cooperative breeding in the vast majority of species. First, families formed by prolonging parent–offspring associations beyond nutritional independency, and second, retained offspring began helping at the nest. These findings suggest that assessment of the conditions that favor the evolution of cooperative breeding can be confounded if this process is not considered to include 2 steps. Specifically, phylogenetic linear mixed models show that the formation of families was associated with more productive and seasonal environments, where prolonged parent–offspring associations are likely to be less costly. However, our data show that the subsequent evolution of cooperative breeding was instead linked to environments with variable productivity, where helpers at the nest can buffer reproductive failure in harsh years. The proposed 2-step framework helps resolve current disagreements about the role of environmental forces in the evolution of cooperative breeding and better explains the geographic distribution of this trait. Many geographic hotspots of cooperative breeding have experienced a historical decline in productivity, suggesting that a higher proportion of family-living species could have been able to avoid extinction under harshening conditions through the evolution of cooperative breeding. These findings underscore the importance of considering the potentially different factors that drive different steps in the evolution of complex adaptations. PMID:28636615

Family living sets the stage for cooperative breeding and ecological resilience in birds.

PubMed

Griesser, Michael; Drobniak, Szymon M; Nakagawa, Shinichi; Botero, Carlos A

2017-06-01

Cooperative breeding is an extreme form of cooperation that evolved in a range of lineages, including arthropods, fish, birds, and mammals. Although cooperative breeding in birds is widespread and well-studied, the conditions that favored its evolution are still unclear. Based on phylogenetic comparative analyses on 3,005 bird species, we demonstrate here that family living acted as an essential stepping stone in the evolution of cooperative breeding in the vast majority of species. First, families formed by prolonging parent-offspring associations beyond nutritional independency, and second, retained offspring began helping at the nest. These findings suggest that assessment of the conditions that favor the evolution of cooperative breeding can be confounded if this process is not considered to include 2 steps. Specifically, phylogenetic linear mixed models show that the formation of families was associated with more productive and seasonal environments, where prolonged parent-offspring associations are likely to be less costly. However, our data show that the subsequent evolution of cooperative breeding was instead linked to environments with variable productivity, where helpers at the nest can buffer reproductive failure in harsh years. The proposed 2-step framework helps resolve current disagreements about the role of environmental forces in the evolution of cooperative breeding and better explains the geographic distribution of this trait. Many geographic hotspots of cooperative breeding have experienced a historical decline in productivity, suggesting that a higher proportion of family-living species could have been able to avoid extinction under harshening conditions through the evolution of cooperative breeding. These findings underscore the importance of considering the potentially different factors that drive different steps in the evolution of complex adaptations.

Evolutionary relationships in the sand-dwelling cichlid lineage of lake tanganyika suggest multiple colonization of rocky habitats and convergent origin of biparental mouthbrooding.

PubMed

Koblmüller, Stephan; Salzburger, Walter; Sturmbauer, Christian

2004-01-01

The cichlid species flock of Lake Tanganyika is comprised of seven seeding lineages that evolved in step with changes of the lake environment. One seeding lineage diversified into at least six lineages within a short period of time. Our study focuses on the diversification of one of these lineages, the Ectodini, comprising highly specialized, sand- and rock-dwelling species. They display two distinct breeding styles: maternal and biparental mouthbrooding. By analyzing three mtDNA gene segments in 30 species representing all 13 described genera, we show that the Ectodini rapidly diversified into four clades at the onset of their radiation. The monotypic genus Grammatotria is likely to represent the most ancestral split, followed by the almost contemporary origin of three additional clades, the first comprising the benthic genus Callochromis, the second comprising the benthic genera Asprotilapia, Xenotilapia, Enantiopus, and Microdontochromis, and the third comprising the semi-pelagic genera Ophthalmotilapia, Cardiopharynx, Cyathopharynx, Ectodus, Aulonocranus, Lestradea, and Cunningtonia. Our study confirms the benthic and sand-dwelling life-style as ancestral. Rocky habitats were colonized independently in the Xenotilapia- and Ophthalmotilapia-clade. The Xenotilapia-clade comprises both maternal and biparental mouthbrooders. Their mode of breeding appears to be highly plastic: biparental mouthbrooding either evolved once in the common ancestor of the clade, to be reverted at least three times, or evolved at least five times independently from a maternally mouthbrooding ancestor. Furthermore, the genera Xenotilapia, Microdontochromis, Lestradea, and Ophthalmotilapia appeared paraphyletic in our analyses, suggesting the need of taxonomic revision.

Migration and the evolution of duetting in songbirds.

PubMed

Logue, David M; Hall, Michelle L

2014-05-07

Many groups of animals defend shared resources with coordinated signals. The best-studied of these signals are the vocal duets produced by mated pairs of birds. Duets are believed to be more common among tropical-breeding species, but a comprehensive test of this hypothesis is lacking, and the mechanisms that generate latitudinal patterns in duetting are not known. We used a stratified sample of 372 songbird species to conduct the first broad-scale, phylogenetically explicit analysis of duet evolution. We found that duetting evolves in association with the absence of migration, but not with sexual monochromatism or tropical breeding. We conclude that the evolution of migration exerts a major influence on the evolution of duetting. The perceived association between tropical breeding and duetting may be a by-product of the migration-duetting relationship. Migration reduces the average duration of partnerships, potentially reducing the benefits of cooperative behaviour, including duetting. Ultimately, the evolution of coordinated resource-defence signals in songbirds may be driven by ecological conditions that favour sedentary lifestyles and social stability.

Migration and the evolution of duetting in songbirds

PubMed Central

Logue, David M.; Hall, Michelle L.

2014-01-01

Many groups of animals defend shared resources with coordinated signals. The best-studied of these signals are the vocal duets produced by mated pairs of birds. Duets are believed to be more common among tropical-breeding species, but a comprehensive test of this hypothesis is lacking, and the mechanisms that generate latitudinal patterns in duetting are not known. We used a stratified sample of 372 songbird species to conduct the first broad-scale, phylogenetically explicit analysis of duet evolution. We found that duetting evolves in association with the absence of migration, but not with sexual monochromatism or tropical breeding. We conclude that the evolution of migration exerts a major influence on the evolution of duetting. The perceived association between tropical breeding and duetting may be a by-product of the migration–duetting relationship. Migration reduces the average duration of partnerships, potentially reducing the benefits of cooperative behaviour, including duetting. Ultimately, the evolution of coordinated resource-defence signals in songbirds may be driven by ecological conditions that favour sedentary lifestyles and social stability. PMID:24619447

USE OF NEUTRON IRRADIATIONS IN THE BROOKHAVEN MUTATIONS PROGRAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miksche, J.P.; Shapiro, S.

1963-01-01

Many plant species were irradiated with x rays, thermal and fast neutrons, andd gamma radiation during the past 10 yr of the cooperative mutations program and adjunct mutation breeding program. Four major concepts and/ or approaches related to the use of mutagenic agents in plant breeding that have evolved are discussed. It was concluded that outcrossing between treated and nontreated populations must be reckoned with, and consequently the two populations should be separated before a true measure of mutation induction can be ascertained; chromosome rearrangement studies are useful, with particular emphasis on inducing disease resistance; work concerned with tissue reorgandizationmore » and rearrangement as related to chimera production and basic understanding of tissue ontogeny, particularly with fruit crops andd horticultural crops is promising; and the effectiveness of responses of plant tissues to neutrons and other mutagenic agents is extremely variable and more basic work is needed before the full potentialities of mutation breeding as a tool in crop improvement can be appreciated. (auth)« less

Protracted treatment with corticosterone reduces breeding success in a long-lived bird.

PubMed

Nelson, Bethany F; Daunt, Francis; Monaghan, Pat; Wanless, Sarah; Butler, Adam; Heidinger, Britt J; Newell, Mark; Dawson, Alistair

2015-01-01

Determining the physiological mechanisms underpinning life-history decisions is essential for understanding the constraints under which life-history strategies can evolve. In long-lived species, where the residual reproductive value of breeders is high, adult survival is a key contributor to lifetime reproductive success. We therefore expect that when adult survival is compromised during reproduction, mechanisms will evolve to redirect resources away from reproduction, with implications for reproductive hormones, adult body mass, nest attendance behaviour and breeding success. We investigated whether manipulating corticosterone, to simulate exposure to an environmental stressor, affected the secretion of prolactin and breeding success in the black-legged kittiwake Rissa tridactyla. We used implanted Alzet® osmotic pumps to administer corticosterone to incubating kittiwakes at a constant rate over a period of approximately 8days. Manipulated birds were compared with sham implanted birds and control birds, which had no implants. There was no significant difference in the body mass of captured individuals at the time of implantation and implant removal. Corticosterone-implanted males showed lower nest attendance during the chick rearing period compared to sham-implanted males; the opposite pattern was found in females. Corticosterone treated birds showed a marginally significant reduction in breeding success compared to sham-implanted individuals, with all failures occurring at least 1week after implant removal. However, prolactin concentrations at implant removal were not significantly different from initial values. We were unable to measure the profile of change in corticosterone during the experiment. However, our results suggest a delayed effect of elevated corticosterone on breeding success rather than an immediate suppression of prolactin concentrations causing premature failure. Copyright © 2014 Elsevier Inc. All rights reserved.

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

PubMed

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Social organization of the Alaotran gentle lemur (Hapalemur griseus alaotrensis).

PubMed

Mutschler, T; Nievergelt, C M; Feistner, A T

2000-01-01

Knowledge of the social organization of lemurs is still limited for most species. Where there is sufficient information, it has been shown that lemur social organization differs in essential points from that of other primates. In the field study reported here, demographic structure and life-history processes were investigated in order to characterize the social organization of the Alaotran gentle lemur (Hapalemur griseus alaotrensis). Data were obtained through captures and observations. Alaotran gentle lemurs were found in small groups of up to nine individuals. Although most groups contained just one breeding female, a substantial proportion of groups (35%) had two breeding females. Therefore, Alaotran gentle lemurs cannot be classed as being organized in monogamous family groups. An extended birth season was found, and groups with two breeding females had significantly higher breeding output per adult than groups with a single adult female. Limited data suggest that females emigrate from their natal group while still subadult, whereas males can stay in the natal group until they are fully grown and disperse as adults. Variability in group composition, significantly higher reproductive output per adult in groups with two breeding females, and delayed dispersal of males suggest that Alaotran gentle lemurs pursue a resource-defense mating strategy, rather than a female-defense mating strategy. The suggestion that extant social lemurs may have evolved from a monogamous system, could explain the differences between lemur social systems and those of other primates.

Effects of a social cue on reproductive development and pre-alternate molt in seasonally breeding migrant and resident female songbirds (Zonotrichia leucophrys).

PubMed

Chmura, Helen E; Meddle, Simone L; Wingfield, John C; Hahn, Thomas P

2017-08-15

To time reproduction optimally, birds have evolved diverse mechanisms by which they respond to environmental changes that help them anticipate and prepare for the breeding season. While residents initiate reproductive preparation and breed in the same geographic location, migrant birds simultaneously prepare for breeding and migration far from their breeding grounds. As a result, it is hypothesized that migrant and resident birds use environmental cues differently to prepare to breed and that there is adaptive specialization in mechanisms regulating reproductive preparation. Specifically, residents are expected to rely more on non-photic cues (e.g. food, temperature, social cues) than migrants. We tested this general prediction using a social cue manipulation. First, we compared the effects of subspecies-appropriate recorded male song on reproductive development in migrants and residents on a naturally increasing photoperiod. Second, we tested the sensitivity of migrant-specific life history events (fattening and pre-alternate molt) to song treatment. After 82 days, residents had higher luteinizing hormone and greater ovarian development than migrants, but song treatment had no effect on these metrics in either subspecies. Song advanced pre-alternate molt but had no effect on fattening in migrants. While our study does not support specialization in social cue use in migrants and residents, it is consistent with findings in the literature of specialization in photoperiodic response. It also demonstrates for the first time that social cues can influence molt in a migrant species. Additional findings from a pilot study looking at responses to a live male suggest it is important to test other kinds of social cues. © 2017. Published by The Company of Biologists Ltd.

Future animal improvement programs applied to global populations

USDA-ARS?s Scientific Manuscript database

Breeding programs evolved gradually from within-herd phenotypic selection to local and regional cooperatives to national evaluations and now international evaluations. In the future, breeders may adapt reproductive, computational, and genomic methods to global populations as easily as with national ...

The effects of stress and sex on selection, genetic covariance, and the evolutionary response.

PubMed

Holman, L; Jacomb, F

2017-10-01

The capacity of a population to adapt to selection (evolvability) depends on whether the structure of genetic variation permits the evolution of fitter trait combinations. Selection, genetic variance and genetic covariance can change under environmental stress, and males and females are not genetically independent, yet the combined effects of stress and dioecy on evolvability are not well understood. Here, we estimate selection, genetic (co)variance and evolvability in both sexes of Tribolium castaneum flour beetles under stressful and benign conditions, using a half-sib breeding design. Although stress uncovered substantial latent heritability, stress also affected genetic covariance, such that evolvability remained low under stress. Sexual selection on males and natural selection on females favoured a similar phenotype, and there was positive intersex genetic covariance. Consequently, sexual selection on males augmented adaptation in females, and intralocus sexual conflict was weak or absent. This study highlights that increased heritability does not necessarily increase evolvability, suggests that selection can deplete genetic variance for multivariate trait combinations with strong effects on fitness, and tests the recent hypothesis that sexual conflict is weaker in stressful or novel environments. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Allopreening in birds is associated with parental cooperation over offspring care and stable pair bonds across years.

PubMed

Kenny, Elspeth; Birkhead, Tim R; Green, Jonathan P

2017-01-01

Individuals of many species form bonds with their breeding partners, yet the mechanisms maintaining these bonds are poorly understood. In birds, allopreening is a conspicuous feature of interactions between breeding partners and has been hypothesized to play a role in strengthening and maintaining pair bonds within and across breeding attempts. Many avian species, however, do not allopreen and the relationship between allopreening and pair bonding across species remains unexplored. In a comparative analysis of allopreening and pair bond behavior, we found that allopreening between breeding partners was more common among species where parents cooperate to rear offspring. The occurrence of allopreening was also associated with an increased likelihood that partners would remain together over successive breeding seasons. However, there was no strong evidence for an association between allopreening and sexual fidelity within seasons or time spent together outside the breeding season. Allopreening between partners was also no more common in colonial or cooperatively breeding species than in solitary species. Analyses of evolutionary transitions indicated that allopreening evolved from an ancestral state of either high parental cooperation or high partner retention, and we discuss possible explanations for this. Overall, our results are consistent with an important role for allopreening in the maintenance of avian pair bonds.

Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance.

PubMed

Taye, Mengistie; Lee, Wonseok; Caetano-Anolles, Kelsey; Dessie, Tadelle; Hanotte, Olivier; Mwai, Okeyo Ally; Kemp, Stephen; Cho, Seoae; Oh, Sung Jong; Lee, Hak-Kyo; Kim, Heebal

2017-12-01

As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light-colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross-population composite likelihood ratio (XP-CLR) and cross-population extended haplotype homozygosity (XP-EHH) statistical methods. We identified 296 (XP-EHH) and 327 (XP-CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study. © 2017 Japanese Society of Animal Science.

DLA-DRB1, DQA1, and DQB1 alleles and haplotypes in North American Gray Wolves.

PubMed

Kennedy, Lorna J; Angles, John M; Barnes, Annette; Carmichael, Lindsey E; Radford, Alan D; Ollier, William E R; Happ, George M

2007-01-01

The canine major histocompatibility complex contains highly polymorphic genes, many of which are critical in regulating immune response. Since domestic dogs evolved from Gray Wolves (Canis lupus), common DLA class II alleles should exist. Sequencing was used to characterize 175 Gray Wolves for DLA class II alleles, and data from 1856 dogs, covering 85 different breeds of mostly European origin, were available for comparison. Within wolves, 28 new alleles were identified, all occurring in at least 2 individuals. Three DLA-DRB1, 8 DLA-DQA1, and 6 DLA-DQB1 alleles also identified in dogs were present. Twenty-eight haplotypes were identified, of which 2 three-locus haplotypes, and many DLA-DQA1/DQB1 haplotypes, are also found in dogs. The wolves studied had relatively few dog DLA alleles and may therefore represent a remnant population descended from Asian wolves. The single European wolf included carried a haplotype found in both these North American wolves and in many dog breeds. Furthermore, one wolf DQB1 allele has been found in Shih Tzu, a breed of Asian origin. These data suggest that the wolf ancestors of Asian and European dogs may have had different gene pools, currently reflected in the DLA alleles present in dog breeds.

A 'slow pace of life' in Australian old-endemic passerine birds is not accompanied by low basal metabolic rates.

PubMed

Bech, Claus; Chappell, Mark A; Astheimer, Lee B; Londoño, Gustavo A; Buttemer, William A

2016-05-01

Life history theory suggests that species experiencing high extrinsic mortality rates allocate more resources toward reproduction relative to self-maintenance and reach maturity earlier ('fast pace of life') than those having greater life expectancy and reproducing at a lower rate ('slow pace of life'). Among birds, many studies have shown that tropical species have a slower pace of life than temperate-breeding species. The pace of life has been hypothesized to affect metabolism and, as predicted, tropical birds have lower basal metabolic rates (BMR) than temperate-breeding birds. However, many temperate-breeding Australian passerines belong to lineages that evolved in Australia and share 'slow' life-history traits that are typical of tropical birds. We obtained BMR from 30 of these 'old-endemics' and ten sympatric species of more recently arrived passerine lineages (derived from Afro-Asian origins or introduced by Europeans) with 'faster' life histories. The BMR of 'slow' temperate-breeding old-endemics was indistinguishable from that of new-arrivals and was not lower than the BMR of 'fast' temperate-breeding non-Australian passerines. Old-endemics had substantially smaller clutches and longer maximal life spans in the wild than new arrivals, but neither clutch size nor maximum life span was correlated with BMR. Our results suggest that low BMR in tropical birds is not functionally linked to their 'slow pace of life' and instead may be a consequence of differences in annual thermal conditions experienced by tropical versus temperate species.

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies.

PubMed

Gopal, Murali; Gupta, Alka

2016-01-01

" No plant is an island too …" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.

MaizeGDB: everything old is new again! [abstract

USDA-ARS?s Scientific Manuscript database

The focus of genetic, genomic, and breeding research evolves over time, making it necessary to continually redefine the paradigm for data access and data analysis tools. Here we report the reinvention of MaizeGDB, the maize genetics and genomics database, to meet maize researchers’ ever changing nee...

Host responses to interspecific brood parasitism: a by-product of adaptations to conspecific parasitism?

PubMed Central

2014-01-01

Background Why have birds evolved the ability to reject eggs? Typically, foreign egg discrimination is interpreted as evidence that interspecific brood parasitism (IP) has selected for the host’s ability to recognize and eliminate foreign eggs. Fewer studies explore the alternative hypothesis that rejection of interspecific eggs is a by-product of host defenses, evolved against conspecific parasitism (CP). We performed a large scale study with replication across taxa (two congeneric Turdus thrushes), space (populations), time (breeding seasons), and treatments (three types of experimental eggs), using a consistent design of egg rejection experiments (n = 1057 nests; including controls), in areas with potential IP either present (Europe; native populations) or absent (New Zealand; introduced populations). These comparisons benefited from the known length of allopatry (one and a half centuries), with no gene flow between native and introduced populations, which is rarely available in host-parasite systems. Results Hosts rejected CP at unusually high rates for passerines (up to 60%). CP rejection rates were higher in populations with higher conspecific breeding densities and no risks of IP, supporting the CP hypothesis. IP rejection rates did not covary geographically with IP risk, contradicting the IP hypothesis. High egg rejection rates were maintained in the relatively long-term isolation from IP despite non-trivial rejection costs and errors. Conclusions These egg rejection patterns, combined with recent findings that these thrushes are currently unsuitable hosts of the obligate parasitic common cuckoo (Cuculus canorus), are in agreement with the hypothesis that the rejection of IP is a by-product of fine-tuned egg discrimination evolved due to CP. Our study highlights the importance of considering both IP and CP simultaneously as potential drivers in the evolution of egg discrimination, and illustrates how populations introduced to novel ecological contexts can provide critical insights into brood parasite-host coevolution. PMID:24834103

Host responses to interspecific brood parasitism: a by-product of adaptations to conspecific parasitism?

PubMed

Samas, Peter; Hauber, Mark E; Cassey, Phillip; Grim, Tomas

2014-01-01

Why have birds evolved the ability to reject eggs? Typically, foreign egg discrimination is interpreted as evidence that interspecific brood parasitism (IP) has selected for the host's ability to recognize and eliminate foreign eggs. Fewer studies explore the alternative hypothesis that rejection of interspecific eggs is a by-product of host defenses, evolved against conspecific parasitism (CP). We performed a large scale study with replication across taxa (two congeneric Turdus thrushes), space (populations), time (breeding seasons), and treatments (three types of experimental eggs), using a consistent design of egg rejection experiments (n = 1057 nests; including controls), in areas with potential IP either present (Europe; native populations) or absent (New Zealand; introduced populations). These comparisons benefited from the known length of allopatry (one and a half centuries), with no gene flow between native and introduced populations, which is rarely available in host-parasite systems. Hosts rejected CP at unusually high rates for passerines (up to 60%). CP rejection rates were higher in populations with higher conspecific breeding densities and no risks of IP, supporting the CP hypothesis. IP rejection rates did not covary geographically with IP risk, contradicting the IP hypothesis. High egg rejection rates were maintained in the relatively long-term isolation from IP despite non-trivial rejection costs and errors. These egg rejection patterns, combined with recent findings that these thrushes are currently unsuitable hosts of the obligate parasitic common cuckoo (Cuculus canorus), are in agreement with the hypothesis that the rejection of IP is a by-product of fine-tuned egg discrimination evolved due to CP. Our study highlights the importance of considering both IP and CP simultaneously as potential drivers in the evolution of egg discrimination, and illustrates how populations introduced to novel ecological contexts can provide critical insights into brood parasite-host coevolution.

Temporal flexibility of reproduction in temperate-breeding dabbling ducks

USGS Publications Warehouse

Krapu, Gary L.

2000-01-01

I compared nesting intervals during three consecutive years in five species of temperate-nesting dabbling ducks (Mallard [Anas platyrhynchos], Northern Pintail [Anas acuta], Northern Shoveler [Anas clypeata], Blue-winged Teal [Anas discors], Gadwall [Anas strepera]) and assessed whether differences existed in timing of refractoriness. Most nesting by females of all five species ended by the summer solstice. Nesting ended earliest for Northern Shovelers and Northern Pintails and latest for Gadwalls. Some Mallards, Blue-winged Teal, and Gadwalls continued to nest into mid- and late summer, whereas Northern Shovelers and Northern pintails did not. Mallards, Blue-winged Teal, and Gadwalls accounted for 99% (81 of 82) of flightless broods resulting from nests initiated during mid- or late summer in North Dakota and 98% (58 of 59) of flightless juveniles shot on or after 1 October by a random sample of duck hunters from across the United States. Early cessation of breeding by Northern Shovelers may have evolved in response to the species' limited flexibility in diet. Photorefractory mechanisms that limit most breeding to spring presumably evolved in response to severe constraints on reproductive success when nesting continued through summer(e.g. mortality of late-hatched young and molting females due to low temperatures). Interspecific differences in photosensitivity may account for variation in timing of cessation of nesting in late spring, but controlled experiments are needed to assess the possible role of non-photic influences. My results suggest that the refractory mechanisms controlling length of the breeding in temperate-nesting dabbling ducks are more varied and complex than previously thought, with non-photic influences (e.g. water conditions, food availability, food quality) having a larger role than indicated by earlier research.

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica.

PubMed

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.

Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

PubMed Central

Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

2015-01-01

Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

How cooperatively breeding birds identify relatives and avoid incest: New insights into dispersal and kin recognition.

PubMed

Riehl, Christina; Stern, Caitlin A

2015-12-01

Cooperative breeding in birds typically occurs when offspring - usually males - delay dispersal from their natal group, remaining with the family to help rear younger kin. Sex-biased dispersal is thought to have evolved in order to reduce the risk of inbreeding, resulting in low relatedness between mates and the loss of indirect fitness benefits for the dispersing sex. In this review, we discuss several recent studies showing that dispersal patterns are more variable than previously thought, often leading to complex genetic structure within cooperative avian societies. These empirical findings accord with recent theoretical models suggesting that sex- biased dispersal is neither necessary, nor always sufficient, to prevent inbreeding. The ability to recognize relatives, primarily by learning individual or group-specific vocalizations, may play a more important role in incest avoidance than currently appreciated. © 2015 WILEY Periodicals, Inc.

Evolution of uni- and bifactorial sexual compatibility systems in fungi

PubMed Central

Nieuwenhuis, B P S; Billiard, S; Vuilleumier, S; Petit, E; Hood, M E; Giraud, T

2013-01-01

Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems. PMID:23838688

Variation in chromosome number and breeding systems: implications for diversification in Pachycereus pringlei (Cactaceae).

PubMed

Gutiérrez-Flores, Carina; la Luz, José L León-de; León, Francisco J García-De; Cota-Sánchez, J Hugo

2018-01-01

Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP). However, several important evolutionary questions, such as the distribution of chromosome numbers and whether the diploid condition is dominant over a potential polyploid condition driving the evolution and diversity in floral morphology and breeding systems in this cactus, are still unclear. In this study, we determined chromosome numbers in 11 localities encompassing virtually the entire geographic range of distribution of P. pringlei . Our data revealed the first diploid (2n = 22) count in this species restricted to the hermaphroditic populations of Catalana (ICA) and Cerralvo (ICE) Islands, whereas the tetraploid (2n = 44) condition is consistently distributed throughout the BCP and mainland Sonora populations distinguished by a non-hermaphroditic breeding system. These results validate a wider distribution of polyploid relative to diploid individuals and a shift in breeding systems coupled with polyploidisation. Considering that the diploid base number and hermaphroditism are the proposed ancestral conditions in Cactaceae, we suggest that ICE and ICA populations represent the relicts of a southern diploid ancestor from which both polyploidy and unisexuality evolved in mainland BCP, facilitating the northward expansion of this species. This cytogeographic distribution in conjunction with differences in floral attributes suggests the distinction of the diploid populations as a new taxonomic entity. We suggest that chromosome doubling in conjunction with allopatric distribution, differences in neutral genetic variation, floral traits, and breeding systems has driven the reproductive isolation, evolution, and diversification of this columnar cactus.

Variation in chromosome number and breeding systems: implications for diversification in Pachycereus pringlei (Cactaceae)

PubMed Central

Gutiérrez-Flores, Carina; la Luz, José L. León-de; León, Francisco J. García-De; Cota-Sánchez, J. Hugo

2018-01-01

Abstract Polyploidy, the possession of more than two sets of chromosomes, is a major biological process affecting plant evolution and diversification. In the Cactaceae, genome doubling has also been associated with reproductive isolation, changes in breeding systems, colonization ability, and speciation. Pachycereus pringlei (S. Watson, 1885) Britton & Rose, 1909, is a columnar cactus that has long drawn the attention of ecologists, geneticists, and systematists due to its wide distribution range and remarkable assortment of breeding systems in the Mexican Sonoran Desert and the Baja California Peninsula (BCP). However, several important evolutionary questions, such as the distribution of chromosome numbers and whether the diploid condition is dominant over a potential polyploid condition driving the evolution and diversity in floral morphology and breeding systems in this cactus, are still unclear. In this study, we determined chromosome numbers in 11 localities encompassing virtually the entire geographic range of distribution of P. pringlei. Our data revealed the first diploid (2n = 22) count in this species restricted to the hermaphroditic populations of Catalana (ICA) and Cerralvo (ICE) Islands, whereas the tetraploid (2n = 44) condition is consistently distributed throughout the BCP and mainland Sonora populations distinguished by a non-hermaphroditic breeding system. These results validate a wider distribution of polyploid relative to diploid individuals and a shift in breeding systems coupled with polyploidisation. Considering that the diploid base number and hermaphroditism are the proposed ancestral conditions in Cactaceae, we suggest that ICE and ICA populations represent the relicts of a southern diploid ancestor from which both polyploidy and unisexuality evolved in mainland BCP, facilitating the northward expansion of this species. This cytogeographic distribution in conjunction with differences in floral attributes suggests the distinction of the diploid populations as a new taxonomic entity. We suggest that chromosome doubling in conjunction with allopatric distribution, differences in neutral genetic variation, floral traits, and breeding systems has driven the reproductive isolation, evolution, and diversification of this columnar cactus. PMID:29675137

The evolution of reproductive diversity in Afrobatrachia: A phylogenetic comparative analysis of an extensive radiation of African frogs.

PubMed

Portik, Daniel M; Blackburn, David C

2016-09-01

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift toward using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Evolutionary transitions towards eusociality in snapping shrimps.

PubMed

Chak, Solomon Tin Chi; Duffy, J Emmett; Hultgren, Kristin M; Rubenstein, Dustin R

2017-03-20

Animal social organization varies from complex societies where reproduction is dominated by a single individual (eusociality) to those where reproduction is more evenly distributed among group members (communal breeding). Yet, how simple groups transition evolutionarily to more complex societies remains unclear. Competing hypotheses suggest that eusociality and communal breeding are alternative evolutionary endpoints, or that communal breeding is an intermediate stage in the transition towards eusociality. We tested these alternative hypotheses in sponge-dwelling shrimps, Synalpheus spp. Although species varied continuously in reproductive skew, they clustered into pair-forming, communal and eusocial categories based on several demographic traits. Evolutionary transition models suggested that eusocial and communal species are discrete evolutionary endpoints that evolved independently from pair-forming ancestors along alternative paths. This 'family-centred' origin of eusociality parallels observations in insects and vertebrates, reinforcing the role of kin selection in the evolution of eusociality and suggesting a general model of animal social evolution.

What can be Learned from Silage Breeding Programs?

NASA Astrophysics Data System (ADS)

Lorenz, Aaron J.; Coors, James G.

Improving the quality of cellulosic ethanol feedstocks through breeding and genetic manipulation could significantly impact the economics of this industry. Attaining this will require comprehensive and rapid characterization of large numbers of samples. There are many similarities between improving corn silage quality for dairy production and improving feedstock quality for cellulosic ethanol. It was our objective to provide insight into what is needed for genetic improvement of cellulosic feedstocks by reviewing the development and operation of a corn silage breeding program. We discuss the evolving definition of silage quality and relate what we have learned about silage quality to what is needed for measuring and improving feedstock quality. In addition, repeatability estimates of corn stover traits are reported for a set of hybrids. Repeatability of theoretical ethanol potential measured by near-infrared spectroscopy is high, suggesting that this trait may be easily improved through breeding. Just as cell wall digestibility has been factored into the latest measurements of silage quality, conversion efficiency should be standardized and included in indices of feedstock quality to maximize overall, economical energy availability.

African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

PubMed Central

Mwai, Okeyo; Hanotte, Olivier; Kwon, Young-Jun; Cho, Seoae

2015-01-01

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers. PMID:26104394

When the ball is in the female's court: How the scramble-competition mating system of the North American red squirrel has shaped male physiology and testosterone dynamics.

PubMed

Boonstra, Rudy; Dušek, Adam; Lane, Jeffrey E; Boutin, Stan

2017-10-01

Male reproductive success in most mammals is determined by their success in direct inter-male competition through aggression and conflict, resulting in female-defense mating systems being predominant. This is linked to male testosterone levels and its dynamics. However, in certain environments, a scramble-competition mating system has evolved, where female reproductive behavior takes precedence and male testosterone dynamics are unlikely to be related to inter-male competition. We studied the North American red squirrel (Tamiasciurus hudsonicus), a species with a well-established scramble-competition system. Using an ACTH hormonal challenge protocol as a proxy for competitive interactions, we compared the testosterone dynamics in breeding males in late winter with that in nonbreeding males in late spring in the Yukon. To gain an integrated picture of their physiological state, we also assessed changes in their stress response, body mass, energy mobilization, and indices of immune function. Testosterone levels at the base bleed were high in breeding males (2.72ng/mL) and virtually absent in non-breeding males (0.04ng/mL). Breeding males were in better condition (heavier body mass, higher hematocrit, and higher erythrocytes), had higher indices of immune function (neutrophil:lymphocyte ratio), but a similar ability to mobilize energy (glucose) compared with non-breeding males. Though total cortisol was higher in non-breeding males, free cortisol was twice as high in breeding males as their corticosteroid binding globulin levels were half as high. In response to the ACTH challenge, testosterone levels in breeding males declined 49% over the first hour and increased 36% over the next hour; in non-breeding males levels showed no change. Free cortisol increased only modestly (26% in breeding males; 23% in non-breeding males). Glucose levels changed similarly in breeding and nonbreeding males, declining for the first 30min and then increasing for the next 60min. Thus, testosterone and components of the stress axis function in a profoundly different manner in male red squirrels than in males of mammals with female-defense mating systems. There are four probable interrelated reasons for these adaptations in male red squirrels: the marginal benefits of each mating, the constraints of mate searching away from their own resource-based territories, energy mobilization in a harsh environment, and a long life span. Copyright © 2017 Elsevier Inc. All rights reserved.

Control of the annual cycle in birds: endocrine constraints and plasticity in response to ecological variability.

PubMed

Dawson, Alistair

2008-05-12

This paper reviews information from ecological and physiological studies to assess how extrinsic factors can modulate intrinsic physiological processes. The annual cycle of birds is made up of a sequence of life-history stages: breeding, moult and migration. Each stage has evolved to occur at the optimum time and to last for the whole duration of time available. Some species have predictable breeding seasons, others are more flexible and some breed opportunistically in response to unpredictable food availability. Photoperiod is the principal environmental cue used to time each stage, allowing birds to adapt their physiology in advance of predictable environmental changes. Physiological (neuroendocrine and endocrine) plasticity allows non-photoperiodic cues to modulate timing to enable individuals to cope with, and benefit from, short-term environmental variability. Although the timing and duration of the period of full gonadal maturation is principally controlled by photoperiod, non-photoperiodic cues, such as temperature, rainfall or food availability, could potentially modulate the exact time of breeding either by fine-tuning the time of egg-laying within the period of full gonadal maturity or, more fundamentally, by modulating gonadal maturation and/or regression. The timing of gonadal regression affects the time of the start of moult, which in turn may affect the duration of the moult. There are many areas of uncertainty. Future integrated studies are required to assess the scope for flexibility in life-history strategies as this will have a critical bearing on whether birds can adapt sufficiently rapidly to anthropogenic environmental changes, in particular climate change.

Territory choice during the breeding tenure of male sedge warblers.

PubMed

Zając, Tadeusz; Bielański, Wojciech; Solarz, Wojciech

2011-12-01

A territorial male can shift the location of its territory from year to year in order to increase its quality. The male can base its decision on environmental cues or else on its breeding experiences (when territory shift is caused by breeding failure in previous seasons). We tested these possible mechanisms of territory choice in the sedge warbler (Acrocephalus schoenobaenus), a territorial migrating passerine that occupies wetlands. This species bases its territory choices on an environmental cue: tall wetland vegetation cover. We found that the magnitude of territory quality improvement between seasons (measured as the area of tall wetland vegetation) increased throughout the early stages of a male's breeding career as a result of territory shifts dependent on the earliness of arrival. The distance the territory was shifted between seasons depended negatively on the previous year's territory quality and, less clearly, on the previous year's mating success. On the other hand, previous mating or nesting success had no influence on territory quality improvement between seasons as measured in terms of vegetation. The results imply that tall wetland vegetation is a long-term, effective environmental cue and that a preference for territories in which this type of landcover prevails has evolved into a rigid behavioral mechanism, supplemented by short-term individual experiences of breeding failure.

Breeding for resistance to gastrointestinal nematodes - the potential in low-input/output small ruminant production systems.

PubMed

Zvinorova, P I; Halimani, T E; Muchadeyi, F C; Matika, O; Riggio, V; Dzama, K

2016-07-30

The control of gastrointestinal nematodes (GIN) is mainly based on the use of drugs, grazing management, use of copper oxide wire particles and bioactive forages. Resistance to anthelmintic drugs in small ruminants is documented worldwide. Host genetic resistance to parasites, has been increasingly used as a complementary control strategy, along with the conventional intervention methods mentioned above. Genetic diversity in resistance to GIN has been well studied in experimental and commercial flocks in temperate climates and more developed economies. However, there are very few report outputs from the more extensive low-input/output smallholder systems in developing and emerging countries. Furthermore, results on quantitative trait loci (QTL) associated with nematode resistance from various studies have not always been consistent, mainly due to the different nematodes studied, different host breeds, ages, climates, natural infections versus artificial challenges, infection level at sampling periods, among others. The increasing use of genetic markers (Single Nucleotide Polymorphisms, SNPs) in GWAS or the use of whole genome sequence data and a plethora of analytic methods offer the potential to identify loci or regions associated nematode resistance. Genomic selection as a genome-wide level method overcomes the need to identify candidate genes. Benefits in genomic selection are now being realised in dairy cattle and sheep under commercial settings in the more advanced countries. However, despite the commercial benefits of using these tools, there are practical problems associated with incorporating the use of marker-assisted selection or genomic selection in low-input/output smallholder farming systems breeding schemes. Unlike anthelmintic resistance, there is no empirical evidence suggesting that nematodes will evolve rapidly in response to resistant hosts. The strategy of nematode control has evolved to a more practical manipulation of host-parasite equilibrium in grazing systems by implementation of various strategies, in which improvement of genetic resistance of small ruminant should be included. Therefore, selection for resistant hosts can be considered as one of the sustainable control strategy, although it will be most effective when used to complement other control strategies such as grazing management and improving efficiency of anthelmintics currently. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Fungus cultivation by ambrosia beetles: Behavior and laboratory breeding success in three Xyleborine species

Treesearch

Peter Biedermann; Kier Klepzig; Taborsky Michael

2009-01-01

Fungus cultivation by ambrosia beetles is one of the four independently evolved cases of agriculture known in animals. Such cultivation is most advanced in the highly social subtribe Xyleborina (Scolytinae), which is characterized by haplodiploidy and extreme levels of inbreeding. Despite their ubiquity in forests worldwide, the behavior of these beetles remains poorly...

Migration confers winter survival benefits in a partially migratory songbird

PubMed Central

Zúñiga, Daniel; Gager, Yann; Kokko, Hanna; Fudickar, Adam Michael; Schmidt, Andreas; Naef-Daenzer, Beat; Wikelski, Martin

2017-01-01

To evolve and to be maintained, seasonal migration, despite its risks, has to yield fitness benefits compared with year-round residency. Empirical data supporting this prediction have remained elusive in the bird literature. To test fitness related benefits of migration, we studied a partial migratory population of European blackbirds (Turdus merula) over 7 years. Using a combination of capture-mark-recapture and radio telemetry, we compared survival probabilities between migrants and residents estimated by multi-event survival models, showing that migrant blackbirds had 16% higher probability to survive the winter compared to residents. A subsequent modelling exercise revealed that residents should have 61.25% higher breeding success than migrants, to outweigh the survival costs of residency. Our results support theoretical models that migration should confer survival benefits to evolve, and thus provide empirical evidence to understand the evolution and maintenance of migration. PMID:29157357

Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat.

PubMed

Mao, Donghai; Yu, Li; Chen, Dazhou; Li, Lanying; Zhu, Yuxing; Xiao, Yeqing; Zhang, Dechun; Chen, Caiyan

2015-07-01

Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

Evolutionary genomics of dog domestication.

PubMed

Wayne, Robert K; vonHoldt, Bridgett M

2012-02-01

We review the underlying principles and tools used in genomic studies of domestic dogs aimed at understanding the genetic changes that have occurred during domestication. We show that there are two principle modes of evolution within dogs. One primary mode that accounts for much of the remarkable diversity of dog breeds is the fixation of discrete mutations of large effect in individual lineages that are then crossed to various breed groupings. This transfer of mutations across the dog evolutionary tree leads to the appearance of high phenotypic diversity that in actuality reflects a small number of major genes. A second mechanism causing diversification involves the selective breeding of dogs within distinct phenotypic or functional groups, which enhances specific group attributes such as heading or tracking. Such progressive selection leads to a distinct genetic structure in evolutionary trees such that functional and phenotypic groups cluster genetically. We trace the origin of the nuclear genome in dogs based on haplotype-sharing analyses between dogs and gray wolves and show that contrary to previous mtDNA analyses, the nuclear genome of dogs derives primarily from Middle Eastern or European wolves, a result more consistent with the archeological record. Sequencing analysis of the IGF1 gene, which has been the target of size selection in small breeds, further supports this conclusion. Finally, we discuss how a black coat color mutation that evolved in dogs has transformed North American gray wolf populations, providing a first example of a mutation that appeared under domestication and selectively swept through a wild relative.

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China.

PubMed

Jia, Guanqing; Liu, Xiaotong; Schnable, James C; Niu, Zhengang; Wang, Chunfang; Li, Yuhui; Wang, Shujun; Wang, Suying; Liu, Jinrong; Guo, Erhu; Zhi, Hui; Diao, Xianmin

2015-01-01

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

PubMed Central

Schnable, James C.; Niu, Zhengang; Wang, Chunfang; Li, Yuhui; Wang, Shujun; Wang, Suying; Liu, Jinrong; Guo, Erhu; Zhi, Hui; Diao, Xianmin

2015-01-01

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species. PMID:25932649

Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny

PubMed Central

2013-01-01

Background The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information. Results The increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage. Conclusions A large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species. PMID:23597112

Genetic evidence supports song learning in the three-wattled bellbird Procnias tricarunculata (Cotingidae).

PubMed

Saranathan, Vinodkumar; Hamilton, Deborah; Powell, George V N; Kroodsma, Donald E; Prum, Richard O

2007-09-01

Vocal learning is thought to have evolved in three clades of birds (parrots, hummingbirds, and oscine passerines), and three clades of mammals (whales, bats, and primates). Behavioural data indicate that, unlike other suboscine passerines, the three-wattled bellbird Procnias tricarunculata (Cotingidae) is capable of vocal learning. Procnias tricarunculata shows conspicuous vocal ontogeny, striking geographical variation in song, and rapid temporal change in song within a population. Deprivation studies of vocal development in P. tricarunculata are impractical. Here, we report evidence from mitochondrial DNA sequences and nuclear microsatellite loci that genetic variation within and among the four allopatric breeding populations of P. tricarunculata is not congruent with variation in vocal behaviour. Sequences of the mitochondrial DNA control region document extensive haplotype sharing among localities and song types, and no phylogenetic resolution of geographical populations or behavioural groups. The vocally differentiated, allopatric breeding populations of P. tricarunculata are only weakly genetically differentiated populations, and are not distinct taxa. Mitochondrial DNA and microsatellite variation show small (2.9% and 13.5%, respectively) but significant correlation with geographical distance, but no significant residual variation by song type. Estimates of the strength of selection that would be needed to maintain the observed geographical pattern in vocal differentiation if songs were genetically based are unreasonably high, further discrediting the hypothesis of a genetic origin of vocal variation. These data support a fourth, phylogenetically independent origin of avian vocal learning in Procnias. Geographical variations in P. tricarunculata vocal behaviour are likely culturally evolved dialects.

Best of Breed

NASA Technical Reports Server (NTRS)

Lohn, Jason

2004-01-01

No team of engineers, no matter how much time they took or how many bottles of cabernet they consumed, would dream up an antenna that looked like a deer antler on steroids. Yet that's what a group at NASA Ames Research Center came up with-thanks to a little help from Darwin. NASA's Space Technology 5 nanosatellites, which are scheduled to start measuring Earth's magnetosphere in late 2004, requires an antenna that can receive a wide range of frequencies regardless of the spacecraft's orientation. Rather than leave such exacting requirements in the hands of a human, the engineers decided to breed a design using genetic algorithms and 32 Linux PCs. The computers generated small antenna-constructing programs (the genotypes) and executed them to produce designs (the phenotypes). Then the designs were evaluated using an antenna simulator. The team settled on the form pictured here. You won't find this kind of antenna in any textbook, design guide, or research paper. But its innovative structure meets a challenging set of specifications. If successfully deployed, it will be the first evolved antenna to make it out of the lab and the first piece of evolved hardware ever to fly in space.

Ospreys do not teach offspring how to kill prey at the nest.

PubMed

Howard, Megan; Hoppitt, Will

2017-08-01

There is strong evidence for teaching in only a handful of species, most of which are cooperative breeders, leading some researchers to suggest that teaching may be more likely to evolve in such species. Alternatively, this initial distribution could be an artefact of the popularity and tractability of cooperative breeders as behavioural study systems. Therefore, establishing or refuting this potential evolutionary link requires researchers to assess potential cases of teaching in more non-cooperatively breeding species. We tested for teaching in the osprey ( Pandion haliaetus ), a non-cooperatively-breeding bird anecdotally reported to teach hunting skills to their offspring. We tested whether parents brought back more live prey to the nest as their offspring got older, allowing the latter to practice killing prey in a manner analogous to the progressive teaching seen in meerkats. We found the opposite trend to that predicted by the teaching hypothesis, indicating that ospreys do not teach their young at the nest. © 2017 The Author(s).

Antipredator strategies in breeding Bristle-thighed Curlews

USGS Publications Warehouse

McCaffery, Brian J.; Gill, Robert E.

1992-01-01

Each fall the world’s breeding population of Bristle-thighed Curlews (Numenius tahitiensis) arrives on the central Pacific wintering grounds following a migration that entails a non- stop flight of over 5000 kilometers. Sun-drenched, palm-shrouded atolls will be their home for the ensuing eight months. Even in the avian world, however, such apparant luxury is not without costs. For the Bristle-thighed Curlew these costs are incurred on the breeding grounds. From the time they arrive there in early May until they depart again for the wintering grounds in August and September, curlews are exposed to a host of predators. Gyrfalcons (Falco rusticolus), Golden Eagles (Aquila chrysaetos), Rough-legged Hawks (Buteo lagopus), Northern Harriers (Circus cyaneus), Parasitic Jaegers (Stercorarius parasiticus), Short-eared Owls (Asio flammeus), Common Ravens (Corvus corax) and Red Foxes (Vulpes vulpes) are potential predators of curlews and their offspring. To combat these threats, the Bristle-thighed Curlew has evolved an elaborate suite of antipredator defenses. Depending on the threat and the phase of the breeding cycle, Bristle-thighed Curlews may respond to potential predators by fleeing or flocking, by camouflage or combat. Given the variety of predators on the tundra, a variety of options is critical.

The ecology of cooperative breeding behaviour.

PubMed

Shen, Sheng-Feng; Emlen, Stephen T; Koenig, Walter D; Rubenstein, Dustin R

2017-06-01

Ecology is a fundamental driving force for the evolutionary transition from solitary living to breeding cooperatively in groups. However, the fact that both benign and harsh, as well as stable and fluctuating, environments can favour the evolution of cooperative breeding behaviour constitutes a paradox of environmental quality and sociality. Here, we propose a new model - the dual benefits framework - for resolving this paradox. Our framework distinguishes between two categories of grouping benefits - resource defence benefits that derive from group-defended critical resources and collective action benefits that result from social cooperation among group members - and uses insider-outsider conflict theory to simultaneously consider the interests of current group members (insiders) and potential joiners (outsiders) in determining optimal group size. We argue that the different grouping benefits realised from resource defence and collective action profoundly affect insider-outsider conflict resolution, resulting in predictable differences in the per capita productivity, stable group size, kin structure and stability of the social group. We also suggest that different types of environmental variation (spatial vs. temporal) select for societies that form because of the different grouping benefits, thus helping to resolve the paradox of why cooperative breeding evolves in such different types of environments. © 2017 John Wiley & Sons Ltd/CNRS.

Beyond promiscuity: mate-choice commitments in social breeding

PubMed Central

Boomsma, Jacobus J.

2013-01-01

Obligate eusociality with distinct caste phenotypes has evolved from strictly monogamous sub-social ancestors in ants, some bees, some wasps and some termites. This implies that no lineage reached the most advanced form of social breeding, unless helpers at the nest gained indirect fitness values via siblings that were identical to direct fitness via offspring. The complete lack of re-mating promiscuity equalizes sex-specific variances in reproductive success. Later, evolutionary developments towards multiple queen-mating retained lifetime commitment between sexual partners, but reduced male variance in reproductive success relative to female's, similar to the most advanced vertebrate cooperative breeders. Here, I (i) discuss some of the unique and highly peculiar mating system adaptations of eusocial insects; (ii) address ambiguities that remained after earlier reviews and extend the monogamy logic to the evolution of soldier castes; (iii) evaluate the evidence for indirect fitness benefits driving the dynamics of (in)vertebrate cooperative breeding, while emphasizing the fundamental differences between obligate eusociality and cooperative breeding; (iv) infer that lifetime commitment is a major driver towards higher levels of organization in bodies, colonies and mutualisms. I argue that evolutionary informative definitions of social systems that separate direct and indirect fitness benefits facilitate transparency when testing inclusive fitness theory. PMID:23339241

Population-Scale Foraging Segregation in an Apex Predator of the North Atlantic

PubMed Central

Paiva, Vitor H.; Fagundes, Ana I.; Romão, Vera; Gouveia, Cátia; Ramos, Jaime A.

2016-01-01

In this work we investigated the between-colony spatial, behavioural and trophic segregation of two sub-populations of the elusive Macaronesian shearwaters Puffinus baroli breeding only ~340 km apart in Cima Islet (Porto Santo Island) and Selvagem Grande Island. Global location sensing (gls) loggers were used in combination with the trophic ecology of tracked individuals, inferred from the isotopic signatures of wing feathers. Results suggest that these two Macaronesian shearwater sub-populations do segregate during the non-breeding period in some ‘sub-population-specific’ regions, by responding to different oceanographic characteristics (habitat modelling). Within these disparate areas, both sub-populations behave differently (at-sea activity) and prey on disparate trophic niches (stable isotope analysis). One hypothesis would be that each sub-population have evolved and adapted to feed on particular and ‘sub-population-specific’ resources, and the segregation observed at the three different levels (spatial, behavioural and trophic) might be in fact a result of such adaptation, from the emergence of ‘cultural foraging patterns’. Finally, when comparing to the results of former studies reporting on the spatial, behavioural and trophic choices of Macaronesian shearwater populations breeding on Azores and Canary Islands, we realized the high ecological plasticity of this species inhabiting and foraging over the North-East Atlantic Ocean. PMID:27003687

Flight calls signal group and individual identity but not kinship in a cooperatively breeding bird.

PubMed

Keen, Sara C; Meliza, C Daniel; Rubenstein, Dustin R

2013-11-01

In many complex societies, intricate communication and recognition systems may evolve to help support both direct and indirect benefits of group membership. In cooperatively breeding species where groups typically comprise relatives, both learned and innate vocal signals may serve as reliable cues for kin recognition. Here, we investigated vocal communication in the plural cooperatively breeding superb starling, Lamprotornis superbus , where flight calls-short, stereotyped vocalizations used when approaching conspecifics-may communicate kin relationships, group membership, and/or individual identity. We found that flight calls were most similar within individual repertoires but were also more similar within groups than within the larger population. Although starlings responded differently to playback of calls from their own versus other neighboring and distant social groups, call similarity was uncorrelated with genetic relatedness. Additionally, immigrant females showed similar patterns to birds born in the study population. Together, these results suggest that flight calls are learned signals that reflect social association but may also carry a signal of individuality. Flight calls, therefore, provide a reliable recognition mechanism for groups and may also be used to recognize individuals. In complex societies comprising related and unrelated individuals, signaling individuality and group association, rather than kinship, may be a route to cooperation.

Evolution of breeding systems and fruits in New World Galium and relatives (Rubiaceae).

PubMed

Soza, Valerie L; Olmstead, Richard G

2010-10-01

Dioecy occurs in only about 6% of angiosperms, yet it has evolved many times from hermaphroditism. Polygamy is an even more uncommon condition within angiosperms, in which both unisexual and bisexual flowers occur within a species. Polygamy, dioecy, and hermaphroditism all occur within a New World clade of Galium (Rubiaceae), in which dioecy is hypothesized to have evolved from hermaphroditism via polygamy. At least five sections of Galium as traditionally defined by fruit morphology occur within this group. We tested the monophyly of sections defined by fruit morphology and sought to determine origins and pathways of breeding systems within this group. • We obtained chloroplast (rpoB-trnC, trnC-psbM, trnL-ndhJ) and nuclear ribosomal (external transcribed spacer) DNA sequences for 89 taxa from the Cruciata-Galium-Valantia (CGV) clade to estimate the phylogeny. Ancestral states for breeding systems, fruit types, and fruit hairs were reconstructed using parsimony and likelihood analyses. • We identified nine well-supported lineages of New World Galium taxa. However, none of the sections traditionally defined by fruit morphology are monophyletic. Dioecy is inferred to have arisen at least three times from hermaphroditism; polygamy is inferred to have arisen at least twice from dioecy and at least six times from hermaphroditism. • Polygamy appears to be a terminal condition in the CGV clade and not a pathway to dioecy. Fruit characters traditionally used in the taxonomy of this group have arisen multiple times within this clade of Galium and are not reliable indicators of shared evolutionary history.

Analysis of the complete mitochondrial genome of the Zhedong White goose and characterization of NUMTs: Reveal domestication history of goose in China and Euro.

PubMed

Ren, Ting; Liang, Shiri; Zhao, Ayong; He, Ke

2016-02-10

To understand the phyletic evolution of geese, the complete mitogenome of the Zhedong goose was sequenced for the first time. It is composed of 37 genes and 1 control region, and the structure and arrangement of all genes sequenced are identical to those of other goose breeds. We confirmed the accuracy of the mitogenome sequence through RT-PCR and found numts from amplification in genomic DNA. Comparisons of the phylogenetic trees and sequences of geese that were suggested a clade of Chinese geese, except the Yili goose, were classified in the Euro clade. Several breed-specific mutations and Chinese breed-specific mutations were found. Our results suggest that Chinese geese evolved from the swan goose, splitting from their common ancestors at different times, which was consistent with studies before. Furthermore, numts in most genes of Zhedong goose clustered with European geese in the phylogenetic tree, suggesting that the haplotypes in the Euro clade might be more ancient. However, the mitogenome of the swan goose shows distinctive evolutionary positions in some genes, which suggest its unclear relationship with Chinese geese and European geese. The current study added to the understanding of the evolution of geese and provided evidence that the typing of numts is an encouraging way for the evolutionary study of geese and the mitochondrial genomes of geese deserve further investigation. Copyright © 2015 Elsevier B.V. All rights reserved.

Hamilton's rule and the causes of social evolution

PubMed Central

Bourke, Andrew F. G.

2014-01-01

Hamilton's rule is a central theorem of inclusive fitness (kin selection) theory and predicts that social behaviour evolves under specific combinations of relatedness, benefit and cost. This review provides evidence for Hamilton's rule by presenting novel syntheses of results from two kinds of study in diverse taxa, including cooperatively breeding birds and mammals and eusocial insects. These are, first, studies that empirically parametrize Hamilton's rule in natural populations and, second, comparative phylogenetic analyses of the genetic, life-history and ecological correlates of sociality. Studies parametrizing Hamilton's rule are not rare and demonstrate quantitatively that (i) altruism (net loss of direct fitness) occurs even when sociality is facultative, (ii) in most cases, altruism is under positive selection via indirect fitness benefits that exceed direct fitness costs and (iii) social behaviour commonly generates indirect benefits by enhancing the productivity or survivorship of kin. Comparative phylogenetic analyses show that cooperative breeding and eusociality are promoted by (i) high relatedness and monogamy and, potentially, by (ii) life-history factors facilitating family structure and high benefits of helping and (iii) ecological factors generating low costs of social behaviour. Overall, the focal studies strongly confirm the predictions of Hamilton's rule regarding conditions for social evolution and their causes. PMID:24686934

Hamilton's rule and the causes of social evolution.

PubMed

Bourke, Andrew F G

2014-05-19

Hamilton's rule is a central theorem of inclusive fitness (kin selection) theory and predicts that social behaviour evolves under specific combinations of relatedness, benefit and cost. This review provides evidence for Hamilton's rule by presenting novel syntheses of results from two kinds of study in diverse taxa, including cooperatively breeding birds and mammals and eusocial insects. These are, first, studies that empirically parametrize Hamilton's rule in natural populations and, second, comparative phylogenetic analyses of the genetic, life-history and ecological correlates of sociality. Studies parametrizing Hamilton's rule are not rare and demonstrate quantitatively that (i) altruism (net loss of direct fitness) occurs even when sociality is facultative, (ii) in most cases, altruism is under positive selection via indirect fitness benefits that exceed direct fitness costs and (iii) social behaviour commonly generates indirect benefits by enhancing the productivity or survivorship of kin. Comparative phylogenetic analyses show that cooperative breeding and eusociality are promoted by (i) high relatedness and monogamy and, potentially, by (ii) life-history factors facilitating family structure and high benefits of helping and (iii) ecological factors generating low costs of social behaviour. Overall, the focal studies strongly confirm the predictions of Hamilton's rule regarding conditions for social evolution and their causes.

Update on exotic ash collection for hybrid breeding and survey for EAB-resistance in native North American species

Treesearch

Mary E. Mason; Daniel A. Herms; David W. Carey; Kathleen S. Knight; Nurul I. Faridi; Jennifer. Koch

2011-01-01

Contrary to the high levels of devastation observed on North American ash species infested with emerald ash borer (EAB) (Agrilus planipennis Fairmaire), reports from Asia indicate that EAB-induced destruction of Asian ash species is limited to stressed trees. This indicates that Asian ash species have co-evolved resistance, or at least a high degree...

Effects of flow regimes altered by dams on survival, population declines, and range-wide losses of California river-breeding frogs

Treesearch

Sarah J. Kupferberg; Wendy J. Palen; Amy J. Lind; Steve Bobzien; Alessandro Catenazzi; Joe Drennan; Mary.  Power

2012-01-01

Widespread alteration of natural hydrologic patterns by large dams combined with peak demands for power and water delivery during summer months have resulted in frequent aseasonal flow pulses in rivers of western North America. Native species in these ecosystems have evolved with predictable annual flood-drought cycles; thus, their likelihood of persistence may...

The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis.

PubMed

Cugno, Graziano; Parreira, José R; Ferlizza, Enea; Hernández-Castellano, Lorenzo E; Carneiro, Mariana; Renaut, Jenny; Castro, Noemí; Arguello, Anastasio; Capote, Juan; Campos, Alexandre M O; Almeida, André M

2016-01-01

Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer's incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15-20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up-regulated in the Palmera breed), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 (up-regulated in the Majorera breed) and cytochrome b-c1 complex subunit 1, mitochondrial and Chain D, Bovine F1-C8 Sub-Complex Of Atp Synthase (down-regulated in the Majorera breed) as a consequence of weight loss.

The Goat (Capra hircus) Mammary Gland Mitochondrial Proteome: A Study on the Effect of Weight Loss Using Blue-Native PAGE and Two-Dimensional Gel Electrophoresis

PubMed Central

Cugno, Graziano; Parreira, José R.; Ferlizza, Enea; Hernández-Castellano, Lorenzo E.; Carneiro, Mariana; Renaut, Jenny; Castro, Noemí; Arguello, Anastasio; Capote, Juan

2016-01-01

Seasonal weight loss (SWL) is the most important limitation to animal production in the Tropical and Mediterranean regions, conditioning producer’s incomes and the nutritional status of rural communities. It is of importance to produce strategies to oppose adverse effects of SWL. Breeds that have evolved in harsh climates have acquired tolerance to SWL through selection. Most of the factors determining such ability are related to changes in biochemical pathways as affected by SWL. In this study, a gel based proteomics strategy (BN: Blue-Native Page and 2DE: Two-dimensional gel electrophoresis) was used to characterize the mitochondrial proteome of the secretory tissue of the goat mammary gland. In addition, we have conducted an investigation of the effects of weight loss in two goat breeds with different levels of adaptation to nutritional stress: Majorera (tolerant) and Palmera (susceptible). The study used Majorera and Palmera dairy goats, divided in 4 sets, 2 for each breed: underfed group fed on wheat straw (restricted diet, so their body weight would be 15–20% reduced by the end of experiment), and a control group fed with an energy-balanced diet. At the end of the experimental period (22 days), mammary gland biopsies were obtained for all experimental groups. The proteomic analysis of the mitochondria enabled the resolution of a total of 277 proteins, and 148 (53%) were identified by MALDI-TOF/TOF mass spectrometry. Some of the proteins were identified as subunits of the glutamate dehydrogenase complex and the respiratory complexes I, II, IV, V from mitochondria, as well as numerous other proteins with functions in: metabolism, development, localization, cellular organization and biogenesis, biological regulation, response to stimulus, among others, that were mapped in both BN and 2DE gels. The comparative proteomics analysis enabled the identification of several proteins: NADH-ubiquinone oxidoreductase 75 kDa subunit and lamin B1 mitochondrial (up-regulated in the Palmera breed), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2 (up-regulated in the Majorera breed) and cytochrome b-c1 complex subunit 1, mitochondrial and Chain D, Bovine F1-C8 Sub-Complex Of Atp Synthase (down-regulated in the Majorera breed) as a consequence of weight loss. PMID:27031334

Additive genetic variance in polyandry enables its evolution, but polyandry is unlikely to evolve through sexy or good sperm processes.

PubMed

Travers, L M; Simmons, L W; Garcia-Gonzalez, F

2016-05-01

Polyandry is widespread despite its costs. The sexually selected sperm hypotheses ('sexy' and 'good' sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2 ) while controlling for sampling variance due to male × male × female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest that the evolution of polyandry may not be driven by sexy sperm or good sperm processes. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Field techniques and methods of data collection used in studies of wood storks of the Birdsville Colony and swamps of the Savannah River Plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coulter, M.C.; Bryan, A.L. Jr.

1988-10-01

The United States population of Wood Storks (Mycteria americana) has been declining over the last 50 years, although there has been disagreement as to the magnitude of the decrease. In 1984, the US Fish and Wildlife Service listed the US breeding population as endangered. In that year the University of Georgia's Savannah River Ecology Laboratory began an extensive research program on the breeding biology and foraging ecology of Wood Storks of the Birdsville colony in Millen, Jenkins county, east-central Georgia, USA. The SREL Wood Stork program was designed to evaluate the importance of foraging habitat on the Savannah River Plantmore » to storks, and to design and develop management plans for artificial foraging ponds at the National Audubon Society's Silver Bluff Plantation Sanctuary. It was necessary to develop an understanding of the general foraging ecology of the birds, and to understand their forage needs during the breeding season. We have summarized the methods that we developed during this program as an aid to researchers studying storks or other wading birds. Although the methods described here were designed to answer questions important to our program, we hope that they are general enough to be helpful to others. Some of the methods were designed in 1983, during a preliminary part of the study. All the methods have evolved during the program, improving from our experience. Many people have been involved in the study and all have contributed to the methods and their improvement.« less

Reduction of Ethanol Yield and Improvement of Glycerol Formation by Adaptive Evolution of the Wine Yeast Saccharomyces cerevisiae under Hyperosmotic Conditions

PubMed Central

Tilloy, Valentin; Ortiz-Julien, Anne

2014-01-01

There is a strong demand from the wine industry for methodologies to reduce the alcohol content of wine without compromising wine's sensory characteristics. We assessed the potential of adaptive laboratory evolution strategies under hyperosmotic stress for generation of Saccharomyces cerevisiae wine yeast strains with enhanced glycerol and reduced ethanol yields. Experimental evolution on KCl resulted, after 200 generations, in strains that had higher glycerol and lower ethanol production than the ancestral strain. This major metabolic shift was accompanied by reduced fermentative capacities, suggesting a trade-off between high glycerol production and fermentation rate. Several evolved strains retaining good fermentation performance were selected. These strains produced more succinate and 2,3-butanediol than the ancestral strain and did not accumulate undesirable organoleptic compounds, such as acetate, acetaldehyde, or acetoin. They survived better under osmotic stress and glucose starvation conditions than the ancestral strain, suggesting that the forces that drove the redirection of carbon fluxes involved a combination of osmotic and salt stresses and carbon limitation. To further decrease the ethanol yield, a breeding strategy was used, generating intrastrain hybrids that produced more glycerol than the evolved strain. Pilot-scale fermentation on Syrah using evolved and hybrid strains produced wine with 0.6% (vol/vol) and 1.3% (vol/vol) less ethanol, more glycerol and 2,3-butanediol, and less acetate than the ancestral strain. This work demonstrates that the combination of adaptive evolution and breeding is a valuable alternative to rational design for remodeling the yeast metabolic network. PMID:24532067

Sterilization versus segregation: control of the 'feebleminded', 1900-1938.

PubMed

Radford, J P

1991-01-01

This paper presents a model designed to contextualize studies of the specialized custodial mental handicap institutions which evolved in Britain and North America during the early decades of this century. The frame of reference adopted is the eugenics movement, and particularly the debate over sterilization vs segregation as the preferred means of controlling the breeding of the 'unfit'. The rise of farm colonies is seen as epitomizing the expression of eugenic ideologies in the social and physical landscapes. The geographical manifestation of eugenically-driven policy is illustrated in a case study of the Langdon colony, an extension of the Royal Western Counties Institution at Starcross near Exeter, as it developed between 1931 and 1938.

Evolution of the hemiascomycete yeasts: on life styles and the importance of inbreeding.

PubMed

Knop, Michael

2006-07-01

The term 'breeding system' is used to describe the morphological and behavioural aspects of the sexual life cycle of a species. The yeast breeding system provides three alternatives that enable hapoids to return to the diploid state that is necessary for meiosis: mating of unrelated haploids (amphimixis), mating between spores from the same tetrad (intratetrad mating, automixis) and mother daughter mating upon mating type switching (haplo-selfing). The frequency of specific mating events affects the level of heterozygosity present in individuals and the genetic diversity of populations. This review discusses the reproductive strategies of yeasts, in particular S. cerevisiae (Bakers' or budding yeast). Emphasis is put on intratetrad mating, its implication for diversity, and how the particular genome structure could have evolved to ensure the preservation of a high degree of heterozygosity in conjunction with frequent intratetrad matings. I also discuss how the ability of yeast to control the number of spores that are formed accounts for high intratetrad mating rates and for enhanced transmission of genomic variation. I extend the discussion to natural genetic variation and propose that a high level of plasticity is inherent in the yeast breeding system, which may allow variation of the breeding behaviour in accordance with the needs imposed by the environment. (c) 2006 Wiley Periodicals, Inc.

Regional analysis of population trajectories from the North American Breeding Bird Survey

USGS Publications Warehouse

Sauer, J.R.; Link, W.A.; Helbig, Andreas J.; Flade, Martin

1999-01-01

The North American Breeding Bird Survey (BBS) was started in 1966, and provides information on population change and distribution for most of the birds in North America. The geographic extent of the survey, and the logistical compromises needed to survey such a large area, present many challenges for estimation from BBS data. In this paper, we describe the survey and discuss some of the limitations of the survey design and implementation. Analysis of the survey has evolved over time as new statistical methods and insights into the analysis of count data are developed. Survey results and analysis tools for the BBS are now available over intemet; we present new methods that use generalized linear models for estimation of population change and empirical Bayes procedures for regional summaries.

Complex Mhc-based mate choice in a wild passerine

PubMed Central

Bonneaud, Camille; Chastel, Olivier; Federici, Pierre; Westerdahl, Helena; Sorci, Gabriele

2006-01-01

The extreme polymorphism of the vertebrate major histocompatibility complex (Mhc) is famous for protecting hosts against constantly evolving pathogens. Mate choice is often evoked as a means of maintaining Mhc variability through avoidance of partners with similar Mhc alleles or preference for heterozygotes. Evidence for these two hypotheses mostly comes from studies on humans and laboratory mice. Here, we tested these hypotheses in a wild outbred population of house sparrows (Passer domesticus). Females were not more or less closely related to the males they paired with when considering neutral genetic variation. However, males failed to form breeding pairs when they had too few Mhc alleles and when they were too dissimilar from females at Mhc loci (i.e. had no common alleles). Furthermore, pairs did not form at random as Mhc diversity positively correlated in mating pairs. These results suggest that mate choice evolves in response to (i) benefits in terms of parasite resistance acquired from allelic diversity, and (ii) costs associated with the disruption of co-adapted genes. PMID:16600889

Complex Mhc-based mate choice in a wild passerine.

PubMed

Bonneaud, Camille; Chastel, Olivier; Federici, Pierre; Westerdahl, Helena; Sorci, Gabriele

2006-05-07

The extreme polymorphism of the vertebrate major histocompatibility complex (Mhc) is famous for protecting hosts against constantly evolving pathogens. Mate choice is often evoked as a means of maintaining Mhc variability through avoidance of partners with similar Mhc alleles or preference for heterozygotes. Evidence for these two hypotheses mostly comes from studies on humans and laboratory mice. Here, we tested these hypotheses in a wild outbred population of house sparrows (Passer domesticus). Females were not more or less closely related to the males they paired with when considering neutral genetic variation. However, males failed to form breeding pairs when they had too few Mhc alleles and when they were too dissimilar from females at Mhc loci (i.e. had no common alleles). Furthermore, pairs did not form at random as Mhc diversity positively correlated in mating pairs. These results suggest that mate choice evolves in response to (i) benefits in terms of parasite resistance acquired from allelic diversity, and (ii) costs associated with the disruption of co-adapted genes.

Life History Correlates and Extinction Risk of Capital-Breeding Fishes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jager, Yetta; Vila-Gispert, Dr Anna; Rose, Kenneth A.

2008-03-01

We consider a distinction for fishes, often made for birds and reptiles, between capital-breeding and income-breeding species. Species that follow a capital-breeding strategy tend to evolve longer intervals between reproductive events and tend to have characteristics that we associate with higher extinction risk. To examine whether these ideas are relevant for fishes, we assembled life-history data for fish species, including an index of extinction risk, the interval between spawning events, the degree of parental care, and whether or not the species migrates to spawn. These data were used to evaluate two hypotheses: 1) fish species with a major accessory activitymore » to spawning (migration or parental care) spawn less often and 2) fish species that spawn less often are at greater risk of extinction. We tested these hypotheses by applying two alternative statistical methods that account for phylogenetic correlation in cross-taxon comparisons. The two methods predicted average intervals between spawning events 0.13 to 0.20 years longer for fishes with a major accessory activity. Both accessories, above-average parental care and spawning migration, were individually associated with longer average spawning intervals. We conclude that the capital-breeding paradigm is relevant for fishes. We also confirmed the second hypothesis, that species in higher IUCN extinction risk categories had longer average spawning intervals. Further research is needed to understand the relationship between extinction risk and spawning interval, within the broader context of life history traits and aquatic habitats.« less

The evolution of reproductive diversity in Afrobatrachia: A phylogenetic comparative analysis of an extensive radiation of African frogs

PubMed Central

Portik, Daniel M.; Blackburn, David C.

2016-01-01

The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co‐evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift toward using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans. PMID:27402182

Enhance beef cattle improvement by embryo biotechnologies.

PubMed

Wu, B; Zan, L

2012-10-01

Embryo biotechnology has become one of the prominent high businesses worldwide. This technology has evolved through three major changes, that is, traditional embryo transfer (in vivo embryo production by donor superovulation), in vitro embryo production by ovum pick up with in vitro fertilization and notably current cloning technique by somatic cell nuclear transfer and transgenic animal production. Embryo biotechnology has widely been used in dairy and beef cattle industry and commercial bovine embryo transfer has become a large international business. Currently, many developed biotechnologies during the period from early oocyte stage to pre-implantation embryos can be used to create new animal breeds and accelerate genetic progression. Based on recent advances in embryo biotechnologies and authors current studies, this review will focus on a description of the application of this technology to beef cattle improvement and discuss how to use this technology to accelerate beef cattle breeding and production. The main topics of this presentation include the following: (i) how to increase calf production numbers from gametes including sperm and oocyte; (ii) multiple ovulation and embryo transfer breeding schemes; (iii) in vitro fertilization and intracytoplasm sperm injection in bovine; (iv) pronuclear development and transgenic animals; (v) sex selection from sperm and embryos; (vi) cloning and androgenesis; (vii) blastocyst development and embryonic stem cells; (viii) preservation of beef cattle genetic resources; and (ix) conclusions. © 2011 Blackwell Verlag GmbH.

The evolution of altruistic social preferences in human groups

PubMed Central

Silk, Joan B.; House, Bailey R.

2016-01-01

In this paper, we consider three hypotheses to account for the evolution of the extraordinary capacity for large-scale cooperation and altruistic social preferences within human societies. One hypothesis is that human cooperation is built on the same evolutionary foundations as cooperation in other animal societies, and that fundamental elements of the social preferences that shape our species' cooperative behaviour are also shared with other closely related primates. Another hypothesis is that selective pressures favouring cooperative breeding have shaped the capacity for cooperation and the development of social preferences, and produced a common set of behavioural dispositions and social preferences in cooperatively breeding primates and humans. The third hypothesis is that humans have evolved derived capacities for collaboration, group-level cooperation and altruistic social preferences that are linked to our capacity for culture. We draw on naturalistic data to assess differences in the form, scope and scale of cooperation between humans and other primates, experimental data to evaluate the nature of social preferences across primate species, and comparative analyses to evaluate the evolutionary origins of cooperative breeding and related forms of behaviour. PMID:26729936

Interaction between the Hawaiian dark-rumped petrel and the Argentine ant in Haleakala National Park, Maui, Hawaii

USGS Publications Warehouse

Krushelnycky, Paul D.; Hodges, Cathleen S.N.; Medeiros, Arthur C.; Loope, Lloyd L.

2001-01-01

The endemic biota of the Hawaiian islands is believed to have evolved in the absence of ant predation. However, it was suspected that this endemic biota is highly vulnerable to the effect of immigrant ants especially with regard to an aggressive predator known as the Argentine ant (Linepithema humile). First recorded in the Haleakala National Park on the island of Maui in 1967, this ant was believed to have reduced populations of native arthropods in high-elevation subalpine shrublands. In addition, concerns were raised that this immigrant ant may have also reduced the breeding success of the endangered Hawaiian Dark-rumped Petrel (Pterodroma phaeopygia sandwichensis), a native seabird. If so, then it was believe that this ant could become another major threat to the survival of this endangered seabird in addition to the threat that was caused by the introduction of introduced mammals, the advent of hunting by the Polynesians, and a loss of breeding habitat. As a result, the purpose of this study was to determine if the Argentine ant affects the nesting success of this native Hawaiian seabird.

Meiotic recombination hotspots - a comparative view.

PubMed

Choi, Kyuha; Henderson, Ian R

2015-07-01

During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Sex-biased oviposition by a nursery pollinator on a gynodioecious host plant: Implications for breeding system evolution and evolution of mutualism.

PubMed

Doubleday, Laura A D; Adler, Lynn S

2017-07-01

Dioecy, a breeding system where individual plants are exclusively male or female, has evolved repeatedly. Extensive theory describes when dioecy should arise from hermaphroditism, frequently through gynodioecy, where females and hermaphrodites coexist, and when gynodioecy should be stable. Both pollinators and herbivores often prefer the pollen-bearing sex, with sex-specific fitness effects that can affect breeding system evolution. Nursery pollination, where adult insects pollinate flowers but their larvae feed on plant reproductive tissues, is a model for understanding mutualism evolution but could also yield insights into plant breeding system evolution. We studied a recently established nursery pollination interaction between native Hadena ectypa moths and introduced gynodioecious Silene vulgaris plants in North America to assess whether oviposition was biased toward females or hermaphrodites, which traits were associated with oviposition, and the effect of oviposition on host plant fitness. Oviposition was hermaphrodite-biased and associated with deeper flowers and more stems. Sexual dimorphism in flower depth, a trait also associated with oviposition on the native host plant ( Silene stellata ), explained the hermaphrodite bias. Egg-receiving plants experienced more fruit predation than plants that received no eggs, but relatively few fruits were lost, and egg receipt did not significantly alter total fruit production at the plant level. Oviposition did not enhance pollination; egg-receiving flowers usually failed to expand and produce seeds. Together, our results suggest that H. ectypa oviposition does not exert a large fitness cost on host plants, sex-biased interactions can emerge from preferences developed on a hermaphroditic host species, and new nursery pollination interactions can arise as negative or neutral rather than as mutualistic for the plant.

The effects of climate change on harp seals (Pagophilus groenlandicus).

PubMed

Johnston, David W; Bowers, Matthew T; Friedlaender, Ari S; Lavigne, David M

2012-01-01

Harp seals (Pagophilus groenlandicus) have evolved life history strategies to exploit seasonal sea ice as a breeding platform. As such, individuals are prepared to deal with fluctuations in the quantity and quality of ice in their breeding areas. It remains unclear, however, how shifts in climate may affect seal populations. The present study assesses the effects of climate change on harp seals through three linked analyses. First, we tested the effects of short-term climate variability on young-of-the year harp seal mortality using a linear regression of sea ice cover in the Gulf of St. Lawrence against stranding rates of dead harp seals in the region during 1992 to 2010. A similar regression of stranding rates and North Atlantic Oscillation (NAO) index values was also conducted. These analyses revealed negative correlations between both ice cover and NAO conditions and seal mortality, indicating that lighter ice cover and lower NAO values result in higher mortality. A retrospective cross-correlation analysis of NAO conditions and sea ice cover from 1978 to 2011 revealed that NAO-related changes in sea ice may have contributed to the depletion of seals on the east coast of Canada during 1950 to 1972, and to their recovery during 1973 to 2000. This historical retrospective also reveals opposite links between neonatal mortality in harp seals in the Northeast Atlantic and NAO phase. Finally, an assessment of the long-term trends in sea ice cover in the breeding regions of harp seals across the entire North Atlantic during 1979 through 2011 using multiple linear regression models and mixed effects linear regression models revealed that sea ice cover in all harp seal breeding regions has been declining by as much as 6 percent per decade over the time series of available satellite data.

The Effects of Climate Change on Harp Seals (Pagophilus groenlandicus)

PubMed Central

Johnston, David W.; Bowers, Matthew T.; Friedlaender, Ari S.; Lavigne, David M.

2012-01-01

Harp seals (Pagophilus groenlandicus) have evolved life history strategies to exploit seasonal sea ice as a breeding platform. As such, individuals are prepared to deal with fluctuations in the quantity and quality of ice in their breeding areas. It remains unclear, however, how shifts in climate may affect seal populations. The present study assesses the effects of climate change on harp seals through three linked analyses. First, we tested the effects of short-term climate variability on young-of-the year harp seal mortality using a linear regression of sea ice cover in the Gulf of St. Lawrence against stranding rates of dead harp seals in the region during 1992 to 2010. A similar regression of stranding rates and North Atlantic Oscillation (NAO) index values was also conducted. These analyses revealed negative correlations between both ice cover and NAO conditions and seal mortality, indicating that lighter ice cover and lower NAO values result in higher mortality. A retrospective cross-correlation analysis of NAO conditions and sea ice cover from 1978 to 2011 revealed that NAO-related changes in sea ice may have contributed to the depletion of seals on the east coast of Canada during 1950 to 1972, and to their recovery during 1973 to 2000. This historical retrospective also reveals opposite links between neonatal mortality in harp seals in the Northeast Atlantic and NAO phase. Finally, an assessment of the long-term trends in sea ice cover in the breeding regions of harp seals across the entire North Atlantic during 1979 through 2011 using multiple linear regression models and mixed effects linear regression models revealed that sea ice cover in all harp seal breeding regions has been declining by as much as 6 percent per decade over the time series of available satellite data. PMID:22238591

The Evolving Arctic: Current State of U.S. Arctic Policy

DTIC Science & Technology

2013-09-01

global warming on the fragile Arctic ecosystem, Canada has taken a proactive approach to protect the environment and its inhabitants. For example in...Whether you are an expert in global warming or not, the fact is there is more water there every day than there has been in the past; that breeds...Environmental Damage, and Interruption of Native Subsistence Whaling /Fishing Due to a Lack of Oil Spill- Response Equipment

Repeatable and heritable behavioural variation in a wild cooperative breeder

PubMed Central

Burke, Terry; Dugdale, Hannah L.

2017-01-01

Abstract Quantifying consistent differences in behaviour among individuals is vital to understanding the ecological and evolutionary significance of animal personality. To quantify personality, the phenotypic variation of a behavioural trait is partitioned to assess how it varies among individuals, which is also known as repeatability. If pedigree data are available, the phenotypic variation can then be further partitioned to estimate the additive genetic variance and heritability. Assessing the repeatability and heritability of personality traits therefore allows for a better understanding of what natural selection can act upon, enabling evolution. In a natural population of facultative cooperatively breeding Seychelles warbler (Acrocephalus sechellensis) on Cousin Island, a lack of breeding vacancies forces individuals into different life-history strategies, and these differences in reproductive state could generate behavioural differences among individuals in the population. We used this population to estimate the repeatability of 4 behavioural traits (novel environment exploration, novel object exploration, obstinacy/struggle rate, and escape response), and narrow-sense heritability (of behavior, h2B; behavior minus observer variance; and personality), and evolvability, of the repeatable behavioural traits. We also tested for an among-individual correlation between the repeatable traits. We found that, compared to estimates in other study species, the exploratory behaviours were moderately repeatable (0.23–0.37), there was a positive among-individual correlation (0.51) between novel environment and novel object exploration, and that novel environment exploration was moderately heritable (0.17; h2B was low as it includes observer variance). This study further clarifies the additive genetic variance available for selection to act upon in this cooperatively breeding bird. PMID:29622921

Temporal Feeding Pattern May Influence Reproduction Efficiency, the Example of Breeding Mares

PubMed Central

Benhajali, Haifa; Ezzaouia, Mohammed; Lunel, Christophe; Charfi, Faouzia; Hausberger, Martine

2013-01-01

Discomfort in farm animals may be induced by inappropriate types or timing of food supplies. Thus, time restriction of meals and lack of roughage have been shown to be one source of emergence of oral stereotypies and abnormal behaviour in horses which have evolved to eat high-fibre diets in small amounts over long periods of time. This feeding pattern is often altered in domestic environment where horses are often fed low fibre meals that can be rapidly consumed. This study aimed at determining the effect of the temporal pattern of feeding on reproductive efficiency of breeding mares, One hundred Arab breeding mares were divided into two groups that differed only in the temporal pattern of roughage availability: only at night for the standard feeding pattern group (SFP mares), night and day for the “continuous feeding” group (CF mares). The total amount of roughage provided was the same as the CF mares received half of the hay during the day while in paddock (haynets). Mares were tested for oestrus detection by teasing with one stallion and were then examined clinically by rectal palpations and ultrasound before being mated naturally or inseminated by fresh or frozen semen. Multivariate logistic regression was used to analyse data. The treatment affected significantly the reproductive efficiency of the mares with fewer oestrus abnormalities (p = 0.0002) and more fertility (p = 0.024) in CF mares (conception rate = 81% versus 55% in SFP mares). Ensuring semi-continous feeding by providing roughage may be a way of fulfilling the basic physiological needs of the horses' digestive system, reducing stress and associated inhibitors of reproduction. To our knowledge, this study provides the first evidence of an impact of temporal feeding patterns on reproductive success in a Mammal. Temporal patterns of feeding may be a major and underestimated factor in breeding. PMID:24098636

Effects of photoperiod and food restriction on the reproductive physiology of female California mice

PubMed Central

Steinman, Michael Q.; Knight, Jennifer A.; Trainor, Brian C.

2012-01-01

Many temperate-zone animals use changes in photoperiod to time breeding. Shorter term cues, like food availability, are integrated with photoperiod to adjust reproductive timing under unexpected conditions. Many mice of the genus Peromyscus breed in the summer. California mice (Peromyscus californicus), however, can breed year round, but tend to begin breeding in the winter. Glial cells may be involved in transduction of environmental signals that regulate gonadotrophin releasing hormone (GnRH) activity. We examined the effects of diet and photoperiod on reproduction in female California mice. Mice placed on either short days (8L:16D) or long days (16L:8D) were food restricted (80% of normal intake) or fed ad libitum. Short day-food restricted mice showed significant regression of the reproductive system. GnRH-immunoreactivity was increased in the tuberal hypothalamus of long day-food restricted mice. This may be associated with the sparing effect long days have when mice are food restricted. The number of GFAP-immunoreactive fibers in proximity to GnRH nerve terminals correlated negatively with uterine size in ad libitum but not food restricted mice, suggesting diet may alter glial regulation of the reproductive axis. There was a trend towards food restriction increasing uterine expression of c-fos mRNA, an estrogen dependent gene. Similar to other seasonally breeding rodents, short days render the reproductive system of female California mice more susceptible to effects of food restriction. This may be vestigial, or it may have evolved to mitigate consequences of unexpectedly poor winter food supplies. PMID:22245263

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches

PubMed Central

Mondal, Suchismita; Rutkoski, Jessica E.; Velu, Govindan; Singh, Pawan K.; Crespo-Herrera, Leonardo A.; Guzmán, Carlos; Bhavani, Sridhar; Lan, Caixia; He, Xinyao; Singh, Ravi P.

2016-01-01

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance. PMID:27458472

Long-term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance.

PubMed

Alves, Mara Lisa; Belo, Maria; Carbas, Bruna; Brites, Cláudia; Paulo, Manuel; Mendes-Moreira, Pedro; Brites, Carla; Bronze, Maria do Rosário; Šatović, Zlatko; Vaz Patto, Maria Carlota

2018-02-01

Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic-climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long-term participatory breeding/on-farm conservation program was established in Portugal. In this program, maize populations were subject to stratified mass selection. This work aimed to estimate the effect of on-farm stratified mass selection on the agronomic performance, quality, and molecular diversity of two historical maize populations. Multilocation field trials, comparing the initial populations with the derived selection cycles, showed that this selection methodology led to agronomic improvement for one of the populations. The molecular diversity analysis, using microsatellites, revealed that overall genetic diversity in both populations was maintained throughout selection. The comparison of quality parameters between the initial populations and the derived selection cycles was made using kernel from a common-garden experiment. This analysis showed that the majority of the quality traits evaluated progressed erratically over time. In conclusion, this breeding approach, through simple and low-cost methodologies, proved to be an alternative strategy for genetic resources' on-farm conservation.

Isotope signatures in winter moulted feathers predict malaria prevalence in a breeding avian host.

PubMed

Yohannes, Elizabeth; Hansson, Bengt; Lee, Raymond W; Waldenström, Jonas; Westerdahl, Helena; Akesson, Mikael; Hasselquist, Dennis; Bensch, Staffan

2008-11-01

It is widely accepted that animal distribution and migration strategy might have co-evolved in relation to selection pressures exerted by parasites. Here, we first determined the prevalence and types of malaria blood parasites in a breeding population of great reed warblers Acrocephalus arundinaceus using PCR. Secondly, we tested for differences in individual feather stable isotope signatures (delta (13)C, delta (15)N, deltaD and delta (34)S) to investigate whether malaria infected and non-infected birds had occupied different areas in winter. We show that birds moulting in Afro-tropical habitats with significantly higher delta (13)C and delta (15)N but lower deltaD and delta(34)S values were more frequently infected with malaria parasites. Based on established patterns of isotopic distributions, our results indicate that moulting sites with higher incidence of malaria are generally drier and situated further to the north in West Africa than sites with lower incidence of malaria. Our findings are pertinent to the general hypothesis that animal distribution and particularly avian migration strategy might evolve in response to selection pressures exerted by parasites at different geographic scales. Tradeoffs between investment in energy demanding life history traits (e.g. migration and winter moult) and immune function are suggested to contribute to the particular choice of habitat during migration and at wintering sites.

Functional Conservation and Divergence among Homoeologs of TaSPL20 and TaSPL21, Two SBP-Box Genes Governing Yield-Related Traits in Hexaploid Wheat1[OPEN

PubMed Central

Mao, Xinguo; Li, Ang; Wang, Jingyi; Chang, Xiaoping; Zhang, Xueyong

2017-01-01

Maintaining high and stable yields has become an increasing challenge in wheat breeding due to climate change. Although Squamosa-promoter binding protein (SBP)-box genes have important roles in plant development, very little is known about the actual biological functions of wheat SBP-box family members. Here, we dissect the functional conservation, divergence, and exploitation of homoeologs of two paralogous TaSPL wheat loci during domestication and breeding. TaSPL20 and TaSPL21 were highly expressed in the lemma and palea. Ectopic expressions of TaSPL20/21 in rice exhibited similar functions in terms of promoting panicle branching but had different functions during seed development. We characterized all six TaSPL20/21 genes located across the three homoeologous (A, B, and D) genomes. According to the functional analysis of naturally occurring variants in 20 environments, four favorable haplotypes were identified. Together, they reduced plant height by up to 27.5%, and TaSPL21-6D-HapII increased 1000-grain weight by 9.73%. Our study suggests that TaSPL20 and TaSPL21 homoeologs underwent diversification in function with each evolving its own distinctive characteristics. During domestication and breeding of wheat in China, favorable haplotypes of each set were selected and exploited to varying degrees due to their large effects on plant height and 1000-grain weight. PMID:28424214

Kidnapping of chicks in emperor penguins: a hormonal by-product?

PubMed

Angelier, Frédéric; Barbraud, Christophe; Lormée, Hervé; Prud'homme, François; Chastel, Olivier

2006-04-01

The function and causes of kidnapping juveniles are little understood because individuals sustain some breeding costs to rear an unrelated offspring. Here we focus on the proximal causes of this behaviour in emperor penguins (Aptenodytes forsteri), whose failed breeders often kidnap chicks. We experimentally tested the hypothesis that kidnapping behaviour was the result of high residual levels of prolactin (PRL), a hormone involved in parental behaviour. Penguins with artificially decreased PRL levels by bromocriptine administration kidnapped chicks less often than control penguins. Within the bromocriptine treated group, kidnapping behaviour was not totally suppressed and the probability of kidnapping a chick was positively correlated to PRL levels measured before treatment. During breeding, emperor penguins have to forage in remote ice-free areas. In these birds, PRL secretion is poorly influenced by chick stimuli and has probably evolved to maintain a willingness to return to the colony after a long absence at sea. Therefore, penguins that have lost their chick during a foraging trip still maintain high residual PRL levels and this, combined with colonial breeding, probably facilitates kidnapping. We suggest that kidnapping in non-cooperative systems may result from a hormonal byproduct of a reproductive adaptation to extreme conditions.

The Evolution of Clutch Size in Hosts of Avian Brood Parasites.

PubMed

Medina, Iliana; Langmore, Naomi E; Lanfear, Robert; Kokko, Hanna

2017-11-01

Coevolution with avian brood parasites shapes a range of traits in their hosts, including morphology, behavior, and breeding systems. Here we explore whether brood parasitism is also associated with the evolution of host clutch size. Several studies have proposed that hosts of highly virulent parasites could decrease the costs of parasitism by evolving a smaller clutch size, because hosts with smaller clutches will lose fewer progeny when their clutch is parasitized. We describe a model of the evolution of clutch size, which challenges this logic and shows instead that an increase in clutch size (or no change) should evolve in hosts. We test this prediction using a broad-scale comparative analysis to ask whether there are differences in clutch size within hosts and between hosts and nonhosts. Consistent with our model, this analysis revealed that host species do not have smaller clutches and that hosts that incur larger costs from raising a parasite lay larger clutches. We suggest that brood parasitism might be an influential factor in clutch-size evolution and could potentially select for the evolution of larger clutches in host species.

Study on Reproductive Biology of Rhododendron longipedicellatum: A Newly Discovered and Special Threatened Plant Surviving in Limestone Habitat in Southeast Yunnan, China.

PubMed

Li, Taiqiang; Liu, Xiongfang; Li, Zhenghong; Ma, Hong; Wan, Youming; Liu, Xiuxian; Fu, Liyong

2018-01-01

Rhododendron longipedicellatum is a narrow endemic species and a subject of urgent demand in the domestic market and overseas. Its fascinating shapes, brilliantly gilvous flowers, and unusual flowering time endow this species with extremely high ornamental value. However, only five wild populations of R. longipedicellatum surviving in limestone habitat have been found through elaborate field investigation, and the number of the populations decreases further or is even confronted with risk of extinction due to the damage of human activities. To enhance the protection and utilization of R. longipedicellatum , this study systematically investigated several important aspects of reproductive biology, including floral syndrome, pollen viability and stigma receptivity, petal color reflectance, breeding system, and pollination biology. The results demonstrated that arched styles not only create obvious herkogamy that avoide self-pollination, but also effectively reduce rain damage to the intrinsic characteristics of the stigma surface secretions, promoting the female fitness of R. longipedicellatum in poor weather. Pollen viability maintained a high level over the flowering period. The reflectance spectrum of petals had two peaks at wavelengths of 360 and 580 nm. Tests of OCI, P/O and artificial pollination all indicated that R. longipedicellatum was self-compatible and that the breeding system was mixed mating. Geitonogamy mediated by Bombus braccatus was the primary pollination route in the natural environment, which suggested that the breeding system of R. longipedicellatum might be evolving from selfing to outcrossing. The pollination vector of R. longipedicellatum was very specific, in that only B. braccatus was confirmed to deliver pollen to the stigmas. Visitation frequency was influenced by the activity rhythms and resource requirements of the different castes (i.e., sex). B. braccatus workers were the most effective pollinators because of higher visitation frequency and more effective contribution to fruit production, whereas the presence of B. braccatus males might enhance pollen flow within the population to a certain extent. Finally, these findings not only provided a reliable theoretical basis for hybridization breeding of R. longipedicellatum as parents, but also laid a solid foundation for further molecular biology studies to more broadly reveal the mechanisms of its endangerment in the future.

New Insights on Plant Salt Tolerance Mechanisms and Their Potential Use for Breeding

PubMed Central

Hanin, Moez; Ebel, Chantal; Ngom, Mariama; Laplaze, Laurent; Masmoudi, Khaled

2016-01-01

Soil salinization is a major threat to agriculture in arid and semi-arid regions, where water scarcity and inadequate drainage of irrigated lands severely reduce crop yield. Salt accumulation inhibits plant growth and reduces the ability to uptake water and nutrients, leading to osmotic or water-deficit stress. Salt is also causing injury of the young photosynthetic leaves and acceleration of their senescence, as the Na+ cation is toxic when accumulating in cell cytosol resulting in ionic imbalance and toxicity of transpiring leaves. To cope with salt stress, plants have evolved mainly two types of tolerance mechanisms based on either limiting the entry of salt by the roots, or controlling its concentration and distribution. Understanding the overall control of Na+ accumulation and functional studies of genes involved in transport processes, will provide a new opportunity to improve the salinity tolerance of plants relevant to food security in arid regions. A better understanding of these tolerance mechanisms can be used to breed crops with improved yield performance under salinity stress. Moreover, associations of cultures with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi could serve as an alternative and sustainable strategy to increase crop yields in salt-affected fields. PMID:27965692

Is heterostyly rare on oceanic islands?

PubMed Central

Watanabe, Kenta; Sugawara, Takashi

2015-01-01

Heterostyly has been considered rare or absent on oceanic islands. However, there has been no comprehensive review on this issue. Is heterostyly truly rare on oceanic islands? What makes heterostyly rare on such islands? To answer these questions, we review the reproductive studies on heterostyly on oceanic islands, with special emphasis on the heterostylous genus Psychotria in the Pacific Ocean as a model system. Overall, not many reproductive studies have been performed on heterostylous species on oceanic islands. In Hawaiian Psychotria, all 11 species are thought to have evolved dioecy from distyly. In the West Pacific, three species on the oceanic Bonin and Lanyu Islands are distylous (Psychotria homalosperma, P. boninensis and P. cephalophora), whereas three species on the continental Ryukyu Islands show various breeding systems, such as distyly (P. serpens), dioecy (P. rubra) and monoecy (P. manillensis). On some other Pacific oceanic islands, possibilities of monomorphy have been reported. For many Psychotria species, breeding systems are unknown, although recent studies indicate that heterostylous species may occur on some oceanic islands. A shift from heterostyly to other sexual systems may occur on some oceanic islands. This tendency may also contribute to the rarity of heterostyly, in addition to the difficulty in colonization/autochthonous evolution of heterostylous species on oceanic islands. Further investigation of reproductive systems of Psychotria on oceanic islands using robust phylogenetic frameworks would provide new insights into plant reproduction on oceanic islands. PMID:26199401

Population and life-stage-specific effects of two herbicide formulations on the aquatic development of European common frogs (Rana temporaria).

PubMed

Wagner, Norman; Veith, Michael; Lötters, Stefan; Viertel, Bruno

2017-01-01

Environmental contamination is suggested to contribute to amphibian population declines. However, the effects of a contaminant on a particular amphibian species can differ among populations. The authors investigated the toxic effects of 2 herbicide formulations on different populations and on representative developmental stages of the European common frog (Rana temporaria). Larvae from forest populations were more sensitive to a commonly used glyphosate-based herbicide compared with individuals from agrarian land. Median lethal concentrations correlated with measured glyphosate levels in the breeding ponds, which may be a sign of evolved tolerances. The reverse result was observed for a less commonly used cycloxydim-based herbicide. Effects of the glyphosate-based herbicide were stronger for earlier larval stages compared with later larval stages. Hence, applications in early spring (when early larvae are present in breeding ponds) pose greater risk concerning acute toxic effects on R. temporaria. With regard to late larval stages, short exposure (96 h) of prometamorphic larvae prolonged time to metamorphosis, but only at the highest test concentration that did not significantly induce mortality. This could be due to impairment of the thyroid axis. Notably, nearly all test concentrations of the 2 herbicides provoked growth retardation. Further research on how evolved or induced tolerances are acquired, actual contamination levels of amphibian habitats, and potential endocrine effects of glyphosate-based herbicides is necessary. Environ Toxicol Chem 2017;36:190-200. © 2016 SETAC. © 2016 SETAC.

Herbage intake of dairy cows in mixed sequential grazing with breeding ewes as followers.

PubMed

Jiménez-Rosales, Juan Daniel; Améndola-Massiotti, Ricardo Daniel; Burgueño-Ferreira, Juan Andrés; Ramírez-Valverde, Rodolfo; Topete-Pelayo, Pedro; Huerta-Bravo, Maximino

2018-03-01

This study aimed to evaluate the hypothesis that mixed sequential grazing of dairy cows and breeding ewes is beneficial. During the seasons of spring-summer 2013 and autumn-winter 2013-2014, 12 (spring-summer) and 16 (autumn-winter) Holstein Friesian cows and 24 gestating (spring-summer) and lactating (autumn-winter) Pelibuey ewes grazed on six (spring-summer) and nine (autumn-winter) paddocks of alfalfa and orchard grass mixed pastures. The treatments "single species cow grazing" (CowG) and "mixed sequential grazing with ewes as followers of cows" (MixG) were evaluated, under a completely randomized design with two replicates per paddock. Herbage mass on offer (HO) and residual herbage mass (RH) were estimated by cutting samples. The estimate of herbage intake (HI) of cows was based on the use of internal and external markers; the apparent HI of ewes was calculated as the difference between HO (RH of cows) and RH. Even though HO was higher in CowG, the HI of cows was higher in MixG during spring-summer and similar in both treatments during autumn-winter, implying that in MixG the effects on the cows HI of higher alfalfa proportion and herbage accumulation rate evolving from lower residual herbage mass in the previous cycle counteracted that of a higher HO in CowG. The HI of ewes was sufficient to enable satisfactory performance as breeding ewes. Thus, the benefits of mixed sequential grazing arose from higher herbage accumulation, positive changes in botanical composition, and the achievement of sheep production without negative effects on the herbage intake of cows.

Extended Longevity of Reproductives Appears to be Common in Fukomys Mole-Rats (Rodentia, Bathyergidae)

PubMed Central

Dammann, Philip; Šumbera, Radim; Maßmann, Christina; Scherag, André; Burda, Hynek

2011-01-01

African mole-rats (Bathyergidae, Rodentia) contain several social, cooperatively breeding species with low extrinsic mortality and unusually high longevity. All social bathyergids live in multigenerational families where reproduction is skewed towards a few breeding individuals. Most of their offspring remain as reproductively inactive “helpers” in their natal families, often for several years. This “reproductive subdivision” of mole-rat societies might be of interest for ageing research, as in at least one social bathyergid (Ansell's mole-rats Fukomys anselli), breeders have been shown to age significantly slower than non-breeders. These animals thus provide excellent conditions for studying the epigenetics of senescence by comparing divergent longevities within the same genotypes without the inescapable short-comings of inter-species comparisons. It has been claimed that many if not all social mole-rat species may have evolved similar ageing patterns, too. However, this remains unclear on account of the scarcity of reliable datasets on the subject. We therefore analyzed a 20-year breeding record of Giant mole-rats Fukomys mechowii, another social bathyergid species. We found that breeders indeed lived significantly longer than helpers (ca. 1.5–2.2fold depending on the sex), irrespective of social rank or other potentially confounding factors. Considering the phylogenetic positions of F. mechowii and F. anselli and unpublished data on a third Fukomys-species (F. damarensis) showing essentially the same pattern, it seems probable that the reversal of the classic trade-off between somatic maintenance and sexual reproduction is characteristic of the whole genus and hence of the vast majority of social mole-rats. PMID:21533255

Variation in migratory behavior influences regional genetic diversity and structure among American kestrel populations (Falco sparverius) in North America

USGS Publications Warehouse

Miller, Mark P.; Mullins, Thomas D.; Parrish, John G.; Walters, Jeffrey R.; Haig, Susan M.

2012-01-01

Birds employ numerous strategies to cope with seasonal fluctuations in high-quality habitat availability. Long distance migration is a common tactic; however, partial migration is especially common among broadly distributed species. Under partial migration systems, a portion of a species migrates, whereas the remainder inhabits breeding grounds year round. In this study, we identified effects of migratory behavior variation on genetic structure and diversity of American Kestrels (Falco sparverius), a widespread partial migrant in North America. American Kestrels generally migrate; however, a resident group inhabits the southeastern United States year round. The southeastern group is designated as a separate subspecies (F. s. paulus) from the migratory group (F. s. sparverius). Using mitochondrial DNA and microsatellites from 183 and 211 individuals, respectively, we illustrate that genetic structure is stronger among nonmigratory populations, with differentiation measures ranging from 0.060 to 0.189 depending on genetic marker and analysis approach. In contrast, measures from western North American populations ranged from 0 to 0.032. These findings suggest that seasonal migratory behavior is also associated with natal and breeding dispersal tendencies. We likewise detected significantly lower genetic diversity within nonmigratory populations, reflecting the greater influence of genetic drift in small populations. We identified the signal of population expansion among nonmigratory populations, consistent with the recent establishment of higher latitude breeding locations following Pleistocene glacial retreat. Differentiation of F. s. paulus and F. s. sparverius reflected subtle differences in allele frequencies. Because migratory behavior can evolve quickly, our analyses suggest recent origins of migratory American Kestrel populations in North America.

Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding.

PubMed

Thieme, Michael; Lanciano, Sophie; Balzergue, Sandrine; Daccord, Nicolas; Mirouze, Marie; Bucher, Etienne

2017-07-07

Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on transcriptional activity of the host RNA polymerase II (Pol II) for their mobility, it was so far unclear whether Pol II is directly involved in repressing their activity. Here we show that plants defective in Pol II activity lose DNA methylation at repeat sequences and produce more extrachromosomal retrotransposon DNA upon stress in Arabidopsis and rice. We demonstrate that combined inhibition of both DNA methylation and Pol II activity leads to a strong stress-dependent mobilization of the heat responsive ONSEN retrotransposon in Arabidopsis seedlings. The progenies of these treated plants contain up to 75 new ONSEN insertions in their genome which are stably inherited over three generations of selfing. Repeated application of heat stress in progeny plants containing increased numbers of ONSEN copies does not result in increased activation of this transposon compared to control lines. Progenies with additional ONSEN copies show a broad panel of environment-dependent phenotypic diversity. We demonstrate that Pol II acts at the root of transposon silencing. This is important because it suggests that Pol II can regulate the speed of plant evolution by fine-tuning the amplitude of transposon mobility. Our findings show that it is now possible to study induced transposon bursts in plants and unlock their use to induce epigenetic and genetic diversity for crop breeding.

Monogamy and high relatedness do not preferentially favor the evolution of cooperation.

PubMed

Nonacs, Peter

2011-03-04

Phylogenetic analyses strongly associate nonsocial ancestors of cooperatively-breeding or eusocial species with monogamy. Because monogamy creates high-relatedness family groups, kin selection has been concluded to drive the evolution of cooperative breeding (i.e., the monogamy hypothesis). Although kin selection is criticized as inappropriate for modeling and predicting the evolution of cooperation, there are no examples where specific inclusive fitness-based predictions are intrinsically wrong. The monogamy hypothesis may be the first case of such a flawed calculation. A simulation model mutated helping alleles into non-cooperative populations where females mated either once or multiply. Although multiple mating produces sibling broods of lower relatedness, it also increases the likelihood that one offspring will adopt a helper role. Examining this tradeoff showed that under a wide range of conditions polygamy, rather than monogamy, allowed helping to spread more rapidly through populations. Further simulations with mating strategies as heritable traits confirmed that multiple-mating is selectively advantageous. Although cooperation evolves similarly regardless of whether dependent young are close or more distant kin, it does not evolve if they are unrelated. The solitary ancestral species to cooperative breeders may have been predominantly monogamous, but it cannot be concluded that monogamy is a predisposing state for the evolution of helping behavior. Monogamy may simply be coincidental to other more important life history characteristics such as nest defense or sequential provisioning of offspring. The differing predictive outcome from a gene-based model also supports arguments that inclusive fitness formulations poorly model some evolutionary questions. Nevertheless, cooperation only evolves when benefits are provided for kin: helping alleles did not increase in frequency in the absence of potential gains in indirect fitness. The key question, therefore, is not whether kin selection occurs, but how best to elucidate the differing evolutionary advantages of genetic relatedness versus genetic diversity.

Monogamy and high relatedness do not preferentially favor the evolution of cooperation

PubMed Central

2011-01-01

Background Phylogenetic analyses strongly associate nonsocial ancestors of cooperatively-breeding or eusocial species with monogamy. Because monogamy creates high-relatedness family groups, kin selection has been concluded to drive the evolution of cooperative breeding (i.e., the monogamy hypothesis). Although kin selection is criticized as inappropriate for modeling and predicting the evolution of cooperation, there are no examples where specific inclusive fitness-based predictions are intrinsically wrong. The monogamy hypothesis may be the first case of such a flawed calculation. Results A simulation model mutated helping alleles into non-cooperative populations where females mated either once or multiply. Although multiple mating produces sibling broods of lower relatedness, it also increases the likelihood that one offspring will adopt a helper role. Examining this tradeoff showed that under a wide range of conditions polygamy, rather than monogamy, allowed helping to spread more rapidly through populations. Further simulations with mating strategies as heritable traits confirmed that multiple-mating is selectively advantageous. Although cooperation evolves similarly regardless of whether dependent young are close or more distant kin, it does not evolve if they are unrelated. Conclusions The solitary ancestral species to cooperative breeders may have been predominantly monogamous, but it cannot be concluded that monogamy is a predisposing state for the evolution of helping behavior. Monogamy may simply be coincidental to other more important life history characteristics such as nest defense or sequential provisioning of offspring. The differing predictive outcome from a gene-based model also supports arguments that inclusive fitness formulations poorly model some evolutionary questions. Nevertheless, cooperation only evolves when benefits are provided for kin: helping alleles did not increase in frequency in the absence of potential gains in indirect fitness. The key question, therefore, is not whether kin selection occurs, but how best to elucidate the differing evolutionary advantages of genetic relatedness versus genetic diversity. PMID:21375755

Phylogeography of a vanishing North American songbird: The Painted Bunting (Passerina ciris)

USGS Publications Warehouse

Herr, C.A.; Sykes, P.W.; Klicka, J.

2011-01-01

The breeding distribution of Painted Buntings (Passerina ciris) is comprised of two allopatric populations separated by a 550-km distributional gap in the southeastern United States. Curiously, the boundary between the two recognized P. ciris subspecies does not separate the two allopatric breeding populations but instead runs roughly through the center of the interior population. Genetic relationships among these subspecies, and the allopatric breeding populations of Painted Bunting, have not been assessed. Given the recent decline in overall abundance of this species, such an assessment is warranted. We sampled birds from 15 localities (138 individuals) and identified 35 distinct haplotypes, six belonging to the Atlantic Coast population and 26 to the interior population, with three shared by both populations. AMOVA results showed that a significantly greater portion of the total genetic variance is explained when grouping birds by the interior and Atlantic Coast populations rather than by subspecies. Furthermore, our data indicate that the Atlantic Coast and interior populations represent independently evolving taxa, with no measureable gene flow between them. Although recently diverged (26,000-115,000 years ago), these isolated bunting populations represent incipient species. For development of conservation strategies, we suggest that the Atlantic Coast and interior populations be recognized as separate management units. ?? 2011 Springer Science+Business Media B.V.

Extra-Pair Mating and Evolution of Cooperative Neighbourhoods

PubMed Central

Eliassen, Sigrunn; Jørgensen, Christian

2014-01-01

A striking but unexplained pattern in biology is the promiscuous mating behaviour in socially monogamous species. Although females commonly solicit extra-pair copulations, the adaptive reason has remained elusive. We use evolutionary modelling of breeding ecology to show that females benefit because extra-pair paternity incentivizes males to shift focus from a single brood towards the entire neighbourhood, as they are likely to have offspring there. Male-male cooperation towards public goods and dear enemy effects of reduced territorial aggression evolve from selfish interests, and lead to safer and more productive neighbourhoods. The mechanism provides adaptive explanations for the common empirical observations that females engage in extra-pair copulations, that neighbours dominate as extra-pair sires, and that extra-pair mating correlates with predation mortality and breeding density. The models predict cooperative behaviours at breeding sites where males cooperate more towards public goods than females. Where maternity certainty makes females care for offspring at home, paternity uncertainty and a potential for offspring in several broods make males invest in communal benefits and public goods. The models further predict that benefits of extra-pair mating affect whole nests or neighbourhoods, and that cuckolding males are often cuckolded themselves. Derived from ecological mechanisms, these new perspectives point towards the evolution of sociality in birds, with relevance also for mammals and primates including humans. PMID:24987839

Darbishire expands his vision of heredity from Mendelian genetics to inherited memory.

PubMed

Wood, Roger J

2015-10-01

The British biologist A.D. Darbishire (1879-1915) responded to the rediscovery in 1900 of Mendel's theory of heredity by testing it experimentally, first in Oxford, then in Manchester and London. He summarised his conclusions in a textbook 'Breeding and the Mendelian Discovery' (1911), in which he questioned whether Mendelism alone could explain all aspects of practical breeding experience. Already he had begun to think about an alternative theory to give greater emphasis to the widely held conviction among breeders regarding the inheritance of characteristics acquired during an individual's life. Redefining heredity in terms of a germ-plasm based biological memory, he used vocabulary drawn partly from sources outside conventional science, including the metaphysical/vitalistic writings of Samuel Butler and Henri Bergson. An evolving hereditary memory fitted well with the conception of breeding as a creative art aimed at greater economic efficiency. For evolution beyond human control he proposed a self-modifying process, claiming it to surpass in efficiency the chancy mechanism of natural selection proposed by Darwin. From his writings, including early chapters of an unfinished book entitled 'An Introduction to a Biology', we consider how he reached these concepts and how they relate to later advances in understanding the genome and the genetic programme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of fire on bird populations in mixed-grass prairie: Chapter 8

USGS Publications Warehouse

Johnson, Douglas H.; Knopf, F.L.; Samson, F.B.

1997-01-01

The mixed-grass prairie is one of the largest ecosystems in North America, originally covering about 69 million hectares (Bragg and Steuter 1995). Although much of the natural vegetation has been replaced by cropland and other uses (Samson and Knopf 1994, Bragg and Steuter 1995), significant areas have been preserved in national wildlife refuges, waterfowl production areas, state game management areas, and nature preserves. Mixed-grass prairie evolved with fire (Bragg 1995), and fire is frequently used as a management tool for prairie (Berkey et al. 1993). Much of the mixed-grass prairie that has been protected is managed to enhance the reproductive success of waterfowl and other gamebirds, but nongame birds now are receiving increasing emphasis. Despite the importance of the area to numerous species of birds and the aggressive management applied to many sites, relatively little is known about the effects of fire on the suitability of mixed-grass prairie for breeding birds. Several studies have examined effects of fire on breeding birds in the tallgrass prairie (e.g., Tester and Marshall 1961, Eddleman 1974, Halvorsen and Anderson 1983, Westenmeier and Buhnerkempe 1983, Zimmerman 1992, Herkert 1994), in western sagebrush grasslands (Peterson and Best 1987), and in shrubsteppe (Bock and Bock 1987). Studies of fire effects in the mixed-grass prairie are limited. Huber and Steuter (1984) examined the effects on birds during the breeding season following an early-May prescribed burn on a 122-ha site in South Dakota. They contrasted the bird populations on that site to those on a nearby 462-ha unburned site that had been lightly grazed by bison (Bison bison). Pylypec (1991) monitored breeding bird populations occurring in fescue prairies of Canada on a single 12.9-ha burned area and on an adjacent 5.6-ha unburned fescue prairie for three years after a prescribed burn. This chapter describes the effects of prescribed fire on common terrestrial birds at a mixed-grass prairie site in east-central North Dakota. Birds were censused annually during 1972-95 on seven plots subjected to various regimes of prescribed fire.

Bird populations as sentinels of endocrine disrupting chemicals.

PubMed

Carere, Claudio; Costantini, David; Sorace, Alberto; Santucci, Daniela; Alleva, Enrico

2010-01-01

Exposure to endocrine disrupting chemicals (EDCs) is a widespread phenomenon in nature. Although the mechanisms of action of EDCs are actively studied, the consequences of endocrine disruption (ED) at the population level and the adaptations evolved to cope with chronic EDC exposure have been overlooked. Birds probably represent the animal taxon most successfully adapted to synanthropic life. Hence, birds share with humans a similar pattern of exposure to xenobiotics. In this article, we review case studies on patterns of behaviour that deviate from the expectation in bird species exposed to EDCs. We provide behavioural and ecological parameters to be used as endpoints of ED; methodological requirements and caveats based on species-specific life-history traits, behavioural repertoires, developmental styles, and possibility of captive breeding; a list of species that could be used as sentinels to assess the quality of man-made environment.

Subsocial Cockroaches Nauphoeta cinerea Mate Indiscriminately with Kin Despite High Costs of Inbreeding.

PubMed

Bouchebti, Sofia; Durier, Virginie; Pasquaretta, Cristian; Rivault, Colette; Lihoreau, Mathieu

Many animals have evolved strategies to reduce risks of inbreeding and its deleterious effects on the progeny. In social arthropods, such as the eusocial ants and bees, inbreeding avoidance is typically achieved by the dispersal of breeders from their native colony. However studies in presocial insects suggest that kin discrimination during mate choice may be a more common mechanism in socially simpler species with no reproductive division of labour. Here we examined this possibility in the subsocial cockroach Nauphoeta cinerea, a model species for research in sexual selection, where males establish dominance hierarchies to access females and control breeding territories. When given a binary choice between a sibling male and a non-sibling male that had the opportunity to establish a hierarchy prior to the tests, females mated preferentially with the dominant male, irrespective of kinship or body size. Despite the lack of kin discrimination during mate choice, inbred-mated females incurred significant fitness costs, producing 20% less offspring than outbred-mated females. We discuss how the social mating system of this territorial cockroach may naturally limit the probability of siblings to encounter and reproduce, without the need for evolving active inbreeding avoidance mechanisms, such as kin recognition.

Subsocial Cockroaches Nauphoeta cinerea Mate Indiscriminately with Kin Despite High Costs of Inbreeding

PubMed Central

Bouchebti, Sofia; Durier, Virginie; Pasquaretta, Cristian; Rivault, Colette; Lihoreau, Mathieu

2016-01-01

Many animals have evolved strategies to reduce risks of inbreeding and its deleterious effects on the progeny. In social arthropods, such as the eusocial ants and bees, inbreeding avoidance is typically achieved by the dispersal of breeders from their native colony. However studies in presocial insects suggest that kin discrimination during mate choice may be a more common mechanism in socially simpler species with no reproductive division of labour. Here we examined this possibility in the subsocial cockroach Nauphoeta cinerea, a model species for research in sexual selection, where males establish dominance hierarchies to access females and control breeding territories. When given a binary choice between a sibling male and a non-sibling male that had the opportunity to establish a hierarchy prior to the tests, females mated preferentially with the dominant male, irrespective of kinship or body size. Despite the lack of kin discrimination during mate choice, inbred-mated females incurred significant fitness costs, producing 20% less offspring than outbred-mated females. We discuss how the social mating system of this territorial cockroach may naturally limit the probability of siblings to encounter and reproduce, without the need for evolving active inbreeding avoidance mechanisms, such as kin recognition. PMID:27655156

Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action.

PubMed

Griswold, Cortland K

2015-12-21

Epistatic gene action occurs when mutations or alleles interact to produce a phenotype. Theoretically and empirically it is of interest to know whether gene interactions can facilitate the evolution of diversity. In this paper, we explore how epistatic gene action affects the additive genetic component or heritable component of multivariate trait variation, as well as how epistatic gene action affects the evolvability of multivariate traits. The analysis involves a sexually reproducing and recombining population. Our results indicate that under stabilizing selection conditions a population with a mixed additive and epistatic genetic architecture can have greater multivariate additive genetic variation and evolvability than a population with a purely additive genetic architecture. That greater multivariate additive genetic variation can occur with epistasis is in contrast to previous theory that indicated univariate additive genetic variation is decreased with epistasis under stabilizing selection conditions. In a multivariate setting, epistasis leads to less relative covariance among individuals in their genotypic, as well as their breeding values, which facilitates the maintenance of additive genetic variation and increases a population׳s evolvability. Our analysis involves linking the combinatorial nature of epistatic genetic effects to the ancestral graph structure of a population to provide insight into the consequences of epistasis on multivariate trait variation and evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Litter size at birth in purebred dogs--a retrospective study of 224 breeds.

PubMed

Borge, Kaja Sverdrup; Tønnessen, Ragnhild; Nødtvedt, Ane; Indrebø, Astrid

2011-03-15

Despite the long history of purebred dogs and the large number of existing breeds, few studies of canine litter size based upon a large number of breeds exist. Previous studies are either old or include only one or a few selected breeds. The aim of this large-scale retrospective study was to estimate the mean litter size in a large population of purebred dogs and to describe some factors that might influence the litter size. A total of 10,810 litters of 224 breeds registered in the Norwegian Kennel Club from 2006 to 2007 were included in the study. The overall mean litter size at birth was 5.4 (± 0.025). A generalized linear mixed model with a random intercept for breed revealed that the litter size was significantly influenced by the size of the breed, the method of mating and the age of the bitch. A significant interaction between breed size and age was detected, in that the expected number of puppies born decreased more for older bitches of large breeds. Mean litter size increased with breed size, from 3.5 (± 0.04) puppies in miniature breeds to 7.1 (± 0.13) puppies in giant breeds. No effect on litter size was found for the season of birth or the parity of the bitch. The large number of breeds and the detail of the registered information on the litters in this study are unique. In conclusion, the size of the breed, the age of the bitch and the method of mating were found to influence litter size in purebred dogs when controlling for breed, with the size of the breed as the strongest determinant. Copyright © 2011 Elsevier Inc. All rights reserved.

Plant Glandular Trichomes as Targets for Breeding or Engineering of Resistance to Herbivores

PubMed Central

Glas, Joris J.; Schimmel, Bernardus C. J.; Alba, Juan M.; Escobar-Bravo, Rocío; Schuurink, Robert C.; Kant, Merijn R.

2012-01-01

Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant’s secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant’s resistance to pests. PMID:23235331

Many to flower, few to fruit: the reproductive biology of Hamamelis virginiana (Hamamelidaceae).

PubMed

Anderson, Gregory J; Hill, James D

2002-01-01

Hamamelis virginiana flowers from late September to late November. In 1977, we began studying the reproductive biology of this eastern North American arborescent shrub by examining floral phenology and rewards, pollen-ovule ratios, breeding system, pollination, pollinator and resource limitation, and seed dispersal. The homogamous, self-incompatible flowers emit a faint odor, bear nectar with sucrose ratios typical of bee- and fly-pollinated flowers, and produce abundant sticky pollen. Flowers were visited infrequently by insects representing six orders. Flies were the most common floral visitors, specifically members of the genus Bradysia, but small bees also carried high percentages of Hamamelis pollen. Despite high pollen/ovule ratios (11 445 grains/ovule), bees and flies are likely pollinators, as experiments indicate wind pollination is less likely. Pollen quantity and resource availability did not appear to limit reproductive output, but pollen quality did. Tests of >40 000 flowers showed natural fruit set to be <1%. The flowering time, breeding system, and clumped distribution of plants, likely due in part to limited seed dispersal, combine to yield this remarkably low fruit set. Because all other species of Hamamelis flower from late winter to early summer, it may be that H. virginiana evolved a fall flowering phenology to avoid competition for pollinators with the closely related H. vernalis.

Canine parvovirus 2c infection in central Portugal.

PubMed

João Vieira, Maria; Silva, Eliane; Oliveira, João; Luísa Vieira, Ana; Decaro, Nicola; Desario, Costantina; Muller, Alexandra; Carvalheira, Júlio; Buonavoglia, Canio; Thompson, Gertrude

2008-07-01

Canine parvovirus (CPV) has been evolving, generating new genetic and antigenic variants throughout the world. This study was conducted to determine the types of CPV circulating in dogs in Figueira da Foz, Portugal. Thirty fecal samples, collected between 2006 and 2007 from dogs with clinical signs of CPV infection, were tested for CPV by a rapid, in-clinic, enzyme-linked immunosorbent assay (ELISA)/immunomigration test, by conventional real-time polymerase chain reaction (PCR), and by minor-groove binding TaqMan PCR. Of the 29 PCR-positive samples, 15 were identified as CPV-2b and 14 as CPV-2c. No CPV-2a was detected. The sensitivity of the ELISA test was 82.76% compared with the PCR assays. No significant associations were found between CPV type, clinical outcome, breed, vaccination status, or age.

Terrestrial reproduction as an adaptation to steep terrain in African toads

PubMed Central

Müller, Hendrik; Hafner, Julian; Penner, Johannes; Mazuch, Tomáš; Rödel, Mark-Oliver; Loader, Simon P.

2017-01-01

How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters. We reconstruct and date the most complete species-level molecular phylogeny and estimate ancestral states for reproductive modes. By correlating continuous habitat measurements from remote sensing data and locality records with life-history transitions, we discover that terrestrial modes of reproduction, including viviparity evolved multiple times in this group, most often directly from fully aquatic modes. Terrestrial modes of reproduction are strongly correlated with steep terrain and low availability of accumulated water sources. Evolutionary transitions to terrestrial modes of reproduction occurred synchronously with or after transitions in habitat, and we, therefore, interpret terrestrial breeding as an adaptation to these abiotic conditions, rather than an exaptation that facilitated the colonization of montane habitats. PMID:28356450

Behavioural adaptations of birds to environments where evaporation is high and water is in short supply.

PubMed

Davies, S J

1982-01-01

1. Behaviour that reduces the heat load or evaporation experienced by birds living in arid areas is reviewed. Many species have evolved hunting behaviour that enables them to remain inactive during the hottest parts of the day and thus greatly reduce the amount of metabolic heat that they need to dissipate. Flights to water are made at low ambient temperatures, either early in the morning or late in the evening. Fighting is rare in many species of desert birds, avoiding the excess generation of heat by this activity. Many arid zone birds maintain long-lasting pair bonds, avoiding the necessity for active, elaborate display before breeding and again reducing activity. 2. The observations on nomadism are discussed. No unifying principles that might control the behaviour of birds seeking widely separated areas of abundance of food have yet emerged. 3. Some species have evolved mechanisms, embodied in behavioural characteristics, that ensure that the eggs and chicks are sheltered from high temperatures and are provided with adequate moisture. 4. Birds have evolved many different kinds of behavioural adaptation to arid zones and representatives from many avian families live there, apparently successfully.

Terrestrial reproduction as an adaptation to steep terrain in African toads.

PubMed

Liedtke, H Christoph; Müller, Hendrik; Hafner, Julian; Penner, Johannes; Gower, David J; Mazuch, Tomáš; Rödel, Mark-Oliver; Loader, Simon P

2017-03-29

How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters. We reconstruct and date the most complete species-level molecular phylogeny and estimate ancestral states for reproductive modes. By correlating continuous habitat measurements from remote sensing data and locality records with life-history transitions, we discover that terrestrial modes of reproduction, including viviparity evolved multiple times in this group, most often directly from fully aquatic modes. Terrestrial modes of reproduction are strongly correlated with steep terrain and low availability of accumulated water sources. Evolutionary transitions to terrestrial modes of reproduction occurred synchronously with or after transitions in habitat, and we, therefore, interpret terrestrial breeding as an adaptation to these abiotic conditions, rather than an exaptation that facilitated the colonization of montane habitats. © 2017 The Author(s).

Experimental demonstration of the fitness consequences of an introduced parasite of Darwin's finches.

PubMed

Koop, Jennifer A H; Huber, Sarah K; Laverty, Sean M; Clayton, Dale H

2011-05-11

Introduced parasites are a particular threat to small populations of hosts living on islands because extinction can occur before hosts have a chance to evolve effective defenses. An experimental approach in which parasite abundance is manipulated in the field can be the most informative means of assessing a parasite's impact on the host. The parasitic fly Philornis downsi, recently introduced to the Galápagos Islands, feeds on nestling Darwin's finches and other land birds. Several correlational studies, and one experimental study of mixed species over several years, reported that the flies reduce host fitness. Here we report the results of a larger scale experimental study of a single species at a single site over a single breeding season. We manipulated the abundance of flies in the nests of medium ground finches (Geospiza fortis) and quantified the impact of the parasites on nestling growth and fledging success. We used nylon nest liners to reduce the number of parasites in 24 nests, leaving another 24 nests as controls. A significant reduction in mean parasite abundance led to a significant increase in the number of nests that successfully fledged young. Nestlings in parasite-reduced nests also tended to be larger prior to fledging. Our results confirm that P. downsi has significant negative effects on the fitness of medium ground finches, and they may pose a serious threat to other species of Darwin's finches. These data can help in the design of management plans for controlling P. downsi in Darwin's finch breeding populations.

Study on Reproductive Biology of Rhododendron longipedicellatum: A Newly Discovered and Special Threatened Plant Surviving in Limestone Habitat in Southeast Yunnan, China

PubMed Central

Li, Taiqiang; Liu, Xiongfang; Li, Zhenghong; Ma, Hong; Wan, Youming; Liu, Xiuxian; Fu, Liyong

2018-01-01

Rhododendron longipedicellatum is a narrow endemic species and a subject of urgent demand in the domestic market and overseas. Its fascinating shapes, brilliantly gilvous flowers, and unusual flowering time endow this species with extremely high ornamental value. However, only five wild populations of R. longipedicellatum surviving in limestone habitat have been found through elaborate field investigation, and the number of the populations decreases further or is even confronted with risk of extinction due to the damage of human activities. To enhance the protection and utilization of R. longipedicellatum, this study systematically investigated several important aspects of reproductive biology, including floral syndrome, pollen viability and stigma receptivity, petal color reflectance, breeding system, and pollination biology. The results demonstrated that arched styles not only create obvious herkogamy that avoide self-pollination, but also effectively reduce rain damage to the intrinsic characteristics of the stigma surface secretions, promoting the female fitness of R. longipedicellatum in poor weather. Pollen viability maintained a high level over the flowering period. The reflectance spectrum of petals had two peaks at wavelengths of 360 and 580 nm. Tests of OCI, P/O and artificial pollination all indicated that R. longipedicellatum was self-compatible and that the breeding system was mixed mating. Geitonogamy mediated by Bombus braccatus was the primary pollination route in the natural environment, which suggested that the breeding system of R. longipedicellatum might be evolving from selfing to outcrossing. The pollination vector of R. longipedicellatum was very specific, in that only B. braccatus was confirmed to deliver pollen to the stigmas. Visitation frequency was influenced by the activity rhythms and resource requirements of the different castes (i.e., sex). B. braccatus workers were the most effective pollinators because of higher visitation frequency and more effective contribution to fruit production, whereas the presence of B. braccatus males might enhance pollen flow within the population to a certain extent. Finally, these findings not only provided a reliable theoretical basis for hybridization breeding of R. longipedicellatum as parents, but also laid a solid foundation for further molecular biology studies to more broadly reveal the mechanisms of its endangerment in the future. PMID:29445383

Two distinct classes of QTL determine rust resistance in sorghum.

PubMed

Wang, Xuemin; Mace, Emma; Hunt, Colleen; Cruickshank, Alan; Henzell, Robert; Parkes, Heidi; Jordan, David

2014-12-31

Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

Comparison of molecular breeding values based on within- and across-breed training in beef cattle.

PubMed

Kachman, Stephen D; Spangler, Matthew L; Bennett, Gary L; Hanford, Kathryn J; Kuehn, Larry A; Snelling, Warren M; Thallman, R Mark; Saatchi, Mahdi; Garrick, Dorian J; Schnabel, Robert D; Taylor, Jeremy F; Pollak, E John

2013-08-16

Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported. Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype. With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero. Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set.

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

PubMed Central

Makina, Sithembile O.; Muchadeyi, Farai C.; van Marle-Köster, Este; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds. PMID:25295053

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel.

PubMed

Makina, Sithembile O; Muchadeyi, Farai C; van Marle-Köster, Este; MacNeil, Michael D; Maiwashe, Azwihangwisi

2014-01-01

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.

Race Characterization of Phytophthora root rot on Capsicum in Taiwan as a Basis for Anticipatory Resistance Breeding.

PubMed

Barchenger, Derek W; Sheu, Zong-Ming; Kumar, Sanjeet; Lin, Shih-Wen; Burlakoti, Rishi R; Bosland, Paul W

2018-02-27

Peppers (Capsicum sp.) are an increasingly important crop because of their use as a vegetable, spice, and food colorant. The oomycete Phytophthora capsici is one of the most devastating pathogens to pepper production worldwide, causing more than $100 million in losses annually. Developing cultivars resistant to P. capsici is challenging because of the many physiological races that exist and new races that are continuously evolving. This problem is confounded by the lack of a universal system of race characterization. As a basis to develop a global anticipatory breeding program, New Mexico Recombinant Inbred Lines (NMRILs) functioned as a host differential for Phytophthora root rot to characterize the race structure of P. capsici populations in Taiwan. Using the NMRILs, 24 new races were identified, illustrating the utility and usefulness of the NMRILs for anticipatory breeding. Virulence of P. capsici was observed to be geographically specific and in two virulence clusters. Interestingly, all but two isolates collected in 2016 were the A2 mating type, which is a shift from the predominantly A1 mating type isolates collected prior to 2008. The NMRILs host differential provides an approach for scientists to work together on a global scale when breeding for resistance as well as on a local level for regional gene deployment. Additionally, we propose that the current race numbering system, which has no biological meaning, be supplemented with the virulence phenotype, based on the susceptible NMRILs to a given isolate. This work provides insights into the population dynamics of P. capsici and interactions within the highly complex Capsicum-Phytophthora pathosystem, and offers a basis for similar research in other crops.

Genetic variation in resistance of the preimplantation bovine embryo to heat shock.

PubMed

Hansen, Peter J

2014-12-01

Reproduction is among the physiological functions in mammals most susceptible to disruption by hyperthermia. Many of the effects of heat stress on function of the oocyte and embryo involve direct effects of elevated temperature (i.e. heat shock) on cellular function. Mammals limit the effects of heat shock by tightly regulating body temperature. This ability is genetically controlled: lines of domestic animals have been developed with superior ability to regulate body temperature during heat stress. Through experimentation in cattle, it is also evident that there is genetic variation in the resistance of cells to the deleterious effects of elevated temperature. Several breeds that were developed in hot climates, including Bos indicus (Brahman, Gir, Nelore and Sahiwal) and Bos taurus (Romosinuano and Senepol) are more resistant to the effects of elevated temperature on cellular function than breeds that evolved in cooler climates (Angus, Holstein and Jersey). Genetic differences are expressed in the preimplantation embryo by Day 4-5 of development (after embryonic genome activation). It is not clear whether genetic differences are expressed in cells in which transcription is repressed (oocytes >100 µm in diameter or embryos at stages before embryonic genome activation). The molecular basis for cellular thermotolerance has also not been established, although there is some suggestion for involvement of heat shock protein 90 and the insulin-like growth factor 1 system. Given the availability of genomic tools for genetic selection, identification of genes controlling cellular resistance to elevated temperature could be followed by progress in selection for those genes within the populations in which they exist. It could also be possible to introduce genes from thermotolerant breeds into thermally sensitive breeds. The ability to edit the genome makes it possible to design new genes that confer protection of cells from stresses like heat shock.

Sharing mates and nest boxes is associated with female "friendship" in European starlings, Sturnus vulgaris.

PubMed

Henry, Laurence; Bourguet, Cécile; Coulon, Marion; Aubry, Christine; Hausberger, Martine

2013-02-01

Breeding decisions in birds involve both mate and nest choice, and there is increasing evidence that social influences may modulate individual choices. Female preferences may be affected by other females' preferences and mutual choice cannot always be excluded, which makes the whole pattern more complex than assumed by most sexual selection models. Social transmission may be facilitated by particular social bonds, therefore prebreeding social networks may influence later mate choices. The other case where females share mate or resources is polygyny, generally viewed to only benefit males. If mutual benefits may arise then mechanisms should evolve to reduce the reproductive cost for females such as to reduce the cost of aggression by sharing their mate with a preferred same-sex social partner. We tested the hypothesis that females' mating decisions may be influenced by the prebreeding social network and that social partner relations established prior to breeding may share decisions (mate/sites) in a facultatively polygynous species, the European starling. Two experiments were designed to test the relative importance of male or nest by following the whole dynamics of the breeding cycle from the prebreeding period until mate and nest selection. In both cases socially isolated females tended to be excluded from breeding, while prebreeding social partners tended to share mates and to nest in close proximity, mate copying leading in some case to polygyny. The final pattern resulted both from female "likes and dislikes" and male preferences for some females. Aggressive interactions between females were rare. Vocal sharing between females may have been a clue for males as to the degree of social integration of these females. PsycINFO Database Record (c) 2013 APA, all rights reserved

Pivoting the Plant Immune System from Dissection to Deployment

PubMed Central

Dangl, Jeffery L.; Horvath, Diana M.; Staskawicz, Brian J.

2013-01-01

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls. PMID:23950531

Laser safety management.

PubMed

Champion, J

2000-08-01

LASER is an acronym for Light Amplification by Stimulated Emission of Radiation. Since the first working laser was demonstrated in 1960 the laser has evolved from being viewed as a weapon, courtesy of the film industry, to its current position as a commonplace medical device within the healthcare industry. As perioperative staff we have become very familiar with the therapeutic use of this device. It is my experience however that, just occasionally, we are guilty of the old adage 'familiarity breeds contempt'. We must remember that the very same features which make lasers so useful in healthcare may also represent major health hazards to patients, staff and others.

Population structure and inbreeding from pedigree analysis of purebred dogs.

PubMed

Calboli, Federico C F; Sampson, Jeff; Fretwell, Neale; Balding, David J

2008-05-01

Dogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, >90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Psi for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers.

PubMed

Bigi, D; Marelli, S P; Randi, E; Polli, M

2015-12-01

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.

Corticosterone manipulation reveals differences in hierarchical organization of multidimensional reproductive trade-offs in r-strategist and K-strategist females.

PubMed

Lancaster, L T; Hazard, L C; Clobert, J; Sinervo, B R

2008-03-01

Life history trade-offs are often hierarchical with decisions at one level affecting lower level trade-offs. We investigated trade-off structure in female side-blotched lizards (Uta stansburiana), which exhibit two evolved strategies: yellow-throated females are K-strategists and orange-throated are r-strategists. Corticosterone treatment was predicted to differentially organize these females' reproductive decisions. Corticosterone-treated yellow females suppressed reproduction but survived well, and augmented egg mass without decreasing clutch size. Conversely, corticosterone enhanced mortality and reproductive rates in orange females, and increased egg mass only after lengthy exposure. Corticosterone did not affect post-laying condition, suggesting that corticosterone increased egg mass through enhanced energy acquisition (income breeding). Corticosterone enhanced survival of lightweight females, but decreased survival of heavy females, introducing a foraging vs. predation trade-off. We conclude that rather than being a direct, functional relationship, observed trade-offs between offspring size and number represent evolved differences in hierarchical organization of multidimensional trade-offs, particularly in response to stress.

Evolution of Parasitism in Insect-transmitted Plant Nematodes

PubMed Central

Giblin-Davis, R. M.; Davies, K. A.; Morris, K.; Thomas, W. K.

2003-01-01

Nematode-insect associations have evolved many times in the phylum Nematoda, but these lineages involve plant parasitism only in the Secernentean orders Aphelenchida and Tylenchida. In the Aphelenchida (Aphelenchoidoidea), Bursaphelenchus xylophilus (Pine wood nematode), B. cocophilus (Red ring or Coconut palm nematode) (Parasitaphelenchidae), and the many potential host-specific species of Schistonchus (fig nematodes) (Aphelenchoididae) nematode-insect interactions probably evolved independently from dauer-forming, mycophagous ancestors that were phoretically transmitted to breeding sites of their insect hosts in plants. Mycophagy probably gave rise to facultative or obligate plant-parasitism because of opportunities due to insect host switches or peculiarities in host behavior. In the Tylenchida, there is one significant radiation of insect-associated plant parasites involving Fergusobia nematodes (Fergusobiinae: Neotylenchidae) and Fergusonina (Fergusoninidae) flies as mutualists that gall myrtaceous plant buds or leaves. These dicyclic nematodes have different phases that are parasitic in either the insect or the plant hosts. The evolutionary origin of this association is unclear. PMID:19265987

Estimation of mating system parameters in an evolving gynodioecous population of cultivated sunflower (Helianthus annuus L.)

PubMed Central

Roumet, M; Ostrowski, M-F; David, J; Tollon, C; Muller, M-H

2012-01-01

Cultivated plants have been molded by human-induced selection, including manipulations of the mating system in the twentieth century. How these manipulations have affected realized parameters of the mating system in freely evolving cultivated populations is of interest for optimizing the management of breeding populations, predicting the fate of escaped populations and providing material for experimental evolution studies. To produce modern varieties of sunflower (Helianthus annuus L.), self-incompatibility has been broken, recurrent generations of selfing have been performed and male sterility has been introduced. Populations deriving from hybrid-F1 varieties are gynodioecious because of the segregation of a nuclear restorer of male fertility. Using both phenotypic and genotypic data at 11 microsatellite loci, we analyzed the consanguinity status of plants of the first three generations of such a population and estimated parameters related to the mating system. We showed that the resource reallocation to seed in male-sterile individuals was not significant, that inbreeding depression on seed production averaged 15–20% and that cultivated sunflower had acquired a mixed-mating system, with ∼50% of selfing among the hermaphrodites. According to theoretical models, the female advantage and the inbreeding depression at the seed production stage were too low to allow the persistence of male sterility. We discuss our methods of parameter estimation and the potential of such study system in evolutionary biology. PMID:21915147

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

PubMed

Kim, Nam-Hoon; Jayakodi, Murukarthick; Lee, Sang-Choon; Choi, Beom-Soon; Jang, Woojong; Lee, Junki; Kim, Hyun Hee; Waminal, Nomar E; Lakshmanan, Meiyappan; van Nguyen, Binh; Lee, Yun Sun; Park, Hyun-Seung; Koo, Hyun Jo; Park, Jee Young; Perumal, Sampath; Joh, Ho Jun; Lee, Hana; Kim, Jinkyung; Kim, In Seo; Kim, Kyunghee; Koduru, Lokanand; Kang, Kyo Bin; Sung, Sang Hyun; Yu, Yeisoo; Park, Daniel S; Choi, Doil; Seo, Eunyoung; Kim, Seungill; Kim, Young-Chang; Hyun, Dong Yun; Park, Youn-Il; Kim, Changsoo; Lee, Tae-Ho; Kim, Hyun Uk; Soh, Moon Soo; Lee, Yi; In, Jun Gyo; Kim, Heui-Soo; Kim, Yong-Min; Yang, Deok-Chun; Wing, Rod A; Lee, Dong-Yup; Paterson, Andrew H; Yang, Tae-Jin

2018-03-31

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Comparison of molecular breeding values based on within- and across-breed training in beef cattle

PubMed Central

2013-01-01

Background Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed predictors for the technology to be fully applied in the beef industry. The efficacies of genomic predictors trained in one breed and utilized to predict genetic merit in differing breeds based on simulation studies have been reported, as have the efficacies of predictors trained using data from multiple breeds to predict the genetic merit of purebreds. However, comparable studies using beef cattle field data have not been reported. Methods Molecular breeding values for weaning and yearling weight were derived and evaluated using a database containing BovineSNP50 genotypes for 7294 animals from 13 breeds in the training set and 2277 animals from seven breeds (Angus, Red Angus, Hereford, Charolais, Gelbvieh, Limousin, and Simmental) in the evaluation set. Six single-breed and four across-breed genomic predictors were trained using pooled data from purebred animals. Molecular breeding values were evaluated using field data, including genotypes for 2227 animals and phenotypic records of animals born in 2008 or later. Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype. Results With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training. Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30). When molecular breeding values were evaluated in breeds that were not in the training set, estimated genetic correlations clustered around zero. Conclusions Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set. For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set. PMID:23953034

A simple language to script and simulate breeding schemes: the breeding scheme language

USDA-ARS?s Scientific Manuscript database

It is difficult for plant breeders to determine an optimal breeding strategy given that the problem involves many factors, such as target trait genetic architecture and breeding resource availability. There are many possible breeding schemes for each breeding program. Although simulation study may b...

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

PubMed

Agha, S H; Pilla, F; Galal, S; Shaat, I; D'Andrea, M; Reale, S; Abdelsalam, A Z A; Li, M H

2008-06-01

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.

Description and typology of intensive Chios dairy sheep farms in Greece.

PubMed

Gelasakis, A I; Valergakis, G E; Arsenos, G; Banos, G

2012-06-01

The aim was to assess the intensified dairy sheep farming systems of the Chios breed in Greece, establishing a typology that may properly describe and characterize them. The study included the total of the 66 farms of the Chios sheep breeders' cooperative Macedonia. Data were collected using a structured direct questionnaire for in-depth interviews, including questions properly selected to obtain a general description of farm characteristics and overall management practices. A multivariate statistical analysis was used on the data to obtain the most appropriate typology. Initially, principal component analysis was used to produce uncorrelated variables (principal components), which would be used for the consecutive cluster analysis. The number of clusters was decided using hierarchical cluster analysis, whereas, the farms were allocated in 4 clusters using k-means cluster analysis. The identified clusters were described and afterward compared using one-way ANOVA or a chi-squared test. The main differences were evident on land availability and use, facility and equipment availability and type, expansion rates, and application of preventive flock health programs. In general, cluster 1 included newly established, intensive, well-equipped, specialized farms and cluster 2 included well-established farms with balanced sheep and feed/crop production. In cluster 3 were assigned small flock farms focusing more on arable crops than on sheep farming with a tendency to evolve toward cluster 2, whereas cluster 4 included farms representing a rather conservative form of Chios sheep breeding with low/intermediate inputs and choosing not to focus on feed/crop production. In the studied set of farms, 4 different farmer attitudes were evident: 1) farming disrupts sheep breeding; feed should be purchased and economies of scale will decrease costs (mainly cluster 1), 2) only exercise/pasture land is necessary; at least part of the feed (pasture) must be home-grown to decrease costs (clusters 1 and 4), 3) providing pasture to sheep is essential; on-farm feed production decreases costs (mainly cluster 3), and 4) large-scale farming (feed production and cash crops) does not disrupt sheep breeding; all feed must be produced on-farm to decrease costs (mainly cluster 3). Conducting a profitability analysis among different clusters, exploring and discovering the most beneficial levels of intensified management and capital investment should now be considered. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

"Boldness" in the domestic dog differs among breeds and breed groups.

PubMed

Starling, Melissa J; Branson, Nicholas; Thomson, Peter C; McGreevy, Paul D

2013-07-01

"Boldness" in dogs is believed to be one end of the shy-bold axis, representing a super-trait. Several personality traits fall under the influence of this super-trait. Previous studies on boldness in dogs have found differences among breeds, but grouping breeds on the basis of behavioural similarities has been elusive. This study investigated differences in the expression of boldness among dog breeds, kennel club breed groups, and sub-groups of kennel club breed groups by way of a survey on dog personality circulated among Australian dog-training clubs and internet forums and lists. Breed had a significant effect on boldness (F=1.63, numDF=111, denDF=272, p<0.001), as did breed group (F=10.66, numDF=8, denDF=772, p<0.001). Herding and gundog groups were broken into sub-groups based on historic breed purpose. Retrievers were significantly bolder than flushing and pointing breeds (Reg. Coef.=2.148; S.E.=0.593; p<0.001), and tending and loose-eyed herding breeds were bolder than heading and cattle-herding breeds (Reg. Coef.=1.744; S.E.=0.866; p=0.045 and Reg. Coef.=1.842; S.E.=0.693; p=0.0084, respectively). This study supports the existence of the shy-bold continuum in dogs. Differences in boldness among groups and sub-groups suggest that behavioural tendencies may be influenced by historical purpose regardless of whether that purpose still factors in selective breeding. Copyright © 2013 Elsevier B.V. All rights reserved.

Ancestrality and evolution of trait syndromes in finches (Fringillidae).

PubMed

Ponge, Jean-François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre-Yves; Théry, Marc; Guilbert, Éric

2017-12-01

Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from "ancestral" to "derived" strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabilized (collectively called B strategy). We analyzed the correlated evolution of four syndromes, summarizing the covariation between 53 traits, respectively, involved in ecological specialization, r-K gradient, sexual selection, and dispersal/social behaviors in 81 species representative of Fringillidae, a bird family with available natural history information and that shows variability for all these traits. The ancestrality of strategy A was supported for three of the four syndromes, the ancestrality of generalism having a weaker support, except for the core group Carduelinae (69 species). It appeared that two different B-strategies evolved from the ancestral state A, both associated with highly predictable environments: one in poorly seasonal environments, called B1, with species living permanently in lowland tropics, with "slow pace of life" and weak sexual dimorphism, and one in highly seasonal environments, called B2, with species breeding out-of-the-tropics, migratory, with a "fast pace of life" and high sexual dimorphism.

Fitness consequences of parental compatibility in the frog Crinia georgiana.

PubMed

Dziminski, Martin A; Roberts, J Dale; Simmons, Leigh W

2008-04-01

Theory suggests that multiple mating by females can evolve as a mechanism for acquiring compatible genes that promote offspring fitness. Genetic compatibility models predict that differences in fitness among offspring arise from interactions between male and female haplotypes. Using a cross-classified breeding design and in vitro fertilization, we raised families of maternal and paternal half-siblings of the frog Crinia georgiana, a species with a polyandrous breeding system and external fertilization. After controlling for variation in maternal provisioning, we found significant effects of interacting parental haplotypes on fertilization success, and nonadditive genetic effects on measures of offspring fitness such as embryo survival, and survival to, size at, and time to metamorphosis. Additive genetic variation due to males and females was negligible, and not statistically significant for any of the fitness traits measured. Combinations of parental haplotypes that resulted in high rates of fertilization produced offspring with higher embryo survival and rapid juvenile development. We suggest that a gamete recognition mechanism for selective fertilization by compatible sperm may promote offspring fitness in this system.

Female transference and mate choice among Tana River red colobus.

PubMed

Marsh, C W

1979-10-18

Red colobus are one of a small number of primate species in which females have been reported to transfer between breeding groups more commonly than males. Several authors have hypothesised that in such species transference may serve to reduce the risk to females of producing offspring of lower fitness through inbreeding. The hypothesis offers no explanation of why females rather than males are responsible for outbreeding in these species, but remains plausible so long as male membership of breeding groups is relatively stable; for once members of one sex have evolved dispersal mechanisms reducing the risk of inbreeding, pressures on the other sex to do likewise will be lowered. Hence, if both sexes commonly migrate, the hypothesis is weakened. I describe here the membership dynamics of a group of Tana River red colobus, Colobus badius rufomitratus, which provide the first evidence of high rates of membership turnover by both sexes in primates, and speculate that the function of female transference in this case may be related to mate choice and the avoidance of infanticide.

Cuckoos host range is associated positively with distribution range and negatively with evolutionary uniqueness.

PubMed

Morelli, Federico; Benedetti, Yanina; Møller, Anders Pape; Liang, Wei; Carrascal, Luis M

2018-05-01

The evolutionary distinctiveness (ED) score is a measure of phylogenetic isolation that quantifies the evolutionary uniqueness of a species. Here, we compared the ED score of parasitic and non-parasitic cuckoo species world-wide, to understand whether parental care or parasitism represents the largest amount of phylogenetic uniqueness. Next, we focused only on 46 cuckoo species characterized by brood parasitism with a known number of host species, and we explored the associations among ED score, number of host species and breeding range size for these species. We assessed these associations using phylogenetic generalized least squares (PGLS) models, taking into account the phylogenetic signal. Parasitic cuckoo species were not more unique in terms of ED than non-parasitic species. However, we found a significant negative association between the evolutionary uniqueness and host range and a positive correlation between the number of host species and range size of parasitic cuckoos, probably suggesting a passive sampling of hosts by parasitic species as the breeding range broadens. The findings of this study showed that more generalist brood parasites occupied very different positions in a phylogenetic tree, suggesting that they have evolved independently within the Cuculiformes order. Finally, we demonstrated that specialist cuckoo species also represent the most evolutionarily unique species in the order of Cuculiformes. © 2018 The Authors. Journal of Animal Ecology © 2018 British Ecological Society.

Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account.

PubMed

Hulsegge, B; Calus, M P L; Oldenbroek, J K; Windig, J J

2017-02-01

From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds. © 2016 Blackwell Verlag GmbH.

Burrow limitations and group living in the communally rearing rodent, Octodon degus

PubMed Central

Ebensperger, Luis A.; Chesh, Adrian S.; Castro, Rodrigo A.; Tolhuysen, Liliana Ortiz; Quirici, Verónica; Burger, Joseph Robert; Sobrero, Raúl; Hayes, Loren D.

2012-01-01

Group living is thought to evolve whenever individuals attain a net fitness advantage due to reduced predation risk or enhanced foraging efficiency, but also when individuals are forced to remain in groups, which often occurs during high-density conditions due to limitations of critical resources for independent breeding. The influence of ecological limitations on sociality has been studied little in species in which reproduction is more evenly shared among group members. Previous studies in the caviomorph rodent Octodon degus (a New World hystricognath) revealed no evidence that group living confers an advantage and suggest that burrow limitations influence formation of social groups. Our objective was to examine the relevance of ecological limitations on sociality in these rodents. Our 4-year study revealed no association between degu density and use of burrow systems. The frequency with which burrow systems were used by degus was not related to the quality of these structures; only in 1 of the 4 years did the frequency of burrow use decrease with decreasing abundance of food. Neither the number of females per group nor total group size (related measures of degu sociality) changed with yearly density of degus. Although the number of males within social groups was lower in 2008, this variation was not related clearly to varying density. The percentage of females in social groups that bred was close to 99% and did not change across years of varying density. Our results suggest that sociality in degus is not the consequence of burrow limitations during breeding. Whether habitat limitations contribute to variation in vertebrate social systems is discussed. PMID:22328789

Will genomic selection be a practical method for plant breeding?

PubMed

Nakaya, Akihiro; Isobe, Sachiko N

2012-11-01

Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory.

Inconsistent identification of pit bull-type dogs by shelter staff.

PubMed

Olson, K R; Levy, J K; Norby, B; Crandall, M M; Broadhurst, J E; Jacks, S; Barton, R C; Zimmerman, M S

2015-11-01

Shelter staff and veterinarians routinely make subjective dog breed identification based on appearance, but their accuracy regarding pit bull-type breeds is unknown. The purpose of this study was to measure agreement among shelter staff in assigning pit bull-type breed designations to shelter dogs and to compare breed assignments with DNA breed signatures. In this prospective cross-sectional study, four staff members at each of four different shelters recorded their suspected breed(s) for 30 dogs; there was a total of 16 breed assessors and 120 dogs. The terms American pit bull terrier, American Staffordshire terrier, Staffordshire bull terrier, pit bull, and their mixes were included in the study definition of 'pit bull-type breeds.' Using visual identification only, the median inter-observer agreements and kappa values in pair-wise comparisons of each of the staff breed assignments for pit bull-type breed vs. not pit bull-type breed ranged from 76% to 83% and from 0.44 to 0.52 (moderate agreement), respectively. Whole blood was submitted to a commercial DNA testing laboratory for breed identification. Whereas DNA breed signatures identified only 25 dogs (21%) as pit bull-type, shelter staff collectively identified 62 (52%) dogs as pit bull-type. Agreement between visual and DNA-based breed assignments varied among individuals, with sensitivity for pit bull-type identification ranging from 33% to 75% and specificity ranging from 52% to 100%. The median kappa value for inter-observer agreement with DNA results at each shelter ranged from 0.1 to 0.48 (poor to moderate). Lack of consistency among shelter staff indicated that visual identification of pit bull-type dogs was unreliable. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers.

PubMed

Campos, Bárbara Machado; do Carmo, Adriana Santana; do Egito, Andrea Alves; da Mariante, Arthur Silva; do Albuquerque, Maria Socorro Muaés; de Gouveia, João José Simoni; Malhado, Carlos Henrique Mendes; Verardo, Lucas Lima; da Silva, Marcos Vinícius Gualberto Barbosa; Carneiro, Paulo Luiz Souza

2017-12-01

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST ), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

A comparative study of clinical manifestations, haematological and serological responses after experimental infection with Anaplasma phagocytophilum in two Norwegian sheep breeds

PubMed Central

2011-01-01

Background It has been questioned if the old native Norwegian sheep breed, Old Norse Sheep (also called Norwegian Feral Sheep), normally distributed on coastal areas where ticks are abundant, is more protected against tick-borne infections than other Norwegian breeds due to a continuously high selection pressure on pasture. The aim of the present study was to test this hypothesis in an experimental infection study. Methods Five-months-old lambs of two Norwegian sheep breeds, Norwegian White (NW) sheep and Old Norse (ON) sheep, were experimentally infected with a 16S rRNA genetic variant of Anaplasma phagocytophilum (similar to GenBank accession number M73220). The experiment was repeated for two subsequent years, 2008 and 2009, with the use of 16 lambs of each breed annually. Ten lambs of each breed were inoculated intravenously each year with 0.4 ml A. phagocytophilum-infected blood containing approximately 0.5 × 106 infected neutrophils/ml. Six lambs of each breed were used as uninfected controls. Half of the primary inoculated lambs in each breed were re-challenged with the same infectious dose at nine (2008) and twelve (2009) weeks after the first challenge. The clinical, haematological and serological responses to A. phagocytophilum infection were compared in the two sheep breeds. Results The present study indicates a difference in fever response and infection rate between breeds of Norwegian sheep after experimental infection with A. phagocytophilum. Conclusion Although clinical response seems to be less in ON-lambs compared to NW-lambs, further studies including more animals are needed to evaluate if the ON-breed is more protected against tick-borne infections than other Norwegian breeds. PMID:21314927

Space use by Forster's Terns breeding in South San Francisco Bay

USGS Publications Warehouse

Bluso-Demers, J.; Colwell, M.A.; Takekawa, John Y.; Ackerman, Joshua T.

2008-01-01

Parental care behaviors often differ in dimorphic seabirds, leading to sex-specific differences in foraging behaviors. However, few studies have examined sex-specific foraging behaviors in monomorphic seabirds. Using radio-telemetry, we studied Forster's Terns (Sterna forsteri) - a monomorphic and socially monogamous seabird - breeding in the South San Francisco Bay, California. Space use did not differ between males and females. Instead, space use varied by breeding stage and colony affiliation. Forster's Terns were located farthest from the nest during pre-breeding and post-breeding time periods, and closest to the nest during incubation and chick-rearing. Home-range size and core-use areas decreased as the breeding season progressed and were most concentrated in the post-breeding stage. The results of this and other studies indicate that tems, unlike other monomorphic seabirds studied, do not exhibit sex-specific differences in space use.

Characterization of recombination features and the genetic basis in multiple cattle breeds.

PubMed

Shen, Botong; Jiang, Jicai; Seroussi, Eyal; Liu, George E; Ma, Li

2018-04-27

Crossover generated by meiotic recombination is a fundamental event that facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination rate among species, but the characterization of recombination features between cattle breeds has not yet been performed. Cattle populations in North America count millions, and the dairy industry has genotyped millions of individuals with pedigree information that provide a unique opportunity to study breed-level variations in recombination. Based on large pedigrees of Jersey, Ayrshire and Brown Swiss cattle with genotype data, we identified over 3.4 million maternal and paternal crossover events from 161,309 three-generation families. We constructed six breed- and sex-specific genome-wide recombination maps using 58,982 autosomal SNPs for two sexes in the three dairy cattle breeds. A comparative analysis of the six recombination maps revealed similar global recombination patterns between cattle breeds but with significant differences between sexes. We confirmed that male recombination map is 10% longer than the female map in all three cattle breeds, consistent with previously reported results in Holstein cattle. When comparing recombination hotspot regions between cattle breeds, we found that 30% and 10% of the hotspots were shared between breeds in males and females, respectively, with each breed exhibiting some breed-specific hotspots. Finally, our multiple-breed GWAS found that SNPs in eight loci affected recombination rate and that the PRDM9 gene associated with hotspot usage in multiple cattle breeds, indicating a shared genetic basis for recombination across dairy cattle breeds. Collectively, our results generated breed- and sex-specific recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded our understanding of the breed-level variations in recombination features within an important livestock species.

Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

PubMed

Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

2005-01-01

In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

Inter- and intra-breed comparative study of sperm motility and viability in Iberian and Duroc boar semen during long-term storage in MR-A and XCell extenders.

PubMed

Martín-Hidalgo, D; Barón, F J; Robina, A; Bragado, M J; Llera, A Hurtado de; García-Marín, L J; Gil, M C

2013-06-01

During boar semen liquid preservation, extender is one of the factors that influence storage tolerance of spermatozoa. However, there are few studies about intra-breed variation in the preservation of semen quality during storage in different extenders. Similarly, boar breed is generally not considered a possible factor influencing variation in the semen storage tolerance in a particular extender. The aim of this study was to compare boar semen storage potential, in terms of the ability to maintain sperm viability and motility, of two currently used long-term extenders, MR-A and XCell. Extended semen from two breeds, Iberian and Duroc that had been stored at 17°C for up to 7 days was used. Intra- and inter-breed effect was studied. On Days 1, 4 and 7 (Day 0=day of semen collection), motility parameters and the percentage of total motile sperm and progressively motile sperm using a CASA system was evaluated. Viability (SYBR-14/PI) was evaluated by flow cytometry. Within each breed and for each storage day, there were differences between extenders, although semen tolerance to preservation was more influenced by the extender in the Iberian than in the Duroc breed. Neither breed nor extender influenced the percentage of viable spermatozoa during the storage time. Moreover, differences in motility parameters were observed between breeds, although the differences were greater when the XCell extender was used. In conclusion, both extender and breed influence motility characteristics of liquid-stored boar semen, so both aspects have to be considered in the design of comparative studies about stored boar semen quality from different breeds or with different extenders. Further studies are needed to corroborate these findings. Copyright © 2013 Elsevier B.V. All rights reserved.

The evolution of social monogamy in mammals.

PubMed

Lukas, D; Clutton-Brock, T H

2013-08-02

The evolution of social monogamy has intrigued biologists for over a century. Here, we show that the ancestral condition for all mammalian groups is of solitary individuals and that social monogamy is derived almost exclusively from this social system. The evolution of social monogamy does not appear to have been associated with a high risk of male infanticide, and paternal care is a consequence rather than a cause of social monogamy. Social monogamy has evolved in nonhuman mammals where breeding females are intolerant of each other and female density is low, suggesting that it represents a mating strategy that has developed where males are unable to defend access to multiple females.

A new Method for the Estimation of Initial Condition Uncertainty Structures in Mesoscale Models

NASA Astrophysics Data System (ADS)

Keller, J. D.; Bach, L.; Hense, A.

2012-12-01

The estimation of fast growing error modes of a system is a key interest of ensemble data assimilation when assessing uncertainty in initial conditions. Over the last two decades three methods (and variations of these methods) have evolved for global numerical weather prediction models: ensemble Kalman filter, singular vectors and breeding of growing modes (or now ensemble transform). While the former incorporates a priori model error information and observation error estimates to determine ensemble initial conditions, the latter two techniques directly address the error structures associated with Lyapunov vectors. However, in global models these structures are mainly associated with transient global wave patterns. When assessing initial condition uncertainty in mesoscale limited area models, several problems regarding the aforementioned techniques arise: (a) additional sources of uncertainty on the smaller scales contribute to the error and (b) error structures from the global scale may quickly move through the model domain (depending on the size of the domain). To address the latter problem, perturbation structures from global models are often included in the mesoscale predictions as perturbed boundary conditions. However, the initial perturbations (when used) are often generated with a variant of an ensemble Kalman filter which does not necessarily focus on the large scale error patterns. In the framework of the European regional reanalysis project of the Hans-Ertel-Center for Weather Research we use a mesoscale model with an implemented nudging data assimilation scheme which does not support ensemble data assimilation at all. In preparation of an ensemble-based regional reanalysis and for the estimation of three-dimensional atmospheric covariance structures, we implemented a new method for the assessment of fast growing error modes for mesoscale limited area models. The so-called self-breeding is development based on the breeding of growing modes technique. Initial perturbations are integrated forward for a short time period and then rescaled and added to the initial state again. Iterating this rapid breeding cycle provides estimates for the initial uncertainty structure (or local Lyapunov vectors) given a specific norm. To avoid that all ensemble perturbations converge towards the leading local Lyapunov vector we apply an ensemble transform variant to orthogonalize the perturbations in the sub-space spanned by the ensemble. By choosing different kind of norms to measure perturbation growth, this technique allows for estimating uncertainty patterns targeted at specific sources of errors (e.g. convection, turbulence). With case study experiments we show applications of the self-breeding method for different sources of uncertainty and different horizontal scales.

What’s in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs

PubMed Central

Gunter, Lisa M.; Barber, Rebecca T.; Wynne, Clive D. L.

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters. PMID:27008213

Genomics of a revived breed: Case study of the Belgian campine cattle

PubMed Central

Wijnrocx, Katrien; Colinet, Frédéric G.; Gengler, Nicolas; Hulsegge, Bettine; Windig, Jack J.; Buys, Nadine

2017-01-01

Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e.g. through the use of crosses with similar breeds. However, the remaining populations are expected to contain crossbred individuals resulting from introgressions. They are likely to carry exogenous genes that affect the breed’s authenticity on a genomic level. Using the revived Campine breed as a case study, 289 individuals registered as purebreds were genotyped on the Illumina BovineSNP50. In addition, genomic information on the Illumina BovineHD and Illumina BovineSNP50 of ten breeds was available to assess the current population structure, genetic diversity, and introgression with phenotypically similar and/or historically related breeds. Introgression with Holstein and beef cattle genotypes was limited to only a few farms. While the current population shows a substantial amount of within-breed variation, the majority of genotypes can be separated from other breeds in the study, supporting the re-establishment of the Campine breed. The majority of the population is genetically close to the Deep Red (NL), Improved Red (NL) and Eastern Belgium Red and White (BE) cattle, breeds known for their historical ties to the Campine breed. This would support an open herdbook policy, thereby increasing the population size and consequently providing a more secure future for the breed. PMID:28426822

What's in a Name? Effect of Breed Perceptions & Labeling on Attractiveness, Adoptions & Length of Stay for Pit-Bull-Type Dogs.

PubMed

Gunter, Lisa M; Barber, Rebecca T; Wynne, Clive D L

2016-01-01

Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.

Will genomic selection be a practical method for plant breeding?

PubMed Central

Nakaya, Akihiro; Isobe, Sachiko N.

2012-01-01

Background Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. Scope In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Conclusions Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory. PMID:22645117

Evolutionary history of Lake Tanganyika's scale-eating cichlid fishes.

PubMed

Koblmüller, Stephan; Egger, Bernd; Sturmbauer, Christian; Sefc, Kristina M

2007-09-01

Although Lake Tanganyika is not the most species-rich of the Great East African Lakes it comprises by far the greatest diversity of cichlid fishes in terms of morphology, ecology, and breeding styles. Our study focuses on the Tanganyikan cichlid tribe Perissodini, which exhibits one of the most peculiar feeding strategies found in cichlids-scale-eating. Their evolutionary history was reconstructed from 1416 bp DNA sequence of two mitochondrial genes (ND2 and partial control region) and from 612 AFLP markers. We confirm the inclusion of the zooplanktivorous genus Haplotaxodon in the tribe Perissodini, and species status of Haplotaxodon trifasciatus. Within the Perissodini, the major lineages emerged within a short period roughly 1.5-2 MYA, which makes their radiation slightly younger than that of other Tanganyikan cichlid tribes. Most scale-eaters evolved in deep-water habitat, perhaps associated with the previously documented radiations of other deep-water dwelling cichlid lineages, and colonized the shallow habitat only recently.

Comparative analyses suggest that information transfer promoted sociality in male bats in the temperate zone.

PubMed

Safi, Kamran; Kerth, Gerald

2007-09-01

The evolution of sociality is a central theme in evolutionary biology. The vast majority of bats are social, which has been explained in terms of the benefits of communal breeding. However, the causes for segregated male groups remain unknown. In a comparative study, we tested whether diet and morphological adaptations to specific foraging styles, two factors known to influence the occurrence of information transfer, can predict male sociality. Our results suggest that the species most likely to benefit from information transfer--namely, those preying on ephemeral insects and with morphological adaptations to feeding in open habitat--are more likely to form male groups. Our findings also indicate that solitary life was the ancestral state of males and sociality evolved in several lineages. Beyond their significance for explaining the existence of male groups in bats, our findings highlight the importance of information transfer in the evolution of animal sociality.

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci.

PubMed

Acosta, A C; Uffo, O; Sanz, A; Ronda, R; Osta, R; Rodellar, C; Martin-Burriel, I; Zaragoza, P

2013-02-01

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F(ST)). The exact test for Hardy-Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds. © 2012 Blackwell Verlag GmbH.

Molecular Study of the Amazonian Macabea Cattle History.

PubMed

Vargas, Julio; Landi, Vincenzo; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed.

Molecular Study of the Amazonian Macabea Cattle History

PubMed Central

Vargas, Julio; Martínez, Amparo; Gómez, Mayra; Camacho, María Esperanza; Álvarez, Luz Ángela; Aguirre, Lenin; Delgado, Juan Vicente

2016-01-01

Macabea cattle are the only Bos taurus breed that have adapted to the wet tropical conditions of the Amazon. This breed has integrated into the culture of the indigenous Shuar-Asuar nations probably since its origins, being one of the few European zoogenetic resources assimilated by the deep-jungle Amazon communities. Despite its potential for local endogenous sustainable development, this breed is currently endangered. The present study used molecular genetics tools to investigate the within- and between-breeds diversity, in order to characterize the breed population, define its associations with other breeds, and infer its origin and evolution. The within-breed genetic diversity showed high values, as indicated by all genetic parameters, such as the mean number of alleles (MNA = 7.25±2.03), the observed heterozygosity (Ho = 0.72±0.02) and the expected heterozygosity (He = 0.72±0.02). The between-breeds diversity analysis, which included factorial correspondence analysis, Reynolds genetic distance, neighbor-joining analysis, and genetic structure analysis, showed that the Macabea breed belongs to the group of the American Creoles, with a Southern-Spain origin. Our outcomes demonstrated that the Macabea breed has a high level of purity and null influences of exotic cosmopolitan breeds with European or Asiatic origin. This breed is an important zoogenetic resource of Ecuador, with relevant and unique attributes; therefore, there is an urgent need to develop conservation strategies for the Macabea breed. PMID:27776178

Breed, sex, and litter effects in 2-month old puppies' behaviour in a standardised open-field test.

PubMed

Barnard, Shanis; Marshall-Pescini, Sarah; Pelosi, Annalisa; Passalacqua, Chiara; Prato-Previde, Emanuela; Valsecchi, Paola

2017-05-11

A considerable number of studies have reported differences among dog breeds with respect to their genetic profile, cognitive abilities or personality traits. Each dog breed is normally treated as a homogeneous group, however, researchers have recently questioned whether the behavioural profile of modern breeds still reflects their historical function or if the intense divergent selective pressures and geographical barriers have created a more fragmented picture. The majority of studies attempting to assess and compare modern breeds' personality focused on the evaluation of adult dogs where the potential effects of environmental/human factors on the dogs' behaviour are hard to discern from their genetic heritage. In the following study, we aimed at investigating between- and within-breed differences in the personality of two-months-old puppies by direct behavioural observation of 377 puppies from 12 breeds. Results showed that there was no effect of sex, however both breed and litter, significantly affected all personality traits. Breed on average explained 10% of the variance, whereas the effect of litter was noticeably higher, explaining on average 23% of the variance. Taken together, our results suggest that breed does have some influence on personality traits, but they also highlight the importance of taking litter effects into account.

Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds.

PubMed

Dou, Tengfei; Zhao, Sumei; Rong, Hua; Gu, Dahai; Li, Qihua; Huang, Ying; Xu, Zhiqiang; Chu, Xiaohui; Tao, Linli; Liu, Lixian; Ge, Changrong; Te Pas, Marinus F W; Jia, Junjing

2017-06-20

Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. We conclude that faster growth rates and larger body size are related to increased expression of genes involved in muscle development and immune response in muscle, while slower growth rates and smaller body size are related to increased general cellular metabolism. The liver of the Daweishan breed displayed increased expression of metabolic genes.

Breeding season survival and breeding incidence of female Mottled Ducks on the upper Texas gulf coast

USGS Publications Warehouse

Rigby, Elizabeth A.; Haukos, David A.

2012-01-01

Previous Mottled Duck (Anas fulvigula) studies suggested that high female breeding season survival may be caused by low nesting effort, but few breeding season estimates of survival associated with nesting effort exist on the western Gulf Coast. Here, breeding season survival (N = 40) and breeding incidence (N = 39) were estimated for female Mottled Ducks on the upper Texas coast, 2006–2008. Females were fitted with backpack radio transmitters and visually relocated every 3–4 days. Weekly survival was estimated using the Known Fate procedure of program MARK with breeding incidence estimated as the annual proportion of females observed nesting or with broods. The top-ranked survival model included a body mass covariate and held weekly female survival constant across weeks and years (SW = 0.986, SE = 0.006). When compared to survival across the entire year estimated from previous band recovery and age ratio analysis, survival rate during the breeding season did not differ. Breeding incidence was well below 100% in all years and highly variable among years (15%–63%). Breeding season survival and breeding incidence were similar to estimates obtained with implant transmitters from the mid-coast of Texas. The greatest breeding incidence for both studies occurred when drought indices indicated average environmental moisture during the breeding season. The observed combination of low breeding incidence and high breeding season survival support the hypothesis of a trade-off between the ecological cost of nesting effort and survival for Mottled Duck females. Habitat cues that trigger nesting are unknown and should be investigated.

Physiological mechanisms mediating patterns of reproductive suppression and alloparental care in cooperatively breeding carnivores.

PubMed

Montgomery, Tracy M; Pendleton, Erika L; Smith, Jennifer E

2018-05-02

Although cooperation represents a long-standing evolutionary puzzle, field studies on social carnivores have contributed greatly to our understanding of the selective forces favoring cooperative breeding. Despite these insights, our grasp of the proximate mechanisms facilitating cooperation in carnivores remains surprisingly limited. Here we provide an overview of our current knowledge of the endocrine mechanisms mediating cooperative breeding in terrestrial species belonging to the mammalian order Carnivora. We focus primarily on aspects of reproductive suppression and alloparental care. We find few studies on the topic, with some of the best studies focusing on the behavioral endocrinology of cooperative breeding in canids (dogs) and herpestids (mongooses). Overall, these studies suggest that breeding females typically have higher circulating levels of estrogen, luteinizing hormone, progesterone, and prolactin than do non-breeding adult females. We also find that among males, testosterone levels are often elevated in breeders compared to non-breeding adult males. The effect of glucocorticoids on reproductive suppression in carnivores appears to be sex-specific: breeding males typically have higher glucocorticoid levels than their non-breeding subordinates, but there is no clear pattern for breeding females. Finally, elevated levels of prolactin and oxytocin are consistently associated with alloparental care in cooperatively breeding carnivores, whereas testosterone and glucocorticoids are often lower in individuals who participate in alloparenting. Taken together, our synthesis elucidates striking gaps in our knowledge of carnivore physiology, especially the endocrine mechanisms promoting alloparental care, and we identify important areas for future research. Copyright © 2017 Elsevier Inc. All rights reserved.

Breed distribution of the nt230(del4) MDR1 mutation in dogs.

PubMed

Gramer, Irina; Leidolf, Regina; Döring, Barbara; Klintzsch, Stefanie; Krämer, Eva-Maria; Yalcin, Ebru; Petzinger, Ernst; Geyer, Joachim

2011-07-01

A 4-bp deletion mutation associated with multiple drug sensitivity exists in the canine multidrug resistance (MDR1) gene. This mutation has been detected in more than 10 purebred dog breeds as well as in mixed breed dogs. To evaluate the breed distribution of this mutation in Germany, 7378 dogs were screened, including 6999 purebred and 379 mixed breed dogs. The study included dog breeds that show close genetic relationship or share breeding history with one of the predisposed breeds but in which the occurrence of the MDR1 mutation has not been reported. The breeds comprised Bearded Collies, Anatolian Shepherd Dog, Greyhound, Belgian Tervuren, Kelpie, Borzoi, Australian Cattle Dog and the Irish Wolfhound. The MDR1 mutation was not detected is any of these breeds, although it was found as expected in the Collie, Longhaired Whippet, Shetland Sheepdog, Miniature Australian Shepherd, Australian Shepherd, Wäller, White Swiss Shepherd, Old English Sheepdog and Border Collie with varying allelic frequencies for the mutant MDR1 allele of 59%, 45%, 30%, 24%, 22%, 17%, 14%, 4% and 1%, respectively. Allelic frequencies of 8% and 2% were determined in herding breed mixes and unclassified mixed breeds, respectively. Because of its widespread breed distribution and occurrence in many mixed breed dogs, it is difficult for veterinarians and dog owners to recognise whether MDR1-related drug sensitivity is relevant for an individual animal. This study provides a comprehensive overview of all affected dog breeds and many dog breeds that are probably unaffected on the basis of ∼15,000 worldwide MDR1 genotyping data. Copyright © 2010 Elsevier Ltd. All rights reserved.

Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping.

PubMed

Pariset, L; Mariotti, M; Nardone, A; Soysal, M I; Ozkan, E; Williams, J L; Dunner, S; Leveziel, H; Maróti-Agóts, A; Bodò, I; Valentini, A

2010-12-01

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure. © 2010 Blackwell Verlag GmbH.

[Estimation of Genetic Diversity of Romanov Sheep by the Coefficient of Genetic Originality Based on ISSR-Fingerprinting Data].

PubMed

Nesteruk, L V; Makarova, N N; Svishcheva, G R; Stolpovsky, Yu A

2015-07-01

Estimation of the state of the genetic diversity and the originality of the breed structure is required for the conservation and management of domestic breeds of agricultural animals. The Romanov breed of sheep from the leading breeding and gene pool farms in Yaroslavl oblast (Russia) is the object of our study. ISS R fingerprinting was used as a molecular method of the study of sheep gene pools. Forty-three DNA fragments were detected (25 and 18, respectively) by two primers ((AG)9C and (GA)9C). Of the discovered ISSR markers, 81% were polymorphic. The coefficient of genetic originality was for the first time used for the study of the specificity and originality of the Romanov-breed gene pool. Based on its values, the studied individuals were divided into five classes depending on the frequency of the ISSR fragment. The most original or the rarest, as well as typical genotypes, were singled out in the Romanov sheep gene pool. Use the obtained data on genetic originality was proposed as a means to increase the efficiency of selection and breeding during the breeding of autochthonous breeds of domesticated animal species.

Can non-breeding be a cost of breeding dispersal?

USGS Publications Warehouse

Danchin, E.; Cam, E.

2002-01-01

Breeding habitat selection and dispersal are crucial processes that affect many components of fitness. Breeding dispersal entails costs, one of which has been neglected: dispersing animals may miss breeding opportunities because breeding dispersal requires finding a new nesting site and mate, two time- and energy-consuming activities. Dispersers are expected to be prone to non-breeding. We used the kittiwake (Rissa tridactyla) to test whether breeding dispersal influences breeding probability. Breeding probability was associated with dispersal, in that both were negatively influenced by private information (previous individual reproductive success) and public information (average reproductive success of conspecifics) about patch quality. Furthermore, the probability of skipping breeding was 1.7 times higher in birds that settled in a new patch relative to those that remained on the same patch. Finally, non-breeders that resumed breeding were 4.4 times more likely to disperse than birds that bred in successive years. Although private information may influence breeding probability directly, the link between breeding probability and public information may be indirect, through the influence of public information on breeding dispersal, non-breeding thus being a cost of dispersal. These results support the hypothesis that dispersal may result in not being able to breed. More generally, non-breeding (which can be interpreted as an extreme form of breeding failure) may reveal costs of various previous activities. Because monitoring the non-breeding portion of a population is difficult, non-breeders have been neglected in many studies of reproduction trade-offs.

A unique mating strategy without physical contact during fertilization in Bombay Night Frogs (Nyctibatrachus humayuni) with the description of a new form of amplexus and female call.

PubMed

Willaert, Bert; Suyesh, Robin; Garg, Sonali; Giri, Varad B; Bee, Mark A; Biju, S D

2016-01-01

Anurans show the highest diversity in reproductive modes of all vertebrate taxa, with a variety of associated breeding behaviours. One striking feature of anuran reproduction is amplexus. During this process, in which the male clasps the female, both individuals' cloacae are juxtaposed to ensure successful external fertilization. Several types of amplexus have evolved with the diversification of anurans, and secondary loss of amplexus has been reported in a few distantly related taxa. Within Nyctibatrachus, a genus endemic to the Western Ghats of India, normal axillary amplexus, a complete loss of amplexus, and intermediate forms of amplexus have all been suggested to occur, but many species remain unstudied. Here, we describe the reproductive behaviour of N. humayuni, including a new type of amplexus. The dorsal straddle, here defined as a loose form of contact in which the male sits on the dorsum of the female prior to oviposition but without clasping her, is previously unreported for anurans. When compared to known amplexus types, it most closely resembles the form of amplexus observed in Mantellinae. Furthermore, we prove that, opposed to the situation in most anurans, male semen release happens before egg deposition. We hypothesize that the male ejaculates on the female's dorsum and that sperm subsequently runs from her back and hind legs before fertilizing the eggs. A second feature characterizing anuran breeding is the advertisement call, mostly produced solely by males. Despite recent descriptions of several new Nyctibatrachus species, few studies have explored their vocal repertoire. We describe both the male advertisement call and a female call for N. humayuni. The presence of a female call has not been reported within Nyctibatrachidae, and has been reported in less than 0.5% of anuran species. Altogether, our results highlight a striking diversity and several unique aspects of Nyctibatrachus breeding behaviour.

A unique mating strategy without physical contact during fertilization in Bombay Night Frogs (Nyctibatrachus humayuni) with the description of a new form of amplexus and female call

PubMed Central

Suyesh, Robin; Garg, Sonali; Giri, Varad B.; Bee, Mark A.

2016-01-01

Anurans show the highest diversity in reproductive modes of all vertebrate taxa, with a variety of associated breeding behaviours. One striking feature of anuran reproduction is amplexus. During this process, in which the male clasps the female, both individuals’ cloacae are juxtaposed to ensure successful external fertilization. Several types of amplexus have evolved with the diversification of anurans, and secondary loss of amplexus has been reported in a few distantly related taxa. Within Nyctibatrachus, a genus endemic to the Western Ghats of India, normal axillary amplexus, a complete loss of amplexus, and intermediate forms of amplexus have all been suggested to occur, but many species remain unstudied. Here, we describe the reproductive behaviour of N. humayuni, including a new type of amplexus. The dorsal straddle, here defined as a loose form of contact in which the male sits on the dorsum of the female prior to oviposition but without clasping her, is previously unreported for anurans. When compared to known amplexus types, it most closely resembles the form of amplexus observed in Mantellinae. Furthermore, we prove that, opposed to the situation in most anurans, male semen release happens before egg deposition. We hypothesize that the male ejaculates on the female’s dorsum and that sperm subsequently runs from her back and hind legs before fertilizing the eggs. A second feature characterizing anuran breeding is the advertisement call, mostly produced solely by males. Despite recent descriptions of several new Nyctibatrachus species, few studies have explored their vocal repertoire. We describe both the male advertisement call and a female call for N. humayuni. The presence of a female call has not been reported within Nyctibatrachidae, and has been reported in less than 0.5% of anuran species. Altogether, our results highlight a striking diversity and several unique aspects of Nyctibatrachus breeding behaviour. PMID:27326376

Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds.

PubMed

Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Tortorici, Lina; Sardina, Maria Teresa; Portolano, Baldassare

2014-10-10

The recent availability of sheep genome-wide SNP panels allows providing background information concerning genome structure in domestic animals. The aim of this work was to investigate the patterns of linkage disequilibrium (LD), the genetic diversity and population structure in Valle del Belice, Comisana, and Pinzirita dairy sheep breeds using the Illumina Ovine SNP50K Genotyping array. Average r (2) between adjacent SNPs across all chromosomes was 0.155 ± 0.204 for Valle del Belice, 0.156 ± 0.208 for Comisana, and 0.128 ± 0.188 for Pinzirita breeds, and some variations in LD value across chromosomes were observed, in particular for Valle del Belice and Comisana breeds. Average values of r (2) estimated for all pairwise combinations of SNPs pooled over all autosomes were 0.058 ± 0.023 for Valle del Belice, 0.056 ± 0.021 for Comisana, and 0.037 ± 0.017 for Pinzirita breeds. The LD declined as a function of distance and average r (2) was lower than the values observed in other sheep breeds. Consistency of results among the several used approaches (Principal component analysis, Bayesian clustering, F ST, Neighbor networks) showed that while Valle del Belice and Pinzirita breeds formed a unique cluster, Comisana breed showed the presence of substructure. In Valle del Belice breed, the high level of genetic differentiation within breed, the heterogeneous cluster in Admixture analysis, but at the same time the highest inbreeding coefficient, suggested that the breed had a wide genetic base with inbred individuals belonging to the same flock. The Sicilian breeds were characterized by low genetic differentiation and high level of admixture. Pinzirita breed displayed the highest genetic diversity (He, Ne) whereas the lowest value was found in Valle del Belice breed. This study has reported for the first time estimates of LD and genetic diversity from a genome-wide perspective in Sicilian dairy sheep breeds. Our results indicate that breeds formed non-overlapping clusters and are clearly separated populations and that Comisana sheep breed does not constitute a homogenous population. The information generated from this study has important implications for the design and applications of association studies as well as for development of conservation and/or selection breeding programs.

Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy.

PubMed

Bouwman, Aniek C; Veerkamp, Roel F

2014-10-03

The aim of this study was to determine the consequences of splitting sequencing effort over multiple breeds for imputation accuracy from a high-density SNP chip towards whole-genome sequence. Such information would assist for instance numerical smaller cattle breeds, but also pig and chicken breeders, who have to choose wisely how to spend their sequencing efforts over all the breeds or lines they evaluate. Sequence data from cattle breeds was used, because there are currently relatively many individuals from several breeds sequenced within the 1,000 Bull Genomes project. The advantage of whole-genome sequence data is that it carries the causal mutations, but the question is whether it is possible to impute the causal variants accurately. This study therefore focussed on imputation accuracy of variants with low minor allele frequency and breed specific variants. Imputation accuracy was assessed for chromosome 1 and 29 as the correlation between observed and imputed genotypes. For chromosome 1, the average imputation accuracy was 0.70 with a reference population of 20 Holstein, and increased to 0.83 when the reference population was increased by including 3 other dairy breeds with 20 animals each. When the same amount of animals from the Holstein breed were added the accuracy improved to 0.88, while adding the 3 other breeds to the reference population of 80 Holstein improved the average imputation accuracy marginally to 0.89. For chromosome 29, the average imputation accuracy was lower. Some variants benefitted from the inclusion of other breeds in the reference population, initially determined by the MAF of the variant in each breed, but even Holstein specific variants did gain imputation accuracy from the multi-breed reference population. This study shows that splitting sequencing effort over multiple breeds and combining the reference populations is a good strategy for imputation from high-density SNP panels towards whole-genome sequence when reference populations are small and sequencing effort is limiting. When sequencing effort is limiting and interest lays in multiple breeds or lines this provides imputation of each breed.

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

PubMed

Vouraki, Sotiria; Gelasakis, Athanasios I; Alexandri, Panoraia; Boukouvala, Evridiki; Ekateriniadou, Loukia V; Banos, Georgios; Arsenos, Georgios

2018-01-01

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Microsatellite loci analysis for the genetic variability and the parentage test of five dog breeds in South Korea.

PubMed

Kang, Byeong-Teck; Kim, Kyung-Seok; Min, Mi-Sook; Chae, Young-Jin; Kang, Jung-Won; Yoon, Junghee; Choi, Jihye; Seong, Je-Kyung; Park, Han-Chan; An, Junghwa; Lee, Mun-Han; Park, Hee-Myung; Lee, Hang

2009-06-01

To investigate the population structure of five dog breeds in South Korea and to validate polymorphic microsatellite markers for the parentage test, microsatellite loci analyses were conducted for two Korean native dog breeds, Poongsan and Jindo, and three imported dog breeds, German Shepherd, Beagle and Greyhound. Overall genetic diversity was high across all dog breeds (expected heterozygosity range: 0.71 to 0.85), although breeds differed in deviations from Hardy-Weinberg equilibrium (HWE). Significant reduction of heterozygosity in the Poongsan and Greyhound breeds was caused by non-random mating and population substructure within these breeds (the Wahlund effects). The close relationship and high degree of genetic diversity for two Korean native dog breeds were substantial. The mean polymorphism information content value was highest in Jindos (0.82) and Poongsans (0.81), followed by Beagles (0.74), Greyhounds (0.72), and German Shepherds (0.66). Accumulated exclusion power values, as an indication of marker validity for parentage tests, were varied but very high across breeds, 0.9999 for Jindos, Poongsans, and Beagles, 0.9997 for Greyhounds, and 0.9995 for German Shepherds. Taken together, the microsatellite loci investigated in this study can serve as suitable markers for the parentage test and as individual identification to establish a reliable pedigree verification system of dog breeds in South Korea. This study also stresses that the population subdivision within breeds can become an important cause of deviation from HWE in dog breeds.

Farm-by-farm analysis of microsatellite, mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed.

PubMed

Herrero-Medrano, J M; Megens, H J; Crooijmans, R P; Abellaneda, J M; Ramis, G

2013-06-01

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems - microsatellites, SNPs and mtDNA - were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H(e) = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm-based practices and farm-based breeding stocks can aid in the design of a sustainable breeding program for minority breeds. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds

PubMed Central

Berthier, David; Peylhard, Moana; Dayo, Guiguigbaza-Kossigan; Flori, Laurence; Sylla, Souleymane; Bolly, Seydou; Sakande, Hassane; Chantal, Isabelle; Thevenon, Sophie

2015-01-01

Background Animal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N’Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds. Methodology/Principal Findings This study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU. Conclusions We demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge of host-pathogen interactions and, furthermore, for identifying key biological pathways. PMID:25954819

A comparison of phenotypic traits related to trypanotolerance in five west african cattle breeds highlights the value of shorthorn taurine breeds.

PubMed

Berthier, David; Peylhard, Moana; Dayo, Guiguigbaza-Kossigan; Flori, Laurence; Sylla, Souleymane; Bolly, Seydou; Sakande, Hassane; Chantal, Isabelle; Thevenon, Sophie

2015-01-01

Animal African Trypanosomosis particularly affects cattle and dramatically impairs livestock development in sub-Saharan Africa. African Zebu (AFZ) or European taurine breeds usually die of the disease in the absence of treatment, whereas West African taurine breeds (AFT), considered trypanotolerant, are able to control the pathogenic effects of trypanosomosis. Up to now, only one AFT breed, the longhorn N'Dama (NDA), has been largely studied and is considered as the reference trypanotolerant breed. Shorthorn taurine trypanotolerance has never been properly assessed and compared to NDA and AFZ breeds. This study compared the trypanotolerant/susceptible phenotype of five West African local breeds that differ in their demographic history. Thirty-six individuals belonging to the longhorn taurine NDA breed, two shorthorn taurine Lagune (LAG) and Baoulé (BAO) breeds, the Zebu Fulani (ZFU) and the Borgou (BOR), an admixed breed between AFT and AFZ, were infected by Trypanosoma congolense IL1180. All the cattle were genetically characterized using dense SNP markers, and parameters linked to parasitaemia, anaemia and leukocytes were analysed using synthetic variables and mixed models. We showed that LAG, followed by NDA and BAO, displayed the best control of anaemia. ZFU showed the greatest anaemia and the BOR breed had an intermediate value, as expected from its admixed origin. Large differences in leukocyte counts were also observed, with higher leukocytosis for AFT. Nevertheless, no differences in parasitaemia were found, except a tendency to take longer to display detectable parasites in ZFU. We demonstrated that LAG and BAO are as trypanotolerant as NDA. This study highlights the value of shorthorn taurine breeds, which display strong local adaptation to trypanosomosis. Thanks to further analyses based on comparisons of the genome or transcriptome of the breeds, these results open up the way for better knowledge of host-pathogen interactions and, furthermore, for identifying key biological pathways.

Analysis of breed effects on semen traits in light horse, warmblood, and draught horse breeds.

PubMed

Gottschalk, Maren; Sieme, Harald; Martinsson, Gunilla; Distl, Ottmar

2016-05-01

In the present study, systematic effects on semen quality traits were investigated in 381 stallions representing 22 breeds. All stallions were used for AI either at the Lower Saxon National Stud Celle or the North Rhine-Westphalian National Stud Warendorf. A total of 71,078 fresh semen reports of the years 2001 to 2014 were edited for analysis of gel-free volume, sperm concentration, total number of sperm, progressive motility, and total number of progressively motile sperm. Breed differences were studied for warmblood and light horse breeds of both national studs (model I) and for warmblood breeds and the draught horse breed Rhenish German Coldblood from the North Rhine-Westphalian National stud (model II) using mixed model procedures. The fixed effects of age class, year, and month of semen collection had significant influences on all semen traits in both analyses. A significant influence of the horse breed was found for all semen traits but gel-free volume in both statistical models. Comparing warmblood and light horse stallions of both national studs, we observed highest sperm concentrations, total numbers of sperm, and total numbers of progressively motile sperm in Anglo-Arabian stallions. The draught horse breed Rhenish German Coldblood had the highest least squares means for gel-free volume, whereas all other investigated semen traits were significantly lower in this breed compared to the warmblood stallions under study. The variance components among stallions within breeds were significant for all semen traits and accounted for 40% to 59% of the total variance. The between-breed-variance among stallions was not significant underlining the similar size of the random stallion effect in each of the horse breeds analyzed here. In conclusion, breed and stallion are accounting for a significant proportion of the variation in semen quality. Copyright © 2016 Elsevier Inc. All rights reserved.

DNA typing of Pakistani cattle breeds Tharparkar and Red Sindhi by microsatellite markers.

PubMed

Azam, Amber; Babar, Masroor Ellahi; Firyal, Sehrish; Anjum, Aftab Ahmad; Akhtar, Nabeela; Asif, Muhammad; Hussain, Tanveer

2012-02-01

Microsatellite markers are used for any individual identity and breed characterization in animals that is an efficient and successful way of investigation. They are used for multiple purposes as genetic detectors including, rapid mutation rate, high level of polymorphism, and range of variety of microsatellite markers available. A panel of 19 microsatellite markers was developed for breed characterization in Tharparkar and Red Sindhi breeds of cattle in Pakistan. Forty four blood samples of cattle (each breed) were collected from Department of Livestock Management, Sindh Agriculture University, Tandojam, Tando Qaiser, Tharparkar Cattle Farm Nabi sar Road, Umer Kot, Sindh, and Govt. Red Sindhi Cattle Breeding Farm, Tando Muhammad Khan Pakistan. Breed characterization was 100% successful. Average PIC, He and Power of Exclusion values were found to be 0.91, 0.62 and 13.28, respectively. Pattern of allelic frequencies of most of the microsatellite markers were clearly distinct between two breeds. As a result of present study a reliable, efficient and very informative panel of microsatellite markers was successfully developed which was capable to interpret individual identity, forensic cases and breed characterization in cattle. This facility is ready to be provided to local cattle breeder at commercial level for DNA testing of cattle. This study will also be highly helpful for breed conservation of cattle. In addition this study can also become a basis to open up new disciplines of animal forensics in Pakistan.

The evolution of immunity in relation to colonization and migration.

PubMed

O'Connor, Emily A; Cornwallis, Charlie K; Hasselquist, Dennis; Nilsson, Jan-Åke; Westerdahl, Helena

2018-05-01

Colonization and migration have a crucial effect on patterns of biodiversity, with disease predicted to play an important role in these processes. However, evidence of the effect of pathogens on broad patterns of colonization and migration is limited. Here, using phylogenetic analyses of 1,311 species of Afro-Palaearctic songbirds, we show that colonization events from regions of high (sub-Saharan Africa) to low (the Palaearctic) pathogen diversity were up to 20 times more frequent than the reverse, and that migration has evolved 3 times more frequently from African- as opposed to Palaearctic-resident species. We also found that resident species that colonized the Palaearctic from Africa, as well as African species that evolved long-distance migration to breed in the Palaearctic, have reduced diversity of key immune genes associated with pathogen recognition (major histocompatibility complex class I). These results suggest that changes in the pathogen community that occur during colonization and migration shape the evolution of the immune system, potentially by adjusting the trade-off between the benefits of extensive pathogen recognition and the costs of immunopathology that result from high major histocompatibility complex class I diversity.

Variation in the prion protein sequence in Dutch goat breeds.

PubMed

Windig, J J; Hoving, R A H; Priem, J; Bossers, A; van Keulen, L J M; Langeveld, J P M

2016-10-01

Scrapie is a neurodegenerative disease occurring in goats and sheep. Several haplotypes of the prion protein increase resistance to scrapie infection and may be used in selective breeding to help eradicate scrapie. In this study, frequencies of the allelic variants of the PrP gene are determined for six goat breeds in the Netherlands. Overall frequencies in Dutch goats were determined from 768 brain tissue samples in 2005, 766 in 2008 and 300 in 2012, derived from random sampling for the national scrapie surveillance without knowledge of the breed. Breed specific frequencies were determined in the winter 2013/2014 by sampling 300 breeding animals from the main breeders of the different breeds. Detailed analysis of the scrapie-resistant K222 haplotype was carried out in 2014 for 220 Dutch Toggenburger goats and in 2015 for 942 goats from the Saanen derived White Goat breed. Nine haplotypes were identified in the Dutch breeds. Frequencies for non-wild type haplotypes were generally low. Exception was the K222 haplotype in the Dutch Toggenburger (29%) and the S146 haplotype in the Nubian and Boer breeds (respectively 7 and 31%). The frequency of the K222 haplotype in the Toggenburger was higher than for any other breed reported in literature, while for the White Goat breed it was with 3.1% similar to frequencies of other Saanen or Saanen derived breeds. Further evidence was found for the existence of two M142 haplotypes, M142 /S240 and M142 /P240 . Breeds vary in haplotype frequencies but frequencies of resistant genotypes are generally low and consequently selective breeding for scrapie resistance can only be slow but will benefit from animals identified in this study. The unexpectedly high frequency of the K222 haplotype in the Dutch Toggenburger underlines the need for conservation of rare breeds in order to conserve genetic diversity rare or absent in other breeds. © 2016 Blackwell Verlag GmbH.

Previous success and current body condition determine breeding propensity in Lesser Scaup: evidence for the individual heterogeneity hypothesis

USGS Publications Warehouse

Warren, Jeffrey M.; Cutting, Kyle A.; Takekawa, John Y.; De La Cruz, Susan E. W.; Williams, Tony D.; Koons, David N.

2014-01-01

The decision to breed influences an individual's current and future reproduction, and the proportion of individuals that breed is an important determinant of population dynamics. Age, experience, individual quality, and environmental conditions have all been demonstrated to influence breeding propensity. To elucidate which of these factors exerts the greatest influence on breeding propensity in a temperate waterfowl, we studied female Lesser Scaup (Aythya affinis) breeding in southwestern Montana. Females were captured during the breeding seasons of 2007–2009, and breeding status was determined on the basis of (1) presence of an egg in the oviduct or (2) blood plasma vitellogenin (VTG) levels. Presence on the study site in the previous year, a proxy for adult female success, was determined with stable isotope signatures of a primary feather collected at capture. Overall, 57% of females had evidence of breeding at the time of capture; this increased to 86% for females captured on or after peak nest initiation. Capture date and size-adjusted body condition positively influenced breeding propensity, with a declining body-condition threshold through the breeding season. We did not detect an influence of age on breeding propensity. Drought conditions negatively affected breeding propensity, reducing the proportion of breeding females to 0.85 (SE = 0.05) from 0.94 (SE = 0.03) during normal-water years. A female that was present in the previous breeding season was 5% more likely to breed than a female that was not present then. The positive correlation between age and experience makes it difficult to differentiate the roles of age, experience, and individual quality in reproductive success in vertebrates. Our results indicate that individual quality, as expressed by previous success and current body condition, may be among the most important determinants of breeding propensity in female Lesser Scaup, providing further support for the individual heterogeneity hypothesis.

Genomics-assisted breeding in fruit trees.

PubMed

Iwata, Hiroyoshi; Minamikawa, Mai F; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.

Genomics-assisted breeding in fruit trees

PubMed Central

Iwata, Hiroyoshi; Minamikawa, Mai F.; Kajiya-Kanegae, Hiromi; Ishimori, Motoyuki; Hayashi, Takeshi

2016-01-01

Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding. PMID:27069395

Breed traceability of buffalo meat using microsatellite genotyping technique.

PubMed

Kannur, Bheemashankar H; Fairoze, Md Nadeem; Girish, P S; Karabasanavar, Nagappa; Rudresh, B H

2017-02-01

Although buffalo has emerged as a major meat producing animal in Asia, major research on breed traceability has so far been focused on cattle (beef). This research gap on buffalo breed traceability has impelled development and validation of buffalo breed traceability using a set of eight microsatellite (STR) markers in seven Indian buffalo breeds (Bhadawari, Jaffaarabadi, Murrah, Mehsana, Nagpuri, Pandharpuri and Surti). Probability of sharing same profile by two individuals at a specific locus was computed considering different STR numbers, allele pooling in breed and population. Match probabilities per breed were considered and six most polymorphic loci were genotyped. Out of eight microsatellite markers studied, markers CSSMO47, DRB3 and CSSM060 were found most polymorphic. Developed technique was validated with known and unknown, blood and meat samples; wherein, samples were genetically traced in 24 out of 25 samples tested. Results of this study showed potential applications of the methodology and encourage other researchers to address the problem of buffalo traceability so as to create a world-wide archive of breed specific genotypes. This work is the first report of breed traceability of buffalo meat utilizing microsatellite genotyping technique.

XY females do better than the XX in the African pygmy mouse, Mus minutoides.

PubMed

Saunders, Paul A; Perez, Julie; Rahmoun, Massilva; Ronce, Ophélie; Crochet, Pierre-André; Veyrunes, Frédéric

2014-07-01

All therian mammals have a similar XY/XX sex-determination system except for a dozen species. The African pygmy mouse, Mus minutoides, harbors an unconventional system in which all males are XY, and there are three types of females: the usual XX but also XX* and X*Y ones (the asterisk designates a sex-reversal mutation on the X chromosome). The long-term evolution of such a system is a paradox, because X*Y females are expected to face high reproductive costs (e.g., meiotic disruption and loss of unviable YY embryos), which should prevent invasion and maintenance of a sex-reversal mutation. Hence, mechanisms for compensating for the costs could have evolved in M. minutoides. Data gathered from our laboratory colony revealed that X*Y females do compensate and even show enhanced reproductive performance in comparison to the XX and XX*; they produce significantly more offspring due to (i) a higher probability of breeding, (ii) an earlier first litter, and (iii) a larger litter size, linked to (iv) a greater ovulation rate. These findings confirm that rare conditions are needed for an atypical sex-determination mechanism to evolve in mammals, and provide valuable insight into understanding modifications of systems with highly heteromorphic sex chromosomes. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding

PubMed Central

Ohnuki, Shinsuke; Okada, Hiroki; Friedrich, Anne; Kanno, Yoichiro; Goshima, Tetsuya; Hasuda, Hirokazu; Inahashi, Masaaki; Okazaki, Naoto; Tamura, Hiroyasu; Nakamura, Ryo; Hirata, Dai; Fukuda, Hisashi; Shimoi, Hitoshi; Kitamoto, Katsuhiko; Watanabe, Daisuke; Schacherer, Joseph; Akao, Takeshi; Ohya, Yoshikazu

2017-01-01

Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomyces cerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies. PMID:28642365

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

PubMed

Michailidou, S; Tsangaris, G; Fthenakis, G C; Tzora, A; Skoufos, I; Karkabounas, S C; Banos, G; Argiriou, A; Arsenos, G

2018-06-01

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (F GRM ) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Evaluation of the sustainability of contrasted pig farming systems: breeding programmes.

PubMed

Rydhmer, L; Gourdine, J L; de Greef, K; Bonneau, M

2014-12-01

The sustainability of breeding activities in 15 pig farming systems in five European countries was evaluated. One conventional and two differentiated systems per country were studied. The Conventional systems were the standard systems in their countries. The differentiated systems were of three categories: Adapted Conventional with focus on animal welfare, meat quality or environment (five systems); Traditional with local breeds in small-scale production (three systems) and Organic (two systems). Data were collected with a questionnaire from nine breeding organisations providing animals and semen to the studied farming systems and from, on average, five farmers per farming system. The sustainability assessment of breeding activities was performed in four dimensions. The first dimension described whether the market for the product was well defined, and whether the breeding goal reflected the farming system and the farmers' demands. The second dimension described recording and selection procedures, together with genetic change in traits that were important in the system. The third dimension described genetic variation, both within and between pig breeds. The fourth dimension described the management of the breeding organisation, including communication, transparency, and technical and human resources. The results show substantial differences in the sustainability of breeding activities, both between farming systems within the same category and between different categories of farming systems. The breeding activities are assessed to be more sustainable for conventional systems than for differentiated systems in three of the four dimensions. In most differentiated farming systems, breeding goals are not related to the system, as these systems use the same genetic material as conventional systems. The breeds used in Traditional farming systems are important for genetic biodiversity, but the small scale of these systems renders them vulnerable. It is hoped that, by reflecting on different aspects of sustainability, this study will encourage sustainable developments in pig production.

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

PubMed Central

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

PubMed

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A; Gandolfi, Barbara; Mullikin, James C; Cole, Shelley A; Gruffydd-Jones, Timothy J; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2)) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2) was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2) ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2) ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

Age and breeding success related to nest position in a White stork Ciconia ciconia colony

NASA Astrophysics Data System (ADS)

Vergara, Pablo; Aguirre, José I.

2006-11-01

Coloniality is a breeding system that may produce benefits in terms of breeding success, although these advantages could vary according to factors such as colony size or nest position. We studied breeder's age in relation to nest position (peripheral or central) within the colony. In addition, we studied the relationship between breeding success and nest position, controlling for breeder's age, a highly correlated factor, in a White Stork Ciconia ciconia colony over a 7-year period. Our results show that central nests are mainly occupied by adult birds and had lower failure rates. However, controlling for breeder's age, nest position per se did not explain breeding success. The scarce predation and the lack of human disturbance in the study colony could explain the absence of differences in breeding success between different nest positions within the colony.

Morphometrics within dog breeds are highly reproducible and dispute Rensch’s rule

PubMed Central

Sutter, Nathan B.; Mosher, Dana S.; Gray, Melissa M.

2009-01-01

Using 27 body measurements, we have identified 13 breed-defining metrics for 109 of 159 domestic dog breeds, most of which are recognized by the American Kennel Club (AKC). The data set included 1,155 dogs at least 1 year old (average 5.4 years), and for 53 breed populations, complete measurement data were collected from at least three males and three females. We demonstrate, first, that AKC breed standards are rigorously adhered to for most domestic breeds with little variation observed within breeds. Second, Rensch’s rule, which describes a scaling among taxa such that sexual dimorphism is greater among larger species if males are the larger sex, with less pronounced differences in male versus female body size in smaller species, is not maintained in domestic dog breeds because the proportional size difference between males and females of small and large breeds is essentially the same. Finally, principal components (PCs) analysis describes both the overall body size (PC1) and the shape (length versus width) of the skeleton (PC2). That the integrity of the data set is sufficiently rich to discern PCs has strong implications for mapping studies, suggesting that individual measurements may not be needed for genetic studies of morphologic traits, particularly in the case of breed-defining traits that are typically under strong selection. Rather, phenotypes derived from data sets such as these, collected at a fraction of the effort and cost, may be used to direct whole-genome association studies aimed at understanding the genetic basis of fixed morphologic phenotypes defining distinct dog breeds. PMID:19020935

Avian use of forest habitats in the Pembina Hills of northeastern North Dakota

USGS Publications Warehouse

Faanes, Craig A.; Andrew, Jonathan M.

1983-01-01

North Dakota has the least extensive total area of forested habitats of any of the 50 United States. Although occurring in limited area, forest communities add considerably to the total ecological diversity of the State. The forests of the Pembina Hills region in northeastern North Dakota are one of only three areas large enough to be considered of commercial value. During 1981 we studied the avifauna of the upper valley of the Pembina River in the Pembina Hills. Field work extended from 20 April to 23 July; breeding bird censuses were conducted 7 June to 2 July. Of the 120 bird species recorded during the study period, 79 species were recorded during the breeding season. The total breeding population was estimated at nearly 76,000 breeding pairs. The wood warblers (Parulidae) were the most numerous family, accounting for about 28,000 breeding pairs. The yellow warbler (Dendroica petechia) was the most abundant breeding species, making up 19.4% of the population. American redstart (Setophaga ruticilla) was second in abundance, accounting for 10.5% of the breeding population. Largest breeding densities occurred in the willow (Salix sp.) shrub community. Although supporting the lowest mean breeding density, quaking aspen (Populus tremuloides) forests supported the highest species diversity. First State breeding records were recorded for alder flycatcher (Empidonax alnorum) and golden-winged warbler (Vermivora chrysoptera). Records were obtained for 12 species considered rare or unusual in North Dakota during the breeding season. The status of all species known to have occurred in the study area is described in an annotated species list.

Assortative mating and fragmentation within dog breeds.

PubMed

Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

2008-01-28

There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.

Assortative mating and fragmentation within dog breeds

PubMed Central

2008-01-01

Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds. PMID:18226210

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

PubMed Central

Gutiérrez-Gil, Beatriz; Arranz, Juan J.; Wiener, Pamela

2015-01-01

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity. PMID:26029239

ENSO Bred Vectors in Coupled Ocean-Atmosphere General Circulation Models

NASA Technical Reports Server (NTRS)

Yang, S. C.; Cai, Ming; Kalnay, E.; Rienecker, M.; Yuan, G.; Toth, ZA.

2004-01-01

The breeding method has been implemented in the NASA Seasonal-to-Interannual Prediction Project (NSIPP) Coupled General Circulation Model (CGCM) with the goal of improving operational seasonal to interannual climate predictions through ensemble forecasting and data assimilation. The coupled instability as cap'tured by the breeding method is the first attempt to isolate the evolving ENSO instability and its corresponding global atmospheric response in a fully coupled ocean-atmosphere GCM. Our results show that the growth rate of the coupled bred vectors (BV) peaks at about 3 months before a background ENSO event. The dominant growing BV modes are reminiscent of the background ENSO anomalies and show a strong tropical response with wind/SST/thermocline interrelated in a manner similar to the background ENSO mode. They exhibit larger amplitudes in the eastern tropical Pacific, reflecting the natural dynamical sensitivity associated with the presence of the shallow thermocline. Moreover, the extratropical perturbations associated with these coupled BV modes reveal the variations related to the atmospheric teleconnection patterns associated with background ENSO variability, e.g. over the North Pacific and North America. A similar experiment was carried out with the NCEP/CFS03 CGCM. Comparisons between bred vectors from the NSIPP CGCM and NCEP/CFS03 CGCM demonstrate the robustness of the results. Our results strongly suggest that the breeding method can serve as a natural filter to identify the slowly varying, coupled instabilities in a coupled GCM, which can be used to construct ensemble perturbations for ensemble forecasts and to estimate the coupled background error covariance for coupled data assimilation.

Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers.

PubMed

Streitberger, K; Schweizer, M; Kropatsch, R; Dekomien, G; Distl, O; Fischer, M S; Epplen, J T; Hertwig, S T

2012-10-01

As a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders' preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Genetic covariance components within and among linear type traits differ among contrasting beef cattle breeds.

PubMed

Doyle, Jennifer L; Berry, Donagh P; Walsh, Siobhan W; Veerkamp, Roel F; Evans, Ross D; Carthy, Tara R

2018-05-04

Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P < 0.05) in heritability estimates, between at least two breeds, existed for 13 out of 18 linear type traits. Differences (P < 0.05) also existed between the pairwise within-breed genetic correlations among the linear type traits. Overall, the linear type traits in the continental breeds (i.e., CH, LM, SI) tended to have similar heritability estimates to each other as well as similar genetic correlations among the same pairwise traits, as did the traits in the British breeds (i.e., AA, HE). The correlation between a linear function of breeding values computed conditional on covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.

Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations

PubMed Central

Pierce, Magretha D.; Dzama, Kennedy; Muchadeyi, Farai C.

2018-01-01

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs. PMID:29868114

Sirenian life history

USGS Publications Warehouse

Bonde, Robert K.

2018-01-01

Sirenians, including the manatees and dugongs, are large herbivorous mammals that have evolved to an aquatic form since the Eocene epoch. Sirenians have unique adaptations, including dense bone for ballast and a longitudinal hemidiaphragm separating paired lungs (which aid in maintaining a horizontal posture in the water column), species-specific rostral deflection, and unique dentition for specialized feeding, which all contribute to their success. All sirenians produce one calf per breeding cycle and have long calf-dependency periods. Low reproduction rates are common for long-lived, large mammals, but may compromise their existence in today’s quickly changing world today. All sirenian populations are listed as either threatened or endangered, and some local stocks have been completely extirpated by human activities.

Mating systems and sexual selection in male-pregnant pipefishes and seahorses: insights from microsatellite-based studies of maternity.

PubMed

Jones, A G; Avise, J C

2001-01-01

In pipefishes and seahorses (family Syngnathidae), the males provide all postzygotic care of offspring by brooding embryos on their ventral surfaces. In some species, this phenomenon of male "pregnancy" results in a reversal of the usual direction of sexual selection, such that females compete more than males for access to mates, and secondary sexual characteristics evolve in females. Thus the syngnathids can provide critical tests of theories related to the evolution of sex differences and sexual selection. Microsatellite-based studies of the genetic mating systems of several species of pipefishes and seahorses have provided insights into important aspects of the natural history and evolution of these fishes. First, males of species with completely enclosed pouches have complete confidence of paternity, as might be predicted from parental investment theory for species in which males invest so heavily in offspring. Second, a wide range of genetic mating systems have been documented in nature, including genetic monogamy in a seahorse, polygynandry in two species of pipefish, and polyandry in a third pipefish species. The genetic mating systems appear to be causally related to the intensity of sexual selection, with secondary sex characters evolving most often in females of the more polyandrous species. Third, genetic studies of captive-breeding pipefish suggest that the sexual selection gradient (or Bateman gradient) may be a substantially better method for characterizing the mating system than previously available techniques. Finally, these genetic studies of syngnathid mating systems have led to some general insights into the occurrence of clustered mutations at microsatellite loci, the utility of linked loci in studies of parentage, and the use of parentage data for direct estimation of adult population size.

Global impact of accelerated plant breeding: Evidence from a meta-analysis on rice breeding.

PubMed

Lenaerts, Bert; de Mey, Yann; Demont, Matty

2018-01-01

Rice breeders in Asia and elsewhere in the world have long overlooked trying to shorten the time it takes to develop new varieties. Plant breeders have proposed a technique called Rapid Generation Advance (RGA) as a way to accelerate the results of public rice breeding programs. However, little is known about RGA's potential impact. Here, we present the first results of a global impact study of RGA. More specifically, we calculated the multiplicator effects of RGA on the research benefits generated by conventional rice breeding programs and applied them to a meta-analysis of selected impact studies in the literature. These insights are a first crucial step in developing a targeted approach for disseminating RGA technology among rice breeders to accelerate the impact of their public rice breeding programs around the world. We show that the additional benefits due to time savings are considerable and offer some insights into the economics of breeding. Our results confirm that the adoption of accelerated breeding would lead to substantial advantages to rice breeding programs and the earlier variety release leads to significant economic benefits to society. This can be important to policy makers when reshaping their public breeding methods and optimising their return on research investments in breeding.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds.

PubMed

Makina, Sithembile O; Taylor, Jeremy F; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; MacNeil, Michael D; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r (2)≥ 0.20 would require about 30,000-50,000 SNPs. However, r (2)≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

PubMed Central

Makina, Sithembile O.; Taylor, Jeremy F.; van Marle-Köster, Este; Muchadeyi, Farai C.; Makgahlela, Mahlako L.; MacNeil, Michael D.; Maiwashe, Azwihangwisi

2015-01-01

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa. PMID:26648975

Characterization of local goat breeds using RAP-DNA markers

NASA Astrophysics Data System (ADS)

Al-Barzinji, Yousif M. S.; Hamad, Aram O.

2017-09-01

The present study was conducted on different colors of local goat breeds. A number of 216 does were sampled from the seven groups. Genomic DNA was extracted from the blood samples. From the twenty used RAPD primers 12 of them were amplified, and presence of bands. The total fragment number of 12 primers over all the goat breed samples was 485 fragments. Out of the 485 fragments, 90 of them were Polymorphic fragments numbers (PFN). From all bands obtained, 20 of them possessed unique bands. The highest unique band was found in locus RAP 6 which has 4 unique bands, three of them in the Maraz Brown and one in the local Koor. Nei's gene diversity and Shanon's information index in this study were averaged 0.38 and 0.60, respectively. The genetic distance among several goat breeds ranged from 9.11 to 43.33%. The highest genetic distance 43.33% recorded between Maraz goat and other goat breeds and between local Koor and other goat (except Maraz goats) breeds (37.79%). However, the lowest genetic distance recorded between local white and Pnok. The distance between (local Black and Pnok) and (local Black and local white) was 22.75%. In conclusions, the high distance among these goat breeds, polymorphism and high numbers of unique bands found in present study indicates that these goat breeds have the required amount of genetic variation to made genetic improvement. This study helps us to clarify the image of the genetic diversity of the local goat breeds and the breeders can used it for mating system when need to make the crossing among these goat breeds.

The legacy of Columbus in American horse populations assessed by microsatellite markers.

PubMed

Cortés, O; Dunner, S; Gama, L T; Martínez, A M; Delgado, J V; Ginja, C; Jiménez, L M; Jordana, J; Luis, C; Oom, M M; Sponenberg, D P; Zaragoza, P; Vega-Pla, J L

2017-08-01

Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of "all other Criollo breeds" had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity. © 2017 Blackwell Verlag GmbH.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

PubMed

Wang, G Z; Chen, S S; Chao, T L; Ji, Z B; Hou, L; Qin, Z J; Wang, J M

2017-05-01

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

Elevational gradient in clutch size of Red-faced Warblers

USGS Publications Warehouse

Dillon, Kristen G.; Conway, Courtney J.

2015-01-01

Our understanding of life history evolution has benefited from debates regarding the underlying causes, and geographic ubiquity, of spatial patterns in avian clutch sizes. Past studies have revealed that birds lay smaller clutch sizes at higher elevation. However, in most previous studies, investigators have failed to adequately control for elevational differences in breeding phenology. To better understand the elevational gradient in avian clutch size, we need to know how clutch size changes across the entire elevational breeding range of a species (i.e., the shape of the relationship between elevation and clutch size), and whether the elevational gradient in clutch size is merely an artifact of elevational gradients in breeding phenology or breeding season length. We examined the relationship between breeding elevation and clutch size of Red-faced Warblers (Cardellina rubrifrons) along a 1000-m elevational gradient in Arizona. Our objectives were to determine how clutch size changed with elevation, and if the relationship between clutch size and elevation merely reflected elevational changes in breeding season length or phenology. The proportion of 5-egg clutches decreased and the proportion of 3- and 4-egg clutches increased non-linearly with increasing elevation, even after controlling for the elevational gradient in nest initiation date. Thus, average clutch size declined across the elevational breeding range of Red-faced Warblers, but this decline was not due to elevational variation in breeding phenology. Timing of breeding changed, but the duration of the breeding season did not change appreciably across the elevational gradient. Hence, elevational differences in breeding season length or breeding phenology cannot explain why Red-faced Warblers (and perhaps other birds) breeding at higher elevations have smaller clutches.

Apoptosis-mediated seasonal testicular regression in the Japanese Jungle Crow (Corvus macrorhynchos).

PubMed

Islam, M Nazrul; Tsukahara, N; Sugita, S

2012-06-01

The present study investigated effects of apoptosis observed during seasonal testicular regression in Japanese Jungle Crows. The study was conducted during January to June 2008, 2009. Testes from adults captured during non-breeding (January), prebreeding (February to mid-March), main-breeding (late March to early May), transition (mid-May to late May), and post-breeding (June) seasons were analyzed. Apoptosis was assessed by in situ terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay. Paired-testis volume increased 95-fold from the non-breeding to the main-breeding season (P < 0.05), and subsequently decreased 26-fold from the main breeding to the post-breeding season (P < 0.05). Testicular activity was evaluated from the total germ cell count and sperm index, which increased 42- and 5-fold, respectively, in the main-breeding season, and subsequently decreased 33- and 5-fold in the post-breeding season. In testes, TUNEL-positive germ cells were at low levels in the non-breeding season, absent in the prebreeding and the main-breeding seasons, and highest in mid-May (P < 0.05). In contrast, TUNEL-positive Sertoli cells occurred only in late-April. In addition, TUNEL-positive fibroblast-like cells were observed in the outer zone of the tunica albuginea in the post-breeding season. Collectively, these data suggested that the seasonal rise in the testicular competence occurred slowly in Japanese Jungle Crows; however, testis function was terminated rapidly after the breeding season. Furthermore, we concluded, similar to other avian species, Sertoli cell apoptosis followed by massive germ cell death was responsible for rapid testicular regression in Jungle Crows. Copyright © 2012 Elsevier Inc. All rights reserved.

Ocular biometry by computed tomography in different dog breeds.

PubMed

Chiwitt, Carolin L H; Baines, Stephen J; Mahoney, Paul; Tanner, Andrew; Heinrich, Christine L; Rhodes, Michael; Featherstone, Heidi J

2017-09-01

To (i) correlate B-mode ocular ultrasound (US) and computed tomography (CT) (prospective pilot study), (ii) establish a reliable method to measure the normal canine eye using CT, (iii) establish a reference guide for some dog breeds, (iv) compare eye size between different breeds and breed groups, and (v) investigate the correlation between eye dimensions and body weight, gender, and skull type (retrospective study). B-mode US and CT were performed on ten sheep cadaveric eyes. CT biometry involved 100 adult pure-bred dogs with nonocular and nonorbital disease, representing eleven breeds. Eye length, width, and height were each measured in two of three planes (horizontal, sagittal, and equatorial). B-mode US and CT measurements of sheep cadaveric eyes correlated well (0.70-0.71). The shape of the canine eye was found to be akin to an oblate spheroid (a flattened sphere). A reference guide was established for eleven breeds. Eyes of large breed dogs were significantly larger than those of medium and small breed dogs (P < 0.01), and eyes of medium breed dogs were significantly larger than those of small breed dogs (P < 0.01). Eye size correlated with body weight (0.74-0.82) but not gender or skull type. Computed tomography is a suitable method for biometry of the canine eye, and a reference guide was established for eleven breeds. Eye size correlated with breed size and body weight. Because correlation between B-mode US and CT was shown, the obtained values can be applied in the clinical setting, for example, for the diagnosis of microphthalmos and buphthalmos. © 2016 American College of Veterinary Ophthalmologists.

Charge breeding simulations for radioactive ion beam production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Variale, V.; Raino, A. C.; Clauser, T.

2012-02-15

The charge breeding technique is used for radioactive ion beam (RIB) production in order of optimizing the re-acceleration of the radioactive element ions produced by a primary beam in a thick target. Charge breeding is achieved by means of a device capable of increasing the ion charge state from 1+ to a desired value n+. In order to get high intensity RIB, experiments with charge breeding of very high efficiency could be required. To reach this goal, the charge breeding simulation could help to optimize the high charge state production efficiency by finding more proper parameters for the radioactive 1+more » ions. In this paper a device based on an electron beam ion source (EBIS) is considered. In order to study that problem, a code already developed for studying the ion selective containment in an EBIS with RF quadrupoles, BRICTEST, has been modified to simulate the ion charge state breeding rate for different 1+ ion injection conditions. Particularly, the charge breeding simulations for an EBIS with a hollow electron beam have been studied.« less

Extent of Linkage Disequilibrium in the Domestic Cat, Felis silvestris catus, and Its Breeds

PubMed Central

Alhaddad, Hasan; Khan, Razib; Grahn, Robert A.; Gandolfi, Barbara; Mullikin, James C.; Cole, Shelley A.; Gruffydd-Jones, Timothy J.; Häggström, Jens; Lohi, Hannes; Longeri, Maria; Lyons, Leslie A.

2013-01-01

Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r 2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits. PMID:23308248

Effects of selection for cooperation and attention in dogs.

PubMed

Gácsi, Márta; McGreevy, Paul; Kara, Edina; Miklósi, Adám

2009-07-24

It has been suggested that the functional similarities in the socio-cognitive behaviour of dogs and humans emerged as a consequence of comparable environmental selection pressures. Here we use a novel approach to account for the facilitating effect of domestication in dogs and reveal that selection for two factors under genetic influence (visual cooperation and focused attention) may have led independently to increased comprehension of human communicational cues. In Study 1, we observed the performance of three groups of dogs in utilizing the human pointing gesture in a two-way object choice test. We compared breeds selected to work while visually separated from human partners (N = 30, 21 breeds, clustered as independent worker group), with those selected to work in close cooperation and continuous visual contact with human partners (N = 30, 22 breeds, clustered as cooperative worker group), and with a group of mongrels (N = 30).Secondly, it has been reported that, in dogs, selective breeding to produce an abnormal shortening of the skull is associated with a more pronounced area centralis (location of greatest visual acuity). In Study 2, breeds with high cephalic index and more frontally placed eyes (brachycephalic breeds, N = 25, 14 breeds) were compared with breeds with low cephalic index and laterally placed eyes (dolichocephalic breeds, N = 25, 14 breeds). In Study 1, cooperative workers were significantly more successful in utilizing the human pointing gesture than both the independent workers and the mongrels.In study 2, we found that brachycephalic dogs performed significantly better than dolichocephalic breeds. After controlling for environmental factors, we have provided evidence that at least two independent phenotypic traits with certain genetic variability affect the ability of dogs to rely on human visual cues. This finding should caution researchers against making simple generalizations about the effects of domestication and on dog-wolf differences in the utilization of human visual signals.

Ecohealth System Dynamic Model as a Planning Tool for the Reduction of Breeding Sites

NASA Astrophysics Data System (ADS)

Respati, T.; Raksanagara, A.; Djuhaeni, H.; Sofyan, A.; Shandriasti, A.

2017-03-01

Dengue is still one of major health problem in Indonesia. Dengue transmission is influenced by dengue prevention and eradication program, community participation, housing environment and climate. The complexity of the disease coupled with limited resources necessitates different approach for prevention methods that include factors contribute to the transmission. One way to prevent the dengue transmission is by reducing the mosquito’s breeding sites. Four factors suspected to influence breeding sites are dengue prevention and eradication program, community participation, housing environment, and weather condition. In order to have an effective program in reducing the breeding site it is needed to have a model which can predict existence of the breeding sites while the four factors under study are controlled. The objective of this study is to develop an Ecohealth model using system dynamic as a planning tool for the reduction of breeding sites to prevent dengue transmission with regard to dengue prevention and eradication program, community participation, housing environment, and weather condition. The methodology is a mixed method study using sequential exploratory design. The study comprised of 3 stages: first a qualitative study to 14 respondents using in-depth interview and 6 respondents for focus group discussion. The results from the first stage was used to develop entomology and household survey questionnaires for second stage conducted in 2036 households across 12 sub districts in Bandung City. Ecohealth system dynamic model was developed using data from first and second stages. Analyses used are thematic analysis for qualitative data; spatial, generalized estimating equation (GEE) and structural equation modeling for quantitative data; also average mean error (AME) and average variance error (AVE) for dynamic system model validation. System dynamic model showed that the most effective approach to eliminate breeding places was by ensuring the availability of basic sanitation for all houses. Weather factors such as precipitation can be compensated with the eradication of breeding sites activities which is conducted as scheduled and at the same time for the whole areas. Conclusion of this study is that dengue prevention and eradication program, community participation, and housing environment contributed to breeding places elimination influenced the existence of the breeding sites. The availability of basic sanitation and breeding places eradication program done timely and collectively are the most effective approach to eradicate breeding sites. Ecohealth dynamic system model can be used as a tool for the planning of breeding sites eradication program to prevent disease transmissions at city level.

Disease burden in four populations of dog and cat breeds compared to mixed-breed dogs and European shorthair cats.

PubMed

Keijser, S F A; Meijndert, L E; Fieten, H; Carrière, B J; van Steenbeek, F G; Leegwater, P A J; Rothuizen, J; Nielen, M

2017-05-01

Current public and professional opinion is that many dog breeds suffer from health issues related to inherited diseases or extreme phenotypes. The aim of this historical comparative observational study was to evaluate the breed-related disease burden in three purebred dog populations (Chihuahua, French bulldog, Labrador retriever) and one purebred cat breed (Persian cats) in the Netherlands by comparison to a control population of mixed-breed dogs and European Shorthair cats. A qualitative query was performed, consisting of a literature review and collecting the expert opinions of University veterinary specialists, to gather insight into potential diseases of the study population. Next, a referral clinic case control study of the patients referred to specific medical disciplines in the University Clinic was performed. The odds ratio (OR) was calculated to determine the likelihood of a patient referred to a particular medical discipline being a certain breed. Together, the qualitative query and the case control study resulted in a list of potentially relevant diseases limited to five organ systems per breed. These were analysed in data from primary practices. Patient files from ten primary practices over a period of two years were manually extracted and examined. Four-hundred individual patient records per breed as well as 1000 non-breed records were randomly selected from the 10 practices, weighted per practice size. Records were then examined and the presence or absence of certain diseases was identified. To evaluate the disease burden per breed, proportional difference (PD) was estimated, as well as the animal's age at presentation in months. The results of the referral clinic case control study showed an overrepresentation (Odds Ratio>1.5) of the selected breeds in several medical specialties, while median age at presentation was in some cases significantly lower than in the non-breed animals. Results of the practice-based extended cross-sectional study showed that only a few of the selected diseases contribute to the disease burden in these purebred populations, which was different from the expectations derived from the literature or expert opinion. Additional results included age difference at presentation, which may be interpreted as age of onset, and could indicate a higher disease burden for the individual animal. Also, only a small percentage of purebred dogs was registered with the national kennel club. Our final recommendation is that population-based data mining is needed to evaluate country-specific companion animal health and welfare. Copyright © 2017 Elsevier B.V. All rights reserved.

Goals and hurdles for a successful implementation of genomic selection in breeding programme for selected annual and perennial crops.

PubMed

Jonas, Elisabeth; de Koning, Dirk Jan

Genomic Selection is an important topic in quantitative genetics and breeding. Not only does it allow the full use of current molecular genetic technologies, it stimulates also the development of new methods and models. Genomic selection, if fully implemented in commercial farming, should have a major impact on the productivity of various agricultural systems. But suggested approaches need to be applicable in commercial breeding populations. Many of the published research studies focus on methodologies. We conclude from the reviewed publications, that a stronger focus on strategies for the implementation of genomic selection in advanced breeding lines, introduction of new varieties, hybrids or multi-line crosses is needed. Efforts to find solutions for a better prediction and integration of environmental influences need to continue within applied breeding schemes. Goals of the implementation of genomic selection into crop breeding should be carefully defined and crop breeders in the private sector will play a substantial part in the decision-making process. However, the lack of published results from studies within, or in collaboration with, private companies diminishes the knowledge on the status of genomic selection within applied breeding programmes. Studies on the implementation of genomic selection in plant breeding need to evaluate models and methods with an enhanced emphasis on population-specific requirements and production environments. Adaptation of methods to breeding schemes or changes to breeding programmes for a better integration of genomic selection strategies are needed across species. More openness with a continuous exchange will contribute to successes.

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

PubMed Central

Petersen, Jessica L.; Mickelson, James R.; Cothran, E. Gus; Andersson, Lisa S.; Axelsson, Jeanette; Bailey, Ernie; Bannasch, Danika; Binns, Matthew M.; Borges, Alexandre S.; Brama, Pieter; da Câmara Machado, Artur; Distl, Ottmar; Felicetti, Michela; Fox-Clipsham, Laura; Graves, Kathryn T.; Guérin, Gérard; Haase, Bianca; Hasegawa, Telhisa; Hemmann, Karin; Hill, Emmeline W.; Leeb, Tosso; Lindgren, Gabriella; Lohi, Hannes; Lopes, Maria Susana; McGivney, Beatrice A.; Mikko, Sofia; Orr, Nicholas; Penedo, M. Cecilia T; Piercy, Richard J.; Raekallio, Marja; Rieder, Stefan; Røed, Knut H.; Silvestrelli, Maurizio; Swinburne, June; Tozaki, Teruaki; Vaudin, Mark; M. Wade, Claire; McCue, Molly E.

2013-01-01

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. PMID:23383025

Seasonal fluctuation in the neuronal classes of parahippocampal area of P. krameri (Scopoli, 1769) and E. scolopaceus (Linnaeus, 1758).

PubMed

Srivastava, U C; Singh, S; Singh, D

2012-10-08

Hippocampus in birds is a relatively narrow, curved strip of tissue that lies on the dorsomedial surface of telencephalon. It is widest dorsally at the junction with parahippocampal area, and it tapers with septum. Parahippocampal area (APH), the most prominent field of hippocampus is a long structure that lies at the most rostral level and continues upto caudal extent. It has been indicated by behavioral studies that hippocampus in birds plays an important role in process of learning, memory formation, food storage and spatial navigation. The present study enlightens some interesting fluctuations occurring in the neuronal classes of parahippocampal area of two seasonally breeding birds viz. P. krameri and E. scolopaceus in terms of dendritic thickness, spine density and spine morphology during breeding and non-breeding time period of birds. The Golgi-impregnated sections were used to study these fluctuations and it was noticed that there was a significant increase in dendritic thickness, spine density, spine length and spine head diameter during breeding as compared to non-breeding period. The results obtained were comparable in two different seasonally breeding birds, supporting the view that avian parahippocampal area shows neuroanatomical plasticity associated with breeding and non-breeding period because of variations in endocrinology.

The potential of open learning in animal breeding.

PubMed

Lohuis, M M; Lohuis, C T; Petrongolo, R A

1999-07-01

Animal breeding education is presently facing many challenges. These include rapid changes in breeding knowledge and technology, resource and funding restrictions, and altering demographics of the learner and the animal breeding industry. These challenges can be met via an open learning educational format. This nontraditional approach is based on the needs of individual learners, not the interests of the teacher or the institution. An important feature of open learning is its appropriateness for the professional development audience. Delivery methods include interactive distance courses on the Web, computer-assisted learning, and team-based study. The Canadian dairy breeding industry has expressed the need for ongoing professional development to understand and adopt new animal breeding technologies. The University of Guelph responded by delivering a series of animal breeding short courses (Executive Certificate Program in Animal Breeding) to industry decision makers in 1997. A version modified specifically for farmers and breeding industry personnel was offered in 1998. Through the collaboration of experts from various agricultural institutions and the use of a learner-centered format, this professional development initiative was a pedagogical and financial success. This paper describes how the open learning approach differs from traditional university teaching. Using the University of Guelph example in animal breeding professional development, the framework for a successful open learning program will be examined. The best practices for effective adult education will also be identified and discussed within this case study.

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.

PubMed

Medugorac, Ivica; Medugorac, Ana; Russ, Ingolf; Veit-Kensch, Claudia E; Taberlet, Pierre; Luntz, Bernhard; Mix, Henry M; Förster, Martin

2009-08-01

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

PubMed Central

Anderson, Heidi; Davison, Stephen; Hughes, Angela M.; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M.; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Forman, Oliver P.; Fretwell, Neale; Cole, Cynthia A.; Lohi, Hannes

2018-01-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare. PMID:29708978

Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs.

PubMed

Donner, Jonas; Anderson, Heidi; Davison, Stephen; Hughes, Angela M; Bouirmane, Julia; Lindqvist, Johan; Lytle, Katherine M; Ganesan, Balasubramanian; Ottka, Claudia; Ruotanen, Päivi; Kaukonen, Maria; Forman, Oliver P; Fretwell, Neale; Cole, Cynthia A; Lohi, Hannes

2018-04-01

Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic variants implicated in Mendelian disorders in the largest canine study sample examined to date by examining over 83,000 mixed breed and 18,000 purebred dogs representing 330 breeds for 152 known variants using a custom-designed beadchip microarray. We further announce the creation of MyBreedData (www.mybreeddata.com), an online updated inherited disorder prevalence resource with its foundation in the generated data. We identified the most prevalent, and rare, disease susceptibility variants across the general dog population while providing the first extensive snapshot of the mixed breed disease heritage. Approximately two in five dogs carried at least one copy of a tested disease variant. Most disease variants are shared by both mixed breeds and purebreds, while breed- or line-specificity of others is strongly suggested. Mixed breed dogs were more likely to carry a common recessive disease, whereas purebreds were more likely to be genetically affected with one, providing DNA-based evidence for hybrid vigor. We discovered genetic presence of 22 disease variants in at least one additional breed in which they were previously undescribed. Some mutations likely manifest similarly independently of breed background; however, we emphasize the need for follow up investigations in each case and provide a suggested validation protocol for broader consideration. In conclusion, our study provides unique insight into genetic epidemiology of canine disease risk variants, and their relevance for veterinary medicine, breeding programs and animal welfare.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

PubMed

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-07-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

PubMed Central

Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

2016-01-01

Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved. PMID:27025169

Differences in innate and adaptive immune response traits of Pahari (Indian non-descript indigenous breed) and Jersey crossbred cattle.

PubMed

Verma, Subhash; Thakur, Aneesh; Katoch, Shailja; Shekhar, Chander; Wani, Aasim Habib; Kumar, Sandeep; Dohroo, Shweta; Singh, Geetanjali; Sharma, Mandeep

2017-10-01

Cattle are an integral part of the largely agrarian economy of India. Indigenous breeds of cattle comprise about 80% of total cattle population of the country and contribute significantly to the overall milk production. There are 40 recognized indigenous breeds of cattle and a number of uncharacterized non-descript cattle. Pahari cattle of Himachal Pradesh in Northern India are one such non-descript indigenous breed. Here we describe a comprehensive evaluation of haematobiochemical parameters and innate and adaptive immune response traits of Pahari cattle and a comparison with Jersey crossbred cattle. The study shows demonstrable differences in the two breeds with respect to some innate and adaptive immunological traits. This is a first attempt to characterize immune response traits of Pahari cattle and the results of the study provide an understanding of breed differences in immune status of cattle which could be useful for their breeding and conservations programs. Copyright © 2017 Elsevier B.V. All rights reserved.

The contribution of migrant breeds to the genetic gain of beef traits of German Vorderwald and Hinterwald cattle.

PubMed

Hartwig, S; Wellmann, R; Hamann, H; Bennewitz, J

2014-12-01

During the past decades, migrant contributions have accumulated in many local breeds. Cross-breeding was carried out to mitigate the risk of inbreeding depression and to improve the performance of local breeds. However, breeding activities for local breeds were not as intensive and target oriented as for popular high-yielding breeds. Therefore, even if performance improved, the gap between the performance of local and popular breeds increased for many traits. Furthermore, the genetic originality of local breeds declined due to the increasing contributions of migrant breeds. This study examined the importance of migrant breed influences for the realization of breeding progress of beef traits of German Vorderwald and Hinterwald cattle. The results show that there is a high amount of migrant contributions and their effects on performance are substantial for most traits. The effect of the French cattle breed Montbéliard (p-value 0.014) on daily gain of Vorderwald bulls at test station was positive. The effects of Vorderwald ancestors (p-value for daily gain 0.007 and p-value for net gain 0.004) were positive for both traits under consideration in the population of Hinterwald cattle. Additionally, the effect of remaining breeds (p-value 0.030) on net gain of Hinterwald cattle in the field was also positive. The estimated effect of Fleckvieh ancestors on net gain of Hinterwald cattle was even larger but not significant. Breeding values adjusted for the effects of the migrant breeds showed little genetic trend. © 2014 Blackwell Verlag GmbH.

Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds.

PubMed

van den Berg, Irene; Boichard, Didier; Lund, Mogens Sandø

2016-11-01

The objective of this study was to compare mapping precision and power of within-breed and multibreed genome-wide association studies (GWAS) and to compare the results obtained by the multibreed GWAS with 3 meta-analysis methods. The multibreed GWAS was expected to improve mapping precision compared with a within-breed GWAS because linkage disequilibrium is conserved over shorter distances across breeds than within breeds. The multibreed GWAS was also expected to increase detection power for quantitative trait loci (QTL) segregating across breeds. GWAS were performed for production traits in dairy cattle, using imputed full genome sequences of 16,031 bulls, originating from 6 French and Danish dairy cattle populations. Our results show that a multibreed GWAS can be a valuable tool for the detection and fine mapping of quantitative trait loci. The number of QTL detected with the multibreed GWAS was larger than the number detected by the within-breed GWAS, indicating an increase in power, especially when the 2 Holstein populations were combined. The largest number of QTL was detected when all populations were combined. The analysis combining all breeds was, however, dominated by Holstein, and QTL segregating in other breeds but not in Holstein were sometimes overshadowed by larger QTL segregating in Holstein. Therefore, the GWAS combining all breeds except Holstein was useful to detect such peaks. Combining all breeds except Holstein resulted in smaller QTL intervals on average, but this outcome was not the case when the Holstein populations were included in the analysis. Although no decrease in the average QTL size was observed, mapping precision did improve for several QTL. Out of 3 different multibreed meta-analysis methods, the weighted z-scores model resulted in the most similar results to the full multibreed GWAS and can be useful as an alternative to a full multibreed GWAS. Differences between the multibreed GWAS and the meta-analyses were larger when different breeds were combined than when the 2 Holstein populations were combined. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetically-determined polymorphism of nonspecific esterases and phosphoglucomutase in eight introduced breeds of the silkworm, Bombyx mori, raised in Bulgaria.

PubMed

Staykova, Teodora

2008-01-01

Isoenzymes are very suitable markers for the study of the inter-breed diversity of the silkworm Bombyx mon L. (Lepidoptera: Bombycidae). More than 250 breeds are raised in Bulgaria, which are not very well studied with regard to their isoenzymic polymorphism. Polymorphism of nonspecific esterases from pupal haemolymph was analyzed, as well as of phosphoglucomutase from different organs of larvae, pupae and imago, from eight introduced breeds. Electrophoresis in polyacrylamide gels was used. A polylocus control of nonspecific esterases, and possible monolocus control of phosphoglucomutase was ascertained. Biallele and triallele polymorphism of phosphoglucomutase locus and in three of the esterase loci was determined. The allelic frequencies of the polymorphic loci in each breed were analyzed. Inter-breed differences were found in different allelic frequencies, different heterozygosity and polymorphism.

The impact of increased food availability on reproduction in a long-distance migratory songbird: implications for environmental change?

PubMed

Seward, Adam M; Beale, Colin M; Gilbert, Lucy; Jones, T Hefin; Thomas, Robert J

2014-01-01

Many populations of migratory songbirds are declining or shifting in distribution. This is likely due to environmental changes that alter factors such as food availability that may have an impact on survival and/or breeding success. We tested the impact of experimentally supplemented food on the breeding success over three years of northern wheatears (Oenanthe oenanthe), a species in decline over much of Europe. The number of offspring fledged over the season was higher for food-supplemented birds than for control birds. The mechanisms for this effect were that food supplementation advanced breeding date, which, together with increased resources, allowed further breeding attempts. While food supplementation did not increase the clutch size, hatching success or number of chicks fledged per breeding attempt, it did increase chick size in one year of the study. The increased breeding success was greater for males than females; males could attempt to rear simultaneous broods with multiple females as well as attempting second broods, whereas females could only increase their breeding effort via second broods. Multiple brooding is rare in the study population, but this study demonstrates the potential for changes in food availability to affect wheatear breeding productivity, primarily via phenotypic flexibility in the number of breeding attempts. Our results have implications for our understanding of how wheatears may respond to natural changes in food availability due to climate changes or changes in habitat management.

Frequencies of genes for coat colour and horns in Nordic cattle breeds

PubMed Central

Kantanen, Juha; Olsaker, Ingrid; Brusgaard, Klaus; Eythorsdottir, Emma; Holm, Lars-Erik; Lien, Sigbjørn; Danell, Birgitta; Adalsteinsson, Stefan

2000-01-01

Gene frequencies of coat colour and horn types were assessed in 22 Nordic cattle breeds in a project aimed at establishing genetic profiles of the breeds under study. The coat colour loci yielding information on genetic variation were: extension, agouti, spotting, brindle, dun dilution and colour sided. The polled locus was assessed for two alleles. A profound variation between breeds was observed in the frequencies of both colour and horn alleles, with the older breeds generally showing greater variation in observed colour, horn types and segregating alleles than the modern breeds. The correspondence between the present genetic distance matrix and previous molecular marker distance matrices was low (r = 0.08 – 0.12). The branching pattern of a neighbour-joining tree disagreed to some extent with the molecular data structure. The current data indicates that 70% of the total genetic variation could be explained by differences between the breeds, suggesting a much greater breed differentiation than typically found at protein and microsatellite loci. The marked differentiation of the cattle breeds and observed disagreements with the results from the previous molecular data in the topology of the phylogenetic trees are most likely a result of selection on phenotypic characters analysed in this study. PMID:14736370

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds.

PubMed

Yang, Songbai; Li, Xiuling; Li, Kui; Fan, Bin; Tang, Zhonglin

2014-01-15

Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.

A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

PubMed Central

2014-01-01

Background Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. Results We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. Conclusions In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs. PMID:24422716

GM as a route for delivery of sustainable crop protection.

PubMed

Bruce, Toby J A

2012-01-01

Modern agriculture, with its vast monocultures of lush fertilized crops, provides an ideal environment for adapted pests, weeds, and diseases. This vulnerability has implications for food security: when new pesticide-resistant pest biotypes evolve they can devastate crops. Even with existing crop protection measures, approximately one-third yield losses occur globally. Given the projected increase in demand for food (70% by 2050 according to the UN), sustainable ways of preventing these losses are needed. Development of resistant crop cultivars can make an important contribution. However, traditional crop breeding programmes are limited by the time taken to move resistance traits into elite crop genetic backgrounds and the limited gene pools in which to search for novel resistance. Furthermore, resistance based on single genes does not protect against the full spectrum of pests, weeds, and diseases, and is more likely to break down as pests evolve counter-resistance. Although not necessarily a panacea, GM (genetic modification) techniques greatly facilitate transfer of genes and thus provide a route to overcome these constraints. Effective resistance traits can be precisely and conveniently moved into mainstream crop cultivars. Resistance genes can be stacked to make it harder for pests to evolve counter-resistance and to provide multiple resistances to different attackers. GM-based crop protection could substantially reduce the need for farmers to apply pesticides to their crops and would make agricultural production more efficient in terms of resources used (land, energy, water). These benefits merit consideration by environmentalists willing to keep an open mind on the GM debate.

Comparative analysis of the complete mitochondrial genomes of two types of ducks, peking duck (Anas platyrhychos) and muscovy duck (Cairina moschata).

PubMed

Tu, Jianfeng; Yang, Ying; Yang, Fuhe; Xing, Xiumei

2017-03-01

Peking duck (Anas platyrhychos) and Muscovy duck (Cairina moschata) are two types of domestic ducks and the most popular meat breeds on the world. In this study, we sequenced and compared complete mitochondrial genomes of both breeds. In order to investigate the phylogeny of both breeds within Anseriformes, the sequences of concatenated 12 protein-coding genes were used for phylogenetic analysis. The result was consistent with most of the previous morphological and molecular studies. Our complete mitochondrial genome sequences of both breeds will be useful information in phylogenetics, and be available as basic data for the breeding and genetics.

Admixture and Local Breed Marginalization Threaten Algerian Sheep Diversity

PubMed Central

Ciani, Elena; Kdidi, Samia; Aouissat, Miloud; Dhimi, Laziz; Lafri, Mohamed; Maftah, Abderrahman; Mehtar, Nadhira

2015-01-01

Due to its geo-climatic conditions, Algeria represents a biodiversity hotspot, with sheep breeds well adapted to a patchwork of extremely heterogeneous harsh habitats. The importance of this peculiar genetic reservoir increases as climate change drives the demand for new adaptations. However, the expansion of a single breed (Ouled-Djellal) which occurred in the last decades has generated a critical situation for the other breeds; some of them are being subjected to uncontrolled cross-breeding with the favored breed and/or to marginalization (effective size contraction). This study investigated genetic diversity within and among six of the nine Algerian breeds, by use of 30 microsatellite markers. Our results showed that, in spite of the census contraction experienced by most of the considered breeds, genetic diversity is still substantial (average gene diversity ranging 0.68 to 0.76) and inbreeding was not identified as a problem. However, two breeds (Rembi and Taâdmit) appeared to have lost most of their genetic originality because of intensive cross-breeding with Ouled-Djellal. Based on the above evidence, we suggest Hamra, Sidaoun, and D’man as breeds deserving the highest priority for conservation in Algeria. PMID:25875832

Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

PubMed Central

2012-01-01

Background Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most important and challenging areas of research in animal genetics. However, currently there are relatively few genomic regions identified that have been subject to positive selection. In this study, a genome-wide scan using ~50,000 Single Nucleotide Polymorphisms (SNPs) was performed in an attempt to identify genomic regions associated with fat deposition in fat-tail breeds. This trait and its modification are very important in those countries grazing these breeds. Results Two independent experiments using either Iranian or Ovine HapMap genotyping data contrasted thin and fat tail breeds. Population differentiation using FST in Iranian thin and fat tail breeds revealed seven genomic regions. Almost all of these regions overlapped with QTLs that had previously been identified as affecting fat and carcass yield traits in beef and dairy cattle. Study of selection sweep signatures using FST in thin and fat tail breeds sampled from the Ovine HapMap project confirmed three of these regions located on Chromosomes 5, 7 and X. We found increased homozygosity in these regions in favour of fat tail breeds on chromosome 5 and X and in favour of thin tail breeds on chromosome 7. Conclusions In this study, we were able to identify three novel regions associated with fat deposition in thin and fat tail sheep breeds. Two of these were associated with an increase of homozygosity in the fat tail breeds which would be consistent with selection for mutations affecting fat tail size several thousand years after domestication. PMID:22364287

Within- and between-year dispersal of American Avocets among multiple western Great Basin wetlands

USGS Publications Warehouse

Plissner, Jonathan H.; Haig, Susan M.; Oring, L.W.

1999-01-01

Connectivity of discrete habitat patches may be described in terms of the movements of individual organisms among such patches. To examine connectivity of widely dispersed alkali lake systems, we recorded post-breeding and subsequent breeding locations of color-banded American Avocets (Recurvirostra americana) in the western U.S. Great Basin, from 1995-1997. Among individuals observed during the post-breeding/premigratory season, over half of the 188 breeding adults were observed at lakes other than their breeding locations, whereas 70% of 125 post-fledged young were observed only at their natal lake systems. Of 46 breeding adults observed in consecutive years, only eight (17%) dispersed between different lake systems. Only 8% of chicks were observed after their first year, and only 1.3% returned to the natal area in subsequent breeding seasons. Adult and recently fledged birds from the southernmost breeding site were regularly observed in post-breeding aggregations at lakes several hundred kilometers to the north, suggesting seasonal differences in habitat quality at the lake systems studied. These results indicate the importance of maintaining habitat for post-breeding movements.

Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide.

PubMed

Makina, Sithembile O; Whitacre, Lindsey K; Decker, Jared E; Taylor, Jeremy F; MacNeil, Michael D; Scholtz, Michiel M; van Marle-Köster, Este; Muchadeyi, Farai C; Makgahlela, Mahlako L; Maiwashe, Azwihangwisi

2016-11-15

Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus. Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds. We established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement.

Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds.

PubMed

Ramayo-Caldas, Yuliaxis; Renand, Gilles; Ballester, Maria; Saintilan, Romain; Rocha, Dominique

2016-04-23

Studies to identify markers associated with beef tenderness have focused on Warner-Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d'Aquitaine beef cattle breeds. Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context.

Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex.

PubMed

Wilbe, Maria; Jokinen, Päivi; Truvé, Katarina; Seppala, Eija H; Karlsson, Elinor K; Biagi, Tara; Hughes, Angela; Bannasch, Danika; Andersson, Göran; Hansson-Hamlin, Helene; Lohi, Hannes; Lindblad-Toh, Kerstin

2010-03-01

The unique canine breed structure makes dogs an excellent model for studying genetic diseases. Within a dog breed, linkage disequilibrium is extensive, enabling genome-wide association (GWA) with only around 15,000 SNPs and fewer individuals than in human studies. Incidences of specific diseases are elevated in different breeds, indicating that a few genetic risk factors might have accumulated through drift or selective breeding. In this study, a GWA study with 81 affected dogs (cases) and 57 controls from the Nova Scotia duck tolling retriever breed identified five loci associated with a canine systemic lupus erythematosus (SLE)-related disease complex that includes both antinuclear antibody (ANA)-positive immune-mediated rheumatic disease (IMRD) and steroid-responsive meningitis-arteritis (SRMA). Fine mapping with twice as many dogs validated these loci. Our results indicate that the homogeneity of strong genetic risk factors within dog breeds allows multigenic disorders to be mapped with fewer than 100 cases and 100 controls, making dogs an excellent model in which to identify pathways involved in human complex diseases.

Relationships among and variation within rare breeds of swine.

PubMed

Roberts, K S; Lamberson, W R

2015-08-01

Extinction of rare breeds of livestock threatens to reduce the total genetic variation available for selection in the face of the changing environment and new diseases. Swine breeds facing extinction typically share characteristics such as small size, slow growth rate, and high fat percentage, which limit them from contributing to commercial production. Compounding the risk of loss of variation is the lack of pedigree information for many rare breeds due to inadequate herd books, which increases the chance that producers are breeding closely related individuals. By making genetic data available, producers can make more educated breeding decisions to preserve genetic diversity in future generations, and conservation organizations can prioritize investments in breed preservation. The objective of this study was to characterize genetic variation within and among breeds of swine and prioritize heritage breeds for preservation. Genotypes from the Illumina PorcineSNP60 BeadChip (GeneSeek, Lincoln, NE) were obtained for Guinea, Ossabaw Island, Red Wattle, American Saddleback, Mulefoot, British Saddleback, Duroc, Landrace, Large White, Pietrain, and Tamworth pigs. A whole-genome analysis toolset was used to construct a genomic relationship matrix and to calculate inbreeding coefficients for the animals within each breed. Relatedness and average inbreeding coefficient differed among breeds, and pigs from rare breeds were generally more closely related and more inbred ( < 0.05). A multidimensional scaling diagram was constructed based on the SNP genotypes. Animals within breeds clustered tightly together except for 2 Guinea pigs. Tamworth, Duroc, and Mulefoot tended to not cluster with the other 7 breeds.

Breeding dispersal of Mexican Spotted Owls in the Sacramento Mountains, New Mexico

Treesearch

Joseph L. Ganey; Darrell L. Apprill; Todd A. Rawlinson; Sean C. Kyle; Ryan S. Jonnes; James P. Ward

2014-01-01

Dispersal is a key process influencing population dynamics and gene flow in species. Despite this, little is known about breeding dispersal in threatened Mexican Spotted Owls (Strix occidentalis lucida), here defined as movement of a non-juvenile owl between territories where it had the opportunity to breed. We observed 28 cases of breeding dispersal during a study of...

Non-invasive assessment of glucocorticoid and androgen metabolite levels in cooperatively breeding Damaraland mole-rats (Fukomys damarensis).

PubMed

Medger, Katarina; Bennett, Nigel C; Lutermann, Heike; Ganswindt, Andre

2018-05-18

Dominant females of cooperative breeding species often use aggression to suppress reproduction of subordinate females, resulting in subordinates experiencing stress-related increases in glucocorticoid levels, which may cause reproductive down-regulation. This would suggest a general pattern with higher glucocorticoid levels in subordinate compared to dominant individuals; however, the opposite was found in a number of cooperatively breeding species. Furthermore, breeding females of the cooperatively breeding Damaraland mole-rats (Fukomys damarensis) exhibit very high androgen concentrations during the wet season, presumably to support their breeding monopoly. Hormone analysis in Damaraland mole-rats have typically been measured using plasma and urine, but faecal analysis offers additional advantages especially for field studies on this species. The present study examines the suitability of Damaraland mole-rat faecal samples for determining glucocorticoid metabolite (fGCM) and androgen metabolite (fAM) concentrations using enzyme immunoassays. Using these assays, we further evaluated the effects of breeding status on fGCM and fAM concentrations in wild-caught and captive Damaraland mole-rats. Wild-caught breeding and non-breeding males and females exhibited no differences in fAM concentrations. Immunoreactive fGCM concentrations were only high in male breeders and comparatively low in non-breeders and breeding females. Concentrations of fAMs and fGCMs were similar in captive males and females, but fAM concentrations were elevated in captive compared to wild-caught individuals, which may be related to a higher reproductive activity due to removal from the breeding female. The relatively uniform fAM and fGCM concentrations found in wild-caught mole-rats may be explained by a stable colony structure during the dry season during which this study was conducted. Limited dispersal opportunities result in lower aggression and stress levels within a colony and as a result lower fAM and fGCM concentrations. Copyright © 2018 Elsevier Inc. All rights reserved.

Overlap in genomic variation associated with milk fat composition in Holstein Friesian and Dutch native dual-purpose breeds.

PubMed

Maurice-Van Eijndhoven, M H T; Bovenhuis, H; Veerkamp, R F; Calus, M P L

2015-09-01

The aim of this study was to identify if genomic variations associated with fatty acid (FA) composition are similar between the Holstein-Friesian (HF) and native dual-purpose breeds used in the Dutch dairy industry. Phenotypic and genotypic information were available for the breeds Meuse-Rhine-Yssel (MRY), Dutch Friesian (DF), Groningen White Headed (GWH), and HF. First, the reliability of genomic breeding values of the native Dutch dual-purpose cattle breeds MRY, DF, and GWH was evaluated using single nucleotide polymorphism (SNP) effects estimated in HF, including all SNP or subsets with stronger associations in HF. Second, the genomic variation of the regions associated with FA composition in HF (regions on Bos taurus autosome 5, 14, and 26), were studied in the different breeds. Finally, similarities in genotype and allele frequencies between MRY, DF, GWH, and HF breeds were assessed for specific regions associated with FA composition. On average across the traits, the highest reliabilities of genomic prediction were estimated for GWH (0.158) and DF (0.116) when the 8 to 22 SNP with the strongest association in HF were included. With the same set of SNP, GEBV for MRY were the least reliable (0.022). This indicates that on average only 2 (MRY) to 16% (GWH) of the genomic variation in HF is shared with the native Dutch dual-purpose breeds. The comparison of predicted variances of different regions associated with milk and milk fat composition showed that breeds clearly differed in genomic variation within these regions. Finally, the correlations of allele frequencies between breeds across the 8 to 22 SNP with the strongest association in HF were around 0.8 between the Dutch native dual-purpose breeds, whereas the correlations between the native breeds and HF were clearly lower and around 0.5. There was no consistent relationship between the reliabilities of genomic prediction for a specific breed and the correlation between the allele frequencies of this breed and HF. In conclusion, most of the genomic variation associated with FA composition in the Dutch dual-purpose breeds appears to be breed-specific. Furthermore, the minor allele frequencies of genes having an effect on the milk FA composition in HF were shown to be much smaller in the breeds MRY, DF, and GWH, especially for the MRY breed. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Short communication: Field fertility in Holstein bulls: Can type of breeding strategy (artificial insemination following estrus versus timed artificial insemination) alter service sire fertility?

PubMed

Batista, E O S; Vieira, L M; Sá Filho, M F; Carvalho, P D; Rivera, H; Cabrera, V; Wiltbank, M C; Baruselli, P S; Souza, A H

2016-03-01

The aim of this study was to compare pregnancy per artificial insemination (P/AI) from service sires used on artificial insemination after estrus detection (EAI) or timed artificial insemination (TAI) breedings. Confirmed artificial insemination outcome records from 3 national data centers were merged and used as a data source. Criteria edits were herd's overall P/AI within 20 and 60%, a minimum of 30 breedings reported per herd-year, service sires that were used in at least 10 different herds with no more than 40% of the breedings performed in a single herd, breeding records from lactating Holstein cows receiving their first to fifth postpartum breedings occurring within 45 to 375 d in milk, and cows with 1 to 5 lactations producing a minimum of 6,804 kg. Initially 1,142,859 breeding records were available for analysis. After editing, a subset of the data (n=857,539) was used to classify breeding codes into either EAI or TAI based on weekly insemination profile in each individual herd. The procedure HPMIXED of SAS was used and took into account effects of state, farm, cow identification, breeding month, year, parity, days in milk at breeding, and service sire. This model was used independently for the 2 types osires f breeding codes (EAI vs. TAI), and service sire P/AI rankings within each breeding code were performed for sires with >700 breedings (94 sires) and for with >1,000 breedings (n=56 sires) following both EAI and TAI. Correlation for service sire fertility rankings following EAI and TAI was performed with the PROC CORR of SAS. Service sire P/AI rankings produced with EAI and TAI were 0.81 (for sires with >700 breedings) and 0.84 (for sires with >1,000 breedings). In addition, important changes occurred in service sire P/AI ranking to EAI and TAI for sires with less than 10,000 recorded artificial inseminations. In conclusion, the type of breeding strategy (EAI or TAI) was associated with some changes in service sire P/AI ranking, but ranking changes declined as number of breedings per service sire increased. Future randomized studies need to explore whether changes in P/AI ranking to EAI versus TAI are due to specific semen characteristics. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A global analysis of bird plumage patterns reveals no association between habitat and camouflage

PubMed Central

Marshall, Kate L.A.; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular), scales, bars and spots (regular)—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis. PMID:27867762

A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

PubMed

Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

2016-01-01

Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

Effects of flow regimes altered by dams on survival, population declines, and range-wide losses of California river-breeding frogs.

PubMed

Kupferberg, Sarah J; Palen, Wendy J; Lind, Amy J; Bobzien, Steve; Catenazzi, Alessandro; Drennan, Joe; Power, Mary E

2012-06-01

Widespread alteration of natural hydrologic patterns by large dams combined with peak demands for power and water delivery during summer months have resulted in frequent aseasonal flow pulses in rivers of western North America. Native species in these ecosystems have evolved with predictable annual flood-drought cycles; thus, their likelihood of persistence may decrease in response to disruption of the seasonal synchrony between stable low-flow conditions and reproduction. We evaluated whether altered flow regimes affected 2 native frogs in California and Oregon (U.S.A.) at 4 spatial and temporal extents. We examined changes in species distribution over approximately 50 years, current population density in 11 regulated and 16 unregulated rivers, temporal trends in abundance among populations occupying rivers with different hydrologic histories, and within-year patterns of survival relative to seasonal hydrology. The foothill yellow-legged frog (Rana boylii), which breeds only in flowing water, is more likely to be absent downstream of large dams than in free-flowing rivers, and breeding populations are on average 5 times smaller in regulated rivers than in unregulated rivers. Time series data (range = 8 - 19 years) from 5 populations of yellow-legged frogs and 2 populations of California red-legged frogs (R. draytonii) across a gradient of natural to highly artificial timing and magnitude of flooding indicate that variability of flows in spring and summer is strongly correlated with high mortality of early life stages and subsequent decreases in densities of adult females. Flow management that better mimics natural flow timing is likely to promote persistence of these species and others with similar phenology. ©2012 Society for Conservation Biology.

Migration and the evolution of sexual dichromatism: evolutionary loss of female coloration with migration among wood-warblers.

PubMed

Simpson, Richard K; Johnson, Michele A; Murphy, Troy G

2015-06-22

The mechanisms underlying evolutionary changes in sexual dimorphism have long been of interest to biologists. A striking gradient in sexual dichromatism exists among songbirds in North America, including the wood-warblers (Parulidae): males are generally more colourful than females at northern latitudes, while the sexes are similarly ornamented at lower latitudes. We use phylogenetically controlled comparative analysis to test three non-mutually exclusive hypotheses for the evolution of sexual dichromatism among wood-warblers. The first two hypotheses focus on the loss of female coloration with the evolution of migration, either owing to the costs imposed by visual predators during migration, or owing to the relaxation of selection for female social signalling at higher latitudes. The third hypothesis focuses on whether sexual dichromatism evolved owing to changes in male ornamentation as the strength of sexual selection increases with breeding latitude. To test these hypotheses, we compared sexual dichromatism to three variables: the presence of migration, migration distance, and breeding latitude. We found that the presence of migration and migration distance were both positively correlated with sexual dichromatism, but models including breeding latitude alone were not strongly supported. Ancestral state reconstruction supports the hypothesis that the ancestral wood-warblers were monochromatic, with both colourful males and females. Combined, these results are consistent with the hypotheses that the evolution of migration is associated with the relaxation of selection for social signalling among females and that there are increased predatory costs along longer migratory routes for colourful females. These results suggest that loss of female ornamentation can be a driver of sexual dichromatism and that social or natural selection may be a stronger contributor to variation in dichromatism than sexual selection. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Menopause: no support for an evolutionary explanation among historical Norwegians.

PubMed

Skjærvø, Gine Roll; Røskaft, Eivin

2013-04-01

Life history theory proposes that menopause is either an epiphenomenon or an adaptation. The most recent adaptive hypothesis proposes that menopause in humans has evolved because of conflict between reproducing generations (RCH). Overlapping reproduction between generations may impose fitness costs to older and younger females who co-breed. However, it has yet to be demonstrated by using a measure of evolutionary fitness (i.e. grandchildren). Here, we tested the RCH by using multigenerational life-history data of historical Norwegian women. Our results indicate that both generations seem to experience some fitness benefits with co-breeding (i.e. reproductive overlap and cohabit). This was because both younger and older females who co-bred had more grandchildren than those who did not co-breed. We suggest that younger females may partly had enhanced fitness because they copied behaviour of females of the older generation. Our results do not support the hypothesis that reproductive conflict between generations explains the evolution of menopause in women. Our results, taken together with the growing evidence against several assumptions of the RCH, indicate that 1) the decline in follicle number has no marked increase in women as they reach the age of 38 years; 2) humans do not have an abrupt decline in fertility at mean age of 38 years; 3) menopause is not unique to humans; and 4) there are not high numbers of individuals surviving to older adulthood during our evolutionary past. Finally, we discuss an alternative point of view suggesting that menopause might be understood in the light of both ageing in general as well as our increased lifespan. Copyright © 2013 Elsevier Inc. All rights reserved.

Migration and the evolution of sexual dichromatism: evolutionary loss of female coloration with migration among wood-warblers

PubMed Central

Simpson, Richard K.; Johnson, Michele A.; Murphy, Troy G.

2015-01-01

The mechanisms underlying evolutionary changes in sexual dimorphism have long been of interest to biologists. A striking gradient in sexual dichromatism exists among songbirds in North America, including the wood-warblers (Parulidae): males are generally more colourful than females at northern latitudes, while the sexes are similarly ornamented at lower latitudes. We use phylogenetically controlled comparative analysis to test three non-mutually exclusive hypotheses for the evolution of sexual dichromatism among wood-warblers. The first two hypotheses focus on the loss of female coloration with the evolution of migration, either owing to the costs imposed by visual predators during migration, or owing to the relaxation of selection for female social signalling at higher latitudes. The third hypothesis focuses on whether sexual dichromatism evolved owing to changes in male ornamentation as the strength of sexual selection increases with breeding latitude. To test these hypotheses, we compared sexual dichromatism to three variables: the presence of migration, migration distance, and breeding latitude. We found that the presence of migration and migration distance were both positively correlated with sexual dichromatism, but models including breeding latitude alone were not strongly supported. Ancestral state reconstruction supports the hypothesis that the ancestral wood-warblers were monochromatic, with both colourful males and females. Combined, these results are consistent with the hypotheses that the evolution of migration is associated with the relaxation of selection for social signalling among females and that there are increased predatory costs along longer migratory routes for colourful females. These results suggest that loss of female ornamentation can be a driver of sexual dichromatism and that social or natural selection may be a stronger contributor to variation in dichromatism than sexual selection. PMID:26019159

Astronomy Librarian - Quo Vadis?

NASA Astrophysics Data System (ADS)

Lagerstrom, Jill; Grothkopf, Uta

"You don't look like a librarian" is a phrase we often hear in the astronomy department or observatory library. Astronomy librarians are a breed apart, and are taking on new and non-traditional roles as information technology evolves. This talk will explore the future of librarians and librarianship through the lens of some of the recent talks given at the sixth "Libraries and Information Services in Astronomy" conference held in Pune, India in February 2010. We will explore the librarian's universe, illustrating how librarians use new technologies to perform such tasks as bibliometrics, how we are re-fashioning our library spaces in an increasingly digital world and how we are confronting the brave new world of Open Access, to name but a few topics.

Breed-Predispositions to Cancer in Pedigree Dogs

PubMed Central

Dobson, Jane M.

2013-01-01

Cancer is a common problem in dogs and although all breeds of dog and crossbred dogs may be affected, it is notable that some breeds of pedigree dogs appear to be at increased risk of certain types of cancer suggesting underlying genetic predisposition to cancer susceptibility. Although the aetiology of most cancers is likely to be multifactorial, the limited genetic diversity seen in purebred dogs facilitates genetic linkage or association studies on relatively small populations as compared to humans, and by using newly developed resources, genome-wide association studies in dog breeds are proving to be a powerful tool for unravelling complex disorders. This paper will review the literature on canine breed susceptibility to histiocytic sarcoma, osteosarcoma, haemangiosarcoma, mast cell tumours, lymphoma, melanoma, and mammary tumours including the recent advances in knowledge through molecular genetic, cytogenetic, and genome wide association studies. PMID:23738139

Optimizing the use of breed types in developing country livestock production systems: a neglected research area.

PubMed

Marshall, K

2014-10-01

Developing country livestock production systems are diverse and dynamic, and include those where existing indigenous breeds are currently optimal and likely to remain so, those where non-indigenous breed types are already in common use, and systems that are changing, such as by intensification, where the introduction of new breed types represents significant opportunities. These include opportunities to improve the livelihood of the world's poor, increase food and nutrition security and enhance environmental sustainability. At present, very little research has focused on this issue, such that significant knowledge gaps in relation to breed-change interventions remain. The purpose of this study is to raise awareness of this issue and suggests strategic research areas to begin filling these knowledge gaps. Such strategic research would include (i) assessing the impact of differing breed types in developing country livestock productions systems, from a range of viewpoints including intrahousehold livelihood benefit, food and nutrition security at different scales, and environmental sustainability; (ii) identification of specific livestock production systems within developing countries, and the type of livestock keepers within these system, that are most likely to benefit from new breed types; and (iii) identification of new breed types as candidates for in-situ testing within these systems, such as through the use of spatial analysis to identify similar production environments combined with community acceptance studies. Results of these studies would primarily assist stakeholders in agriculture, including both policy makers and livestock keepers, to make informed decisions on the potential use of new breed types. © 2014 Blackwell Verlag GmbH.

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

PubMed

Gama, Luis T; Martínez, Amparo M; Carolino, Inês; Landi, Vincenzo; Delgado, Juan V; Vicente, Antonio A; Vega-Pla, José L; Cortés, Oscar; Sousa, Conceição O

2013-06-14

Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity. Native pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

Floral contrivances and specialised pollination mechanism strongly influence mixed mating in Wrightia tomentosa (Apocynaceae).

PubMed

Barman, C; Singh, V K; Das, S; Tandon, R

2018-05-01

Reproductive success of a plant species is largely influenced by the outcome of mating pattern in a population. It is believed that a significantly larger proportion of animal-pollinated plants have evolved a mixed-mating strategy, the extent of which may vary among species. It is thus pertinent to investigate the key contributors to mating success, especially to identify the reproductive constraints in depauperate populations of threatened plant species. We examined the contribution of floral architecture, pollination mechanism and breeding system on the extent of outcrossing rate in a near-threatened tree species, Wrightia tomentosa. The breeding system was ascertained from controlled pollination experiments. In order to determine outcrossing rate, 60 open-pollinated progeny were analysed using an AFLP markers. Although the trees are self-compatible, herkogamy and compartmentalisation of pollen and nectar in different chambers of the floral tube effectively prevent spontaneous autogamy. Pollination is achieved through specialised interaction with moths. Differential foraging behaviour of settling moths and hawkmoths leads to different proportions of geitonogamous and xenogamous pollen on the stigma. However, most open-pollinated progeny were the result of xenogamy (outcrossing rate, tm = 0.68). The study shows that floral contrivances and pollination system have a strong influence on mating pattern. The differential foraging behaviour of the pollinators causes deposition of a mixture of self- and cross-pollen to produce a mixed brood. Inbreeding depression and geitonogamy appear to play a significant role in sustaining mixed mating in this species. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

PubMed Central

Fleming, Damarius S.; Weigend, Steffen; Simianer, Henner; Weigend, Annett; Rothschild, Max; Schmidt, Carl; Ashwell, Chris; Persia, Mike; Reecy, James; Lamont, Susan J.

2017-01-01

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST, integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population’s indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions. PMID:28341699

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure.

PubMed

Fleming, Damarius S; Weigend, Steffen; Simianer, Henner; Weigend, Annett; Rothschild, Max; Schmidt, Carl; Ashwell, Chris; Persia, Mike; Reecy, James; Lamont, Susan J

2017-05-05

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed F ST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions. Copyright © 2017 Fleming et al.

Coastlines of the past: clues for our future

NASA Astrophysics Data System (ADS)

Reynolds, L.

2017-12-01

Coastlines are constantly evolving due to the long-term effects of sea-level change and human impacts, as well as in response to high-impact, short duration hazard events such as storms, tsunamis, and earthquakes. The sediments that accumulate in coastal systems such as estuaries, dunes, and beaches archieve the enviornmental record of the past, providing us a baseline with which to predict future coastal hazard magnitude and recurrence intervals. We study this record to understand future hazard potential, as well as to aid restoration efforts. Many coastal systems around the world have been degraded in the last few hundred years by human activity- these regions are important breeding grounds for commercially viable species, natural pollution filters, and barriers against inundation. Efforts to restore coastal systems often rely on data from historical sources to reconstruct past coastal conditions-the geological record can extend the timeframe with which we think about possible restoration points. In addition, studying past coastal response to enviornmental changes can aid the effort to restore systems to a point of sustainability and resilience instead of simply restoring to an arbirtary point in time.

Mother to Offspring Transmission of Chronic Wasting Disease in Reeves’ Muntjac Deer

PubMed Central

Nalls, Amy V.; McNulty, Erin; Powers, Jenny; Seelig, Davis M.; Hoover, Clare; Haley, Nicholas J.; Hayes-Klug, Jeanette; Anderson, Kelly; Stewart, Paula; Goldmann, Wilfred; Hoover, Edward A.; Mathiason, Candace K.

2013-01-01

The horizontal transmission of prion diseases has been well characterized in bovine spongiform encephalopathy (BSE), chronic wasting disease (CWD) of deer and elk and scrapie of sheep, and has been regarded as the primary mode of transmission. Few studies have monitored the possibility of vertical transmission occurring within an infected mother during pregnancy. To study the potential for and pathway of vertical transmission of CWD in the native cervid species, we used a small cervid model–the polyestrous breeding, indoor maintainable, Reeves’ muntjac deer–and determined that the susceptibility and pathogenesis of CWD in these deer reproduce that in native mule and white-tailed deer. Moreover, we demonstrate here that CWD prions are transmitted from doe to fawn. Maternal CWD infection also appears to result in lower percentage of live birth offspring. In addition, evolving evidence from protein misfolding cyclic amplification (PMCA) assays on fetal tissues suggest that covert prion infection occurs in utero. Overall, our findings demonstrate that transmission of prions from mother to offspring can occur, and may be underestimated for all prion diseases. PMID:23977159

Dog Breed Differences in Visual Communication with Humans.

PubMed

Konno, Akitsugu; Romero, Teresa; Inoue-Murayama, Miho; Saito, Atsuko; Hasegawa, Toshikazu

2016-01-01

Domestic dogs (Canis familiaris) have developed a close relationship with humans through the process of domestication. In human-dog interactions, eye contact is a key element of relationship initiation and maintenance. Previous studies have suggested that canine ability to produce human-directed communicative signals is influenced by domestication history, from wolves to dogs, as well as by recent breed selection for particular working purposes. To test the genetic basis for such abilities in purebred dogs, we examined gazing behavior towards humans using two types of behavioral experiments: the 'visual contact task' and the 'unsolvable task'. A total of 125 dogs participated in the study. Based on the genetic relatedness among breeds subjects were classified into five breed groups: Ancient, Herding, Hunting, Retriever-Mastiff and Working). We found that it took longer time for Ancient breeds to make an eye-contact with humans, and that they gazed at humans for shorter periods of time than any other breed group in the unsolvable situation. Our findings suggest that spontaneous gaze behavior towards humans is associated with genetic similarity to wolves rather than with recent selective pressure to create particular working breeds.

Spring temperatures influence selection on breeding date and the potential for phenological mismatch in a migratory bird

PubMed Central

Soukup, Sheryl Swartz; Drilling, Nancy E.; Eckerle, Kevin P.; Sakaluk, Scott K.; Thompson, Charles F.

2016-01-01

Climate change has affected the seasonal phenology of a variety of taxa, including that of migratory birds and their critical food resources. However, whether climate-induced changes in breeding phenology affect individual fitness, and how these changes might, therefore, influence selection on breeding date remain unresolved. Here, we use a 36-year dataset from a long-term, individual-based study of House Wrens (Troglodytes aedon) to test whether the timing of avian breeding seasons is associated with annual changes in temperature, which have increased to a small but significant extent locally since the onset of the study in 1980. Increasing temperature was associated with an advancement of breeding date in the population, as the onset of breeding within years was closely associated with daily spring temperatures. Warmer springs were also associated with a reduced incubation period, but reduced incubation periods were associated with a prolonged duration of nestling provisioning. Nest productivity, in terms of fledgling production, was not associated with temperature, but wetter springs reduced fledging success. Most years were characterized by selection for earlier breeding, but cool and wet years resulted in stabilizing selection on breeding date. Our results indicate that climate change and increasing spring temperatures can affect suites of life-history traits, including selection on breeding date. Increasing temperatures may favor earlier breeding, but the extent to which the phenology of populations might advance may be constrained by reductions in fitness associated with early breeding during cool, wet years. Variability in climatic conditions will, therefore, shape the extent to which seasonal organisms can respond to changes in their environment. PMID:27859132

Characterization of casein gene complex and genetic diversity analysis in Indian goats.

PubMed

Rout, P K; Kumar, A; Mandal, A; Laloe, D; Singh, S K; Roy, R

2010-04-01

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

There is room for selection in a small local pig breed when using optimum contribution selection: a simulation study.

PubMed

Gourdine, J L; Sørensen, A C; Rydhmer, L

2012-01-01

Selection progress must be carefully balanced against the conservation of genetic variation in small populations of local breeds. Well-defined breeding programs with specified selection traits are rare in local pig breeds. Given the small population size, the focus is often on the management of genetic diversity. However, in local breeds, optimum contribution selection can be applied to control the rate of inbreeding and to avoid reduced performance in traits with high market value. The aim of this study was to assess the extent to which a breeding program aiming for improved product quality in a small local breed would be feasible. We used stochastic simulations to compare 25 scenarios. The scenarios differed in size of population, selection intensity of boars, type of selection (random selection, truncation selection based on BLUP breeding values, or optimum contribution selection based on BLUP breeding values), and heritability of the selection trait. It was assumed that the local breed is used in an extensive system for a high-meat-quality market. The simulations showed that in the smallest population (300 female reproducers), inbreeding increased by 0.8% when selection was performed at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P < 0.05), but at a considerably decreased rate of inbreeding (0.7 to 1.2 vs. 2.3 to 5.7%, P < 0.01). This confirmation of the potential utilization of OCS even in small populations is important in the context of sustainable management and the use of animal genetic resources.

Differentiating the evolution of female song and male-female duets in the New World blackbirds: can tropical natural history traits explain duet evolution?

PubMed

Odom, Karan J; Omland, Kevin E; Price, J Jordan

2015-03-01

Female bird song and combined vocal duets of mated pairs are both frequently associated with tropical, monogamous, sedentary natural histories. Little is known, however, about what selects for duetting behavior versus female song. Female song likely preceded duet evolution and could drive apparent relationships between duets and these natural histories. We compared the evolution of female song and male-female duets in the New World blackbirds (Icteridae) by investigating patterns of gains and losses of both traits and their relationships with breeding latitude, mating system, nesting pattern, and migratory behavior. We found that duets evolved only in lineages in which female song was likely ancestral. Both female song and duets were correlated with tropical breeding, social monogamy, territorial nesting, and sedentary behavior when all taxa were included; however, correlations between duets and these natural history traits disappeared when comparisons were limited to taxa with female song. Also, likelihood values supported stronger relationships between the natural history traits and female song than between these traits and duets. Our results suggest that the natural histories thought to favor the evolution of duetting may in fact be associated with female song and that additional selection pressures are responsible for the evolution of duets. © 2015 The Author(s).

Humpback whale song on the Southern Ocean feeding grounds: implications for cultural transmission.

PubMed

Garland, Ellen C; Gedamke, Jason; Rekdahl, Melinda L; Noad, Michael J; Garrigue, Claire; Gales, Nick

2013-01-01

Male humpback whales produce a long, complex, and stereotyped song on low-latitude breeding grounds; they also sing while migrating to and from these locations, and occasionally in high-latitude summer feeding areas. All males in a population sing the current version of the constantly evolving display and, within an ocean basin, populations sing similar songs; however, this sharing can be complex. In the western and central South Pacific region there is repeated cultural transmission of song types from eastern Australia to other populations eastward. Song sharing is hypothesized to occur through several possible mechanisms. Here, we present the first example of feeding ground song from the Southern Ocean Antarctic Area V and compare it to song from the two closest breeding populations. The early 2010 song contained at least four distinct themes; these matched four themes from the eastern Australian 2009 song, and the same four themes from the New Caledonian 2010 song recorded later in the year. This provides evidence for at least one of the hypothesized mechanisms of song transmission between these two populations, singing while on shared summer feeding grounds. In addition, the feeding grounds may provide a point of acoustic contact to allow the rapid horizontal cultural transmission of song within the western and central South Pacific region and the wider Southern Ocean.

Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population.

PubMed

Pulido, Francisco; Berthold, Peter

2010-04-20

Global warming is impacting biodiversity by altering the distribution, abundance, and phenology of a wide range of animal and plant species. One of the best documented responses to recent climate change is alterations in the migratory behavior of birds, but the mechanisms underlying these phenotypic adjustments are largely unknown. This knowledge is still crucial to predict whether populations of migratory birds will adapt to a rapid increase in temperature. We monitored migratory behavior in a population of blackcaps (Sylvia atricapilla) to test for evolutionary responses to recent climate change. Using a common garden experiment in time and captive breeding we demonstrated a genetic reduction in migratory activity and evolutionary change in phenotypic plasticity of migration onset. An artificial selection experiment further revealed that residency will rapidly evolve in completely migratory bird populations if selection for shorter migration distance persists. Our findings suggest that current alterations of the environment are favoring birds wintering closer to the breeding grounds and that populations of migratory birds have strongly responded to these changes in selection. The reduction of migratory activity is probably an important evolutionary process in the adaptation of migratory birds to climate change, because it reduces migration costs and facilitates the rapid adjustment to the shifts in the timing of food availability during reproduction.

Self-compatibility is over-represented on islands.

PubMed

Grossenbacher, Dena L; Brandvain, Yaniv; Auld, Josh R; Burd, Martin; Cheptou, Pierre-Olivier; Conner, Jeffrey K; Grant, Alannie G; Hovick, Stephen M; Pannell, John R; Pauw, Anton; Petanidou, Theodora; Randle, April M; Rubio de Casas, Rafael; Vamosi, Jana; Winn, Alice; Igic, Boris; Busch, Jeremiah W; Kalisz, Susan; Goldberg, Emma E

2017-07-01

Because establishing a new population often depends critically on finding mates, individuals capable of uniparental reproduction may have a colonization advantage. Accordingly, there should be an over-representation of colonizing species in which individuals can reproduce without a mate, particularly in isolated locales such as oceanic islands. Despite the intuitive appeal of this colonization filter hypothesis (known as Baker's law), more than six decades of analyses have yielded mixed findings. We assembled a dataset of island and mainland plant breeding systems, focusing on the presence or absence of self-incompatibility. Because this trait enforces outcrossing and is unlikely to re-evolve on short timescales if it is lost, breeding system is especially likely to reflect the colonization filter. We found significantly more self-compatible species on islands than mainlands across a sample of > 1500 species from three widely distributed flowering plant families (Asteraceae, Brassicaceae and Solanaceae). Overall, 66% of island species were self-compatible, compared with 41% of mainland species. Our results demonstrate that the presence or absence of self-incompatibility has strong explanatory power for plant geographical patterns. Island floras around the world thus reflect the role of a key reproductive trait in filtering potential colonizing species in these three plant families. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

A key ecological trait drove the evolution of biparental care and monogamy in an amphibian.

PubMed

Brown, Jason L; Morales, Victor; Summers, Kyle

2010-04-01

Linking specific ecological factors to the evolution of parental care pattern and mating system is a difficult task of key importance. We provide evidence from comparative analyses that an ecological factor (breeding pool size) is associated with the evolution of parental care across all frogs. We further show that the most intensive form of parental care (trophic egg feeding) evolved in concert with the use of small pools for tadpole deposition and that egg feeding was associated with the evolution of biparental care. Previous research on two Peruvian poison frogs (Ranitomeya imitator and Ranitomeya variabilis) revealed similar life histories, with the exception of breeding pool size. This key ecological difference led to divergence in parental care patterns and mating systems. We present ecological field experiments that demonstrate that biparental care is essential to tadpole survival in small (but not large) pools. Field observations demonstrate social monogamy in R. imitator, the species that uses small pools. Molecular analyses demonstrate genetic monogamy in R. imitator, the first example of genetic monogamy in an amphibian. In total, this evidence constitutes the most complete documentation to date that a single ecological factor drove the evolution of biparental care and genetic and social monogamy in an animal.

The oxidative costs of parental care in cooperative and pair-breeding African starlings.

PubMed

Guindre-Parker, Sarah; Rubenstein, Dustin R

2018-06-01

The cost of parental care has long been thought to favor the evolution of cooperative breeding, because breeders can provide reduced parental care when aided by alloparents. Oxidative stress-the imbalance between reactive oxygen species and neutralizing antioxidants-has been proposed to mediate the cost of parental care, though results from empirical studies remain equivocal. We measured changes in oxidative status during reproduction in cooperatively breeding superb starlings (Lamprotornis superbus) to gain insight into the relationships among breeding status, parental care, and oxidative stress. We also compared the oxidative cost of reproduction in the cooperatively breeding superb starling to that in a sympatric non-cooperatively breeding species, the greater blue-eared glossy starling (L. chalybaeus), to determine whether cooperatively breeding individuals face reduced oxidative costs of parental care relative to non-cooperatively breeding individuals. Breeders and alloparents of the cooperative species did not differ in oxidative status throughout a breeding attempt. However, individuals of the non-cooperative species incurred an increase in reactive oxygen metabolites proportionally to an individual's workload during offspring care. These findings suggest that non-cooperative starlings experience an oxidative cost of parental care, whereas cooperatively breeding starlings do not. It is possible that high nest predation risk and multi-brooding in the cooperatively breeding species may have favored reduced physiological costs of parental care more strongly compared to pair-breeding starlings. Reduced physiological costs of caring for young may thus represent a direct benefit that promotes cooperative breeding.

Application of microsatellite markers as potential tools for traceability of Girgentana goat breed dairy products.

PubMed

Sardina, Maria Teresa; Tortorici, Lina; Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Portolano, Baldassare

2015-08-01

In livestock, breed assignment may play a key role in the certification of products linked to specific breeds. Traceability of farm animals and authentication of their products can contribute to improve breed profitability and sustainability of animal productions with significant impact on the rural economy of particular geographic areas and on breed and biodiversity conservation. With the goal of developing a breed genetic traceability system for Girgentana dairy products, the aim of this study was to identify specific microsatellite markers able to discriminate among the most important Sicilian dairy goat breeds, in order to detect possible adulteration in Girgentana dairy products. A total of 20 microsatellite markers were analyzed on 338 individual samples from Girgentana, Maltese, and Derivata di Siria goat breeds. Specific microsatellite markers useful for traceability of dairy products were identified. Eight microsatellite markers showed alleles present at the same time in Maltese and Derivata di Siria and absent in Girgentana and, therefore, they were tested on DNA pools of the three breeds. Considering the electropherograms' results, only FCB20, SRCRSP5, and TGLA122 markers were tested on DNA samples extracted from cheeses of Girgentana goat breed. These three microsatellite markers could be applied in a breed genetic traceability system of Girgentana dairy products in order to detect adulteration due to Maltese and Derivata di Siria goat breeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

The genome-wide structure of two economically important indigenous Sicilian cattle breeds.

PubMed

Mastrangelo, S; Saura, M; Tolone, M; Salces-Ortiz, J; Di Gerlando, R; Bertolini, F; Fontanesi, L; Sardina, M T; Serrano, M; Portolano, B

2014-11-01

Genomic technologies, such as high-throughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (Ne), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of Ne were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r(2) in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

Ephemeral lekking behavior in the buff-breasted sandpiper, Tryngites subruficollis

USGS Publications Warehouse

Lanctot, Richard B.; Weatherhead, Patrick J.

1997-01-01

We studied male reproductive behavior of the buff-breasted sandpiper Tryngites subruficoills for three yean on a 16-km2 study site in northern Alaska to document variation in male lekking behavior and to explore the causes of that variation. During the breeding season, about 75% of males on the study area displayed on leks, with the remainder displaying solitarily. Leks averaged between 2.3 and 3.0 males each (maximum size = 20). Most leks (69%) were present in only one year and about one-tenth were active all three years. Half of the leks were active for only one survey (maximum of 3-4 days) in a given year. Individual male behavior varied substantially, from remaining at a tingle lek for most of the breeding season or attending multiple leks during the season, to displaying solitarily or displaying both on leks and solitarily. Some males (30% or fewer) displayed near nests during the later part of the breeding season, perhaps attempting to copulate with females during egg-laying. The pro-portion of males that displayed on leks remained consistently high throughout the breeding season despite changes in the operational sex ratio and in the intensity of male-male competition. However, the absolute number of males (lekking and solitary) in the study area was positively correlated with the number of fertile females during both breeding seasons. We suggest that buff-breasted sandpipers may be unusual among lek-breeding birds in that males have the option of leaving areas when the number of fertile females becomes depressed and flying to new areas where breeding opportunities are still available. Breeding opportunities may be especially variable in the high arctic because of uneven snow accumulation and differential melt-off that can delay breeding by two or more weeks. This interpretation suggests that the mating system of the buff-breasted sandpiper must be viewed at a much larger scale than what has typically been used in mating system studies.

Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil.

PubMed

Brasil, B S A F; Coelho, E G A; Drummond, M G; Oliveira, D A A

2013-11-18

The Brazilian cattle population is mainly composed of breeds of zebuine origin and their American derivatives. Comprehensive knowledge about the genetic diversity of these populations is fundamental for animal breeding programs and the conservation of genetic resources. This study aimed to assess the phylogenetic relationships, levels of genetic diversity, and patterns of taurine/zebuine admixture among 9 commercial cattle breeds raised in Brazil. Analysis of DNA polymorphisms was performed on 2965 animals using the 11 microsatellite markers recommended by the International Society of Animal Genetics. High genetic diversity was detected in all breeds, even though significant inbreeding was observed within some. Differences among the breeds accounted for 14.72% of the total genetic variability, and genetic differentiation was higher among taurine than among zebuine cattle. Of note, Nelore cattle presented with high levels of admixture, which is consistent with the history of frequent gene flow during the establishment of this breed in Brazil. Furthermore, significant genetic variability was partitioned within the commercial cattle breeds formed in America, which, therefore, comprise important resources of genetic diversity in the tropics. The genetic characterization of these important Brazilian breeds may now facilitate the development of management and breeding programs for these populations.

Progesterone concentration and lambing rate of Karakul ewes treated with prostaglandin and GnRH combined with the ram effect during breeding and non-breeding seasons.

PubMed

Mirzaei, A; Mohebbi-Fani, M; Omidi, A; Boostani, A; Nazifi, S; Mahmoodian-Fard, H R; Chahardahcherik, M

2017-09-15

The combination of ram effect with two injections of PGF 2α 10-days apart and the same protocol plus an additional injection of GnRH prior to the first injection of PGF 2α were examined in Karakul ewes during breeding and non-breeding seasons, respectively. Plasma progesterone (P 4 ) concentrations (to detect the presence of active corpus luteum), twin lambing, litter size and synchronization of lambing were evaluated. In each study 70 ewes (2-4 years old) were divided to a treatment (n = 40) and a control (n = 30) group. During the breeding season, on days -10 and 0 before ram release, the treatment group was injected intramuscularly with PGF 2α (D-Cloprostenol; 0.15 mg). During the non-breeding season, on day -15 before ram release the treatment group was injected with GnRH (buserelin; 4.2 μg) intramuscularly followed by two injections of PGF 2α on days -10 and 0. In both studies, the rams were released into the ewe flock after the second prostaglandin injection (day 0). Blood samples of ewes were collected on days -10, 0, 20 and 70 of the study in breeding season and on days -15, -10, 0, 20 and 70 during non-breeding season. The treatment group had higher P 4 concentrations compared to the control ewes on day 0 in the breeding season (5.80 ± 0.61 vs. 5.0 ± 0.93 ng/mL) and day -10 in the non-breeding season (3.50 ± 0.33 vs. 2.70 ± 0.35 ng/mL) though the differences were not significant (P > 0.05). Based on plasma P 4 concentrations (>1 ng/mL) on day 70, in the breeding season all control ewes (100%) and 91.9% of the treatment ewes were detected to have active corpus luteum (P = 0.09). An almost inverse result (90% vs. 97.5%; P = 0.2) was detected in the non-breeding season. The lambing rate was higher (P = 0.03) in the treatment group compared to the control ewes during the non-breeding season (90% vs. 70%), but tended to be lower (P = 0.07) in the breeding season (73% vs. 90%). Twin lambing rate was higher in the treatment group compared to the control ewes in the breeding (40.7% vs. 0.0%; P < 0.05) and non-breeding (22.2% vs. 0.0%; P < 0.05) seasons. The litter size of the control and treated ewes were 1.0 ± 0.0 vs. 1.40 ± 0.10 in the breeding and 1.0 ± 0.0 vs. 1.22 ± 0.10 in the non-breeding season (P < 0.05). No effect was observed regard to synchronization of the treated ewes. In the breeding season two injections of PGF 2α ten days apart combined with ram effect, may lower the lambing rate, but may enhance twin pregnancies and litter size in Karakul ewes. In the non-breeding season, however, the GnRH-PGF 2α treatment plus ram effect may enhance the lambing rate, twin pregnancies and litter size. Copyright © 2017. Published by Elsevier Inc.

Genetic relationships among Vietnamese local pigs investigated using genome-wide SNP markers.

PubMed

Ishihara, S; Arakawa, A; Taniguchi, M; Luu, Q M; Pham, D L; Nguyen, B V; Mikawa, S; Kikuchi, K

2018-02-01

Vietnam is one of the most important countries for pig domestication, and a total of 26 local breeds have been reported. In the present study, genetic relationships among the various pig breeds were investigated using 90 samples collected from local pigs (15 breeds) in 15 distantly separated, distinct areas of the country and six samples from Landrace pigs in Hanoi as an out-group of a common Western breed. All samples were genotyped using the Illumina Porcine SNP60 v2 Genotyping BeadChip. We used 15 160-15 217 SNPs that showed a high degree of polymorphism in the Vietnamese breeds for identifying genetic relationships among the Vietnamese breeds. Principal components analysis showed that most pigs indigenous to Vietnam formed clusters correlated with their original geographic locations. Some Vietnamese breeds formed a cluster that was genetically related to the Western breed Landrace, suggesting the possibility of crossbreeding. These findings will be useful for the conservation and management of Vietnamese local pig breeds. © 2018 Stichting International Foundation for Animal Genetics.

A Game-Theoretic Model of Marketing Skin Whiteners.

PubMed

Mendoza, Roger Lee

2015-01-01

Empirical studies consistently find that people in less developed countries tend to regard light or "white" skin, particularly among women, as more desirable or superior. This is a study about the marketing of skin whiteners in these countries, where over 80 percent of users are typically women. It proceeds from the following premises: a) Purely market or policy-oriented approaches toward the risks and harms of skin whitening are cost-inefficient; b) Psychosocial and informational factors breed uninformed and risky consumer choices that favor toxic skin whiteners; and c) Proliferation of toxic whiteners in a competitive buyer's market raises critical supplier accountability issues. Is intentional tort a rational outcome of uncooperative game equilibria? Can voluntary cooperation nonetheless evolve between buyers and sellers of skin whiteners? These twin questions are key to addressing the central paradox in this study: A robust and expanding buyer's market, where cheap whitening products abound at a high risk to personal and societal health and safety. Game-theoretic modeling of two-player and n-player strategic interactions is proposed in this study for both its explanatory and predictive value. Therein also lie its practical contributions to the economic literature on skin whitening.

Genetic analysis of prolactin gene in Pakistani cattle.

PubMed

Uddin, Raza Mohy; Babar, Masroor Ellahi; Nadeem, Asif; Hussain, Tanveer; Ahmad, Shakil; Munir, Sadia; Mehboob, Riffat; Ahmad, Fridoon Jawad

2013-10-01

Prolactin (PRL) is a polypeptide hormone, secreted mainly by the anterior pituitary gland. It is involved in many endocrine activities. The key functions of PRL are related to reproduction and lactation in mammals. To ascertain the presence of polymorphisms in the bovine PRL gene (bPRL), the bPRL gene was sequenced. Five mutations were identified in exonic region and eleven in associated intronic regions in 100 cattle from four Pakistani cattle breeds. Haplotype of predicted amino acid changes represent a common alteration at codon 222 from R-Arginine into K-Lysine in all four breeds. Significant statistical variations were observed in the distribution of single nucleotide polymorphism (SNP) in various cattle populations. However, on basis of present study, an association of these SNPs with milk performance traits in four Pakistani cow breeds cannot be truly replicated but at least can be effective DNA markers for some of the breeds studied. Linkage analysis between these SNPs on larger populations can be useful for the association with milk production traits. Furthermore, present study may be used for marker-assisted selection and management in cattle breeding program in local cattle breeds.

Survival rates and lifetime reproduction of breeding male Cooper’s Hawks in Wisconsin, 1980-2005

USGS Publications Warehouse

Rosenfield, Robert N.; Bielefeldt, John; Rosenfield, Laura J.; Booms, Travis L.; Bozek, Michael A.

2009-01-01

There are few published data on annual survival and no reports of lifetime reproduction for breeding Cooper's Hawks (Accipiter cooperii). Breeding males (n  =  105) in central and southeastern Wisconsin had an annual mortality rate of 19%, or a survival rate of 81% for birds ≤10 years of age. We did not detect significant differences in mortality rates between urban and rural habitats, nor between the earlier 13 years and later 13 years of this study. Male Cooper's Hawks produced from zero to 32 nestlings during their lifetimes. Body mass or size appeared unrelated to annual survivorship and lifetime reproduction, although lifetime reproduction was correlated strongly with longevity of breeding males. Fifteen of 66 males (23%) produced most (53%) of the nestlings. Our studies occurred in an area where breeding populations may be increasing with some of the highest reported productivity indices and nesting densities for this species. Habitat used for nesting on our Wisconsin study areas may be less important for survivorship and lifetime reproduction than acquisition of a nesting area in which a male will breed throughout his life.

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

PubMed Central

Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

2001-01-01

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

Importance of determining the climatic domains of sheep breeds.

PubMed

Petit, D; Boujenane, I

2018-07-01

The main purpose of the study was to compare the capacity of the major sheep breeds in Morocco to cope with climate changes through the ranges of several climate parameters in which they can be found. We first delimitated the climatic 'domains' of each breed by constructing a database including altitude and climatic parameters (minima mean of the coldest month, maxima mean of the hottest month, annual rainfall, pluviothermic coefficient of Emberger Q 2, annual minima mean and annual maxima mean) on a 30-year period using the representative stations of each breed distribution. The overlap between each breed combination was quantified through a canonical analysis that extracted the most discriminant parameters. The variance analysis of each climatic parameter evidenced two breeds remarkable by their tolerance. The first one is the Timahdite, mainly settled in areas over 1100 m, which can tolerate the greatest variations in annual rainfall and pluviothermic coefficient. In spite of this feature, this breed is endangered owing to the decreasing quality of pastures. The second one is the D'man which apparently can support high variations in extreme temperatures. In fact, this breed is not well adapted to pastures and requires a special microclimate offered by oases. The information reported in this study will be the basis for the establishment of characterization and selection strategies for Moroccan sheep.

Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping.

PubMed

Dreger, Dayna L; Rimbault, Maud; Davis, Brian W; Bhatnagar, Adrienne; Parker, Heidi G; Ostrander, Elaine A

2016-12-01

In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. © 2016. Published by The Company of Biologists Ltd.

Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping

PubMed Central

Dreger, Dayna L.; Rimbault, Maud; Davis, Brian W.; Bhatnagar, Adrienne; Parker, Heidi G.

2016-01-01

ABSTRACT In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. PMID:27874836

Distribution of extrahepatic congenital portosystemic shunt morphology in predisposed dog breeds

PubMed Central

2012-01-01

Background An inherited basis for congenital extrahepatic portosystemic shunts (EHPSS) has been demonstrated in several small dog breeds. If in general both portocaval and porto-azygous shunts occur in breeds predisposed to portosystemic shunts then this could indicate a common genetic background. This study was performed to determine the distribution of extrahepatic portocaval and porto-azygous shunts in purebred dog populations. Results Data of 135 client owned dogs diagnosed with EHPSS at the Faculty of Veterinary Medicine of Utrecht University from 2001 – 2010 were retrospectively analyzed. The correlation between shunt localization, sex, age, dog size and breed were studied. The study group consisted of 54 males and 81 females from 24 breeds. Twenty-five percent of dogs had porto-azygous shunts and 75% had portocaval shunts. Of the dogs with porto-azygous shunts only 27% was male (P = 0.006). No significant sex difference was detected in dogs with a portocaval shunt. Both phenotypes were present in almost all breeds represented with more than six cases. Small dogs are mostly diagnosed with portocaval shunts (79%) whereas both types are detected. The age at diagnosis in dogs with porto-azygous shunts was significantly higher than that of dogs with portocaval shunts (P < 0.001). Conclusion The remarkable similarity of phenotypic variation in many dog breeds may indicate common underlying genes responsible for EHPSS across breeds. The subtype of EHPSS could be determined by a minor genetic component or modulating factors during embryonic development. PMID:22784395

Distribution of extrahepatic congenital portosystemic shunt morphology in predisposed dog breeds.

PubMed

Van den Bossche, Lindsay; van Steenbeek, Frank G; Favier, Robert P; Kummeling, Anne; Leegwater, Peter A J; Rothuizen, Jan

2012-07-11

An inherited basis for congenital extrahepatic portosystemic shunts (EHPSS) has been demonstrated in several small dog breeds. If in general both portocaval and porto-azygous shunts occur in breeds predisposed to portosystemic shunts then this could indicate a common genetic background. This study was performed to determine the distribution of extrahepatic portocaval and porto-azygous shunts in purebred dog populations. Data of 135 client owned dogs diagnosed with EHPSS at the Faculty of Veterinary Medicine of Utrecht University from 2001 - 2010 were retrospectively analyzed. The correlation between shunt localization, sex, age, dog size and breed were studied. The study group consisted of 54 males and 81 females from 24 breeds. Twenty-five percent of dogs had porto-azygous shunts and 75% had portocaval shunts. Of the dogs with porto-azygous shunts only 27% was male (P = 0.006). No significant sex difference was detected in dogs with a portocaval shunt. Both phenotypes were present in almost all breeds represented with more than six cases. Small dogs are mostly diagnosed with portocaval shunts (79%) whereas both types are detected. The age at diagnosis in dogs with porto-azygous shunts was significantly higher than that of dogs with portocaval shunts (P < 0.001). The remarkable similarity of phenotypic variation in many dog breeds may indicate common underlying genes responsible for EHPSS across breeds. The subtype of EHPSS could be determined by a minor genetic component or modulating factors during embryonic development.

[Polymorphisms of bGH, RORC, and DGAT1 genes in Russian beef cattle breeds].

PubMed

Gorlov, I F; Fedunin, A A; Randelin, D A; Sulimova, G E

2014-12-01

We examined the allelic and genotypic polymorphisms of genes of the retinoic acid receptor-related orphan receptor C (RORC), diacylglycerol acyltransferase-1 (DGAT1), and growth hormone (bGH) in Russian beef cattle breeds in two populations of Kazakh white-headed cattle (of Kazakh and Russian selection) and in the Kalmyk cattle breed and Mongolian hogorogo breed, which is related to Kalmyk breed. The studied genes are associated with parameters of meat quality: marbleness (bGH and RORC) and tenderness (DGAT1). They are also associated with an increase in carcass weight (bGH). We found that Russian and Kazakh populations of the Kazakh white-headed.breed were characterized by a high content of the AA genotype of RORC (0.713 and 0.608, respectively) and of the AA genotype of DGAT1 (0.913 and 0.975), both of which are preferable for meat quality. The total frequencies for the combined genotypes for the bGH and RORC genes, which provide for superior meat quality and carcass weight, in the populations of Kazakh white-headed cattle (GG/AA and GC/AA-68.8% and 57% in the Russian and Kazakh populations, respectively) exceeded the frequencies in the two other studied breeds by two times. Overall, the obtained results point to the high genetic potential of both populations of Kazakh white-headed cattle breeds in beef production. Results of this study can be used to improve the selection of meat traits in industrial livestock.

Improving Charging-Breeding Simulations with Space-Charge Effects

NASA Astrophysics Data System (ADS)

Bilek, Ryan; Kwiatkowski, Ania; Steinbrügge, René

2016-09-01

Rare-isotope-beam facilities use Highly Charged Ions (HCI) for accelerators accelerating heavy ions and to improve measurement precision and resolving power of certain experiments. An Electron Beam Ion Trap (EBIT) is able to create HCI through successive electron impact, charge breeding trapped ions into higher charge states. CBSIM was created to calculate successive charge breeding with an EBIT. It was augmented by transferring it into an object-oriented programming language, including additional elements, improving ion-ion collision factors, and exploring the overlap of the electron beam with the ions. The calculation is enhanced with the effects of residual background gas by computing the space charge due to charge breeding. The program assimilates background species, ionizes and charge breeds them alongside the element being studied, and allows them to interact with the desired species through charge exchange, giving fairer overview of realistic charge breeding. Calculations of charge breeding will be shown for realistic experimental conditions. We reexamined the implementation of ionization energies, cross sections, and ion-ion interactions when charge breeding.

Relative prevalence of upper respiratory tract obstructive disorders in two breeds of harness racehorses (185 cases: 1998-2006).

PubMed

Strand, E; Fjordbakk, C T; Sundberg, K; Spangen, L; Lunde, H; Hanche-Olsen, S

2012-09-01

Two genetically and phenotypically distinct horse breeds are used for harness racing in Scandinavia: the Standardbred (SB) and Coldblooded Trotter. These racehorses have identical environmental, management and racing conditions. Therefore, this study was undertaken to identify and compare the relative prevalence of upper respiratory tract (URT) obstructive disorders in these 2 breeds. To determine whether these 2 phenotypically different breeds of harness racehorses have different predispositions for URT disorders. Retrospective study of 88 Norwegian Coldblooded Trotters (NCT) and 97 SBs referred to this hospital for URT evaluation between 1998 and 2006. Case records of all horses diagnosed with an URT disorder during resting endoscopy, and all horses undergoing high-speed treadmill videoendoscopy (HSTV) with one or more periods of induced poll flexion were evaluated. The relative prevalence of URT disorders between the 2 breeds was analysed using a Fisher's exact test. There was a significant (P<0.05) breed predisposition regarding 6 URT disorders. Bilateral dynamic laryngeal collapse associated with poll flexion and flaccid epiglottis was significantly more frequent in the NCT. Alar fold collapse and nasopharyngeal collapse were significantly more frequent in SBs. Epiglottic entrapment and nasal flutter were only diagnosed in the SBs. Dynamic disorders were more common than resting disorders in both breeds. URT obstructive disorders (dynamic laryngeal collapse associated with poll flexion, flaccid epiglottis, pharyngeal collapse, alar fold collapse, nasal flutter and epiglottic entrapment) are breed related, indicating an anatomic or functional cause. Periods of induced poll flexion during HSTV was essential to declare harness racehorses free of URT disorders. Further anatomic or physiological studies comparing these breeds could potentially provide insight into the pathogenesis of certain URT obstructive disorders. Induced poll flexion should be included in routine HSTV examinations of all harness racehorses. © 2011 EVJ Ltd.

Influence of behavioural tactics on recruitment and reproductive trajectory in the kittiwake

USGS Publications Warehouse

Cam, E.; Cadiou, B.; Hines, J.E.

2002-01-01

Many studies have provided evidence that, in birds, inexperienced breeders have a lower probability of breeding successfully. This is often explained by lack of skills and knowledge, and sometimes late laying dates in the first breeding attempt. There is growing evidence that in many species with deferred reproduction, some prebreeders attend breeding places, acquire territories and form pairs. Several behavioural tactics assumed to be associated with territory acquisition have been described in different species. These tactics may influence the probability of recruiting in the breeding segment of the population, age of first breeding, and reproductive success in the first breeding attempt. Here we addressed the influence of behaviour ('squatting') during the prebreeding period on demographic parameters (survival and recruitment probability) in a long-lived colonial seabird species: the kittiwake. We also investigated the influence of behaviour on reproductive trajectory. Squatters have a higher survival and recruitment probability, and a higher probability of breeding successfully in the first breeding attempt in all age-classes where this category is represented. The influence of behaviour is mainly expressed in the first reproduction. However, there is a relationship between breeding success in the first occasion and subsequent occasions. The influence of breeding success in the first breeding attempt on the rest of the trajectory may indirectly reflect the influence of behaviour on breeding success in the first occasion. The shape of the reproductive trajectory is influenced by behaviour and age of first breeding. There is substantial individual variation from the mean reproductive trajectory, which is accounted for by heterogeneity in performance among individuals in the first attempt, but there is no evidence of individual heterogeneity in the rate of change over time in performance in subsequent breeding occasions

Dispersal in the communally breeding groove-billed ani (Crotophaga sulcirostris)

USGS Publications Warehouse

Bowen, B.S.; Koford, Rolf R.; Vehrencamp, S.L.

1989-01-01

We studied dispersal in a color-banded population of the Groove-billed Ani (Crotophaga sulcirostris) in Costa Rica. Eight percent of the young alive at the end of the breeding season bred on their natal territories the next year and 4% remained but did not breed. Thirteen percent dispersed successfully within the study area and bred in communal groups or simple pairs. The remaining 75% of the young birds disappeared from the study area. Young males remained in the study area as breeders more frequently than did young females. Breeding dispersal occurred, with at least 9% of the adult population moving to a new territory each year.We used a demographic model to estimate the following dispersal fates for young birds. For both males and females, 62% of the young alive at the end of the breeding season in which they hatched obtained a breeding position the next year. Of those that dispersed from their natal territories, 59 to 70% of the males and 64 to 74% of the females obtained breeding positions. Of those that bred the year after they hatched, 22% of the males and 2% of the females bred in their natal units, 34% of the males and 6% of the females bred within the study area but outside their natal units, and 44% of the males and 92% of the females bred outside the study area. We estimated that all of the males and 28% of the females that bred the year after they hatched were within three territories of their natal sites.

Mammary gland and milk fatty acid composition of two dairy goat breeds under feed-restriction.

PubMed

Palma, Mariana; Alves, Susana P; Hernández-Castellano, Lorenzo E; Capote, Juan; Castro, Noemí; Argüello, Anastasio; Matzapetakis, Manolis; Bessa, Rui J B; de Almeida, André M

2017-08-01

Goat dairy products are an important source of animal protein in the tropics. During the dry season, pasture scarcity leads animals to lose up to 40% of their body weight, a condition known as Seasonal Weight Loss (SWL) that is one of the major constraints in ruminant production. Breeds with high tolerance to SWL are relevant to understand the physiological responses to pasture scarcity so they could be used in programs for animal breeding. In the Canary Islands there are two dairy goat breeds with different levels of tolerance to SWL: the Palmera, susceptible to SWL; and the Majorera, tolerant to SWL. Fat is one of the milk components most affected by environmental and physiological conditions. This study hypothesises that feed-restriction affects Majorera and Palmera breeds differently, leading to different fatty acid profiles in the mammary gland and milk. An interaction between breed and feed-restriction was observed in the mammary gland. Feed-restriction was associated with an increase in oleic acid and a decrease in palmitic acid percentage in the Palmera breed whereas no differences were observed in the Majorera breed. Palmitic and oleic acids together constituted around 60% of the total fatty acids identified, which suggests that Palmera breed is more susceptible to SWL. In milk, feed-restriction affected both breeds similarly. Regarding the interaction of the breed with the treatment, we also observed similar responses in both breeds, but this influence affects only around 2% of the total fatty acids. In general, Majorera breed is more tolerant to feed-restriction.

Identification of breeding objectives for Begait goat in western Tigray, North Ethiopia.

PubMed

Abraham, Hagos; Gizaw, Solomon; Urge, Mengistu

2018-06-21

A sound breeding objective is the basis for genetic improvement in overall economic merit of farm animals. Begait goat is one of the identified breeds in Ethiopia, which is a multipurpose breed as it serves as source of cash income and source of food (meat and milk). Despite its importance, no formal breeding objectives exist for Begait goat. The objective of the present study was to identify breeding objectives for the breed through two approaches: using own-flock ranking experiment and developing deterministic bio-economic models as a preliminary step towards designing sustainable breeding programs for the breed. In the own-flock ranking experiment, a total of 45 households were visited at their homesteads and were asked to select, with reasons, the first best, second best, third best, and the most inferior does from their own flock. Age, previous reproduction, and production information of the identified animals were inquired; live body weight and some linear body measurements were taken. The bio-economic model included performance traits (weights, daily weight gain, kidding interval, litter size, milk yield, kid mortality, pregnancy, and replacement rates) and economic (revenue and costs) parameters. It was observed that there was close agreement between the farmers' ranking and bio-economic model results. In general, the results of the present study indicated that Begait goat owners could improve performance of their goats and profitability of their farms by selecting for 6-month weight, litter size, pre-weaning kid survival rate, and milk yield.

New World cattle show ancestry from multiple independent domestication events

PubMed Central

McTavish, Emily Jane; Decker, Jared E.; Schnabel, Robert D.; Taylor, Jeremy F.; Hillis, David M.

2013-01-01

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment. PMID:23530234

Dog sperm head morphometry: its diversity and evolution.

PubMed

Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

2017-01-01

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds' sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics.

Rethinking dog domestication by integrating genetics, archeology, and biogeography.

PubMed

Larson, Greger; Karlsson, Elinor K; Perri, Angela; Webster, Matthew T; Ho, Simon Y W; Peters, Joris; Stahl, Peter W; Piper, Philip J; Lingaas, Frode; Fredholm, Merete; Comstock, Kenine E; Modiano, Jaime F; Schelling, Claude; Agoulnik, Alexander I; Leegwater, Peter A; Dobney, Keith; Vigne, Jean-Denis; Vilà, Carles; Andersson, Leif; Lindblad-Toh, Kerstin

2012-06-05

The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs with the geographic locations of 14 so-called "ancient" breeds (defined by their genetic differentiation) resulted in a counterintuitive pattern. First, none of the ancient breeds derive from regions where the oldest archeological remains have been found. Second, three of the ancient breeds (Basenjis, Dingoes, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog's wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds is a lack of recent admixture with other breeds likely facilitated by geographic and cultural isolation. Furthermore, these genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins. We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication.

Defining a breeding objective for Nile tilapia that takes into account the diversity of smallholder production systems.

PubMed

Omasaki, S K; van Arendonk, J A M; Kahi, A K; Komen, H

2016-10-01

In general, livestock and fish farming systems in developing countries tend to be highly diverse in terms of agro-ecological conditions and market orientation. There are no studies that have investigated if and how this diversity translates to varying preferences for breeding objective traits. This is particularly important for breeding programmes that are organized on a national level (e.g. government-supported nucleus breeding programmes). The aim of this study was to investigate whether Nile tilapia farmers with diverse production systems and economic constraints have different preferences for breeding objective traits. The second objective was to derive a consensus breeding goal, using weighted goal programming that could be used for a national breeding programme for Nile tilapia. A survey was conducted among 100 smallholder Nile tilapia farmers in Kenya to obtain preference values for traits of economic importance, by using multiple pairwise comparisons. Individual and group preference values were estimated using analytical hierarchy process. Low-income farmers preferred harvest weight, while medium- and high-income farmers preferred growth rate and survival. Grouping farmers according to market objective (fingerling production or fattening) showed that fingerling producers preferred growth rate and survival, while fattening farmers preferred harvest weight, height and thickness. Weighted goal programming was used to obtain consensus preference values, and these were used to derive desired gains for a breeding goal of a national breeding programme that takes into account the diversity of smallholder production systems. © 2016 Blackwell Verlag GmbH.

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

PubMed Central

Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R.

2015-01-01

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models. PMID:25785447

Trends in popularity of some morphological traits of purebred dogs in Australia.

PubMed

Teng, Kendy T; McGreevy, Paul D; Toribio, Jenny-Ann L M L; Dhand, Navneet K

2016-01-01

The morphology of dogs can provide information about their predisposition to some disorders. For example, larger breeds are predisposed to hip dysplasia and many neoplastic diseases. Therefore, longitudinal trends in popularity of dog morphology can reveal potential disease pervasiveness in the future. There have been reports on the popularity of particular breeds and behavioural traits but trends in the morphological traits of preferred breeds have not been studied. This study investigated trends in the height, dog size and head shape (cephalic index) of Australian purebred dogs. One hundred eighty-one breeds derived from Australian National Kennel Council (ANKC) registration statistics from 1986 to 2013 were analysed. Weighted regression analyses were conducted to examine trends in the traits by using them as outcome variables, with year as the explanatory variable and numbers of registered dogs as weights. Linear regression investigated dog height and cephalic index (skull width/skull length), and multinomial logistic regression studied dog size. The total number of ANKC registration had decreased gradually from 95,792 in 1986 to 66,902 in 2013. Both weighted minimal height (p = 0.014) and weighted maximal height (p < 0.001) decreased significantly over time, and the weighted cephalic index increased significantly (p < 0.001). The odds of registration of medium and small breeds increased by 5.3 % and 4.2 %, respectively, relative to large breeds (p < 0.001) and by 12.1 % and 11.0 %, respectively, relative to giant breeds (p < 0.001) for each 5-year block of time. Compared to taller and larger breeds, shorter and smaller breeds have become relatively popular over time. Mean cephalic index has increased, which indicates that Australians have gradually favoured breeds with shorter and wider heads (brachycephalic). These significant trends indicate that the dog morphological traits reported here may potentially influence how people select companion dogs in Australia and provide valuable predictive information on the pervasiveness of diseases in dogs.

The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

PubMed Central

Purfield, Deirdre C.; McParland, Sinead; Wall, Eamon; Berry, Donagh P.

2017-01-01

Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production. PMID:28463982

What shall I do now? State-dependent variations of life-history traits with aging in Wandering Albatrosses.

PubMed

Pardo, Deborah; Barbraud, Christophe; Weimerskirch, Henri

2014-02-01

Allocation decisions depend on an organism's condition which can change with age. Two opposite changes in life-history traits are predicted in the presence of senescence: either an increase in breeding performance in late age associated with terminal investment or a decrease due to either life-history trade-offs between current breeding and future survival or decreased efficiency at old age. Age variation in several life-history traits has been detected in a number of species, and demographic performances of individuals in a given year are influenced by their reproductive state the previous year. Few studies have, however, examined state-dependent variation in life-history traits with aging, and they focused mainly on a dichotomy of successful versus failed breeding and non-breeding birds. Using a 50-year dataset on the long-lived quasi-biennial breeding wandering albatross, we investigated variations in life-history traits with aging according to a gradient of states corresponding to potential costs of reproduction the previous year (in ascending order): non-breeding birds staying at sea or present at breeding grounds, breeding birds that failed early, late or were successful. We used multistate models to study survival and decompose reproduction into four components (probabilities of return, breeding, hatching, and fledging), while accounting for imperfect detection. Our results suggest the possible existence of two strategies in the population: strict biennial breeders that exhibited almost no reproductive senescence and quasi-biennial breeders that showed an increased breeding frequency with a strong and moderate senescence on hatching and fledging probabilities, respectively. The patterns observed on survival were contrary to our predictions, suggesting an influence of individual quality rather than trade-offs between reproduction and survival at late ages. This work represents a step further into understanding the evolutionary ecology of senescence and its relationship with costs of reproduction at the population level. It paves the way for individual-based studies that could show the importance of intra-population heterogeneity in those processes.

Breed distribution of the ABCB1-1Delta (multidrug sensitivity) polymorphism among dogs undergoing ABCB1 genotyping.

PubMed

Mealey, Katrina L; Meurs, Kathryn M

2008-09-15

To evaluate the breed distribution of the ABCB1-1Delta polymorphism in a large number of dogs in North America, including dogs of several herding breeds in which this polymorphism has been detected and other breeds in which this polymorphism has not yet been identified. Cross-sectional study. 5,368 dogs from which buccal swab samples were collected for purposes of ABCB1 genotyping. From May 1, 2004, to September 30, 2007, DNA specimens derived from buccal swab samples collected from 5,368 dogs underwent ABCB1 genotyping. These data were reviewed, and results for each dog were recorded in a spreadsheet, along with the dog's breed. The genotypes for each breed were tallied by use of a sorting function. The ABCB1-1Delta allele was identified in 9 breeds of dogs and in many mixed-breed dogs. Breeds that had the ABCB1-1Delta allele included Collie, Longhaired Whippet, Australian Shepherd (standard and miniature), Shetland Sheepdog, Old English Sheepdog, Border Collie, Silken Windhound, and German Shepherd Dog (a breed in which this mutation had not been detected previously). The ABCB1-1Delta polymorphism is associated with increased susceptibility to many adverse drug reactions and with suppression of the hypothalamic-pituitary-adrenal axis and is present in many herding breeds of dog. Veterinarians should be familiar with the breeds that have the ABCB1-1Delta polymorphism to make appropriate pharmacologic choices for these patients.

Owner perceived differences between mixed-breed and purebred dogs.

PubMed

Turcsán, Borbála; Miklósi, Ádám; Kubinyi, Enikő

2017-01-01

Studies about the behaviours of mixed-breed dogs are rare, although mixed-breeds represent the majority of the world's dog population. We have conducted two surveys to investigate the behavioural, demographic, and dog keeping differences between purebred and mixed-breed companion dogs. Questionnaire data were collected on a large sample of dogs living in Germany (N = 7,700 purebred dogs representing more than 200 breeds, and N = 7,691 mixed-breeds). We found that according to their owners, mixed-breeds were (1) less calm, (2) less sociable toward other dogs, and (3) showed more problematic behaviour than purebreds (p < 0.001 for all). Mixed-breeds and purebreds were similar in trainability and boldness scores. However, twelve out of 20 demographic and dog keeping factors differed between purebred and mixed-breed dogs, and two factors showed considerable (> 10%) differences: neutering was more frequent among mixed-breeds, and they were acquired at older ages than purebreds (p < 0.001 for both), which could result in the observed behaviour differences. After controlling for the distribution of the demographic and dog keeping factors, we found that mixed-breeds were (1) more trainable than purebreds, (2) less calm, and (3) showed more problematic behaviour than purebreds (p < 0.001 for all). We discuss that these differences at least partly might be due to selective forces. Our results suggest that instead of being the "average" dogs, mixed-breeds represent a special group with characteristic behavioural traits.

Iteroparity in the variable environment of the salamander Ambystoma tigrinum

USGS Publications Warehouse

Church, D.R.; Bailey, L.L.; Wilbur, H.M.; Kendall, W.L.; Hines, J.E.

2007-01-01

Simultaneous estimation of survival, reproduction, and movement is essential to understanding how species maximize lifetime reproduction in environments that vary across space and time. We conducted a four-year, capture–recapture study of three populations of eastern tiger salamanders (Ambystoma tigrinum tigrinum) and used multistate mark–recapture statistical methods to estimate the manner in which movement, survival, and breeding probabilities vary under different environmental conditions across years and among populations and habitats. We inferred how individuals may mitigate risks of mortality and reproductive failure by deferring breeding or by moving among populations. Movement probabilities among populations were extremely low despite high spatiotemporal variation in reproductive success and survival, suggesting possible costs to movements among breeding ponds. Breeding probabilities varied between wet and dry years and according to whether or not breeding was attempted in the previous year. Estimates of survival in the nonbreeding, forest habitat varied among populations but were consistent across time. Survival in breeding ponds was generally high in years with average or high precipitation, except for males in an especially ephemeral pond. A drought year incurred severe survival costs in all ponds to animals that attempted breeding. Female salamanders appear to defer these episodic survival costs of breeding by choosing not to breed in years when the risk of adult mortality is high. Using stochastic simulations of survival and breeding under historical climate conditions, we found that an interaction between breeding probabilities and mortality limits the probability of multiple breeding attempts differently between the sexes and among populations.

Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers.

PubMed

Aberle, K S; Hamann, H; Drögemüller, C; Distl, O

2004-08-01

We compared the genetic diversity and distance among six German draught horse breeds to wild (Przewalski's Horse), primitive (Icelandic Horse, Sorraia Horse, Exmoor Pony) or riding horse breeds (Hanoverian Warmblood, Arabian) by means of genotypic information from 30 microsatellite loci. The draught horse breeds included the South German Coldblood, Rhenish German Draught Horse, Mecklenburg Coldblood, Saxon Thuringa Coldblood, Black Forest Horse and Schleswig Draught Horse. Despite large differences in population sizes, the average observed heterozygosity (H(o)) differed little among the heavy horse breeds (0.64-0.71), but was considerably lower than in the Hanoverian Warmblood or Icelandic Horse population. The mean number of alleles (N(A)) decreased more markedly with declining population sizes of German draught horse breeds (5.2-6.3) but did not reach the values of Hanoverian Warmblood (N(A) = 6.7). The coefficient of differentiation among the heavy horse breeds showed 11.6% of the diversity between the heavy horse breeds, as opposed to 21.2% between the other horse populations. The differentiation test revealed highly significant genetic differences among all draught horse breeds except the Mecklenburg and Saxon Thuringa Coldbloods. The Schleswig Draught Horse was the most distinct draught horse breed. In conclusion, the study demonstrated a clear distinction among the German draught horse breeds and even among breeds with a very short history of divergence like Rhenish German Draught Horse and its East German subpopulations Mecklenburg and Saxon Thuringa Coldblood.

Owner perceived differences between mixed-breed and purebred dogs

PubMed Central

Turcsán, Borbála; Miklósi, Ádám; Kubinyi, Enikő

2017-01-01

Studies about the behaviours of mixed-breed dogs are rare, although mixed-breeds represent the majority of the world’s dog population. We have conducted two surveys to investigate the behavioural, demographic, and dog keeping differences between purebred and mixed-breed companion dogs. Questionnaire data were collected on a large sample of dogs living in Germany (N = 7,700 purebred dogs representing more than 200 breeds, and N = 7,691 mixed-breeds). We found that according to their owners, mixed-breeds were (1) less calm, (2) less sociable toward other dogs, and (3) showed more problematic behaviour than purebreds (p < 0.001 for all). Mixed-breeds and purebreds were similar in trainability and boldness scores. However, twelve out of 20 demographic and dog keeping factors differed between purebred and mixed-breed dogs, and two factors showed considerable (> 10%) differences: neutering was more frequent among mixed-breeds, and they were acquired at older ages than purebreds (p < 0.001 for both), which could result in the observed behaviour differences. After controlling for the distribution of the demographic and dog keeping factors, we found that mixed-breeds were (1) more trainable than purebreds, (2) less calm, and (3) showed more problematic behaviour than purebreds (p < 0.001 for all). We discuss that these differences at least partly might be due to selective forces. Our results suggest that instead of being the “average” dogs, mixed-breeds represent a special group with characteristic behavioural traits. PMID:28222103

Grooming as a reward? Social function of grooming between females in cooperatively breeding marmosets

PubMed Central

LAZARO-PEREA, CRISTINA; DE FÁTIMA ARRUDA, MARIA; SNOWDON, CHARLES T.

2006-01-01

Classical models of grooming predict that subordinate primates will direct grooming towards dominants to receive coalitionary support from them. In contrast, recent reviews suggest that grooming asymmetries can change with social system and ecological conditions and should reflect asymmetries in services provided by different members of the dyad. We studied grooming patterns between females in six wild groups of common marmosets, Callithrix jacchus, to investigate the relation between social structure and grooming between females in a cooperatively breeding species. We observed grooming frequently and consistently in all study groups. Breeding females groomed nonbreeding females more than vice versa, and grooming between breeding and nonbreeding females was not related to agonistic behaviour. Our results provide some support to the hypothesis that grooming asymmetries are related to differences in services provided by different group members. We suggest that, in cooperatively breeding systems, breeding females may use grooming as an incentive for helper females to stay in the group. PMID:17237884

Initial insights on the performances and management of dairy cattle herds combining two breeds with contrasting features.

PubMed

Magne, M A; Thénard, V; Mihout, S

2016-05-01

Finding ways of increasing animal production with low external inputs and without compromising reproductive performances is a key issue of livestock systems sustainability. One way is to take advantage of the diversity and interactions among components within livestock systems. Among studies that investigate the influence of differences in animals' individual abilities in a herd, few focus on combinations of cow breeds with contrasting features in dairy cattle herds. This study aimed to analyse the performances and management of such multi-breed dairy cattle herds. These herds were composed of two types of dairy breeds: 'specialist' (Holstein) and 'generalist' (e.g. Montbeliarde, Simmental, etc.). Based on recorded milk data in southern French region, we performed (i) to compare the performances of dairy herds according to breed-type composition: multi-breed, single specialist breed or single generalist breed and (ii) to test the difference of milk performances of specialist and generalist breed cows (n = 10 682) per multi-breed dairy herd within a sample of 22 farms. The sampled farmers were also interviewed to characterise herd management through multivariate analysis. Multi-breed dairy herds had a better trade-off among milk yield, milk fat and protein contents, herd reproduction and concentrate-conversion efficiency than single-breed herds. Conversely, they did not offer advantages in terms of milk prices and udder health. Compared to specialist dairy herds, they produce less milk with the same concentrate-conversion efficiency but have better reproductive performances. Compared to generalist dairy herds, they produce more milk with better concentrate-conversion efficiency but have worse reproductive performances. Within herds, specialist and generalist breed cows significantly differed in milk performances, showing their complementarity. The former produced more milk for a longer lactation length while the latter produced milk with higher protein and fat contents and had a slightly longer lactation rank. Our results also focus on the farmers' management of multi-breed dairy herds underlying herd performances. Three strategies of management were identified and structured along two main axes. The first differentiates farmers according to their animal-selection practices in relation with their objectives of production: adapting animal to produce milk with low-feeding inputs v. focussing on milk yield trait to intensify milk production. The second refers to the purpose farmers give to multi-breed dairy herds: milk v. milk/meat production. These initial insights on the performances and management of multi-breed dairy herds contribute to better understanding the functioning of ruminant livestock systems based on individual variability.

Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.

PubMed

Rahmatalla, Siham A; Arends, Danny; Reissmann, Monika; Said Ahmed, Ammar; Wimmers, Klaus; Reyer, Henry; Brockmann, Gudrun A

2017-10-23

Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (F IS ) did not differ from zero. F st coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei's genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high F st values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system. The information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high F st values in Taggar goat and allowed to identify candidate genes which can be used in the development of breed selection programs to improve local breeds and find genetic factors contributing to the adaptation to harsh environments.

Effect of Particular Breed on the Chemical Composition, Texture, Color, and Sensorial Characteristics of Dry-cured Ham

PubMed Central

Seong, Pil Nam; Park, Kuyng Mi; Kang, Sun Moon; Kang, Geun Ho; Cho, Soo Hyun; Park, Beom Young; Van Ba, Hoa

2014-01-01

The present study demonstrates the impact of specific breed on the characteristics of dry-cured ham. Eighty thighs from Korean native pig (KNP), crossbreed (Landrace×Yorkshire)♀×Duroc♂ (LYD), Berkshire (Ber), and Duroc (Du) pig breeds (n = 10 for each breed) were used for processing of dry-cured ham. The thighs were salted with 6% NaCl (w/w) and 100 ppm NaNO2, and total processing time was 413 days. The effects of breed on the physicochemical composition, texture, color and sensory characteristics were assessed on the biceps femoris muscle of the hams. The results revealed that the highest weight loss was found in the dry-cured ham of LYD breed and the lowest weight loss was found in Ber dry-cured ham. The KNP dry-cured ham contain higher intramuscular fat level than other breed hams (p<0.05). It was observed that the dry-cured ham made from KNP breed had the lowest water activity value and highest salt content, while the LYD dry-cure ham had higher total volatile basic nitrogen content than the Ber and Du hams (p<0.05). Zinc, iron and total monounsaturated fatty acids levels were higher in KNP ham while polyunsaturated fatty acids levels were higher in Du ham when compared to other breed hams (p<0.05). Additionally, the KNP dry-cured ham possessed higher Commission International de l’Eclairage (CIE) a* value, while the Du dry-cured ham had higher L*, CIE b* and hue angle values (p<0.05). Furthermore, breed significantly affected the sensory attributes of dry-cured hams with higher scores for color, aroma and taste found in KNP dry-cured ham as compared to other breed hams (p<0.05). The overall outcome of the study is that the breed has a potential effect on the specific chemical composition, texture, color and sensorial properties of dry-cured hams. These data could be useful for meat processors to select the suitable breeds for economical manufacturing of high quality dry-cured hams. PMID:25083111

Effect of Particular Breed on the Chemical Composition, Texture, Color, and Sensorial Characteristics of Dry-cured Ham.

PubMed

Seong, Pil Nam; Park, Kuyng Mi; Kang, Sun Moon; Kang, Geun Ho; Cho, Soo Hyun; Park, Beom Young; Van Ba, Hoa

2014-08-01

The present study demonstrates the impact of specific breed on the characteristics of dry-cured ham. Eighty thighs from Korean native pig (KNP), crossbreed (Landrace×Yorkshire)♀×Duroc♂ (LYD), Berkshire (Ber), and Duroc (Du) pig breeds (n = 10 for each breed) were used for processing of dry-cured ham. The thighs were salted with 6% NaCl (w/w) and 100 ppm NaNO2, and total processing time was 413 days. The effects of breed on the physicochemical composition, texture, color and sensory characteristics were assessed on the biceps femoris muscle of the hams. The results revealed that the highest weight loss was found in the dry-cured ham of LYD breed and the lowest weight loss was found in Ber dry-cured ham. The KNP dry-cured ham contain higher intramuscular fat level than other breed hams (p<0.05). It was observed that the dry-cured ham made from KNP breed had the lowest water activity value and highest salt content, while the LYD dry-cure ham had higher total volatile basic nitrogen content than the Ber and Du hams (p<0.05). Zinc, iron and total monounsaturated fatty acids levels were higher in KNP ham while polyunsaturated fatty acids levels were higher in Du ham when compared to other breed hams (p<0.05). Additionally, the KNP dry-cured ham possessed higher Commission International de l'Eclairage (CIE) a* value, while the Du dry-cured ham had higher L*, CIE b* and hue angle values (p<0.05). Furthermore, breed significantly affected the sensory attributes of dry-cured hams with higher scores for color, aroma and taste found in KNP dry-cured ham as compared to other breed hams (p<0.05). The overall outcome of the study is that the breed has a potential effect on the specific chemical composition, texture, color and sensorial properties of dry-cured hams. These data could be useful for meat processors to select the suitable breeds for economical manufacturing of high quality dry-cured hams.

Avian cooperative breeding: Old hypotheses and new directions.

PubMed

Heinsohn, R G; Cockburn, A; Mulder, R A

1990-12-01

In cooperatively breeding birds, individuals that appear capable of reproducing on their own may instead assist others with their breeding efforts. Research into avian cooperative breeding has attempted to reconcile the apparent altruism of this behaviour with maximization of inclusive fitness. Most explanations of cooperative breeding have suggested that philopatry is enforced by ecological constraints, such as a shortage of resources critical to breeding. Non-dispersers may then benefit both directly and indirectly from contributing at the nest. Recent research has shown that such benefits may be sufficient to promote philopatry, without the need for ecological constraints, and emphasizes that consideration of both costs and benefits of philopatry is essential for a comprehensive approach to the problem. The growing body of data from long-term studies of different species should combine with an improved phylogenetic perspective on cooperative breeding, to provide a useful base for future comparative analyses and experimentation. Copyright © 1990. Published by Elsevier Ltd.

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology.

PubMed

Pareek, Chandra Shekhar; Błaszczyk, Paweł; Dziuba, Piotr; Czarnik, Urszula; Fraser, Leyland; Sobiech, Przemysław; Pierzchała, Mariusz; Feng, Yaping; Kadarmideen, Haja N; Kumar, Dibyendu

2017-01-01

RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver tissue of young bulls of the Polish Red, Polish Holstein-Friesian (HF) and Hereford breeds, and to understand the genomic variation in the three cattle breeds that may reflect differences in production traits. The RNA-seq experiment on bovine liver produced 107,114,4072 raw paired-end reads, with an average of approximately 60 million paired-end reads per library. Breed-wise, a total of 345.06, 290.04 and 436.03 million paired-end reads were obtained from the Polish Red, Polish HF, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed that 81.35%, 82.81% and 84.21% of the mapped sequencing reads were properly paired to the Polish Red, Polish HF, and Hereford breeds, respectively. This study identified 5,641,401 SNPs and insertion and deletion (indel) positions expressed in the bovine liver with an average of 313,411 SNPs and indel per young bull. Following the removal of the indel mutations, a total of 195,3804, 152,7120 and 205,3184 raw SNPs expressed in bovine liver were identified for the Polish Red, Polish HF, and Hereford breeds, respectively. Breed-wise, three highly reliable breed-specific SNP-databases (SNP-dbs) with 31,562, 24,945 and 28,194 SNP records were constructed for the Polish Red, Polish HF, and Hereford breeds, respectively. Using a combination of stringent parameters of a minimum depth of ≥10 mapping reads that support the polymorphic nucleotide base and 100% SNP ratio, 4,368, 3,780 and 3,800 SNP records were detected in the Polish Red, Polish HF, and Hereford breeds, respectively. The SNP detections using RNA-seq data were successfully validated by kompetitive allele-specific PCR (KASPTM) SNP genotyping assay. The comprehensive QTL/CG analysis of 110 QTL/CG with RNA-seq data identified 20 monomorphic SNP hit loci (CARTPT, GAD1, GDF5, GHRH, GHRL, GRB10, IGFBPL1, IGFL1, LEP, LHX4, MC4R, MSTN, NKAIN1, PLAG1, POU1F1, SDR16C5, SH2B2, TOX, UCP3 and WNT10B) in all three cattle breeds. However, six SNP loci (CCSER1, GHR, KCNIP4, MTSS1, EGFR and NSMCE2) were identified as highly polymorphic among the cattle breeds. This study identified breed-specific SNPs with greater SNP ratio and excellent mapping coverage, as well as monomorphic and highly polymorphic putative SNP loci within QTL/CGs of bovine liver tissue. A breed-specific SNP-db constructed for bovine liver yielded nearly six million SNPs. In addition, a KASPTM SNP genotyping assay, as a reliable cost-effective method, successfully validated the breed-specific putative SNPs originating from the RNA-seq experiments.

Dog Breed Differences in Visual Communication with Humans

PubMed Central

Konno, Akitsugu; Romero, Teresa; Inoue-Murayama, Miho; Saito, Atsuko; Hasegawa, Toshikazu

2016-01-01

Domestic dogs (Canis familiaris) have developed a close relationship with humans through the process of domestication. In human-dog interactions, eye contact is a key element of relationship initiation and maintenance. Previous studies have suggested that canine ability to produce human-directed communicative signals is influenced by domestication history, from wolves to dogs, as well as by recent breed selection for particular working purposes. To test the genetic basis for such abilities in purebred dogs, we examined gazing behavior towards humans using two types of behavioral experiments: the ‘visual contact task’ and the ‘unsolvable task’. A total of 125 dogs participated in the study. Based on the genetic relatedness among breeds subjects were classified into five breed groups: Ancient, Herding, Hunting, Retriever-Mastiff and Working). We found that it took longer time for Ancient breeds to make an eye-contact with humans, and that they gazed at humans for shorter periods of time than any other breed group in the unsolvable situation. Our findings suggest that spontaneous gaze behavior towards humans is associated with genetic similarity to wolves rather than with recent selective pressure to create particular working breeds. PMID:27736990

Progress in the molecular and genetic modification breeding of beef cattle in China.

PubMed

Tong, Bin; Zhang, Li; Li, Guang-Peng

2017-11-20

The studies of beef cattle breeding in China have been greatly improved with the rapid development of the international beef cattle industrialization. The beef cattle breeding technologies have rapidly transformed from traditional breeding to molecular marker-assisted breeding, genomic selection and genetic modification breeding. Hundreds of candidate genes and molecular markers associated with growth, meat quality, reproduction performance and diseases resistance have been identified, and some of them have already been used in cattle breeding. Genes and molecular markers associated with growth and development are focused on the growth hormone, muscle regulatory factors, myostatin and insulin-like growth factors. Meat quality is mediated by fatty acid transport and deposition related signals, calpains and calpain system, muscle regulatory factors and muscle growth regulation pathways. Reproduction performance is regulated by GnRH-FSH-LH, growth differentiation factor 9, prolactin receptor and forkhead box protein O1. Disease resistance is modulated by the major histocompatibility complex gene family, toll-like receptors, mannose-binding lectin and interferon gene signals. In this review, we summarize the most recent progress in beef cattle breeding in marker-assisted selection, genome-wide selection and genetic modification breeding, aiming to provide a reference for further genetic breeding research of beef cattle in China.

A Test of Canine Olfactory Capacity: Comparing Various Dog Breeds and Wolves in a Natural Detection Task

PubMed Central

Polgár, Zita; Kinnunen, Mari; Újváry, Dóra; Miklósi, Ádám; Gácsi, Márta

2016-01-01

Many dog breeds are bred specifically for increased performance in scent-based tasks. Whether dogs bred for this purpose have higher olfactory capacities than other dogs, or even wolves with whom they share a common ancestor, has not yet been studied. Indeed, there is no standard test for assessing canine olfactory ability. This study aimed to create a simple procedure that requires no pre-training and to use it to measure differences in olfactory capacity across four groups of canines: (1) dog breeds that have been selected for their scenting ability; (2) dog breeds that have been bred for other purposes; (3) dog breeds with exaggerated short-nosed features; and (4) hand-reared grey wolves. The procedure involved baiting a container with raw turkey meat and placing it under one of four identical ceramic pots. Subjects were led along the row of pots and were tasked with determining by olfaction alone which of them contained the bait. There were five levels of increasing difficulty determined by the number of holes on the container’s lid. A subsample of both dogs and wolves was retested to assess reliability. The results showed that breeds selected for scent work were better than both short-nosed and non-scent breeds. In the most difficult level, wolves and scenting breeds performed better than chance, while non-scenting and short-nosed breeds did not. In the retested samples wolves improved their success; however, dogs showed no change in their performances indicating that a single test may be reliable enough to assess their capacity. Overall, we revealed measurable differences between dog breeds in their olfactory abilities and suggest that the Natural Detection Task is a good foundation for developing an efficient way of quantifying them. PMID:27152412

A Test of Canine Olfactory Capacity: Comparing Various Dog Breeds and Wolves in a Natural Detection Task.

PubMed

Polgár, Zita; Kinnunen, Mari; Újváry, Dóra; Miklósi, Ádám; Gácsi, Márta

2016-01-01

Many dog breeds are bred specifically for increased performance in scent-based tasks. Whether dogs bred for this purpose have higher olfactory capacities than other dogs, or even wolves with whom they share a common ancestor, has not yet been studied. Indeed, there is no standard test for assessing canine olfactory ability. This study aimed to create a simple procedure that requires no pre-training and to use it to measure differences in olfactory capacity across four groups of canines: (1) dog breeds that have been selected for their scenting ability; (2) dog breeds that have been bred for other purposes; (3) dog breeds with exaggerated short-nosed features; and (4) hand-reared grey wolves. The procedure involved baiting a container with raw turkey meat and placing it under one of four identical ceramic pots. Subjects were led along the row of pots and were tasked with determining by olfaction alone which of them contained the bait. There were five levels of increasing difficulty determined by the number of holes on the container's lid. A subsample of both dogs and wolves was retested to assess reliability. The results showed that breeds selected for scent work were better than both short-nosed and non-scent breeds. In the most difficult level, wolves and scenting breeds performed better than chance, while non-scenting and short-nosed breeds did not. In the retested samples wolves improved their success; however, dogs showed no change in their performances indicating that a single test may be reliable enough to assess their capacity. Overall, we revealed measurable differences between dog breeds in their olfactory abilities and suggest that the Natural Detection Task is a good foundation for developing an efficient way of quantifying them.

The Shepherds' Tale: A Genome-Wide Study across 9 Dog Breeds Implicates Two Loci in the Regulation of Fructosamine Serum Concentration in Belgian Shepherds.

PubMed

Forsberg, Simon K G; Kierczak, Marcin; Ljungvall, Ingrid; Merveille, Anne-Christine; Gouni, Vassiliki; Wiberg, Maria; Lundgren Willesen, Jakob; Hanås, Sofia; Lequarré, Anne-Sophie; Mejer Sørensen, Louise; Tiret, Laurent; McEntee, Kathleen; Seppälä, Eija; Koch, Jørgen; Battaille, Géraldine; Lohi, Hannes; Fredholm, Merete; Chetboul, Valerie; Häggström, Jens; Carlborg, Örjan; Lindblad-Toh, Kerstin; Höglund, Katja

2015-01-01

Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated haemoglobin (HbA1c) are two major biomarkers of glycaemia, where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds. Considering all breeds together, we did not find any genome-wide significant associations to fructosamine serum concentration. However, by performing breed-specific analyses we revealed an association on chromosome 3 (pcorrected ≈ 1:68 × 10-6) in Belgian shepherd dogs of the Malinois subtype. The associated region and its close neighbourhood harbours interesting candidate genes such as LETM1 and GAPDH that are important in glucose metabolism and have previously been implicated in the aetiology of diabetes mellitus. To further explore the genetics of this breed specificity, we screened the genome for reduced heterozygosity stretches private to the Belgian shepherd breed. This revealed a region with reduced heterozygosity that shows a statistically significant interaction (p = 0.025) with the association region on chromosome 3. This region also harbours some interesting candidate genes and regulatory regions but the exact mechanisms underlying the interaction are still unknown. Nevertheless, this finding provides a plausible explanation for breed-specific genetic effects for complex traits in dogs. Shepherd breeds are at low risk of developing diabetes mellitus. The findings in Belgian shepherds could be connected to a protective mechanism against the disease. Further insight into the regulation of glucose metabolism could improve diagnostic and therapeutic methods for diabetes mellitus.

Interbreed variation in serum serotonin (5-hydroxytryptamine) concentration in healthy dogs.

PubMed

Höglund, K; Häggström, J; Hanås, S; Merveille, A-C; Gouni, V; Wiberg, M; Lundgren Willesen, J; Entee, K Mc; Mejer Sørensen, L; Tiret, L; Seppälä, E H; Lohi, H; Chetboul, V; Fredholm, M; Lequarré, A-S; Ljungvall, I

2018-06-16

Serotonin (5-hydroxytryptamine [5-HT]) has several biological functions. In different species, excessive 5-HT has been linked to valvular lesions, similar to those seen in dogs with myxomatous mitral valve disease. Previous studies suggest higher 5-HT in healthy Cavalier King Charles Spaniels (CKCSs), a breed highly affected by myxomatous mitral valve disease, compared to other breeds. To investigate potential interbreed variation in serum 5-HT in healthy dogs. 483 healthy dogs of nine breeds aged 1-7 years. Dogs were examined at five European centers. Absence of cardiovascular, organ-related, or systemic diseases was ensured by thorough clinical investigations including echocardiography. Serum was frozen and later analyzed by enzyme-linked immunosorbent assay (ELISA). Median 5-HT concentration was 252.5 (interquartile range = 145.5-390.6) ng/mL. Overall breed difference was found (p<0.0001), and 42% of pairwise breed comparisons were significant. Univariate regression analysis showed association between serum 5-HT concentration and breed, center of examination, storage time, and sex, with higher 5-HT in females. In multiple regression analysis, the final model had an adjusted R 2 of 0.27 with breed (p<0.0001), center (p<0.0001), and storage time (p=0.014) remaining significant. Within centers, overall breed differences were found at 3/5 centers (p≤0.028), and pairwise comparisons within those centers showed breed differences in 42% of comparisons. Among the included breeds, Newfoundlands, Belgian Shepherds and CKCSs had highest 5-HT concentrations. Interbreed variation in serum 5-HT concentration was found in healthy dogs aged 1-7 years. These differences should be taken into account when designing clinical studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Improvement of indigenous cattle to modern Japanese Black (Wagyu) cattle

NASA Astrophysics Data System (ADS)

Oikawa, T.

2018-02-01

Wagyu cattle have been improved from indigenous cattle raised in Japan since the country was opened 100 years ago. Characteristics of the breed were formed during that period. Here, the process of the breeding is described, and recent topics about breeding studies are discussed.

Effects of experimentally sustained elevated testosterone on incubation behaviour and reproductive success in female great tits (Parus major).

PubMed

de Jong, Berber; Lens, Luc; Amininasab, Seyed Mehdi; van Oers, Kees; Darras, Veerle M; Eens, Marcel; Pinxten, Rianne; Komdeur, Jan; Groothuis, Ton G G

2016-05-01

In many seasonally breeding birds, female and male testosterone (T) levels peak at the start of the breeding season, coinciding with pair bonding and nesting activities. Shortly after the onset of egg laying, T levels slowly decline to baseline levels in both sexes, but more rapidly so in females. During this period, T in males may still function to facilitate territorial behaviour, mate guarding and extra pair copulations, either via short lasting peaks or elevated basal levels of the hormone. In some species, however, males become insensitive to increased T after the onset of egg laying. It has been postulated that in these species bi-parental care is essential for offspring survival, as T is known to inhibit paternal care. However, only very few studies have analysed this for females. As females are heavily involved in parental care, they too might become insensitive to T after egg laying. Alternatively, because territorial defence, mate guarding and extra pair copulations are expected to be less important for females than for males, they may not have had the need to evolve a mechanism to become insensitive to T during the period of maternal care, because their natural T levels are never elevated during this part of the breeding season anyway. We tested these alternative hypotheses in female great tits (Parus major). Male great tits have previously been shown to be insensitive to T after egg laying with regard to nestling feeding behaviour (but not song rate). When females had started nest building, we experimentally elevated their T levels up to the nestling feeding phase, and measured incubation behaviour (only females incubate) and reproductive success. T did not significantly affect nest building or egg laying behaviour, although egg laying tended to be delayed in T females. Females with experimentally enhanced T maintained lower temperature during incubation but did not spend less time incubating. This might explain the reduced hatching success of their eggs, smaller brood size and lower number of fledglings we found in this study. As in this species T-dependent behaviour by females during the phase of parental care is not needed, the results support the hypothesis that in this species the need for selection in favour of T-insensitivity did not occur. Copyright © 2016 Elsevier Inc. All rights reserved.

Larval traits show temporally consistent constraints, but are decoupled from post-settlement juvenile growth, in an intertidal fish.

PubMed

Thia, Joshua A; Riginos, Cynthia; Liggins, Libby; Figueira, Will F; McGuigan, Katrina

2018-05-05

1.Complex life-cycles may evolve to dissociate distinct developmental phases in an organism's lifetime. However, genetic or environmental factors may restrict trait independence across life stages, constraining ontogenetic trajectories. Quantifying covariance across life-stages and their temporal variability is fundamental in understanding life-history phenotypes and potential distributions and consequences for selection. 2.We studied developmental constraints in an intertidal fish (Bathygobius cocosensis: Gobiidae) with a discrete pelagic larval phase and benthic juvenile phase. We tested whether traits occurring earlier in life affected those expressed later, and whether larval traits were decoupled from post-settlement juvenile traits. Sampling distinct cohorts from three annual breeding seasons afforded tests of temporally variability in trait covariance. 3.From otoliths (fish ear stones), we measured hatch size, larval duration, pelagic growth (larval traits) and early post-settlement growth (juvenile trait) in 124 juvenile B. cocoensis. We used path analyses to model trait relationships with respect to their chronological expression, comparing models among seasons. We also modelled the effect of season and hatch date on each individual trait to quantify their inherent variability. 4.Our path analyses demonstrated a decoupling of larval traits on juvenile growth. Within the larval phase, longer larval durations resulted in greater pelagic growth, and larger size-at-settlement. There was also evidence that larger hatch size might reduce larval durations, but this effect was only marginally significant. Although pelagic and post-settlement growth were decoupled, pelagic growth had post-settlement consequences: individuals with high pelagic growth were among the largest fish at settlement, and remained among the largest early post-settlement. We observed no evidence that trait relationships varied among breeding seasons, but larval duration differed among breeding seasons, and was shorter for larvae hatching later within each season. 5.Overall, we demonstrate mixed support for the expectation that traits in different life-stages are independent. While post-settlement growth was decoupled from larval traits, pelagic development had consequences for the size of newly settled juveniles. Temporal consistency in trait covariances implies that genetic and/or environmental factors influencing them were stable over our three-year study. Our work highlights the importance of individual developmental experiences and temporal variability in understanding population distributions of life-history traits. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Dog bite injuries to humans and the use of breed-specific legislation: a comparison of bites from legislated and non-legislated dog breeds.

PubMed

Creedon, Nanci; Ó'Súilleabháin, Páraic S

2017-01-01

The primary objective of this study was to investigate if differences in dog bite characteristics exist amongst legislated and non-legislated dog breeds listed under breed-specific legislation in Ireland (age when bitten, anatomical bite locations, triggers for biting, victim's relationship with the dog, geographical location and owner presence, history of aggression, reporting bite incident to authorities, medical treatment required following the bite, and type of bite inflicted). A second objective of the current study was to investigate dog control officer's enforcement and perceptions of current legislation. Data for statistical analyses were collated through a nationally advertised survey, with Pearson Chi-square and Fisher's Exact Test statistical methods employed for analyses. A total of 140 incident surveys were assessed comprising of non-legislated ( n  = 100) and legislated ( n  = 40) dog bite incidents. Legislated breeds were significantly more likely to be perceived as aggressive and less fearful as triggers for biting compared to non-legislated breeds ( P  = 0.003). Non-legislated breeds were more likely to inflict a bite with the owner present on own property and on a business premises compared to legislated breeds ( P  = 0.036). Non-legislated breeds were more likely to not be reported to the authorities before ( P  = 0.009), and after ( P  = 0.032) the bite occurred compared to legislated breeds. There were no significant differences observed between both groups for; age when the victim was bitten, bite location, relationship with the dog, history of aggression, outcome for the dog, if the dog bit again, and seeing a professional trainer or behaviourist. No significant difference was observed between both legislated and non-legislated groups for medical treatment required following the bite, and the type of bite inflicted. The present study results did not observe evidence of any differences between legislated and non-legislated for both the medical treatment to victims required following the bite, and the type of bite inflicted. The significant differences in bites being reported to authorities, perceived triggers for biting, and biting locations suggests distinctly differing perceptions relating to risk between legislated and non-legislated dog breeds. Further consequences relating to the introduction of breed-specific legislation in Ireland are discussed.

Ecological relationships of breeding blue-winged teal to prairie potholes

USGS Publications Warehouse

Drewien, R.C.; Springer, P.F.

1969-01-01

Ecology of breeding blue-winged teal (Anas discors) was studied on the Waubay Study Area in Day County, South Dakota, in 1965 and 1966. Breeding pair use of the wetland habitat and importance of Type 1 ponds in the wetland complex were evaluated. Changes in breeding pair densities and wetland habitat conditions on the study area were compared for the 16-year period, 1950-66.Blue-winged teal pair densities of 30.7 and 33.0 per square mile in 1965 and 1966, respectively, were above the 16-year average from 1950 to 1966 and near the maximum for this period. Blue-winged teal comprised 46.7 per cent of the waterfowl breeding population in 1965 and 51.7 per cent in 1966. Number of water areas per square mile through mid-spring 1965 was comparable to the average for the 16-year period, whereas during late spring 1965 and throughout the 1966 spring breeding seasons the number of water areas increased to near optimum conditions.Annual breeding-pair densities from 1950 to 1966 appeared to be largely influenced by water conditions, and pair-density fluctuations resulted from changes in number of wet ponds from late April through mid-May. Variations in water conditions after this period did not appear to have as great an effect on numbers of breeding teal.Use of wetland habitat by pairs changed throughout the spring breeding seasons. During the post-arrival period, teal congregated on larger wetlands. With onset of egg-laying, pairs dispersed into ponds throughout the wetland complex to establish breeding home ranges. Other factors that influenced changes in habitat use included: 1) pond type and size, 2) breeding cycle phenology, 3) availability of wet ponds, and 4) land use. Number of blue-winged teal pairs per unit area of water was highest in 1965 and 1966 on Type 1B ponds, followed in decreasing order by Types 3, 1A, and 4 and 5. Greater use of Type 1B ponds was probably related to larger ratio of edge or shore line to unit area of water. Interspersion of many small wetlands throughout the breeding habitat provided for maximum pair dispersal during egg-laying and early incubation stages of the reproductive cycle.

Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies

PubMed Central

Acland, Gregory M.

2014-01-01

Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision. PMID:22065099

Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies.

PubMed

Miyadera, Keiko; Acland, Gregory M; Aguirre, Gustavo D

2012-02-01

Considerable clinical and molecular variations have been known in retinal blinding diseases in man and also in dogs. Different forms of retinal diseases occur in specific breed(s) caused by mutations segregating within each isolated breeding population. While molecular studies to find genes and mutations underlying retinal diseases in dogs have benefited largely from the phenotypic and genetic uniformity within a breed, within- and across-breed variations have often played a key role in elucidating the molecular basis. The increasing knowledge of phenotypic, allelic, and genetic heterogeneities in canine retinal degeneration has shown that the overall picture is rather more complicated than initially thought. Over the past 20 years, various approaches have been developed and tested to search for genes and mutations underlying genetic traits in dogs, depending on the availability of genetic tools and sample resources. Candidate gene, linkage analysis, and genome-wide association studies have so far identified 24 mutations in 18 genes underlying retinal diseases in at least 58 dog breeds. Many of these genes have been associated with retinal diseases in humans, thus providing opportunities to study the role in pathogenesis and in normal vision. Application in therapeutic interventions such as gene therapy has proven successful initially in a naturally occurring dog model followed by trials in human patients. Other genes whose human homologs have not been associated with retinal diseases are potential candidates to explain equivalent human diseases and contribute to the understanding of their function in vision.

Opposing selection and environmental variation modify optimal timing of breeding.

PubMed

Tarwater, Corey E; Beissinger, Steven R

2013-09-17

Studies of evolution in wild populations often find that the heritable phenotypic traits of individuals producing the most offspring do not increase proportionally in the population. This paradox may arise when phenotypic traits influence both fecundity and viability and when there is a tradeoff between these fitness components, leading to opposing selection. Such tradeoffs are the foundation of life history theory, but they are rarely investigated in selection studies. Timing of breeding is a classic example of a heritable trait under directional selection that does not result in an evolutionary response. Using a 22-y study of a tropical parrot, we show that opposing viability and fecundity selection on the timing of breeding is common and affects optimal breeding date, defined by maximization of fitness. After accounting for sampling error, the directions of viability (positive) and fecundity (negative) selection were consistent, but the magnitude of selection fluctuated among years. Environmental conditions (rainfall and breeding density) primarily and breeding experience secondarily modified selection, shifting optimal timing among individuals and years. In contrast to other studies, viability selection was as strong as fecundity selection, late-born juveniles had greater survival than early-born juveniles, and breeding later in the year increased fitness under opposing selection. Our findings provide support for life history tradeoffs influencing selection on phenotypic traits, highlight the need to unify selection and life history theory, and illustrate the importance of monitoring survival as well as reproduction for understanding phenological responses to climate change.

Selection of Breeding Stock among Australian Purebred Dog Breeders, with Particular Emphasis on the Dam.

PubMed

Czerwinski, Veronika; McArthur, Michelle; Smith, Bradley; Hynd, Philip; Hazel, Susan

2016-11-16

Every year, thousands of purebred domestic dogs are bred by registered dog breeders. Yet, little is known about the rearing environment of these dogs, or the attitudes and priorities surrounding breeding practices of these dog breeders. The objective of this study was to explore some of the factors that dog breeders consider important for stock selection, with a particular emphasis on issues relating to the dam. Two-hundred and seventy-four Australian purebred dog breeders, covering 91 breeds across all Australian National Kennel Club breed groups, completed an online survey relating to breeding practices. Most breeders surveyed (76%) reported specialising in one breed of dog, the median number of dogs and bitches per breeder was two and three respectively, and most breeders bred two litters or less a year. We identified four components, relating to the dam, that were considered important to breeders. These were defined as Maternal Care, Offspring Potential, Dam Temperament, and Dam Genetics and Health. Overall, differences were observed in attitudes and beliefs across these components, showing that there is variation according to breed/breed groups. In particular, the importance of Maternal Care varied according to dog breed group. Breeders of brachycephalic breeds tended to differ the most in relation to Offspring Potential and Dam Genetics and Health. The number of breeding dogs/bitches influenced breeding priority, especially in relation to Dam Temperament, however no effect was found relating to the number of puppies bred each year. Only 24% of breeders used their own sire for breeding. The finding that some breeders did not test for diseases relevant to their breed, such as hip dysplasia in Labrador Retrievers and German Shepherds, provides important information on the need to educate some breeders, and also buyers of purebred puppies, that screening for significant diseases should occur. Further research into the selection of breeding dams and sires will inform future strategies to improve the health and behaviour of our best friend.

Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans.

PubMed

Ceh, E; Dovc, P

2014-08-01

Livestock guard dog (LGD) breeds from the Western Balkans are a good example of how complex genetic diversity pattern observed in dog breeds has been shaped by transition in dog breeding practices. Despite their common geographical origin and relatively recent formal recognition as separate breeds, the Karst Shepherd, Sarplaninac and Tornjak show distinct population dynamics, assessed by pedigree, microsatellite and mtDNA data. We genotyped 493 dogs belonging to five dog breeds using a set of 18 microsatellite markers and sequenced mtDNA from 94 dogs from these breeds. Different demographic histories of the Karst Shepherd and Tornjak breeds are reflected in the pedigree data with the former breed having more unbalanced contributions of major ancestors and a realized effective population size of less than 20 animals. The highest allelic richness was found in Sarplaninac (5.94), followed by Tornjak (5.72), whereas Karst Shepherd dogs exhibited the lowest allelic richness (3.33). Similarly, the highest mtDNA haplotype diversity was found in Sarplaninac, followed by Tornjak and Karst Shepherd, where only one haplotype was found. Based on FST differentiation values and high percentages of animals correctly assigned, all breeds can be considered genetically distinct. However, using microsatellite data, common ancestry between the Karst Shepherd and Sarplaninac could not be reconstructed, despite pedigree and mtDNA evidence of their historical admixture. Using neighbour-joining, STRUCTURE or DAPC methods, Sarplaninac and Caucasian Shepherd breeds could not be separated and additionally showed close proximity in the NeighborNet tree. STRUCTURE analysis of the Tornjak breed demonstrated substructuring, which needs further investigation. Altogether, results of this study show that the official separation of these dog breeds strongly affected the resolution of genetic differentiation and thus suggest that the relationships between breeds are not only determined by breed relatedness, but in small populations even more importantly by stochastic effects. © 2014 Blackwell Verlag GmbH.

Is that dog a pit bull? A cross-country comparison of perceptions of shelter workers regarding breed identification.

PubMed

Hoffman, Christy L; Harrison, Natalie; Wolff, London; Westgarth, Carri

2014-01-01

Bull breeds are commonly kept as companion animals, but the pit bull terrier is restricted by breed-specific legislation (BSL) in parts of the United States and throughout the United Kingdom. Shelter workers must decide which breed(s) a dog is. This decision may influence the dog's fate, particularly in places with BSL. In this study, shelter workers in the United States and United Kingdom were shown pictures of 20 dogs and were asked what breed each dog was, how they determined each dog's breed, whether each dog was a pit bull, and what they expected the fate of each dog to be. There was much variation in responses both between and within the United States and United Kingdom. UK participants frequently labeled dogs commonly considered by U.S. participants to be pit bulls as Staffordshire bull terriers. UK participants were more likely to say their shelters would euthanize dogs deemed to be pit bulls. Most participants noted using dogs' physical features to determine breed, and 41% affected by BSL indicated they would knowingly mislabel a dog of a restricted breed, presumably to increase the dog's adoption chances.

Differences in Trait Impulsivity Indicate Diversification of Dog Breeds into Working and Show Lines.

PubMed

Fadel, Fernanda Ruiz; Driscoll, Patricia; Pilot, Malgorzata; Wright, Hannah; Zulch, Helen; Mills, Daniel

2016-03-10

Impulsiveness describes the inability to inhibit behaviour in the presence of salient cues. Trait-level impulsivity exists on a continuum and individual differences can be adaptive in different contexts. While breed related differences in behavioural tendency in the domestic dog (Canis familiaris) are well established, the phenomenon within lines of a breed which have been selected more recently is not well studied, although it may challenge the popular notion of breed-typical behaviour. We describe differences in impulsivity between and within two dog breeds with working and show lines selected for different levels of impulsivity: Border Collies (herding work) and Labrador Retrievers (gun work). Recent show line selection might have lessened differences in impulsivity between breeds. We tested this hypothesis on a dataset of 1161 individuals assessed using a validated psychometric tool (Dog Impulsivity Assessment Scale--DIAS). Collies were more impulsive on average, consistent with the original purpose of breed selection. Regarding line, working Collies differed from working Labradors, but show lines from the two breeds were not significantly different. Altered or relaxed artificial selection for behavioural traits when appearance rather than behaviour become the primary focus for breeders may reduce average differences in impulsivity between breeds in show lines.

An exploratory analysis on how geographic, socioeconomic, and environmental drivers affect the diversity of livestock breeds worldwide.

PubMed

Leroy, G; Boettcher, P; Hoffmann, I; Mottet, A; Teillard, F; Baumung, R

2016-12-01

This study investigates the relationships between various environmental and geographic, demographic, and socioeconomic factors with the diversity of livestock breeds reported within countries across the world. Statistical analyses were performed considering the numbers of breeds reported by 158 countries for 4 livestock mammalian species (cattle, sheep, goats, and pigs). Organization for Economic Cooperation and Development (OECD) countries reported more breeds than non-OECD countries in general. Strong and positive correlations were found between agricultural area, human population size, species population size, and number of breeds per country. When considering regression models, the species population size was found as the most important explanatory factor for the number of breeds reported by countries in the 4 species. Diversity of production systems in the country had a significant association with the number of breeds reported for sheep, goats, and pigs. The number of ruminant breeds was positively associated with the size of agricultural area and the diversity of land cover in the country. While demographic and cultural importance of a given species is a major factor associated with the number of livestock breeds within countries, this diversity is also connected to the variability in environmental and production conditions.

Is That Dog a Pit Bull? A Cross-Country Comparison of Perceptions of Shelter Workers Regarding Breed Identification

PubMed Central

Hoffman, Christy L.; Harrison, Natalie; Wolff, London; Westgarth, Carri

2014-01-01

Bull breeds are commonly kept as companion animals, but the pit bull terrier is restricted by breed-specific legislation (BSL) in parts of the United States and throughout the United Kingdom. Shelter workers must decide which breed(s) a dog is. This decision may influence the dog's fate, particularly in places with BSL. In this study, shelter workers in the United States and United Kingdom were shown pictures of 20 dogs and were asked what breed each dog was, how they determined each dog's breed, whether each dog was a pit bull, and what they expected the fate of each dog to be. There was much variation in responses both between and within the United States and United Kingdom. UK participants frequently labeled dogs commonly considered by U.S. participants to be pit bulls as Staffordshire bull terriers. UK participants were more likely to say their shelters would euthanize dogs deemed to be pit bulls. Most participants noted using dogs' physical features to determine breed, and 41% affected by BSL indicated they would knowingly mislabel a dog of a restricted breed, presumably to increase the dog's adoption chances. PMID:24673506

Non-dietary risk factors for gastric dilatation-volvulus in large and giant breed dogs.

PubMed

Glickman, L T; Glickman, N W; Schellenberg, D B; Raghavan, M; Lee, T

2000-11-15

To identify non-dietary risk factors for gastric dilatation-volvulus (GDV) in large breed and giant breed dogs. Prospective cohort study. 1,637 dogs > or = 6 months old of the following breeds: Akita, Bloodhound, Collie, Great Dane, Irish Setter, Irish Wolfhound, Newfoundland, Rottweiler, Saint Bernard, Standard Poodle, and Weimaraner. Owners of dogs that did not have a history of GDV were recruited at dog shows, and the dog's length and height and the depth and width of its thorax and abdomen were measured. Information concerning the dog's medical history, genetic background, personality, and diet was obtained from the owners, and owners were contacted by mail and telephone at approximately 1-year intervals to determine whether dogs had developed GDV or died. Incidence of GDV, calculated on the basis of dog-years at risk for dogs that were or were not exposed to potential risk factors, was used to calculate the relative risk of GDV. Cumulative incidence of GDV during the study was 6% for large breed and giant breed dogs. Factors significantly associated with an increased risk of GDV were increasing age, having a first-degree relative with a history of GDV, having a faster speed of eating, and having a raised feeding bowl. Approximately 20 and 52% of cases of GDV among the large breed and giant breed dogs, respectively, were attributed to having a raised feed bowl.

Assessment of the seabird community of the Mozambique Channel and its potential use as an indicator of tuna abundance

NASA Astrophysics Data System (ADS)

Le Corre, Matthieu; Jaquemet, Sébastien

2005-05-01

Tropical seabirds are known to associate with aggregations of surface dwelling predators, like tunas when feeding. Some species are even regarded as near obligate commensals of tunas. As food is one of the main factors that shape breeding strategies and determine breeding success of seabirds, it is of interest to test the hypothesis that variations in tuna abundance may have effects on foraging success and thus on breeding parameters of tropical seabirds. The Mozambique Channel is appropriate for such a study because relative tuna abundance is assessed annually (through fishery catches) and seabird populations are abundant. A regional synopsis shows that at least 3.034 million pairs of seabirds breed on islands of the Mozambique Channel, 99.3% being sooty terns. This super-abundant seabird is strongly associated with tuna and marine mammals when feeding. More than 99% of the sooty tern population of the Mozambique Channel breeds at three remote coralline islands, namely Juan de Nova (66%), Europa (25%) and Glorieuses (9%). Various breeding parameters (breeding population size, breeding time, growth rate of the chicks, daily food intake, diet) are studied at these three sites in order to investigate their relation to the marine environment (including tuna abundance). A preliminary estimate is made of the quantity of food eaten by the sooty tern population.

Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population.

PubMed

Hozé, C; Fritz, S; Phocas, F; Boichard, D; Ducrocq, V; Croiseau, P

2014-01-01

Single-breed genomic selection (GS) based on medium single nucleotide polymorphism (SNP) density (~50,000; 50K) is now routinely implemented in several large cattle breeds. However, building large enough reference populations remains a challenge for many medium or small breeds. The high-density BovineHD BeadChip (HD chip; Illumina Inc., San Diego, CA) containing 777,609 SNP developed in 2010 is characterized by short-distance linkage disequilibrium expected to be maintained across breeds. Therefore, combining reference populations can be envisioned. A population of 1,869 influential ancestors from 3 dairy breeds (Holstein, Montbéliarde, and Normande) was genotyped with the HD chip. Using this sample, 50K genotypes were imputed within breed to high-density genotypes, leading to a large HD reference population. This population was used to develop a multi-breed genomic evaluation. The goal of this paper was to investigate the gain of multi-breed genomic evaluation for a small breed. The advantage of using a large breed (Normande in the present study) to mimic a small breed is the large potential validation population to compare alternative genomic selection approaches more reliably. In the Normande breed, 3 training sets were defined with 1,597, 404, and 198 bulls, and a unique validation set included the 394 youngest bulls. For each training set, estimated breeding values (EBV) were computed using pedigree-based BLUP, single-breed BayesC, or multi-breed BayesC for which the reference population was formed by any of the Normande training data sets and 4,989 Holstein and 1,788 Montbéliarde bulls. Phenotypes were standardized by within-breed genetic standard deviation, the proportion of polygenic variance was set to 30%, and the estimated number of SNP with a nonzero effect was about 7,000. The 2 genomic selection (GS) approaches were performed using either the 50K or HD genotypes. The correlations between EBV and observed daughter yield deviations (DYD) were computed for 6 traits and using the different prediction approaches. Compared with pedigree-based BLUP, the average gain in accuracy with GS in small populations was 0.057 for the single-breed and 0.086 for multi-breed approach. This gain was up to 0.193 and 0.209, respectively, with the large reference population. Improvement of EBV prediction due to the multi-breed evaluation was higher for animals not closely related to the reference population. In the case of a breed with a small reference population size, the increase in correlation due to multi-breed GS was 0.141 for bulls without their sire in reference population compared with 0.016 for bulls with their sire in reference population. These results demonstrate that multi-breed GS can contribute to increase genomic evaluation accuracy in small breeds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Co-breeding Association of Aedes albopictus (Skuse) and Aedes aegypti (Linnaeus) (Diptera: Culicidae) in Relation to Location and Container Size

PubMed Central

Hashim, Nur Aida; Ahmad, Abu Hassan; Talib, Anita; Athaillah, Farida; Krishnan, Kumara Thevan

2018-01-01

The occurrence of major outbreaks of dengue, and other vector borne diseases such as chikungunya and zika in tropical and subtropical regions has rendered control of the diseases a top-priority for many affected countries including Malaysia. Control of the mosquito vectors Aedes aegypti and Aedes albopictus through the reduction of breeding sites and the application of insecticides to kill immature forms and adults are the main control efforts to combat these diseases. The present study describes the association between Ae. albopictus and Ae. aegypti in shared breeding sites. This study is important given that any measure taken against one species may affect the other. A yearlong larval survey was conducted in four dengue endemic areas of Penang Island. Sorenson’s coefficient index indicated that no association between number of the immatures of the two species regardless of container size and study location. Therefore, the mean number Ae. albopictus immature was not decreased in the presence of Ae. aegypti in shared breeding container. However Ae. aegypti appeared to prefer breeding in habitats not occupied by Ae. albopictus, the two species sharing breeding sites only where available containers were limited. In control efforts, eliminating the preferred breeding containers for one species might not affect or reduce the population of the other species. PMID:29644025

Computer, Video, and Rapid-Cycling Plant Projects in an Undergraduate Plant Breeding Course.

ERIC Educational Resources Information Center

Michaels, T. E.

1993-01-01

Studies the perceived effectiveness of four student projects involving videotape production, computer conferencing, microcomputer simulation, and rapid-cycling Brassica breeding for undergraduate plant breeding students in two course offerings in consecutive years. Linking of the computer conferencing and video projects improved the rating of the…

Integration of DNA marker information into breeding value predictions

USDA-ARS?s Scientific Manuscript database

Calves from seven breeds including 20 herds were genotyped with a reduced DNA marker panel for weaning weight. The marker panel used was derived using USMARC Cycle VII animals. The results from the current study suggest marker effects are not robust across breeds and that methodology exists to integ...

Breeding bird communities

Treesearch

Vanessa L. Artman; Randy Dettmers

2003-01-01

Prescribed burning is being applied on an experimental basis to restore and maintain mixed-oak communities in southern Ohio. This chapter describes baseline conditions for the breeding bird community prior to prescribed burning. We surveyed breeding bird populations at four study areas using the territory-mapping method. We observed 35 bird species during the surveys....

Cow genotyping strategies for genomic selection in small dairy cattle population

USDA-ARS?s Scientific Manuscript database

This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds there are few sires with progeny records and genotyping cows can improve the accuracy of genomic EBV. The Guernsey bre...

PRELIMINARY ANALYSIS OF COMMON LOON GENETIC STRUCTURE IN NORTH AMERICA BASED ON FIVE MICROSATELLITE LOCI

EPA Science Inventory

This study seeks to determine fine-scale genetic structure of Common Loon breeding populations in order to link wintering birds with their breeding regions. Common Loons are large piscivorous birds that breed in lakes of northern North America and Iceland. Loons are highly phil...

Breed effect between Mos rooster (Galician indigenous breed) and Sasso T-44 line and finishing feed effect of commercial fodder or corn.

PubMed

Franco, D; Rois, D; Vázquez, J A; Purriños, L; González, R; Lorenzo, J M

2012-02-01

The aim of this research was to study the Mos rooster breed growth performance, carcass, and meat quality. The breed effect (Mos vs. Sasso T-44) and finishing feed in the last month (fodder vs. corn) on animal growth, carcass characteristics, meat quality, and fatty and amino acid profiles were studied using a randomized block design with initial weight as covariance. In total, 80 roosters (n = 30 of Sasso T-44 line and n = 50 of Mos breed) were used. They were separated by breed and allocated to 2 feeding treatment groups (concentrate and corn). Each feeding treatment group consisted of 15 and 25 roosters, for Sasso T-44 line and Mos breed, respectively. Finishing feeding did not affect growth parameters in the 2 genotypes of rooster tested (P > 0.05). Nonetheless, the comparison between both types of roosters led to significant differences in growth parameters (P < 0.05). Regarding carcass characteristics, no significant influences of finishing feeding treatment (P > 0.05) were found, and as expected, carcass weight clearly differed between genotypes due to the lower growth rate of Mos roosters. However, drumstick, thigh, and wing percentages were greater in the Mos breed than in the hybrid line. In color instrumental traits, roosters feeding with corn showed breast meat with significantly (P < 0.001) higher a* and b* values than those of cocks feeding with commercial fodder. Values of shear force were less than 2 kg for both genotypes, thus it can be classified as very tender meat. Finishing with corn significantly increased (P < 0.001) the polyunsaturated fatty acid content in the breast; the Mos breed had a polyunsaturated to saturated fatty acid ratio of 0.73. The amino acid profile of the indigenous breed was not similar to that of the commercial strain. Finishing feeding treatment had a greater influence than breed effect on amino acid profile.

Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip.

PubMed

Cañas-Álvarez, J J; González-Rodríguez, A; Munilla, S; Varona, L; Díaz, C; Baro, J A; Altarriba, J; Molina, A; Piedrafita, J

2015-11-01

The availability of SNP chips for massive genotyping has proven to be useful to genetically characterize populations of domestic cattle and to assess their degree of divergence. In this study, the Illumina BovineHD BeadChip genotyping array was used to describe the genetic variability and divergence among 7 important autochthonous Spanish beef cattle breeds. The within-breed genetic diversity, measured as the marker expected heterozygosity, was around 0.30, similar to other European cattle breeds. The analysis of molecular variance revealed that 94.22% of the total variance was explained by differences within individuals whereas only 4.46% was the result of differences among populations. The degree of genetic differentiation was small to moderate as the pairwise fixation index of genetic differentiation among breeds (F) estimates ranged from 0.026 to 0.068 and the Nei's D genetic distances ranged from 0.009 to 0.016. A neighbor joining (N-J) phylogenetic tree showed 2 main groups of breeds: Pirenaica, Bruna dels Pirineus, and Rubia Gallega on the one hand and Avileña-Negra Ibérica, Morucha, and Retinta on the other. In turn, Asturiana de los Valles occupied an independent and intermediate position. A principal component analysis (PCA) applied to a distance matrix based on marker identity by state, in which the first 2 axes explained up to 17.3% of the variance, showed a grouping of animals that was similar to the one observed in the N-J tree. Finally, a cluster analysis for ancestries allowed assigning all the individuals to the breed they belong to, although it revealed some degree of admixture among breeds. Our results indicate large within-breed diversity and a low degree of divergence among the autochthonous Spanish beef cattle breeds studied. Both N-J and PCA groupings fit quite well to the ancestral trunks from which the Spanish beef cattle breeds were supposed to derive.

Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N'Dama.

PubMed

Kim, Soo-Jin; Ka, Sojeong; Ha, Jung-Woo; Kim, Jaemin; Yoo, DongAhn; Kim, Kwondo; Lee, Hak-Kyo; Lim, Dajeong; Cho, Seoae; Hanotte, Olivier; Mwai, Okeyo Ally; Dessie, Tadelle; Kemp, Stephen; Oh, Sung Jong; Kim, Heebal

2017-05-12

Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied. We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N'Dama cattle. We analysed genetic variation patterns in N'Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N'Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N'Dama may engage in skeletal growth as well as immune systems. Our results imply that N'Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.

The effect of Lameness before and during the breeding season on fertility in 10 pasture-based Irish dairy herds.

PubMed

Somers, Joris R; Huxley, Jon; Lorenz, Ingrid; Doherty, Michael L; O'Grady, Luke

2015-01-01

The effects of lameness on fertility have been documented frequently but few data are available from seasonally breeding, pasture-based herds (such as those used in Ireland) where cows are housed during the winter months but managed at pasture for the remainder of the year. This study determined the prevalence of lameness in a group of 786 cows in 10 pasture-based Irish dairy herds before, during and after the breeding season and assessed the relationship between lameness and the reproductive performance in these herds through serial locomotion scoring during the grazing period. Lameness prevalences of 11.6 % before, 14.6 % during and 11.6 % after the breeding season were found and these compared favourably to results from housed cattle and are similar to other studies carried out in grazing herds. A Cox proportional hazards model with locomotion score as time varying covariate was used. After controlling for the effect of farm, month of calving, body condition score at calving, body condition score loss after calving and economic breeding index, cows identified as lame during the study were less likely to become pregnant. Cows lame before the earliest serve date but no longer lame during the breeding season, cows becoming lame after the earliest serve date and cows identified lame both before and after this date were respectively 12 %, 35 % and 38 % less likely to become pregnant compared to cows never observed lame during the study. However, these findings were only significant for cows becoming lame after the earliest serve date and cows lame both before and after the start of breeding. This study found that the reproductive efficiency was significantly (p < 0.05) lower in cows becoming lame during the breeding season and cows lame before and during the breeding season compared to non-lame cows. Cows no longer lame during the breeding season had a lower Submission Rate to first serve within 3 weeks of earliest serve date. However, the Pregnancy Rate was not significantly (p > 0.05) lower in these animals compared to cows never diagnosed as lame. In addition to lameness status, nutritional status and genetics were found to influence the reproductive performance in pasture-based Irish dairy herds.

Population-Wide Failure to Breed in the Clark's Nutcracker (Nucifraga columbiana).

PubMed

Schaming, Taza D

2015-01-01

In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark's nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark's nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark's nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark's nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.

Rethinking dog domestication by integrating genetics, archeology, and biogeography

PubMed Central

Larson, Greger; Karlsson, Elinor K.; Perri, Angela; Webster, Matthew T.; Ho, Simon Y. W.; Peters, Joris; Stahl, Peter W.; Piper, Philip J.; Lingaas, Frode; Fredholm, Merete; Comstock, Kenine E.; Modiano, Jaime F.; Schelling, Claude; Agoulnik, Alexander I.; Leegwater, Peter A.; Dobney, Keith; Vigne, Jean-Denis; Vilà, Carles; Andersson, Leif; Lindblad-Toh, Kerstin

2012-01-01

The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs with the geographic locations of 14 so-called “ancient” breeds (defined by their genetic differentiation) resulted in a counterintuitive pattern. First, none of the ancient breeds derive from regions where the oldest archeological remains have been found. Second, three of the ancient breeds (Basenjis, Dingoes, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog’s wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds is a lack of recent admixture with other breeds likely facilitated by geographic and cultural isolation. Furthermore, these genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins. We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication. PMID:22615366

Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.

PubMed

Wang, Yanan; Tang, Zhonglin; Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

2014-01-01

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.

Analysis of Genome-Wide Copy Number Variations in Chinese Indigenous and Western Pig Breeds by 60 K SNP Genotyping Arrays

PubMed Central

Sun, Yaqi; Wang, Hongyang; Wang, Chao; Yu, Shaobo; Liu, Jing; Zhang, Yu; Fan, Bin; Li, Kui; Liu, Bang

2014-01-01

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs. PMID:25198154

Mudskippers and Their Genetic Adaptations to an Amphibious Lifestyle.

PubMed

You, Xinxin; Sun, Min; Li, Jia; Bian, Chao; Chen, Jieming; Yi, Yunhai; Yu, Hui; Shi, Qiong

2018-02-07

Mudskippers are the largest group of amphibious teleost fish that are uniquely adapted to live on mudflats. During their successful transition from aqueous life to terrestrial living, these fish have evolved morphological and physiological modifications of aerial vision and olfaction, higher ammonia tolerance, aerial respiration, improved immunological defense against terrestrial pathogens, and terrestrial locomotion using protruded pectoral fins. Comparative genomic and transcriptomic data have been accumulated and analyzed for understanding molecular mechanisms of the terrestrial adaptations. Our current review provides a general introduction to mudskippers and recent research advances of their genetic adaptations to the amphibious lifestyle, which will be helpful for understanding the evolutionary transition of vertebrates from water to land. Our insights into the genomes and transcriptomes will also support molecular breeding, functional identification, and natural compound screening.

Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle.

PubMed

Judge, M M; Kelleher, M M; Kearney, J F; Sleator, R D; Berry, D P

2017-06-01

Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using 300 SNPs (selected using the global index method), the correlation between predicted and actual breed proportion was 0.993 and 0.995 in the Angus and Hereford validation populations, respectively. When SNP panels optimised for breed prediction in one population were used to predict the breed proportion of a separate population, the correlation between predicted and actual breed proportion was 0.034 and 0.044 weaker in the Hereford and Angus populations, respectively (using the 300 SNP panel). It is necessary to include at least 300 to 400 SNPs (per breed) on genotype panels to accurately predict breed proportion from biological samples.

Identification of the mutation causing progressive retinal atrophy in Old Danish Pointing Dog.

PubMed

Karlskov-Mortensen, P; Proschowsky, H F; Gao, F; Fredholm, M

2018-06-01

Progressive retinal atrophy (PRA) is a common cause of blindness in many dog breeds. It is most often inherited as a simple Mendelian trait, but great genetic heterogeneity has been demonstrated both within and between breeds. In many breeds the genetic cause of the disease is not known, and until now, the Old Danish Pointing Dog (ODP) has been one of those breeds. ODP is one of the oldest dog breeds in Europe. Seventy years ago the breed almost vanished, but today a population still exists, primarily in Denmark but with some dogs in Germany and Sweden. PRA has been diagnosed in ODP since the late 1990s. It resembles late onset PRA in other dog breeds, and it is inherited as an autosomal recessive trait. In the present study, we performed whole-genome sequencing and identified a single base insertion (c.3149_3150insC) in exon 1 of C17H2orf71. This is the same mutation previously found to cause PRA in Gordon Setters and Irish Setters, and it was later found in Tibetan Terrier, Standard Poodle and the Polski Owczarek Nizinny. The presence of the mutation in such a diverse range of breeds indicates an origin preceding creation of modern dog breeds. Hence, we screened 262 dogs from 44 different breeds plus four crossbred dogs, and can subsequently add Miniature Poodle and another polish sheepdog, the Polski Owczarek Podhalanski, to the list of affected breeds. © 2018 Stichting International Foundation for Animal Genetics.

Joint genomic evaluation of French dairy cattle breeds using multiple-trait models.

PubMed

Karoui, Sofiene; Carabaño, María Jesús; Díaz, Clara; Legarra, Andrés

2012-12-07

Using a multi-breed reference population might be a way of increasing the accuracy of genomic breeding values in small breeds. Models involving mixed-breed data do not take into account the fact that marker effects may differ among breeds. This study was aimed at investigating the impact on accuracy of increasing the number of genotyped candidates in the training set by using a multi-breed reference population, in contrast to single-breed genomic evaluations. Three traits (milk production, fat content and female fertility) were analyzed by genomic mixed linear models and Bayesian methodology. Three breeds of French dairy cattle were used: Holstein, Montbéliarde and Normande with 2976, 950 and 970 bulls in the training population, respectively and 964, 222 and 248 bulls in the validation population, respectively. All animals were genotyped with the Illumina Bovine SNP50 array. Accuracy of genomic breeding values was evaluated under three scenarios for the correlation of genomic breeding values between breeds (r(g)): uncorrelated (1), r(g) = 0; estimated r(g) (2); high, r(g) = 0.95 (3). Accuracy and bias of predictions obtained in the validation population with the multi-breed training set were assessed by the coefficient of determination (R(2)) and by the regression coefficient of daughter yield deviations of validation bulls on their predicted genomic breeding values, respectively. The genetic variation captured by the markers for each trait was similar to that estimated for routine pedigree-based genetic evaluation. Posterior means for rg ranged from -0.01 for fertility between Montbéliarde and Normande to 0.79 for milk yield between Montbéliarde and Holstein. Differences in R(2) between the three scenarios were notable only for fat content in the Montbéliarde breed: from 0.27 in scenario (1) to 0.33 in scenarios (2) and (3). Accuracies for fertility were lower than for other traits. Using a multi-breed reference population resulted in small or no increases in accuracy. Only the breed with a small data set and large genetic correlation with the breed with a large data set showed increased accuracy for the traits with moderate (milk) to high (fat content) heritability. No benefit was observed for fertility, a lowly heritable trait.

Estimation of test-day model (co)variance components across breeds using New Zealand dairy cattle data.

PubMed

Vanderick, S; Harris, B L; Pryce, J E; Gengler, N

2009-03-01

In New Zealand, a large proportion of cows are currently crossbreds, mostly Holstein-Friesians (HF) x Jersey (JE). The genetic evaluation system for milk yields is considering the same additive genetic effects for all breeds. The objective was to model different additive effects according to parental breeds to obtain first estimates of correlations among breed-specific effects and to study the usefulness of this type of random regression test-day model. Estimates of (co)variance components for purebred HF and JE cattle in purebred herds were computed by using a single-breed model. This analysis showed differences between the 2 breeds, with a greater variability in the HF breed. (Co)variance components for purebred HF and JE and crossbred HF x JE cattle were then estimated by using a complete multibreed model in which computations of complete across-breed (co)variances were simplified by correlating only eigenvectors for HF and JE random regressions of the same order as obtained from the single-breed analysis. Parameter estimates differed more strongly than expected between the single-breed and multibreed analyses, especially for JE. This could be due to differences between animals and management in purebred and non-purebred herds. In addition, the model used only partially accounted for heterosis. The multibreed analysis showed additive genetic differences between the HF and JE breeds, expressed as genetic correlations of additive effects in both breeds, especially in linear and quadratic Legendre polynomials (respectively, 0.807 and 0.604). The differences were small for overall milk production (0.926). Results showed that permanent environmental lactation curves were highly correlated across breeds; however, intraherd lactation curves were also affected by the breed-environment interaction. This result may indicate the existence of breed-specific competition effects that vary through the different lactation stages. In conclusion, a multibreed model similar to the one presented could optimally use the environmental and genetic parameters and provide breed-dependent additive breeding values. This model could also be a useful tool to evaluate crossbred dairy cattle populations like those in New Zealand. However, a routine evaluation would still require the development of an improved methodology. It would also be computationally very challenging because of the simultaneous presence of a large number of breeds.

Joint genomic evaluation of French dairy cattle breeds using multiple-trait models

PubMed Central

2012-01-01

Background Using a multi-breed reference population might be a way of increasing the accuracy of genomic breeding values in small breeds. Models involving mixed-breed data do not take into account the fact that marker effects may differ among breeds. This study was aimed at investigating the impact on accuracy of increasing the number of genotyped candidates in the training set by using a multi-breed reference population, in contrast to single-breed genomic evaluations. Methods Three traits (milk production, fat content and female fertility) were analyzed by genomic mixed linear models and Bayesian methodology. Three breeds of French dairy cattle were used: Holstein, Montbéliarde and Normande with 2976, 950 and 970 bulls in the training population, respectively and 964, 222 and 248 bulls in the validation population, respectively. All animals were genotyped with the Illumina Bovine SNP50 array. Accuracy of genomic breeding values was evaluated under three scenarios for the correlation of genomic breeding values between breeds (rg): uncorrelated (1), rg = 0; estimated rg (2); high, rg = 0.95 (3). Accuracy and bias of predictions obtained in the validation population with the multi-breed training set were assessed by the coefficient of determination (R2) and by the regression coefficient of daughter yield deviations of validation bulls on their predicted genomic breeding values, respectively. Results The genetic variation captured by the markers for each trait was similar to that estimated for routine pedigree-based genetic evaluation. Posterior means for rg ranged from −0.01 for fertility between Montbéliarde and Normande to 0.79 for milk yield between Montbéliarde and Holstein. Differences in R2 between the three scenarios were notable only for fat content in the Montbéliarde breed: from 0.27 in scenario (1) to 0.33 in scenarios (2) and (3). Accuracies for fertility were lower than for other traits. Conclusions Using a multi-breed reference population resulted in small or no increases in accuracy. Only the breed with a small data set and large genetic correlation with the breed with a large data set showed increased accuracy for the traits with moderate (milk) to high (fat content) heritability. No benefit was observed for fertility, a lowly heritable trait. PMID:23216664

Nucleotide Substitution in 3' Arm of Bovine MIR-2467 in Five Cattle Breeds.

PubMed

Łukaszewicz, Aneta; Basiak, Szymon; Proskura, Witold Stanisław; Dybus, Andrzej

2015-01-01

The T > C single nucleotide polymorphism (SNP) in the MIR2467 gene was investigated in order to confirm its presence in cattle genome and to check for possible differences in its genotype distribution among different breeds. Additional purpose of the study was to investigate in silico potential effect of that substitution on the structure and stability of precursor mir-2467. The study involved 634 individuals of five cattle breeds: Angus, Hereford, Holstein-Friesian, Jersey, and Limousin, which were genotyped using PCR-RFLP assay. In this study, the presence of T > C polymorphism at position 24 was observed in all the cattle breeds excepting Hereford. In addition, the differences in the genotype distribution among analyzed breeds were indicated. On the basis of minimum free energy structure prediction, the C allele was indicated to have possible impact on decreasing the stability of the pre-mir-2467, thus altering its ability to regulate target genes expression.

Integrating genomic selection into dairy cattle breeding programmes: a review.

PubMed

Bouquet, A; Juga, J

2013-05-01

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.

Validating the use of intrinsic markers in body feathers to identify inter-individual differences in non-breeding areas of northern fulmars.

PubMed

Quinn, Lucy R; Meharg, Andrew A; van Franeker, Jan A; Graham, Isla M; Thompson, Paul M

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ 13 C and δ 15 N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

The natural resources supply indexes study of the pig breeding scale in China

NASA Astrophysics Data System (ADS)

Leng, Bi-Bin; Zhang, Qi-Zhen; Ji, Xue-Qiang; Xu, Yue-Feng

2017-08-01

For the pollution problem of the pig breeding scale, we took three indexes as evaluation criterion, including arable land per capita, the water resource per capita and per capita share of grain. Then SPSS was used to synthesized the natural resources supply indexes of the pig breeding scale. The results show that with the fast development of technology and the steadily rising of grain production, the natural resources supply indexes of the pig breeding scale are raising constantly.

Production objectives, trait and breed preferences of farmers keeping N'Dama, Fulani Zebu and crossbred cattle and implications for breeding programs.

PubMed

Traoré, S A; Markemann, A; Reiber, C; Piepho, H P; Valle Zárate, A

2017-04-01

Many local livestock breeds in developing countries are being replaced by exotic breeds, leading to a loss of genetic resources. In southern Mali, for the past two decades, a trend towards increasing crossbreeding between the trypanotolerant N'Dama cattle and the trypano-susceptible Fulani Zebu cattle has been taking place. A survey with 160 farmers owning a cattle herd was carried out in southern Mali to investigate their production objectives, as well as trait and breed preferences and correlated socio-economic determinants in order to understand farmers' breeding decisions and to identify comparative advantages of three breed groups (N'Dama, Fulani Zebu and crossbreds) raised in the study area. Data were analyzed using an exploded logit model. The reasons for raising cattle, as well as trait and breed preferences reflected the multiple objectives of the farmers. Draught power and savings were the most important production objectives. Productive traits were ranked highest; farmers reported large body size as the most preferred trait, followed by fertility, draught ability and milk yield. Crossbreds were the favored breed group. Breed preferences were mainly explained by 'resistance to disease' for N'Dama cattle and 'high market price' for Fulani Zebu and crossbred cattle. Production objectives, trait and breed preferences were mainly influenced by farmer group (local farmers and settled transhumants). Local farmers put comparatively more emphasis on livestock functions linked to crop production such as draught power. They had a higher preference for traction ability as a selection trait and preferred N'Dama over Fulani Zebu cattle. Settled transhumants emphasized milk yield as a selection trait and preferred Fulani Zebu over N'Dama. The results indicate that the trend towards more crossbreeding will continue putting the N'Dama breed under high risk of genetic dilution in southern Mali. The N'Dama cattle remain a valuable breed due to their adaptive traits such as disease and drought tolerance and their good traction ability, fulfilling the diverse objectives of local farmers. Crossbreeding was found to be a promising breeding strategy, which might contribute to the maintenance of the local breed, provided that breeding schemes are thoroughly planned and organized.

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin.

PubMed

Di Lorenzo, Piera; Lancioni, Hovirag; Ceccobelli, Simone; Colli, Licia; Cardinali, Irene; Karsli, Taki; Capodiferro, Marco Rosario; Sahin, Emine; Ferretti, Luca; Ajmone Marsan, Paolo; Sarti, Francesca Maria; Lasagna, Emiliano; Panella, Francesco; Achilli, Alessandro

2018-01-01

Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.

PubMed

Metzger, Julia; Tonda, Raul; Beltran, Sergi; Agueda, Lídia; Gut, Marta; Distl, Ottmar

2014-07-04

Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

PubMed Central

Pareek, Chandra Shekhar; Błaszczyk, Paweł; Dziuba, Piotr; Czarnik, Urszula; Fraser, Leyland; Sobiech, Przemysław; Pierzchała, Mariusz; Feng, Yaping; Kadarmideen, Haja N.; Kumar, Dibyendu

2017-01-01

Background RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver tissue of young bulls of the Polish Red, Polish Holstein-Friesian (HF) and Hereford breeds, and to understand the genomic variation in the three cattle breeds that may reflect differences in production traits. Results The RNA-seq experiment on bovine liver produced 107,114,4072 raw paired-end reads, with an average of approximately 60 million paired-end reads per library. Breed-wise, a total of 345.06, 290.04 and 436.03 million paired-end reads were obtained from the Polish Red, Polish HF, and Hereford breeds, respectively. Burrows-Wheeler Aligner (BWA) read alignments showed that 81.35%, 82.81% and 84.21% of the mapped sequencing reads were properly paired to the Polish Red, Polish HF, and Hereford breeds, respectively. This study identified 5,641,401 SNPs and insertion and deletion (indel) positions expressed in the bovine liver with an average of 313,411 SNPs and indel per young bull. Following the removal of the indel mutations, a total of 195,3804, 152,7120 and 205,3184 raw SNPs expressed in bovine liver were identified for the Polish Red, Polish HF, and Hereford breeds, respectively. Breed-wise, three highly reliable breed-specific SNP-databases (SNP-dbs) with 31,562, 24,945 and 28,194 SNP records were constructed for the Polish Red, Polish HF, and Hereford breeds, respectively. Using a combination of stringent parameters of a minimum depth of ≥10 mapping reads that support the polymorphic nucleotide base and 100% SNP ratio, 4,368, 3,780 and 3,800 SNP records were detected in the Polish Red, Polish HF, and Hereford breeds, respectively. The SNP detections using RNA-seq data were successfully validated by kompetitive allele-specific PCR (KASPTM) SNP genotyping assay. The comprehensive QTL/CG analysis of 110 QTL/CG with RNA-seq data identified 20 monomorphic SNP hit loci (CARTPT, GAD1, GDF5, GHRH, GHRL, GRB10, IGFBPL1, IGFL1, LEP, LHX4, MC4R, MSTN, NKAIN1, PLAG1, POU1F1, SDR16C5, SH2B2, TOX, UCP3 and WNT10B) in all three cattle breeds. However, six SNP loci (CCSER1, GHR, KCNIP4, MTSS1, EGFR and NSMCE2) were identified as highly polymorphic among the cattle breeds. Conclusions This study identified breed-specific SNPs with greater SNP ratio and excellent mapping coverage, as well as monomorphic and highly polymorphic putative SNP loci within QTL/CGs of bovine liver tissue. A breed-specific SNP-db constructed for bovine liver yielded nearly six million SNPs. In addition, a KASPTM SNP genotyping assay, as a reliable cost-effective method, successfully validated the breed-specific putative SNPs originating from the RNA-seq experiments. PMID:28234981

Assigning breed origin to alleles in crossbred animals.

PubMed

Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

2016-08-22

For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns breed origin to alleles of crossbred animals, even if their pedigree is not recorded.

Founder representation and effective population size in old versus young breeds-genetic diversity of Finnish and Nordic Spitz.

PubMed

Kumpulainen, M; Anderson, H; Svevar, T; Kangasvuo, I; Donner, J; Pohjoismäki, J

2017-10-01

Finnish Spitz is 130-year-old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f a ) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis (N¯ec) is 168, whereas the genetic effective population size (N eg ) computed the decay of linkage disequilibrium (r 2 ) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz (N¯ec = 98 and N eg  = 49). Interestingly, the r 2 data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed. © 2017 Blackwell Verlag GmbH.

The use of SNP data for the monitoring of genetic diversity in cattle breeds

USDA-ARS?s Scientific Manuscript database

LD between SNPs contains information about effective population size. In this study, we investigate the use of genome-wide SNP data for marker based estimation of effective population size for two taurine cattle breeds of Africa and two local cattle breeds of Switzerland. Estimated recombination rat...

Breeding chronology and reproductive success of Richardson's merlins in southeastern Montana

Treesearch

Dale M. Becker; Carolyn Hull Sieg

1985-01-01

Breeding chronology and reproductive success of the Merlin (Falco columbarius richarsonii) were studied in southeastern Montana from 1978 - 1981. Breeding activity spanned 5 mo from the earliest observation of adults to the latest dispersal of adults and young from nesting areas. Clutch size, brood size and fledging success at active nests were...

Pigs in Toxicology: Breed Differences in Metabolism and Background Findings.

PubMed

Helke, Kristi L; Nelson, Keith N; Sargeant, Aaron M; Jacob, Binod; McKeag, Sean; Haruna, Julius; Vemireddi, Vimala; Greeley, Melanie; Brocksmith, Derek; Navratil, Nicole; Stricker-Krongrad, Alain; Hollinger, Charlotte

2016-06-01

Both a rodent and a nonrodent species are required for evaluation in nonclinical safety studies conducted to support human clinical trials. Historically, dogs and nonhuman primates have been the nonrodent species of choice. Swine, especially the miniature swine or minipigs, are increasingly being used in preclinical safety as an alternate nonrodent species. The pig is an appropriate option for these toxicology studies based on metabolic pathways utilized in xenobiotic biotransformation. Both similarities and differences exist in phase I and phase II biotransformation pathways between humans and pigs. There are numerous breeds of pigs, yet only a few of these breeds are characterized with regard to both xenobiotic-metabolizing enzymes and background pathology findings. Some specific differences in these enzymes based on breed and sex are known. Although swine have been used extensively in biomedical research, there is also a paucity of information in the current literature detailing the incidence of background lesions and differences between commonly used breeds. Here, the xenobiotic-metabolizing enzymes are compared between humans and pigs, and minipig background pathology changes are reviewed with emphasis on breed differences. © The Author(s) 2016.

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

PubMed Central

Xie, Weibo; Wang, Gongwei; Yuan, Meng; Yao, Wen; Lyu, Kai; Zhao, Hu; Yang, Meng; Li, Pingbo; Zhang, Xing; Yuan, Jing; Wang, Quanxiu; Liu, Fang; Dong, Huaxia; Zhang, Lejing; Li, Xinglei; Meng, Xiangzhou; Zhang, Wan; Xiong, Lizhong; He, Yuqing; Wang, Shiping; Yu, Sibin; Xu, Caiguo; Luo, Jie; Li, Xianghua; Xiao, Jinghua; Lian, Xingming; Zhang, Qifa

2015-01-01

Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement. PMID:26358652

A Qualitative Evidence of the Breeding Sites of Anopheles arabiensis Patton (Diptera: Culicidae) in and Around Kassala Town, Eastern Sudan

PubMed Central

Hamza, Asma Mahmoud; El Rayah, El Amin

2016-01-01

Anopheles arabiensis Patton (Diptera: Culicidae) is considered the most efficient malaria vector in eastern Sudan. This study aims to characterize the breeding sites of An. arabiensis throughout the year in and around Kassala town, eastern Sudan. Diverse larval habitat types were visited and characterized based on the habitat type and chemical composition. Mosquito larvae were found in many diverse habitats. During the rainy season, rain pools and water bodies created by the seasonal Gash River serve as the main breeding sites. In the dry season, irrigation canals, seepage from water pipes, neglected wells, artificial containers, and man-made ditches serve as the main breeding sites. Breeding water showed a pH of 7.9 and a low concentration of the total dissolved salts. The results of this study may be considered in planning and implementing larval control programs in the area. PMID:27547039

Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding.

PubMed

Teixeira da Silva, Jaime A; Jin, Xiaohua; Dobránszki, Judit; Lu, Jiangjie; Wang, Huizhong; Zotz, Gerhard; Cardoso, Jean Carlos; Zeng, Songjun

2016-02-01

Orchids of the genus Dendrobium are of great economic importance in global horticultural trade and in Asian traditional medicine. For both areas, research yielding solid information on taxonomy, phylogeny, and breeding of this genus are essential. Traditional morphological and cytological characterization are used in combination with molecular results in classification and identification. Markers may be useful when used alone but are not always reliable in identification. The number of species studied and identified by molecular markers is small at present. Conventional breeding methods are time-consuming and laborious. In the past two decades, promising advances have been made in taxonomy, phylogeny and breeding of Dendrobium species due to the intensive use of molecular markers. In this review, we focus on the main molecular techniques used in 121 published studies and discuss their importance and possibilities in speeding up the breeding of new cultivars and hybrids. Copyright © 2015 Elsevier Inc. All rights reserved.

Obesity in show dogs.

PubMed

Corbee, R J

2013-10-01

Obesity is an important disease with a growing incidence. Because obesity is related to several other diseases, and decreases life span, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain breeds is often suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, we investigated 1379 dogs of 128 different breeds by determining their body condition score (BCS). Overall, 18.6% of the show dogs had a BCS >5, and 1.1% of the show dogs had a BCS>7. There were significant differences between breeds, which could be correlated to the breed standards. It warrants firm discussions with breeders and judges in order to come to different interpretations of the standards to prevent overweight conditions from being the standard of beauty. © 2012 Blackwell Verlag GmbH.

Citrus breeding, genetics and genomics in Japan

PubMed Central

Omura, Mitsuo; Shimada, Takehiko

2016-01-01

Citrus is one of the most cultivated fruits in the world, and satsuma mandarin (Citrus unshiu Marc.) is a major cultivated citrus in Japan. Many excellent cultivars derived from satsuma mandarin have been released through the improvement of mandarins using a conventional breeding method. The citrus breeding program is a lengthy process owing to the long juvenility, and it is predicted that marker-assisted selection (MAS) will overcome the obstacle and improve the efficiency of conventional breeding methods. To promote citrus molecular breeding in Japan, a genetic mapping was initiated in 1987, and the experimental tools and resources necessary for citrus functional genomics have been developed in relation to the physiological analysis of satsuma mandarin. In this paper, we review the progress of citrus breeding and genome researches in Japan and report the studies on genetic mapping, expression sequence tag cataloguing, and molecular characterization of breeding characteristics, mainly in terms of the metabolism of bio-functional substances as well as factors relating to, for example, fruit quality, disease resistance, polyembryony, and flowering. PMID:27069387

Changing nest placement of Hawaiian Common Amakihi during the breeding cycle

USGS Publications Warehouse

van Riper, Charles; Kern, M. D.; Sogge, M. K.

1993-01-01

We studied the nesting behavior of the Common Amakihi (Hemignathus virens) from 1970-1981 on the island of Hawaii to determine if the species alters nest placement over a protracted 9-month breeding season. Birds preferentially chose the southwest quadrant of trees in which to build nests during all phases of the breeding season. It appeared that ambient temperature (Ta) was a contributing factor to differential nest placement between early and late phases of the annual breeding cycle. When Ta is low during the early (December-March) breeding period, Common Amakihi selected exposed nesting locations that benefitted them with maximum solar insolation. However, in the later phase of the breeding period (April-July) when Ta was much higher, renesting birds selected nest sites deeper in the canopy in significantly taller trees. This is one of the few documented examples in which a species changes location of nest during a breeding season, thus allowing exploitation of temporally differing microclimatic conditions.

Climatic effects on breeding grounds are more important drivers of breeding phenology in migrant birds than carry-over effects from wintering grounds.

PubMed

Ockendon, Nancy; Leech, Dave; Pearce-Higgins, James W

2013-01-01

Long-distance migrants may be particularly vulnerable to climate change on both wintering and breeding grounds. However, the relative importance of climatic variables at different stages of the annual cycle is poorly understood, even in well-studied Palaearctic migrant species. Using a national dataset spanning 46 years, we investigate the impact of wintering ground precipitation and breeding ground temperature on breeding phenology and clutch size of 19 UK migrants. Although both spring temperature and arid zone precipitation were significantly correlated with laying date, the former accounted for 3.5 times more inter-annual variation. Neither climate variable strongly affected clutch size. Thus, although carry-over effects had some impact, they were weaker drivers of reproductive traits than conditions on the breeding grounds.

Differences in Voluntary Cow Traffic between Holstein and Illawarra Breeds of Dairy Cattle in a Pasture-based Automatic Milking System

PubMed Central

Clark, C. E. F.; Kwinten, N. B. P.; van Gastel, D. A. J. M.; Kerrisk, K. L.; Lyons, N. A.; Garcia, S. C.

2014-01-01

Automatic milking systems (AMS) rely upon voluntary cow traffic (the voluntary movement of cattle around a farm) for milk harvesting and feed consumption. Previous research on conventional milking systems has shown differences between dairy cow breeds for intake and milk production, however, the ability to manipulate voluntary cow traffic and milking frequency on AMS farms through breed selection is unknown. This study investigated the effect of breed (Holstein Friesian versus Illawarra) on voluntary cow traffic as determined by gate passes at the Camden AMS research farm dairy facility. Daily data on days in milk, milk yield, gate passes and milking frequency for 158 Holstein Friesian cows and 24 Illawarra cows were collated by month for the 2007 and 2008 years. Illawarra cows had 9% more gate passes/day than Holstein cows over the duration of the study; however, the milking frequency and milk yield of both breeds were similar. Gate passes were greatest for both breeds in early lactation and in the winter (June to August) and summer (December to February) seasons. These findings highlight an opportunity to translate increased voluntary cow movement associated with breed selection into increased milking frequencies, milk production and overall pasture-based AMS performance. PMID:25049992

Serum enzymes levels and influencing factors in three indigenous Ethiopian goat breeds.

PubMed

Tibbo, M; Jibril, Y; Woldemeskel, M; Dawo, F; Aragaw, K; Rege, J E O

2008-12-01

Serum enzymes were studied in 163 apparently healthy goats from three indigenous goat breeds of Ethiopia. The effect of breed, age, sex and season on alanine aminotransferase (ALT) / glutamic pyruvic transaminase (GPT), aspartate aminotransferase (AST) / glutamic oxalacetic transaminases (GOT), alkaline phosphatase (ALP) and acid phosphatase (AcP) levels was assessed. The mean serum enzymes levels of the indigenous Arsi-Bale, Central Highland and Long-eared Somali goat breeds ranged from 14.0-20.2 iu L(-1) for ALT/GPT, from 43.2-49.3 iu L(-1) for AST/GOT, from 83.7-98.8 iu L(-1) for ALP, and from 2.99-4.23 iu L(-1) for AcP, were within the normal range for goats elsewhere. Breed had significant influence on AST/GOT values. Sex had significant effect on ALT/GPT for Arsi-Bale goats with higher values in males than females. Age was significant on all serum enzymes studied in the Arsi-Bale goats and on ALP in the Central Highland goats. Season had significant influence on all serum enzymes except for ALT/GPT in the Arsi-Bale goats. The serum enzyme levels of these indigenous goat breeds can be used as normal reference values for Ethiopian goat breeds adapted to similar agro-ecology and production system.

Differences in Voluntary Cow Traffic between Holstein and Illawarra Breeds of Dairy Cattle in a Pasture-based Automatic Milking System.

PubMed

Clark, C E F; Kwinten, N B P; van Gastel, D A J M; Kerrisk, K L; Lyons, N A; Garcia, S C

2014-04-01

Automatic milking systems (AMS) rely upon voluntary cow traffic (the voluntary movement of cattle around a farm) for milk harvesting and feed consumption. Previous research on conventional milking systems has shown differences between dairy cow breeds for intake and milk production, however, the ability to manipulate voluntary cow traffic and milking frequency on AMS farms through breed selection is unknown. This study investigated the effect of breed (Holstein Friesian versus Illawarra) on voluntary cow traffic as determined by gate passes at the Camden AMS research farm dairy facility. Daily data on days in milk, milk yield, gate passes and milking frequency for 158 Holstein Friesian cows and 24 Illawarra cows were collated by month for the 2007 and 2008 years. Illawarra cows had 9% more gate passes/day than Holstein cows over the duration of the study; however, the milking frequency and milk yield of both breeds were similar. Gate passes were greatest for both breeds in early lactation and in the winter (June to August) and summer (December to February) seasons. These findings highlight an opportunity to translate increased voluntary cow movement associated with breed selection into increased milking frequencies, milk production and overall pasture-based AMS performance.

Breed-specific incidence rates of canine primary bone tumors — A population based survey of dogs in Norway

PubMed Central

Anfinsen, Kristin P.; Grotmol, Tom; Bruland, Oyvind S.; Jonasdottir, Thora J.

2011-01-01

This is one of few published population-based studies describing breed specific rates of canine primary bone tumors. Incidence rates related to dog breeds could help clarify the impact of etiological factors such as birth weight, growth rate, and adult body weight/height on development of these tumors. The study population consisted of dogs within 4 large/giant breeds; Irish wolfhound (IW), Leonberger (LB), Newfoundland (NF), and Labrador retriever (LR), born between January 1st 1989 and December 31st 1998. Questionnaires distributed to owners of randomly selected dogs — fulfilling the criteria of breed, year of birth, and registration in the Norwegian Kennel Club — constituted the basis for this retrospective, population-based survey. Of the 3748 questionnaires received by owners, 1915 were completed, giving a response rate of 51%. Forty-three dogs had been diagnosed with primary bone tumors, based upon clinical examination and x-rays. The breeds IW and LB, with 126 and 72 cases per 10 000 dog years at risk (DYAR), respectively, had significantly higher incidence rates of primary bone tumors than NF and LR (P < 0.0001). Incidence rates for the latter were 11 and 2 cases per 10 000 DYAR, respectively. Pursuing a search for risk factors other than body size/weight is supported by the significantly different risks of developing primary bone tumors between similarly statured dogs, like NF and LB, observed in this study. Defining these breed-specific incidence rates enables subsequent case control studies, ultimately aiming to identify specific etiological factors for developing primary bone tumors. PMID:22210997

Toxoplasma gondii seroprevalence varies by cat breed.

PubMed

Must, Kärt; Hytönen, Marjo K; Orro, Toomas; Lohi, Hannes; Jokelainen, Pikka

2017-01-01

Toxoplasma gondii is a widespread zoonotic parasite that is relevant for veterinary and public health. The domestic cat, the definitive host species with the largest worldwide population, has become evolutionarily and epidemiologically the most important host of T. gondii. The outcome of T. gondii infection is influenced by congenital and acquired host characteristics. We detected differences in T. gondii seroprevalence by cat breed in our previous studies. The aims of this study were to estimate T. gondii seroprevalence in selected domestic cat breeds, and to evaluate whether being of a certain breed is associated with T. gondii seropositivity, when the age and lifestyle of the cat are taken into account. The studied breeds were the Birman, British Shorthair, Burmese, Korat, Norwegian Forest Cat, Ocicat, Persian, and Siamese. Plasma samples were analyzed for the presence of immunoglobulin G antibodies against T. gondii with a commercial direct agglutination test at dilution 1:40. The samples were accompanied by owner-completed questionnaires that provided background data on the cats. Overall, 41.12% of the 1121 cats tested seropositive, and the seroprevalence increased with age. The Burmese had the lowest seroprevalence (18.82%) and the Persian had the highest (60.00%). According to the final multivariable logistic regression model, the odds to test seropositive were four to seven times higher in Birmans, Ocicats, Norwegian Forest Cats, and Persians when compared with the Burmese, while older age and receiving raw meat were also risk factors for T. gondii seropositivity. This study showed that T. gondii seroprevalence varies by cat breed and identified being of certain breeds, older age, and receiving raw meat as risk factors for seropositivity.

From sport hunting to breeding success: Patterns of lead ammunition ingestion and its effects on an endangered raptor.

PubMed

Gil-Sánchez, José M; Molleda, Saray; Sánchez-Zapata, José A; Bautista, Jesús; Navas, Isabel; Godinho, Raquel; García-Fernández, Antonio J; Moleón, Marcos

2018-02-01

Lead is highly toxic for wildlife, with pernicious consequences especially in long-lived predators. The causes of lead ammunition ingestion in Bonelli's eagle (Aquila fasciata) and its effects on breeding success were studied in one of the most important populations of this endangered species in Europe. Regurgitated pellets belonging to different pairs from 2004 to 2014 were analyzed, both in the breeding (1363 pellets from 12 territories) and non-breeding (172 pellets from 9 territories) seasons. From these territories, 57 molted feathers to study lead contamination were analyzed, and breeding success was monitored for 41 breeding attempts. The occurrence of lead shots in pellets was detected using X-ray photographs. Pellets were also used to describe eagle diet. Lead shots in pellets were present in 83.3% of the territories. The frequency of occurrence of lead shots in pellets (2.81% in spring and 1.31% in autumn) was primarily related to the consumption of red-legged partridge in the breeding season (when partridges are hunted from blinds using calling lures), and secondarily to rabbit consumption in the non-breeding season (coinciding with the main hunting season). Thus, our results indicate that injured small-game were the main source of lead contamination in the Bonelli's eagle. For the first time for a raptor species, a positive relationship between the frequency of occurrence of lead shots in pellets and lead concentration in eagles' feathers has been documented. Lead concentration in feathers (mean±SD: 816±426μgkg -1 , with no sex-related differences) was high for a species that rarely eats carrion or aquatic birds (the main prey-related lead source for raptors). This had negative effects on breeding success, which could jeopardize Bonelli's eagles in other European populations that are sustained by juvenile dispersal from the study population. Our work shows that some game modalities pose a potential threat to endangered raptors. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic characterization, at the mitochondrial and nuclear DNA levels, of five Canary Island dog breeds.

PubMed

Suárez, N M; Betancor, E; Fregel, R; Pestano, J

2013-08-01

Many studies presenting genetic analysis of dog breeds have been conducted without the inclusion of island dog breeds, although isolation can be one of the main factors in their origin. Here we report the genetic analysis at the nuclear and mitochondrial DNA levels of five Canary Island dog breeds (Canarian Warren Hound, Canary Island Mastiff, Garafiano Shepherd, La Palma Rat-Hunter and El Hierro Wolfhound) to fill this gap and, at the same time, genetically characterize these breeds. We identified 168 alleles in autosomal microsatellites and 16 mitochondrial haplotypes. Observed and expected heterozygosities ranged from 0.556 to 0.783 and from 0.737 to 0.943 respectively. Furthermore, three haplotypes were newly described and exclusive to a particular breed (A17+ in the Canary Island Mastiff; A33+ in the Canarian Warren Hound; Bi in the La Palma Rat-Hunter). The outcome of our analyses also revealed different breed histories consistent with historical documents and hypothetical origin designations. Although mtDNA haplotypes showed poor breed discriminating power, autosomal markers allowed a clear clustering of each single population. We expect that our results, together with further analyses, will help to make the population histories of island dog breeds clearer. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

Short communication: casein haplotype variability in sicilian dairy goat breeds.

PubMed

Gigli, I; Maizon, D O; Riggio, V; Sardina, M T; Portolano, B

2008-09-01

In the Mediterranean region, goat milk production is an important economic activity. In the present study, 4 casein genes were genotyped in 5 Sicilian goat breeds to 1) identify casein haplotypes present in the Argentata dell'Etna, Girgentana, Messinese, Derivata di Siria, and Maltese goat breeds; and 2) describe the structure of the Sicilian goat breeds based on casein haplotypes and allele frequencies. In a sample of 540 dairy goats, 67 different haplotypes with frequency >or=0.01 and 27 with frequency >or=0.03 were observed. The most common CSN1S1-CSN2-CSN1S2-CSN3 haplotype for Derivata di Siria and Maltese was FCFB (0.17 and 0.22, respectively), whereas for Argentata dell'Etna, Girgentana and Messinese was ACAB (0.06, 0.23, and 0.10, respectively). According to the haplotype reconstruction, Argentata dell'Etna, Girgentana, and Messinese breeds presented the most favorable haplotype for cheese production, because the casein concentration in milk of these breeds might be greater than that in Derivata di Siria and Maltese breeds. Based on a cluster analysis, the breeds formed 2 main groups: Derivata di Siria, and Maltese in one group, and Argentata dell'Etna and Messinese in the other; the Girgentana breed was between these groups but closer to the latter.

Birds choose long-term partners years before breeding

USGS Publications Warehouse

Teitelbaum, Claire S.; Converse, Sarah J.; Mueller, Thomas

2017-01-01

Pair bonds can provide social benefits to long-term monogamous species alongside their benefits for reproduction. However, little is known about when these bonds form, in particular how long they are present before breeding. Previous studies of pair formation in long-term monogamous birds have been rather data-limited, but for many migratory birds they report pair formation on the wintering grounds. We provide the first systematic investigation of prebreeding association patterns of long-term monogamous pairs by examining entire life histories based on tracking data of migratory whooping cranes, Grus americana. We found that a substantial portion (62%) of breeding pairs started associating at least 12 months before first breeding, with 16 of 58 breeding pairs beginning to associate over 2 years before first breeding. For most pairs, these associations with future breeding partners also became unique and distinguishable from association patterns with nonpartner individuals 12 months before first breeding. In addition, 60% of pair associations began before at least one partner had reached nominal sexual maturity. Most pairs began associating in the late spring upon arrival at the summer grounds, while associations beginning at other times of the year were rare. Patterns in the associations of pairs prior to breeding can point to the potential benefits of prebreeding relationships, for instance providing support in competitive interactions or increasing partner familiarity.

Sudden acquired retinal degeneration in dogs: breed distribution of 495 canines.

PubMed

Heller, Amanda R; van der Woerdt, Alexandra; Gaarder, James E; Sapienza, John S; Hernandez-Merino, Elena; Abrams, Kenneth; Church, Melanie L; La Croix, Noelle

2017-03-01

The purpose of this study was to describe breed, age, gender, and weight distribution of dogs affected with sudden acquired retinal degeneration (SARD) and to investigate whether SARD is more common in small breed dogs. Medical records of dogs diagnosed with SARD confirmed by an electroretinogram were reviewed. Breed, age, gender, and weight were recorded when available. The same data were obtained for dogs with SARD described in the veterinary literature. Three hundred and two dogs were included from the ophthalmology practices and 193 dogs from the veterinary literature. Sixty breeds were present in the study. Mixed-breed dogs were the most common at 108 dogs (21.8%), followed by the Dachshund (68, 13.7%), Chinese Pug (44, 8.9%), Miniature Schnauzer (39, 7.9%), Maltese (23, 4.6%), Cocker Spaniel (22, 4.4%), Bichon Frise (18, 3.6%), Beagle (16, 3.2%), Brittany (15, 3.0%), and Pomeranian (10, 2.0%). Fifty other breeds were represented by 1-9 dogs each. The median age was 9 years (range = 10 months-16 years). The weight was known for 197 dogs. About 60.9% of dogs were less than 25 pounds, 31.5% were between 25 and 50 pounds, and 7.6% were greater than 50 pounds. Gender was recorded in 393 dogs: 217 female dogs and 176 male dogs. As previously reported, SARD is most common in middle-aged to older dogs. Smaller dogs of less than 25 pounds appear overrepresented, while large/giant breed dogs of greater than 50 pounds are infrequently diagnosed. In this study, there was no statistical significance between female and male dogs. © 2016 American College of Veterinary Ophthalmologists.

Effects of breed and feeding system on milk production, body weight, body condition score, reproductive performance, and postpartum ovarian function.

PubMed

Walsh, S; Buckley, F; Pierce, K; Byrne, N; Patton, J; Dillon, P

2008-11-01

The objective of this study was to investigate the potential differences among Holstein-Friesian (HF), Montbéliarde (MB), Normande (NM), Norwegian Red (NRF), Montbéliarde x Holstein-Friesian (MBX), and Normande x Holstein-Friesian (NMX) across 2 seasonal grass-based systems of milk production. The effects of breed and feeding system on milk production, body weight, body condition score, fertility performance, hormone parameters, ovarian function, and survival were determined by using mixed model methodology, generalized linear models, and survival analysis. The 5-yr study comprised up to 749 lactations on 309 cows in one research herd. The HF produced the greatest yield of solids-corrected milk, the MB and NM produced the least yields, and NRF, MBX, and NMX were intermediate. The NRF had the lowest body weight throughout lactation, the NM had the highest, and the other breeds were intermediate. Body condition score was greatest for MB and NM, least for HF, and intermediate for NRF, MBX, and NMX. The HF had a lower submission rate and overall pregnancy rate compared with the NRF. The NRF survived the longest in the herd, the HF survived the shortest, and the NM, MB, MBX, and NMX were intermediate. Breed of dairy cow had no effect on selected milk progesterone parameters from 5 d postpartum until 26 d after first artificial insemination. Breed of dairy cow did not influence insulin and insulin-like growth factor-1 around parturition or at the start of the breeding season. Animals offered a high-concentrate diet had greater milk yield, but they did not have improved reproductive performance. Differences observed between the different breeds in this study are a likely consequence of the past selection criteria for the respective breeds.

The Effects of Habitat Type and Volcanic Eruptions on the Breeding Demography of Icelandic Whimbrels Numenius phaeopus.

PubMed

Katrínardóttir, Borgný; Alves, José A; Sigurjónsdóttir, Hrefna; Hersteinsson, Páll; Gunnarsson, Tómas G

2015-01-01

Distinct preference of species for habitats is most often driven by long term differences in demographic rates between habitats. Estimating variation in those rates is key for developing successful conservation strategies. Stochastic events can interact with underlying variation in habitat quality in regulating demography but the opportunities to explore such interactions are rare. Whimbrels in Iceland show a strong preference for sparsely vegetated riverplains. Such habitats in Iceland face various threats, e.g., climate change, river regulation and spread of alien plant species. In this study we compared demographic parameters of breeding Whimbrels between riverplains and other habitats before, during and after volcanic eruption events to estimate the importance of the habitats for the species and the effect of ash deposit on breeding success. We found that an estimated minimum of 23% of the Icelandic population of Whimbrels and c. 10% of the world population of the species breed in riverplain habitats in Iceland. Whimbrels bred consistently at much higher densities in riverplain habitats than in other habitats and riverplains also had higher densities of pairs with fledglings although the proportion of successful breeders was similar between habitats. Predation by livestock may have had a considerable negative effect on breeding success on our study sites. Breeding was negatively affected by the volcanic activity, probably through the effects of ash on the invertebrate food supply, with breeding success being gradually worse closer to the eruption. Breeding success was equally affected by volcanism across habitats which differed in underlying habitat quality. This study gives an example of how populations can be regulated by factors which operate at different spatial scales, such as local variation in habitat quality and stochastic events which impact larger areas.

Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency

PubMed Central

Li, Y. H.; Chu, H. P.; Jiang, Y. N.; Lin, C. Y.; Li, S. H.; Li, K. T.; Weng, G. J.; Cheng, C. C.; Lu, D. J.; Ju, Y. T.

2014-01-01

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu’s inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations. PMID:25049996

A comparison of two collection methods for estimating abundance and parity of Anopheles albimanus in breeding sites and villages of southern Mexico.

PubMed

Ulloa, A; Rodríguez, M H; Rodríguez, A D; Roberts, D R

1997-09-01

The abundance and age structure of Anopheles albimanus populations were estimated by UV updraft light traps and human landing catches within villages and in nearby breeding sites of southern México. Four villages and 5 breeding sites were selected for the study. Light trap and human landing catches were simultaneously carried out in each breeding site and each village. Anopheles albimanus was the most abundant malaria vector caught in breeding sites and in villages. Significant differences in overall An. albimanus abundance among villages and among breeding sites were detected only by human landing catches. In both villages and breeding sites, more mosquitoes were captured by 1 human bait (34.3 +/- 6.3 and 14.6 +/- 2.9, respectively) than by one light trap (15.9 +/- 3.3 and 2.4 +/- 0.3 respectively) collection. After pooling, no significant differences were detected in the abundance estimated by each method in breeding sites and villages. A significant correlation of numbers of specimens between methods was detected. Age structure was different between samples from breeding sites and villages, with more gravid females collected in breeding sites, whereas more nulipars were collected in villages. By collection method, age structure was also different both in breeding sites and in villages. In breeding sites, the percentage of parous females was significantly higher in human landing catches, whereas the percentage of gravid females was significantly higher in light traps. In villages, only the percentage of gravid females was significantly higher in light traps. Our results suggests that UV light traps could be used to measure several entomological parameters of An. albimanus populations because both abundance variations and parity rates were similarly detected by both methods.

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding, extensive loss of genetic diversity and lack of correlation between inbreeding and health.

PubMed

Jansson, M; Laikre, L

2014-04-01

One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid-20th century and comprise 5-10 generations and 1 000-50 000 individuals per pedigree over our study period of 1980-2010. We compared levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals during this period in the investigated dog breeds that we classified as 'healthy' (11 breeds) or 'unhealthy' (15) based on statistics on the extent of veterinary care obtained from Sweden's four largest insurance companies for pets. We found extensive loss of genetic variation and moderate levels of recent inbreeding in all breeds examined, but no strong indication of a difference in these parameters between healthy versus unhealthy breeds over this period. Thus, recent breeding history with respect to rate of inbreeding does not appear to be a main cause of poor health in the investigated dog breeds in Sweden. We identified both strengths and weaknesses of the dog pedigree data important to consider in future work of monitoring and conserving genetic diversity of dog breeds. © 2013 The Authors Journal of Animal Breeding and Genetics Published by Blackwell Verlag GmbH.

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

PubMed

Sudrajad, P; Seo, D W; Choi, T J; Park, B H; Roh, S H; Jung, W Y; Lee, S S; Lee, J H; Kim, S; Lee, S H

2017-02-01

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. © 2016 Stichting International Foundation for Animal Genetics.

PrP genotype frequencies and risk evaluation for scrapie in dairy sheep breeds from southern Italy.

PubMed

Martemucci, Giovanni; Iamartino, Daniela; Blasi, Michele; D'Alessandro, Angela Gabriella

2015-12-01

Concerns regarding scrapie in sheep breeding have increased in the last few decades. The present study was carried out in dairy sheep breeds from southern Italy. In order to find breeding animals resistant to scrapie, the PrP genes of 1,205 animals from entire flocks of dairy native Apulian Leccese and Altamurana breeds, and Sicilian Comisana breed, were analysed for polymorphisms at codons 136, 154, and 171 related to scrapie resistance/susceptibility. The Altamurana breed was considered as two populations (Alt-Cav and Alt-Cra-Zoe), based on presumed cross-breeding. A total of five alleles and ten different genotypes were found. The ARQ allele was predominant for all breeds followed by ARR, the most resistant allele to scrapie, which was highly prevalent in Comisana (50%) and in native Alt-Cav (42.4%). The VRQ allele, associated with the highest susceptibility to scrapie, was detected at not negligeable levels in allocthonous Comisana (3.5%), at a low frequency (0.2%) in native Leccese and Alt-Cra-Zoe, while it was absent in Alt-Cav. The frequencies of PrP genotypes with a very low susceptibility risk to scrapie (R1) was higher in Comisana and Alt-Cav. The most susceptible genotype, ARQ/VRQ, was found only in Comisana. Within the Altamurana breed, there were notable differences between Alt-Cav and Alt-Cra-Zoe sheep. The Alt-Cav was characterised by the absence of VRQ and AHQ alleles and by the higher frequency of the ARR/ARR genotype (18.7%). Breeding programs, mainly in endangered breeds such as Altamurana, should be conducted gradually, combining resistance to scrapie, maintenance of genetic variability, and production. Copyright © 2015 Elsevier B.V. All rights reserved.

Population-Wide Failure to Breed in the Clark’s Nutcracker (Nucifraga columbiana)

PubMed Central

Schaming, Taza D.

2015-01-01

In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark’s nutcrackers (Nucifraga Columbiana) in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark’s nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis) cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years) and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years). The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1), a nonbreeding year, as compared to 2012 (6.2 ± 2.0), a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark’s nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark’s nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences. PMID:25970294

Advances and Challenges in Genomic Selection for Disease Resistance.

PubMed

Poland, Jesse; Rutkoski, Jessica

2016-08-04

Breeding for disease resistance is a central focus of plant breeding programs, as any successful variety must have the complete package of high yield, disease resistance, agronomic performance, and end-use quality. With the need to accelerate the development of improved varieties, genomics-assisted breeding is becoming an important tool in breeding programs. With marker-assisted selection, there has been success in breeding for disease resistance; however, much of this work and research has focused on identifying, mapping, and selecting for major resistance genes that tend to be highly effective but vulnerable to breakdown with rapid changes in pathogen races. In contrast, breeding for minor-gene quantitative resistance tends to produce more durable varieties but is a more challenging breeding objective. As the genetic architecture of resistance shifts from single major R genes to a diffused architecture of many minor genes, the best approach for molecular breeding will shift from marker-assisted selection to genomic selection. Genomics-assisted breeding for quantitative resistance will therefore necessitate whole-genome prediction models and selection methodology as implemented for classical complex traits such as yield. Here, we examine multiple case studies testing whole-genome prediction models and genomic selection for disease resistance. In general, whole-genome models for disease resistance can produce prediction accuracy suitable for application in breeding. These models also largely outperform multiple linear regression as would be applied in marker-assisted selection. With the implementation of genomic selection for yield and other agronomic traits, whole-genome marker profiles will be available for the entire set of breeding lines, enabling genomic selection for disease at no additional direct cost. In this context, the scope of implementing genomics selection for disease resistance, and specifically for quantitative resistance and quarantined pathogens, becomes a tractable and powerful approach in breeding programs.

An Age-Associated Decline in Thymic Output Differs in Dog Breeds According to Their Longevity.

PubMed

Holder, Angela; Mella, Stephanie; Palmer, Donald B; Aspinall, Richard; Catchpole, Brian

2016-01-01

The age associated decline in immune function is preceded in mammals by a reduction in thymic output. Furthermore, there is increasing evidence of a link between immune competence and lifespan. One approach to determining thymic output is to quantify signal joint T cell receptor excision circles (sj-TRECs), a method which has been developed and used in several mammalian species. Life expectancy and the rate of aging vary in dogs depending upon their breed. In this study, we quantified sj-TRECs in blood samples from dogs of selected breeds to determine whether there was a relationship between longevity and thymic output. In Labrador retrievers, a breed with a median expected lifespan of 11 years, there was an age-associated decline in sj-TREC values, with the greatest decline occurring before 5 years of age, but with sj-TREC still detectable in some geriatric animals, over 13 years of age. In large short-lived breeds (Burnese mountain dogs, Great Danes and Dogue de Bordeaux), the decline in sj-TREC values began earlier in life, compared with small long-lived breeds (Jack Russell terriers and Yorkshire terriers), and the presence of animals with undetectable sj-TRECs occurred at a younger age in the short-lived breeds. The study findings suggest that age-associated changes in canine sj-TRECs are related to breed differences in longevity, and this research highlights the use of dogs as a potential model of immunosenescence.

First satellite tracks of the Endangered black-capped petrel

USGS Publications Warehouse

Jodice, Patrick G.R.; Ronconi, Robert A.; Rupp, Ernst; Wallace, George E.; Satgé, Yvan

2015-01-01

The black-capped petrel Pterodroma hasitata is an endangered seabird with fewer than 2000 breeding pairs restricted to a few breeding sites in Haiti and the Dominican Republic. To date, use areas at sea have been determined entirely from vessel-based surveys and opportunistic sightings and, as such, spatial and temporal gaps in our understanding of the species’ marine range are likely. To enhance our understanding of marine use areas, we deployed satellite tags on 3 black-capped petrels breeding on Hispaniola, representing the first tracking study for this species and one of the first published tracking studies for any breeding seabird in the Caribbean. During chick rearing, petrels primarily used marine habitats in the southern Caribbean Sea (ca. 18.0° to 11.5°N, 70.0° to 75.5°W) between the breeding site and the coasts of Venezuela and Colombia. Maximum distance from the breeding sites ranged from ca. 500 to 1500 km during the chick-rearing period. During the post-breeding period, each bird dispersed north and used waters west of the Gulf Stream offshore of the mid- and southern Atlantic coasts of the USA as well as Gulf Stream waters and deeper pelagic waters east of the Gulf Stream. Maximum distance from the breeding sites ranged from ca. 2000 to 2200 km among birds during the nonbreeding period. Petrels used waters located within 14 different exclusive economic zones, suggesting that international collaboration will benefit the development of management strategies for this species.

Dog sperm head morphometry: its diversity and evolution

PubMed Central

Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

2017-01-01

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds’ sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics. PMID:27751991

Wayward youth: Trans-Beringian movement and differential southward migration by juvenile sharp-tailed sandpipers

USGS Publications Warehouse

Handel, Colleen M.; Gill, Robert E.

2010-01-01

The sharp-tailed sandpiper (Calidris acuminata) is a long-distance migrant that travels each year from breeding grounds in the Russian Arctic to nonbreeding areas in Australasia. Most adults migrate rapidly from breeding grounds along a largely inland route through Asia. Here we report on the highly unusual migratory strategy of this species in which some juveniles, but virtually no adults, take a pronounced detour to western Alaska before proceeding on southward migration. We analyzed data from our own studies in this region and published and unpublished observations and specimen records of sharp-tailed sandpipers from the entire Pacific Basin. Each autumn, sharp-tailed sandpipers began arriving on coastal graminoid meadows and intertidal habitats throughout western Alaska during the last half of August and the last sandpipers departed from southwestern Alaska during October and November. Body mass of birds banded or collected across multiple years and sites in western Alaska (n = 330) increased by an average of 0.57 ± 0.06 g per day between mid-August and late October. Records suggest a small, regular movement of juveniles (and a very few adults) along the Asiatic coast, but we estimate from surveys that a few tens of thousands of juveniles stage in western Alaska each autumn. The distribution of sight and specimen records from the Pacific Basin during autumn suggests strongly age-segregated migration routes, with the principal migration of juveniles crossing central and western Oceania in a possible nonstop trans-Pacific flight from Alaska. This is only the second well-documented case of differential migration among birds that involves different routes for adults and juveniles, and it raises intriguing questions about how and why this system has evolved.

Phylogeography of a Habitat Specialist with High Dispersal Capability: The Savi’s Warbler Locustella luscinioides

PubMed Central

Neto, Júlio M.; Arroyo, José L.; Bargain, Bruno; Monrós, Juan S.; Mátrai, Norbert; Procházka, Petr; Zehtindjiev, Pavel

2012-01-01

In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi’s Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi’s Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in the Balkans and is currently widespread, showing strong evidence for population expansion; whereas the other is restricted to Iberia and remained stable. Microsatellites agreed with a genetic break around the Pyrenees, but showed considerable introgression and a weaker genetic structure. Both genetic markers showed an isolation-by-distance pattern associated with the population expansion of the eastern clade. Breeding populations seem to be segregated at the wintering sites, but results on migratory connectivity are preliminary. Savi’s Warbler is the only known migratory bird species in which Iberian birds did not expand beyond the Pyrenees after the last glaciation. Despite the long period of independent evolution of western and eastern populations, complete introgression occurred when these groups met in Iberia. Mitochondrial sequences indicated the existence of refugia-within-refugia in the Iberian Peninsula during the last glacial period, which is surprising given the high dispersal capacity of this species. Plumage differences of eastern subspecies seemed to have evolved recently through natural selection, in agreement with the glacial expansion hypothesis. This study supports the great importance of the Iberian Peninsula and its role for the conservation of genetic variation. PMID:22701653

Wayward youth: Trans-Beringian movement and differential southward migration by Juvenile sharp-tailed sandpipers

USGS Publications Warehouse

Handel, C.M.; Gill, R.E.

2010-01-01

The sharp-tailed sandpiper (Calidris acuminata) is a long-distance migrant that travels each year from breeding grounds in the Russian Arctic to nonbreeding areas in Australasia. Most adults migrate rapidly from breeding grounds along a largely inland route through Asia. Here we report on the highly unusual migratory strategy of this species in which some juveniles, but virtually no adults, take a pronounced detour to western Alaska before proceeding on southward migration. We analyzed data from our own studies in this region and published and unpublished observations and specimen records of sharptailed sandpipers from the entire Pacific Basin. Each autumn, sharp-tailed sandpipers began arriving on coastal graminoid meadows and intertidal habitats throughout western Alaska during the last half of August and the last sandpipers departed from southwestern Alaska during October and November. Body mass of birds banded or collected across multiple years and sites in western Alaska (n = 330) increased by an average of 0.57 ?? 0.06 g per day between mid-August and late October. Records suggest a small, regular movement of juveniles (and a very few adults) along the Asiatic coast, but we estimate from surveys that a few tens of thousands of juveniles stage in western Alaska each autumn. The distribution of sight and specimen records from the Pacific Basin during autumn suggests strongly age-segregated migration routes, with the principal migration of juveniles crossing central and western Oceania in a possible nonstop trans-Pacific flight from Alaska. This is only the second well-documented case of differential migration among birds that involves different routes for adults and juveniles, and it raises intriguing questions about how and why this system has evolved. ?? The Arctic Institute of North America.

Ecology of the Ostracode Loxoconcha in Chesapeake Bay: Application to Shell Chemistry Calibration

NASA Astrophysics Data System (ADS)

Vann, C. D.; Cronin, T. M.; Dwyer, G. S.

2001-12-01

The successful application of magnesium/calcium ratios (Mg/Ca) of ostracode shells to paleothermometry depends on understanding both the factors controlling the uptake of Mg into the ostracode calcitic shell and the species' seasonal ecology, which determines the time of year when adult molting occurs. Loxoconcha, a cosmopolitan shallow-water ostracode genus that evolved in the Paleogene, includes more than 500 extant species, many inhabiting temperate regions, making it a potentially valuable tool in Cenozoic paleothermometry. We studied the population ecology of Loxoconcha matagordensis, an epiphytal species common in bays and estuaries along the Atlantic and Gulf Coasts of North America, for application to Holocene paleoclimatology in temperate coastal regions. L. matagordensis populations collected from Zostera marina beds in Chesapeake Bay (N 37° 47'4.3", W 76° 17'44.4"; N 37° 47'4.5", W 76° 17'31.0") show that its population dynamics and Zostera height appear to be regulated primarily by seasonal oscillations in water temperature. As water temperature increased from 14.8° to 24.6° C between April and July 2001, a spring breeding season occurred shifting the age structure of the Loxoconcha population from an entirely adult population (individuals that wintered over) to a predominately juvenile population comprised of all eight growth (molt) stages. Most new adults secreted their shells during May and June, although in some years, a second breeding season may occur in late August/September. Other temperate species of this genus also appear to have spring/early summer adult shell growth. Our results suggest that the Mg/Ca ratios from Holocene adult shells of Loxoconcha obtained from sediment cores provide a record of late spring/early summer water temperature variability linked to decadal and centennial climate processes.

Application of genomic selection in farm animal breeding.

PubMed

Tan, Cheng; Bian, Cheng; Yang, Da; Li, Ning; Wu, Zhen-Fang; Hu, Xiao-Xiang

2017-11-20

Genomic selection (GS) has become a widely accepted method in animal breeding to genetically improve economic traits. With the declining costs of high-density SNP chips and next-generation sequencing, GS has been applied in dairy cattle, swine, poultry and other animals and gained varying degrees of success. Currently, major challenges in GS studies include further reducing the cost of genome-wide SNP genotyping and improving the predictive accuracy of genomic estimated breeding value (GEBV). In this review, we summarize various methods for genome-wide SNP genotyping and GEBV prediction, and give a brief introduction of GS in livestock and poultry breeding. This review will provide a reference for further implementation of GS in farm animal breeding.

Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data.

PubMed

Mao, X; Sahana, G; De Koning, D-J; Guldbrandtsen, B

2016-04-01

Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins ( = 5,519), Jerseys ( = 1,231), and Red Dairy Cattle ( = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; -value = 2.8 × 10) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene , which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.

Metabolic rate and environmental productivity: Well-provisioned animals evolved to run and idle fast

PubMed Central

Mueller, Pamela; Diamond, Jared

2001-01-01

Even among vertebrate species of the same body mass and higher-level taxonomic group, metabolic rates exhibit substantial differences, for which diverse explanatory factors—such as dietary energy content, latitude, altitude, temperature, and rainfall—have been postulated. A unifying underlying factor could be food availability, in turn controlled by net primary productivity (NPP) of the animal's natural environment. We tested this possibility by studying five North American species of Peromyscus mice, all of them similar in diet (generalist omnivores) and in gut morphology but differing by factors of up to 13 in NPP of their habitat of origin. We maintained breeding colonies of all five species in the laboratory under identical conditions and consuming identical diets. Basal metabolic rate (BMR) and daily ad libitum food intake both increased with NPP, which explained 88% and 90% of their variances, respectively. High-metabolism mouse species from high-NPP environments were behaviorally more active than were low-metabolism species from low-NPP environments. Intestinal glucose uptake capacity also increased with NPP (and with BMR and food intake), because species of high-NPP environments had larger small intestines and higher uptake rates. For metabolic rates of our five species, the driving environmental variable is environmental productivity itself (and hence food availability), rather than temporal variability of productivity. Thus, species that have evolved in the presence of abundant food run their metabolism “fast,” both while active and while idling, as compared with species of less productive environments, even when all species are given access to unlimited food. PMID:11606744

Deconstructing sociality, social evolution and relevant nonapeptide functions.

PubMed

Goodson, James L

2013-04-01

Although behavioral neuroendocrinologists often discuss "sociality" as a unitary variable, the term encompasses a wide diversity of behaviors that do not evolve in a linked fashion across species. Thus grouping, monogamy, paternal care, cooperative breeding/alloparental care, and various other forms of social contact are evolutionarily labile and evolve in an almost cafeteria-like fashion, indicating that relevant neural mechanisms are at least partially dissociable. This poses a challenge for the study of the nonapeptides (vasopressin, oxytocin, and homologous neuropeptides), because nonapeptides are known to modulate all of these aspects of sociality in one species or another. Hence, we may expect substantial diversity in the behavioral functions of nonapeptides across species, and indeed this is the case. Further compounding this complexity is the fact that the pleiotropic contributions of nonapeptides to social behavior are matched by pleiotropic contributions to physiology. Given these considerations, single "model systems" approaches to nonapeptide function will likely not have strong predictive validity for humans or other species. Rather, if we are to achieve predictive validity, we must sample a wide diversity of species in an attempt to derive general principles. In the present review, I discuss what is known about functional evolution of nonapeptide systems, and critically evaluate general assumptions about bonding and other functions that are based on the model systems approach. From this analysis I attempt to summarize what can and cannot be generalized across species, and highlight critical gaps in our knowledge about the functional evolution of nonapeptide systems as it relates to dimensions of sociality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Experimental and observational evidence reveals that predators in natural environments do not regulate their prey: They are passengers, not drivers

NASA Astrophysics Data System (ADS)

White, T. C. R.

2013-11-01

Among both ecologists and the wider community there is a tacit assumption that predators regulate populations of their prey. But there is evidence from a wide taxonomic and geographic range of studies that predators that are adapted to co-evolved prey generally do not regulate their prey. This is because predators either cannot reproduce as fast as their prey and/or are inefficient hunters unable to catch enough prey to sustain maximum reproduction. The greater capacity of herbivores to breed successfully is, however, normally restricted by a lack of enough food of sufficient quality to support reproduction. But whenever this shortage is alleviated by a large pulse of food, herbivores increase their numbers to outbreak levels. Their predators are unable to contain this increase, but their numbers, too, surge in response to this increase in food. Eventually both their populations will crash once the food supply runs out, first for the herbivores and then for the predators. Then an “over-run” of predators will further depress the already declining prey population, appearing to be controlling its abundance. This latter phenomenon has led many ecologists to conclude that predators are regulating the numbers of their prey. However, it is the same process that is revealed during outbreaks that limits populations of both predator and prey in “normal” times, although this is usually not readily apparent. Nevertheless, as all the diverse cases discussed here attest, the abundance of predators and their co-evolved prey are both limited by their food: the predators are passengers, not drivers.

Evidence for density dependence in foraging and migratory behavior of a subtropical nearshore seabird

USGS Publications Warehouse

Lamb, Juliet S.; Satgé, Yvan G.; Jodice, Patrick G. R.

2017-01-01

Density-dependent competition for food resources influences both foraging ecology and reproduction in a variety of animals. The relationship between colony size, local prey depletion, and reproductive output in colonial central-place foragers has been extensively studied in seabirds; however, most studies have focused on effects of intraspecific competition during the breeding season, while little is known about whether density-dependent resource depletion influences individual migratory behavior outside the breeding season. Using breeding colony size as a surrogate for intraspecific resource competition, we tested for effects of colony size on breeding home range, nestling health, and migratory patterns of a nearshore colonial seabird, the brown pelican (Pelecanus occidentalis), originating from seven breeding colonies of varying sizes in the subtropical northern Gulf of Mexico. We found evidence for density-dependent effects on foraging behavior during the breeding season, as individual foraging areas increased linearly with the number of breeding pairs per colony. Contrary to our predictions, however, nestlings from more numerous colonies with larger foraging ranges did not experience either decreased condition or increased stress. During nonbreeding, individuals from larger colonies were more likely to migrate, and traveled longer distances, than individuals from smaller colonies, indicating that the influence of density-dependent effects on distribution persists into the nonbreeding period. We also found significant effects of individual physical condition, particularly body size, on migratory behavior, which in combination with colony size suggesting that dominant individuals remain closer to breeding sites during winter. We conclude that density-dependent competition may be an important driver of both the extent of foraging ranges and the degree of migration exhibited by brown pelicans. However, the effects of density-dependent competition on breeding success and population regulation remain uncertain in this system.

Application of selection mapping to identify genomic regions associated with dairy production in sheep.

PubMed

Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

2014-01-01

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of "dairy breeds." This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.

Pre-breeding blood urea nitrogen concentration and reproductive performance of Bonsmara heifers within different management systems.

PubMed

Tshuma, Takula; Holm, Dietmar Erik; Fosgate, Geoffrey Theodore; Lourens, Dirk Cornelius

2014-08-01

This study investigated the association between pre-breeding blood urea nitrogen (BUN) concentration and reproductive performance of beef heifers within different management systems in South Africa. Bonsmara heifers (n = 369) from five herds with different estimated levels of nitrogen intake during the month prior to the commencement of the breeding season were sampled in November and December 2010 to determine BUN concentrations. Body mass, age, body condition score (BCS) and reproductive tract score (RTS) were recorded at study enrolment. Trans-rectal ultrasound and/or palpation was performed 4-8 weeks after a 3-month breeding season to estimate the stage of pregnancy. Days to pregnancy (DTP) was defined as the number of days from the start of the breeding season until the estimated conception date. Logistic regression and Cox proportional hazards survival analysis were performed to estimate the association of pre-breeding BUN concentration with subsequent pregnancy and DTP, respectively. After stratifying for herd and adjusting for age, heifers with relatively higher pre-breeding BUN concentration took longer to become pregnant when compared to those with relatively lower BUN concentration (P = 0.011). In the herd with the highest estimated nitrogen intake (n = 143), heifers with relatively higher BUN were less likely to become pregnant (P = 0.013) and if they did, it was only later during the breeding season (P = 0.017), after adjusting for body mass. These associations were not present in the herd (n = 106) with the lowest estimated nitrogen intake (P > 0.500). It is concluded that Bonsmara heifers with relatively higher pre-breeding BUN concentration, might be at a disadvantage because of this negative impact on reproductive performance, particularly when the production system includes high levels of nitrogen intake.

Prevalence of congenital heart disease in 76,301 mixed-breed dogs and 57,025 mixed-breed cats.

PubMed

Schrope, Donald P

2015-09-01

Assess the prevalence of congenital heart disease (CHD) in a large population of mixed-breed dogs and cats. 76,301 mixed-breed dogs and 57,025 mixed-breed cats. Retrospective review of records and examinations based on specified diagnostic criteria. Among mixed-breed dogs, the prevalence of CHD was 0.13% (51.4% female) and of innocent murmurs was 0.10% (53.0% male). Pulmonic stenosis was the most common defect followed by patent ductus arteriosus, aortic stenosis, and ventricular septal defect. Among mixed-breed cats, prevalence of CHD was 0.14% (55.2% male) and of innocent murmurs was 0.16% (54.4% male). When the 25 cats with dynamic left or right ventricular outflow obstruction were counted with cases of innocent murmurs, the overall prevalence was 0.2%. Ventricular septal defects were the most common feline CHD followed closely by aortic stenosis and hypertrophic obstructive cardiomyopathy. There was no overall sex predilection for CHD in mixed-breed cats or dogs, and no significant difference in CHD prevalence between cats or dogs. Among dogs, subvalvular aortic stenosis and mitral valve dysplasia had a male predisposition while patent ductus arteriosus had a female predisposition. Among cats, valvular pulmonic stenosis, subvalvular and valvular aortic stenosis, and ventricular septal defects had a male predisposition while pulmonary artery stenosis had a female predisposition. The prevalence of CHD in a mixed-breed dogs and cats is lower than for prior studies, perhaps due to the lack of purebreds in the study population or actual changes in disease prevalence. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

PubMed Central

Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

2014-01-01

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. PMID:24788864

Population structure of four Thai indigenous chicken breeds.

PubMed

Mekchay, Supamit; Supakankul, Pantaporn; Assawamakin, Anunchai; Wilantho, Alisa; Chareanchim, Wanwisa; Tongsima, Sissades

2014-03-27

In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

PubMed Central

Parker, Heidi G.; Kukekova, Anna V.; Akey, Dayna T.; Goldstein, Orly; Kirkness, Ewen F.; Baysac, Kathleen C.; Mosher, Dana S.; Aguirre, Gustavo D.; Acland, Gregory M.; Ostrander, Elaine A.

2007-01-01

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. PMID:17916641

[Phenotypic trends and breeding values for canine congenital sensorineural deafness in Dalmatian dogs].

PubMed

Blum, Meike; Distl, Ottmar

2014-01-01

In the present study, breeding values for canine congenital sensorineural deafness, the presence of blue eyes and patches have been predicted using multivariate animal models to test the reliability of the breeding values for planned matings. The dataset consisted of 6669 German Dalmatian dogs born between 1988 and 2009. Data were provided by the Dalmatian kennel clubs which are members of the German Association for Dog Breeding and Husbandry (VDH). The hearing status for all dogs was evaluated using brainstem auditory evoked potentials. The reliability using the prediction error variance of breeding values and the realized reliability of the prediction of the phenotype of future progeny born in each one year between 2006 and 2009 were used as parameters to evaluate the goodness of prediction through breeding values. All animals from the previous birth years were used for prediction of the breeding values of the progeny in each of the up-coming birth years. The breeding values based on pedigree records achieved an average reliability of 0.19 for the future 1951 progeny. The predictive accuracy (R2) for the hearing status of single future progeny was at 1.3%. Combining breeding values for littermates increased the predictive accuracy to 3.5%. Corresponding values for maternal and paternal half-sib groups were at 3.2 and 7.3%. The use of breeding values for planned matings increases the phenotypic selection response over mass selection. The breeding values of sires may be used for planned matings because reliabilities and predictive accuracies for future paternal progeny groups were highest.

Recent breeding history of dog breeds in Sweden: modest rates of inbreeding, extensive loss of genetic diversity and lack of correlation between inbreeding and health

PubMed Central

Jansson, M; Laikre, L

2014-01-01

One problem in modern dogs is a high occurrence of physical diseases, defects and disorders. Many breeds exhibit physical problems that affect individual dogs throughout life. A potential cause of these problems is inbreeding that is known to reduce the viability of individuals. We investigated the possible correlation between recent inbreeding and health problems in dogs and used studbook data from 26 breeds provided by the Swedish Kennel Club for this purpose. The pedigrees date back to the mid-20th century and comprise 5–10 generations and 1 000–50 000 individuals per pedigree over our study period of 1980–2010. We compared levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals during this period in the investigated dog breeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) based on statistics on the extent of veterinary care obtained from Sweden's four largest insurance companies for pets. We found extensive loss of genetic variation and moderate levels of recent inbreeding in all breeds examined, but no strong indication of a difference in these parameters between healthy versus unhealthy breeds over this period. Thus, recent breeding history with respect to rate of inbreeding does not appear to be a main cause of poor health in the investigated dog breeds in Sweden. We identified both strengths and weaknesses of the dog pedigree data important to consider in future work of monitoring and conserving genetic diversity of dog breeds. PMID:24289536

Breeding implications resulting from classification of patellae luxation in dogs.

PubMed

van Grevenhof, E M; Hazewinkel, H A W; Heuven, H C M

2016-08-01

Patellar luxation (PL) is one of the major hereditary orthopaedic abnormalities observed in a variety of dog breeds. When the patellae move sideways out of the trochlear groove, this is called PL. The PL score varies between dogs from normal to very severe. Reducing the prevalence of PL by breeding could prevent surgery, thereby improve welfare. Orthopaedic specialists differentiate between normal and loose patellae, where the patellae can be moved to the edge of the trochlear groove, considering scoring loose patellae as normal in the future. Loose patellae are considered acceptable for breeding so far by the breeding organization. The aim of this study was to analyse the genetic background of PL to decide on the importance of loose patellae when breeding for healthy dogs. Data are available from two dog breeds, that is Flat-coated Retrievers (n = 3808) and Kooiker dogs (n = 794), with a total of 4602 dogs. Results show that loose patellae indicate that dogs are genetically more susceptible to develop PL because family members of the dogs with loose patellae showed more severe PL. In addition, the estimated breeding values for dogs with loose patellae indicate that breeding values of dogs with loose patellae were worse than breeding values obtained for dogs with a normal score. Given these results, it is advised to orthopaedic specialists to continue to score loose patellae as a separate class and to dog breeders to minimize the use of dogs in breeding with a genetically higher susceptibility for PL. © 2015 Blackwell Verlag GmbH.

Optimum allocation of test resources and comparison of breeding strategies for hybrid wheat.

PubMed

Longin, C Friedrich H; Mi, Xuefei; Melchinger, Albrecht E; Reif, Jochen C; Würschum, Tobias

2014-10-01

The use of a breeding strategy combining the evaluation of line per se with testcross performance maximizes annual selection gain for hybrid wheat breeding. Recent experimental studies confirmed a high commercial potential for hybrid wheat requiring the design of optimum breeding strategies. Our objectives were to (1) determine the optimum allocation of the type and number of testers, the number of test locations and the number of doubled haploid lines for different breeding strategies, (2) identify the best breeding strategy and (3) elaborate key parameters for an efficient hybrid wheat breeding program. We performed model calculations using the selection gain for grain yield as target variable to optimize the number of lines, testers and test locations in four different breeding strategies. A breeding strategy (BS2) combining the evaluation of line per se performance and general combining ability (GCA) had a far larger annual selection gain across all considered scenarios than a breeding strategy (BS1) focusing only on GCA. In the combined strategy, the production of testcross seed conducted in parallel with the first yield trial for line per se performance (BS2rapid) resulted in a further increase of the annual selection gain. For the current situation in hybrid wheat, this relative superiority of the strategy BS2rapid amounted to 67 % in annual selection gain compared to BS1. Varying a large number of parameters, we identified the high costs for hybrid seed production and the low variance of GCA in hybrid wheat breeding as key parameters limiting selection gain in BS2rapid.

Habitat selection by breeding red-winged blackbirds

USGS Publications Warehouse

Albers, P.H.

1978-01-01

Habitat preferences of breeding Red-winged Blackbirds in an agricultural area were determined by comparing population density, landscape characteristics, and vegetational descriptions. Observations were made throughout the breeding season. Preferred breeding habitats of Red-wings, in order of preference, were wetlands, hayfields, old fields, and pastures. Males and females occupied old fields and wetlands first, then hayfields, and finally, pastures. Cutting of hayfields caused territorial abandonment by both sexes within 48 h. The apparent movement of displaced females from cut hayfields to uncut hayfields suggests that habitat fidelity of females is strong after the breeding effort has begun. Breeding Red-wings exhibited general preferences for trees, large amounts of habitat edge, erect old vegetation, and sturdy, tall, and dense vegetation. Vegetative forms and species, such as upland grasses, broad- and narrow-leafed monocots in wetlands, and forbs were important to the Red-wing at various times during the breeding season. Landscape and vegetational preferences of breeding adults were easier to observe early in the breeding season (March through May) than later. Vegetational growth and increases in the size of the breeding population probably make these preferences more difficult to detect. Territory size was poorly correlated with landscape and vegetational characteristics in uplands but strongly correlated with broad- and narrow-leafed mono cots and vegetative height in wetlands. Wetland territories were smaller than upland territories. Territories increased in size during the middle and late portions of the breedi g season. Habitat selection by the Red-winged Blackbird can best be studied by evaluating vegetative preferences throughout the breeding season.

The frequency of sex in fungi

PubMed Central

James, Timothy Y.

2016-01-01

Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction. This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’. PMID:27619703

The frequency of sex in fungi.

PubMed

Nieuwenhuis, Bart P S; James, Timothy Y

2016-10-19

Fungi are a diverse group of organisms with a huge variation in reproductive strategy. While almost all species can reproduce sexually, many reproduce asexually most of the time. When sexual reproduction does occur, large variation exists in the amount of in- and out-breeding. While budding yeast is expected to outcross only once every 10 000 generations, other fungi are obligate outcrossers with well-mixed panmictic populations. In this review, we give an overview of the costs and benefits of sexual and asexual reproduction in fungi, and the mechanisms that evolved in fungi to reduce the costs of either mode. The proximate molecular mechanisms potentiating outcrossing and meiosis appear to be present in nearly all fungi, making them of little use for predicting outcrossing rates, but also suggesting the absence of true ancient asexual lineages. We review how population genetic methods can be used to estimate the frequency of sex in fungi and provide empirical data that support a mixed mode of reproduction in many species with rare to frequent sex in between rounds of mitotic reproduction. Finally, we highlight how these estimates might be affected by the fungus-specific mechanisms that evolved to reduce the costs of sexual and asexual reproduction.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'. © 2016 The Author(s).

Group foraging increases foraging efficiency in a piscivorous diver, the African penguin

PubMed Central

McGeorge, Cuan; Ginsberg, Samuel; Pichegru, Lorien; Pistorius, Pierre A.

2017-01-01

Marine piscivores have evolved a variety of morphological and behavioural adaptations, including group foraging, to optimize foraging efficiency when targeting shoaling fish. For penguins that are known to associate at sea and feed on these prey resources, there is nonetheless a lack of empirical evidence to support improved foraging efficiency when foraging with conspecifics. We examined the hunting strategies and foraging performance of breeding African penguins equipped with animal-borne video recorders. Individuals pursued both solitary as well as schooling pelagic fish, and demonstrated independent as well as group foraging behaviour. The most profitable foraging involved herding of fish schools upwards during the ascent phase of a dive where most catches constituted depolarized fish. Catch-per-unit-effort was significantly improved when targeting fish schools as opposed to single fish, especially when foraging in groups. In contrast to more generalist penguin species, African penguins appear to have evolved specialist hunting strategies closely linked to their primary reliance on schooling pelagic fish. The specialist nature of the observed hunting strategies further limits the survival potential of this species if Allee effects reduce group size-related foraging efficiency. This is likely to be exacerbated by diminishing fish stocks due to resource competition and environmental change. PMID:28989785

Development of novel vaccines using DNA shuffling and screening strategies.

PubMed

Locher, Christopher P; Soong, Nay Wei; Whalen, Robert G; Punnonen, Juha

2004-02-01

DNA shuffling and screening technologies recombine and evolve genes in vitro to rapidly obtain molecules with improved biological activity and fitness. In this way, genes from related strains are bred like plants or livestock and their successive progeny are selected. These technologies have also been called molecular breeding-directed molecular evolution. Recent developments in bioinformatics-assisted computer programs have facilitated the design, synthesis and analysis of DNA shuffled libraries of chimeric molecules. New applications in vaccine development are among the key features of DNA shuffling and screening technologies because genes from several strains or antigenic variants of pathogens can be recombined to create novel molecules capable of inducing immune responses that protect against infections by multiple strains of pathogens. In addition, molecules such as co-stimulatory molecules and cytokines have been evolved to have improved T-cell proliferation and cytokine production compared with the wild-type human molecules. These molecules can be used to immunomodulate vaccine responsiveness and have multiple applications in infectious diseases, cancer, allergy and autoimmunity. Moreover, DNA shuffling and screening technologies can facilitate process development of vaccine manufacturing through increased expression of recombinant polypeptides and viruses. Therefore, DNA shuffling and screening technologies can overcome some of the challenges that vaccine development currently faces.

The Architecture of the Pollen Hoarding Syndrome in Honey Bees: Implications for Understanding Social Evolution, Behavioral Syndromes, and Selective Breeding

PubMed Central

Rueppell, Olav

2014-01-01

Social evolution has influenced every aspect of contemporary honey bee biology, but the details are difficult to reconstruct. The reproductive ground plan hypothesis of social evolution proposes that central regulators of the gonotropic cycle of solitary insects have been coopted to coordinate social complexity in honey bees, such as the division of labor among workers. The predicted trait associations between reproductive physiology and social behavior have been identified in the context of the pollen hoarding syndrome, a larger suite of interrelated traits. The genetic architecture of this syndrome is characterized by a partially overlapping genetic architecture with several consistent, pleiotropic QTL. Despite these central QTL and an integrated hormonal regulation, separate aspects of the pollen hoarding syndrome may evolve independently due to peripheral QTL and additionally segregating genetic variance. The characterization of the pollen hoarding syndrome has also demonstrated that this syndrome involves many non-behavioral traits, which may be the case for numerous “behavioral” syndromes. Furthermore, the genetic architecture of the pollen hoarding syndrome has implications for breeding programs for improving honey health and other desirable traits: If these traits are comparable to the pollen hoarding syndrome, consistent pleiotropic QTL will enable marker assisted selection, while sufficient additional genetic variation may permit the dissociation of trade-offs for efficient multiple trait selection. PMID:25506100

The Architecture of the Pollen Hoarding Syndrome in Honey Bees: Implications for Understanding Social Evolution, Behavioral Syndromes, and Selective Breeding.

PubMed

Rueppell, Olav

2014-05-01

Social evolution has influenced every aspect of contemporary honey bee biology, but the details are difficult to reconstruct. The reproductive ground plan hypothesis of social evolution proposes that central regulators of the gonotropic cycle of solitary insects have been coopted to coordinate social complexity in honey bees, such as the division of labor among workers. The predicted trait associations between reproductive physiology and social behavior have been identified in the context of the pollen hoarding syndrome, a larger suite of interrelated traits. The genetic architecture of this syndrome is characterized by a partially overlapping genetic architecture with several consistent, pleiotropic QTL. Despite these central QTL and an integrated hormonal regulation, separate aspects of the pollen hoarding syndrome may evolve independently due to peripheral QTL and additionally segregating genetic variance. The characterization of the pollen hoarding syndrome has also demonstrated that this syndrome involves many non-behavioral traits, which may be the case for numerous "behavioral" syndromes. Furthermore, the genetic architecture of the pollen hoarding syndrome has implications for breeding programs for improving honey health and other desirable traits: If these traits are comparable to the pollen hoarding syndrome, consistent pleiotropic QTL will enable marker assisted selection, while sufficient additional genetic variation may permit the dissociation of trade-offs for efficient multiple trait selection.

Communal breeding promotes a matrilineal social system where husband and wife live apart.

PubMed

Wu, Jia-Jia; He, Qiao-Qiao; Deng, Ling-Ling; Wang, Shi-Chang; Mace, Ruth; Ji, Ting; Tao, Yi

2013-05-07

The matrilineal Mosuo of southwest China live in large communal houses where brothers and sisters of three generations live together, and adult males walk to visit their wives only at night; hence males do not reside with their own offspring. This duolocal residence with 'walking' or 'visiting' marriage is described in only a handful of matrilineal peasant societies. Benefits to women of living with matrilineal kin, who cooperate with child-care, are clear. But why any kinship system can evolve where males invest more in their sister's offspring than their own is a puzzle for evolutionary anthropologists. Here, we present a new hypothesis for a matrilineal bias in male investment. We argue that, when household resources are communal, relatedness to the whole household matters more than relatedness to individual offspring. We use an inclusive fitness model to show that the more sisters (and other closely related females) co-reside, the more effort males should spend working on their sister's farm and less on their wife's farm. The model shows that paternity uncertainty may be a cause of lower overall work rates in males, but it is not likely to be the cause of a matrilineal bias. The bias in work effort towards working on their natal farm, and thus the duolocal residence and 'visiting marriage' system, can be understood as maximizing inclusive fitness in circumstances where female kin breed communally.

Humpback Whale Song on the Southern Ocean Feeding Grounds: Implications for Cultural Transmission

PubMed Central

Garland, Ellen C.; Gedamke, Jason; Rekdahl, Melinda L.; Noad, Michael J.; Garrigue, Claire; Gales, Nick

2013-01-01

Male humpback whales produce a long, complex, and stereotyped song on low-latitude breeding grounds; they also sing while migrating to and from these locations, and occasionally in high-latitude summer feeding areas. All males in a population sing the current version of the constantly evolving display and, within an ocean basin, populations sing similar songs; however, this sharing can be complex. In the western and central South Pacific region there is repeated cultural transmission of song types from eastern Australia to other populations eastward. Song sharing is hypothesized to occur through several possible mechanisms. Here, we present the first example of feeding ground song from the Southern Ocean Antarctic Area V and compare it to song from the two closest breeding populations. The early 2010 song contained at least four distinct themes; these matched four themes from the eastern Australian 2009 song, and the same four themes from the New Caledonian 2010 song recorded later in the year. This provides evidence for at least one of the hypothesized mechanisms of song transmission between these two populations, singing while on shared summer feeding grounds. In addition, the feeding grounds may provide a point of acoustic contact to allow the rapid horizontal cultural transmission of song within the western and central South Pacific region and the wider Southern Ocean. PMID:24278134

The impact of using old germplasm on genetic merit and diversity-A cattle breed case study.

PubMed

Eynard, Sonia E; Windig, Jack J; Hulsegge, Ina; Hiemstra, Sipke-Joost; Calus, Mario P L

2018-05-29

Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long-term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse-Rhine-Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long-term maintenance and selection of breeds. © 2018 The Authors. Journal of Animal Breeding and Genetics Published by Blackwell Verlag GmbH.

Known breeding distribution and abundance of golden eagles in Eastern North America

Treesearch

Francois Morneau; Junior A. Tremblay; Charles Todd; Tony E. Chubbs; Charles Maisonneuve; Jerome Lemaitre; Todd Katzner

2015-01-01

Aquila chrysaetos (Golden Eagle) breeds in both eastern and western North America. However, the former population has received much less attention than the latter. The purpose of this paper is to document the known distribution and abundance of eastern Golden Eagles within their breeding range and to identify gaps in knowledge for future studies....

Selecting loblolly pine parents for seed orchards to minimize the cost of producing pulp

Treesearch

W.J. Lowe; T.D. Byram; F.E. Bridgwater

1999-01-01

Southern pine cooperative breeding programs currently emphasize genetic improvement of growth rates. When a deployment population, typically a seed orchard, is established, there is an opportunity to emphasize traits other than growth rate to maximize the profit of individual cooperators in the breeding program. The authors studied a southeast Texas breeding population...

Breeding bird populations in Missouri Ozark forests with and without clearcutting

Treesearch

Frank R., III Thompson; William D. Dijak; Thomas G. Kulowiec; David A. Hamilton

1992-01-01

Concern has arisen that forest management practices that create edge (such as clearcutting) are contributing to regional declines in neotropical migrant birds that inhabit forest interiors. Consequently, we studied breeding bird populations in an extensively forested region of southern Missouri to determine if the numbers of breeding birds differed between areas (n = 9...

Strategies for selecting and breeding EAB-resistant ash

Treesearch

Jennifer L. Koch; Kathleen Knight; Therese Poland; David W. Carey; Daniel A. Herms; Mary E. Mason

2011-01-01

Breeding for pest resistance in forest trees is a proven approach for managing both native and nonnative insects and diseases. A recent study by the Food and Agriculture Organization of the United Nations reports 255 forest tree breeding programs for insect or disease resistance in 33 diff erent countries (http://www.fao.org/forestry/26445/en/). Advantages to...

Simulation of introgression of the polled allele into the Holstein breed via conventional breeding versus gene editing

USDA-ARS?s Scientific Manuscript database

The objective of this study was to simulate the introgression of the polled allele into a dairy cattle population and compare the impact of using the methods of conventional breeding versus gene editing to increase the frequency of the polled allele. The rate of minor allele frequency (MAF) change, ...

Geographic variation in foraging ecologies of breeding and nonbreeding birds in oak woodlands

Treesearch

William M. Block

1990-01-01

I studied geographic variation in the foraging ecology of four breeding and four non breeding species in three oak (Quercus spp.) woodlands of California. Variations were evident for all species. Variations in tree-species use, foraging tactics, substrates, and behaviors were species-specific. For example, White-breasted Nuthatches (Sitta carolinensis) used...

Design of a DNA panel for genomic studies in Russian cattle breeds

USDA-ARS?s Scientific Manuscript database

A panel of 96 DNA samples (Russian Cattle Genomic Diversity Panel 1.0 or RCGDP 1.0) characterizing the breadth of genetic diversity in popular Russian cattle breeds was designed. The panel contains from four to eight animals from each of 11 dairy and six dairy-meat and meat breeds. The main criterio...

Plant Breeding: Surprisingly, Less Sex Is Better.

PubMed

van Dijk, Peter J; Rigola, Diana; Schauer, Stephen E

2016-02-08

Introduction of apomixis, asexual reproduction through seeds, into crop species has the potential to dramatically transform plant breeding. A new study demonstrates that traits can be stably transferred between generations in newly produced apomictic lines, and heralds a breeding revolution needed to increase food production for the growing planet. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characteristics of urban woodlands affecting breeding bird diversity and abundance

Treesearch

N.G. Tilghman

1987-01-01

Breeding bird communities were studied in 32 forest islands surrounded by urban development. These isolated woodlands in Springfield, Massachusetts, provided breeding habitats for a wider variety of birds (77 species) than previously described for other urban habitats (e.g. four times as many species as found in urban residential areas in the same city in a...

Selection for breed-specific long-bodied phenotypes is associated with increased expression of canine hip dysplasia.

PubMed

Roberts, Taryn; McGreevy, Paul D

2010-03-01

Hip dysplasia (HD) is the most common skeletal disease in purebred dogs. Radiographic schemes developed to reduce prevalence through selective breeding have had limited success, but the role of selecting for morphological characteristics prized in the show-ring and dictated by breed standards has not been fully explored. This study correlated published scores of hip pathology with measurements of body length to height ratio from photographs of Best-of-Breed specimens from 30 breeds (n=12/breed) to establish whether selection criteria could be compromising welfare by increasing susceptibility to HD. Relative body length correlated strongly with higher rates of HD by breed data from the Orthopedic Foundation for Animals (Spearman r=0.727, P<0.001), the British Veterinary Association (r=0.701, P<0.001), and the Australian Veterinary Association (r=0.577, P<0.01). By favouring body shapes that are longer than they are tall, judges may be inadvertently selecting for conformational attributes predisposing dogs to HD, suggesting that ambiguity in breed standards and extreme relative body length phenotypes can engender serious welfare consequences and need to be re-evaluated. 2009 Elsevier Ltd. All rights reserved.

Between-breed variations in resistance/resilience to gastrointestinal nematodes among indigenous goat breeds in Uganda.

PubMed

Onzima, R B; Mukiibi, R; Ampaire, A; Benda, K K; Kanis, E

2017-12-01

Gastrointestinal nematodes (GINs), Haemonchus contortus, are a major health problem in goat production. Resistance to H. contortus, the most prevalent GIN in Uganda, was studied among three indigenous goat breeds to assess their differences. Twelve male goats of each breed approximately 7 months old of small East African (SEA), Mubende, and Kigezi goats from smallholder farmers in Arua, Mubende, and Kabale were assembled for the study. At the station, they were dewormed with a combination therapy of the broad-spectrum dewormers closantel and albendazole to free the goats of gastrointestinal parasites. During experimentation, the goats were kept indoors and ad libitum fed on clean banana peels and napier grass. On attainment of zero-worm-egg status, the goats were artificially infected with 18,000 third-stage (L3) larvae of H. contortus prepared according to Baermann's procedure. Data were collected on fecal egg count (FEC), packed cell volume (PCV), and body weight (BW) on a 2-week basis until 12 weeks post infection and carcass weight and total worm count (WC) in the abomasum at termination of the experiment. The data on FEC, PCV, and BW were subjected to repeated-measure analysis of variance and the others by one-way analysis of variance. FEC between breeds was only significantly different at 12 weeks post infection (p = 0.04). Generally, higher FEC was recorded in Kigezi compared to SEA and Mubende goats. Carcass weight was significantly different among breeds (p < 0.05), with Mubende having the highest carcass weight, followed by Kigezi and SEA. PCV and daily weight gains were significantly different between breeds (p < 0.05). WC was not significantly different between the breeds. FEC and PCV were weakly significant at later stages of the experiment with higher parasite burden suggesting potential variation in resistance to H. contortus. These differences could be exploited in designing breeding programs with disease resistance in indigenous goat breeds.

Relative contribution of lipid sources to eggs of lesser scaup

USGS Publications Warehouse

Cutting, Kyle A.; Hobson, Keith A.; Rotella, Jay J.; Warren, Jeffrey M.; Takekawa, John Y.; De La Cruz, Susan E. W.; Parker, Michael

2014-01-01

Studies of how birds mobilize nutrients to eggs have traditionally considered a continuum of possible allocation strategies ranging from income breeding (rely on food sources found on the breeding grounds) to capital breeding (rely on body reserves stored prior to the breeding season). For capital breeding, stored body reserves can be acquired either on or away from the breeding grounds, but it has been difficult to quantify the relative contribution of each, precluding identification of key habitats for acquiring nutrients for clutch formation. During 2006–2009, we explored the importance of spring-staging habitats versus breeding-area habitats for egg-lipid formation in female lesser scaup Aythya affinis using stable carbon (δ13C) isotope analyses. Although δ13C values for abdominal lipid reserves brought to the breeding grounds overlapped those of local amphipods, we were able to quantify the importance of local plant carbohydrates (seeds of emergent wetland plants) to the production of eggs. We compared the importance of local wetland seeds (overall δ13C: −29.1 ± 0.9‰ SD) to combined lipid stores and lipids from local amphipods (overall δ13C: −23.8 ± 2.2‰). Local seeds and stored body lipids contributed equally to egg lipid formation across years but we found evidence of annual variation in their relative importance. Wetland seeds contributed 39% (SE = 10%) to egg lipid production, and the importance of this source varied by year (90% CI = 47–75% in 2006, 13–42% in 2007, 29–65% in 2008, and 7–30% in 2009). In contrast to earlier studies that suggest lesser scaup predominantly employ a capital breeding strategy, our results suggest that in some years females may attain half of their energy for clutch formation from foods on the breeding grounds.

Productivity of pure- and crossbred cattle in a subtropical environment

NASA Astrophysics Data System (ADS)

van Zyl, J. G. E.; Schoeman, S. J.; Coertze, R. J.; Groeneveld, H. T.

1991-06-01

The influence of different breeds of sire and dam types on cow productivity in an arid, subtropical environment was studied. Cows with calves sired by Simmentaler, Hereford and Bonsmara bulls were more ( P<0.05) productive than those with calves sired by Afrikaner bulls. Simmentaler sires were superior ( P<0.05) to Bonsmara sires. Crossbred cows of predominant (>50%) Bos taurus breeding were generally superior to crossbreds of predominant B. indicus breeding and purebreds. Crossbreeding systems to utilize breed effects to optimise cow productivity within environmental constraints are discussed.

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011–2012)

PubMed Central

Zierath, Sharon; Hughes, Angela M.; Fretwell, Neale; Dibley, Mark

2017-01-01

Background A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. Results From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. Conclusions The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner’s rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs. PMID:29166669

Frequency of five disease-causing genetic mutations in a large mixed-breed dog population (2011-2012).

PubMed

Zierath, Sharon; Hughes, Angela M; Fretwell, Neale; Dibley, Mark; Ekenstedt, Kari J

2017-01-01

A large and growing number of inherited genetic disease mutations are now known in the dog. Frequencies of these mutations are typically examined within the breed of discovery, possibly in related breeds, but nearly always in purebred dogs. No report to date has examined the frequencies of specific genetic disease mutations in a large population of mixed-breed dogs. Further, veterinarians and dog owners typically dismiss inherited/genetic diseases as possibilities for health problems in mixed-breed dogs, assuming hybrid vigor will guarantee that single-gene disease mutations are not a cause for concern. Therefore, the objective of this study was to screen a large mixed-breed canine population for the presence of mutant alleles associated with five autosomal recessive disorders: hyperuricosuria and hyperuricemia (HUU), cystinuria (CYST), factor VII deficiency (FVIID), myotonia congenita (MYC) and phosphofructokinase deficiency (PKFD). Genetic testing was performed in conjunction with breed determination via the commercially-available Wisdom PanelTM test. From a population of nearly 35,000 dogs, homozygous mutant dogs were identified for HUU (n = 57) and FVIID (n = 65). Homozygotes for HUU and FVIID were identified even among dogs with highly mixed breed ancestry. Carriers were identified for all disorders except MYC. HUU and FVIID were of high enough frequency to merit consideration in any mixed-breed dog, while CYST, MYC, and PKFD are vanishingly rare. The assumption that mixed-breed dogs do not suffer from single-gene genetic disorders is shown here to be false. Within the diseases examined, HUU and FVIID should remain on any practitioner's rule-out list, when clinically appropriate, for all mixed-breed dogs, and judicious genetic testing should be performed for diagnosis or screening. Future testing of large mixed-breed dog populations that include additional known canine genetic mutations will refine our knowledge of which genetic diseases can strike mixed-breed dogs.

Development of a genetic tool for product regulation in the diverse British pig breed market.

PubMed

Wilkinson, Samantha; Archibald, Alan L; Haley, Chris S; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Groenen, Martien A M; Wiener, Pamela; Ogden, Rob

2012-11-15

The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.

Development of a genetic tool for product regulation in the diverse British pig breed market

PubMed Central

2012-01-01

Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. Results The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. Conclusion The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. PMID:23150935

General parity between trio and pairwise breeding of laboratory mice in static caging.

PubMed

Kedl, Ross M; Wysocki, Lawrence J; Janssen, William J; Born, Willi K; Rosenbaum, Matthew D; Granowski, Julia; Kench, Jennifer A; Fong, Derek L; Switzer, Lisa A; Cruse, Margaret; Huang, Hua; Jakubzick, Claudia V; Kosmider, Beata; Takeda, Katsuyuki; Stranova, Thomas J; Klumm, Randal C; Delgado, Christine; Tummala, Saigiridhar; De Langhe, Stijn; Cambier, John; Haskins, Katherine; Lenz, Laurel L; Curran-Everett, Douglas

2014-11-15

Changes made in the 8th edition of the Guide for the Care and Use of Laboratory Animals included new recommendations for the amount of space for breeding female mice. Adopting the new recommendations required, in essence, the elimination of trio breeding practices for all institutions. Both public opinion and published data did not readily support the new recommendations. In response, the National Jewish Health Institutional Animal Care and Use Committee established a program to directly compare the effects of breeding format on mouse pup survival and growth. Our study showed an overall parity between trio and pairwise breeding formats on the survival and growth of the litters, suggesting that the housing recommendations for breeding female mice as stated in the current Guide for the Care and Use of Laboratory Animals should be reconsidered. Copyright © 2014 by The American Association of Immunologists, Inc.

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

DOE PAGES

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.; ...

2015-08-28

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstratemore » stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this study, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz.« less

Genome-wide analysis highlights genetic dilution in Algerian sheep.

PubMed

Gaouar, S B S; Lafri, M; Djaout, A; El-Bouyahiaoui, R; Bouri, A; Bouchatal, A; Maftah, A; Ciani, E; Da Silva, A B

2017-03-01

Algeria represents a reservoir of genetic diversity with local sheep breeds adapted to a large range of environments and showing specific features necessary to deal with harsh conditions. This remarkable diversity results from the traditional management of dryland by pastoralists over centuries. Most of these breeds are poorly productive, and the economic pressure leads farmers to realize anarchic cross-breeding (that is, not carried out in the framework of selection plans) with the hope to increase animal's conformation. In this study, eight of the nine local Algerian sheep breeds (D'men, Hamra, Ouled-Djellal, Rembi, Sidaoun, Tazegzawt, Berber and Barbarine) were investigated for the first time by genome-wide single-nucleotide polymorphism genotyping. At an international scale, Algerian sheep occupied an original position shaped by relations with African and European (particularly Italian) breeds. The strong genetic proximity with Caribbean and Brazilian breeds confirmed that the genetic make-up of these American breeds was largely influenced by the Atlantic slave trade. At a national scale, an alarming genetic dilution of the Berber (a primitive breed) and the Rembi was observed, as a consequence of uncontrolled mating practices with Ouled-Djellal. A similar, though less pronounced, phenomenon was also detected for the Barbarine, another ancestral breed. Genetic originality appeared to be better preserved in Tazegzawt, Hamra, D'men and Sidaoun. These breeds should be given high priority in the establishment of conservation plans to halt their progressive loss. For Berber and Barbarine that also occur in the bordering neighbor countries, urgent concerted transnational actions are needed.

Fast and efficient charge breeding of the Californium rare isotope breeder upgrade electron beam ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostroumov, P. N.; Barcikowski, A.; Dickerson, C. A.

The Electron Beam Ion Source (EBIS), developed to breed Californium Rare Isotope Breeder Upgrade (CARIBU) radioactive beams at Argonne Tandem Linac Accelerator System (ATLAS), is being tested off-line. A unique property of the EBIS is a combination of short breeding times, high repetition rates, and a large acceptance. Overall, we have implemented many innovative features during the design and construction of the CARIBU EBIS as compared to the existing EBIS breeders. The off-line charge breeding tests are being performed using a surface ionization source that produces singly charged cesium ions. The main goal of the off-line commissioning is to demonstratemore » stable operation of the EBIS at a 10 Hz repetition rate and a breeding efficiency into single charge state higher than 15%. These goals have been successfully achieved and exceeded. We have measured (20% ± 0.7%) breeding efficiency into the single charge state of 28+ cesium ions with the breeding time of 28 ms. In general, the current CARIBU EBIS operational parameters can provide charge breeding of any ions in the full mass range of periodic table with high efficiency, short breeding times, and sufficiently low charge-to-mass ratio, 1/6.3 for the heaviest masses, for further acceleration in ATLAS. In this study, we discuss the parameters of the EBIS and the charge breeding results in a pulsed injection mode with repetition rates up to 10 Hz.« less

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

Breeding site selection by coho salmon (Oncorhynchus kisutch) in relation to large wood additions and factors that influence reproductive success

USGS Publications Warehouse

Clark, Steven M.; Dunham, Jason B.; McEnroe, Jeffery R.; Lightcap, Scott W.

2014-01-01

The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four fitness components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. We evaluated the relative influences of habitat features linked to these fitness components with respect to selection of breeding sites by coho salmon (Oncorhynchus kisutch). We also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. We used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. Results of this work suggest that female coho salmon likely select breeding sites based on a wide range of habitat features linked to all four hypothesized fitness components. More specifically, model parameter estimates indicated that breeding site selection was most strongly influenced by proximity to pool-tail crests and deeper water (mean and maximum depths). Linkages between large wood and breeding site selection were less clear. Overall, our findings suggest that breeding site selection by coho salmon is influenced by a suite of fitness components in addition to the egg incubation environment, which has been the emphasis of much work in the past.

Epidemiological study of canine parvovirus infection in and around Bhubaneswar, Odisha, India.

PubMed

Behera, Monalisa; Panda, S K; Sahoo, P K; Acharya, A P; Patra, R C; Das, Sweta; Pati, S

2015-01-01

An epidemiological study of canine parvovirus infection in dogs in and around Bhubaneswar, Odisha was conducted between December 2012 to March 2013 and prevalence rate was studied on the basis of age, breed, and sex. A total of 71 fecal samples from suspected diarrheic dogs were collected in sterile phosphate buffer saline (10% W/V) and examined by polymerase chain reaction (PCR) for detection of canine parvo virus infection, followed by epidemiological study in relation to age, breed, and sex. Of 71 samples analyzed, 29 (40.85%) were found to be positive by PCR assay. The infection was higher in Deshi/local breeds (34.48%), followed by German shepherd (17.24%), equal incidences in mixed and Labrador retriever (10.34%), Rottweiler and German spitz showed 6.90% each and finally lower incidences in four breeds (3.45%) such as Dalmatians, Nea politan mastiff, Pug and Great Dane. Age-wise prevalence study revealed the infection being more in the age group of 3-6 months (41.37%), followed by equal incidences of 27.59% in 1-3 months and 6-12 months age group, and a low incidence in age groups above 12 months (3.45%). The incidence was predominantly higher in males (86.21%) than females (13.79%). The epidemiological analysis revealed that the breed wise prevalence was found to be more in Deshi breeds as compared to others, age groups below 6 months were found to be more prone to parvovirus infection and males were mostly infected.

Expression of regulatory neuropeptides in the hypothalamus of red deer (Cervus elaphus) reveals anomalous relationships in the seasonal control of appetite and reproduction.

PubMed

Barrell, G K; Ridgway, M J; Wellby, M; Pereira, A; Henry, B A; Clarke, I J

2016-04-01

Red deer are seasonal with respect to reproduction and food intake, so we tested the hypothesis that their brains would show seasonal changes in numbers of cells containing hypothalamic neuropeptides that regulate these functions. We examined the brains of male and female deer in non-breeding and breeding seasons to quantify the production of kisspeptin, gonadotropin inhibitory hormone (GnIH), neuropeptide Y (NPY) and γ-melanocyte stimulating hormone (γ-MSH - an index of pro-opiomelanocortin production), using immunohistochemistry. These neuropeptides are likely to be involved in the regulation of reproductive function and appetite. During the annual breeding season there were more cells producing kisspeptin in the arcuate nucleus of the hypothalamus than during the non-breeding season in males and females whereas there was no seasonal difference in the expression of GnIH. There were more cells producing the appetite stimulating peptide, NPY, in the arcuate/median eminence regions of the hypothalamus of females during the non-breeding season whereas the levels of an appetite suppressing peptide, γ-MSH, were highest in the breeding season. Male deer brains exhibited the converse, with NPY cell numbers highest in the breeding season and γ-MSH levels highest in the non-breeding season. These results support a role for kisspeptin as an important stimulatory regulator of seasonal breeding in deer, as in other species, but suggest a lack of involvement of GnIH in the seasonality of reproduction in deer. In the case of appetite regulation, the pattern exhibited by females for NPY and γ-MSH was as expected for the breeding and non-breeding seasons, based on previous studies of these peptides in sheep and the seasonal cycle of appetite reported for various species of deer. An inverse result in male deer most probably reflects the response of appetite regulating cells to negative energy balance during the mating season. Differences between the sexes in the seasonal changes in appetite regulating peptide cells of the hypothalamus present an interesting model for future studies. Copyright © 2016 Elsevier Inc. All rights reserved.

Genomic selection for crossbred performance accounting for breed-specific effects.

PubMed

Lopes, Marcos S; Bovenhuis, Henk; Hidalgo, André M; van Arendonk, Johan A M; Knol, Egbert F; Bastiaansen, John W M

2017-06-26

Breed-specific effects are observed when the same allele of a given genetic marker has a different effect depending on its breed origin, which results in different allele substitution effects across breeds. In such a case, single-breed breeding values may not be the most accurate predictors of crossbred performance. Our aim was to estimate the contribution of alleles from each parental breed to the genetic variance of traits that are measured in crossbred offspring, and to compare the prediction accuracies of estimated direct genomic values (DGV) from a traditional genomic selection model (GS) that are trained on purebred or crossbred data, with accuracies of DGV from a model that accounts for breed-specific effects (BS), trained on purebred or crossbred data. The final dataset was composed of 924 Large White, 924 Landrace and 924 two-way cross (F1) genotyped and phenotyped animals. The traits evaluated were litter size (LS) and gestation length (GL) in pigs. The genetic correlation between purebred and crossbred performance was higher than 0.88 for both LS and GL. For both traits, the additive genetic variance was larger for alleles inherited from the Large White breed compared to alleles inherited from the Landrace breed (0.74 and 0.56 for LS, and 0.42 and 0.40 for GL, respectively). The highest prediction accuracies of crossbred performance were obtained when training was done on crossbred data. For LS, prediction accuracies were the same for GS and BS DGV (0.23), while for GL, prediction accuracy for BS DGV was similar to the accuracy of GS DGV (0.53 and 0.52, respectively). In this study, training on crossbred data resulted in higher prediction accuracy than training on purebred data and evidence of breed-specific effects for LS and GL was demonstrated. However, when training was done on crossbred data, both GS and BS models resulted in similar prediction accuracies. In future studies, traits with a lower genetic correlation between purebred and crossbred performance should be included to further assess the value of the BS model in genomic predictions.

Does genomic selection have a future in plant breeding?

PubMed

Jonas, Elisabeth; de Koning, Dirk-Jan

2013-09-01

Plant breeding largely depends on phenotypic selection in plots and only for some, often disease-resistance-related traits, uses genetic markers. The more recently developed concept of genomic selection, using a black box approach with no need of prior knowledge about the effect or function of individual markers, has also been proposed as a great opportunity for plant breeding. Several empirical and theoretical studies have focused on the possibility to implement this as a novel molecular method across various species. Although we do not question the potential of genomic selection in general, in this Opinion, we emphasize that genomic selection approaches from dairy cattle breeding cannot be easily applied to complex plant breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Toxoplasma gondii seroprevalence varies by cat breed

PubMed Central

Hytönen, Marjo K.; Orro, Toomas; Lohi, Hannes; Jokelainen, Pikka

2017-01-01

Toxoplasma gondii is a widespread zoonotic parasite that is relevant for veterinary and public health. The domestic cat, the definitive host species with the largest worldwide population, has become evolutionarily and epidemiologically the most important host of T. gondii. The outcome of T. gondii infection is influenced by congenital and acquired host characteristics. We detected differences in T. gondii seroprevalence by cat breed in our previous studies. The aims of this study were to estimate T. gondii seroprevalence in selected domestic cat breeds, and to evaluate whether being of a certain breed is associated with T. gondii seropositivity, when the age and lifestyle of the cat are taken into account. The studied breeds were the Birman, British Shorthair, Burmese, Korat, Norwegian Forest Cat, Ocicat, Persian, and Siamese. Plasma samples were analyzed for the presence of immunoglobulin G antibodies against T. gondii with a commercial direct agglutination test at dilution 1:40. The samples were accompanied by owner-completed questionnaires that provided background data on the cats. Overall, 41.12% of the 1121 cats tested seropositive, and the seroprevalence increased with age. The Burmese had the lowest seroprevalence (18.82%) and the Persian had the highest (60.00%). According to the final multivariable logistic regression model, the odds to test seropositive were four to seven times higher in Birmans, Ocicats, Norwegian Forest Cats, and Persians when compared with the Burmese, while older age and receiving raw meat were also risk factors for T. gondii seropositivity. This study showed that T. gondii seroprevalence varies by cat breed and identified being of certain breeds, older age, and receiving raw meat as risk factors for seropositivity. PMID:28886182

High altitude flights by ruddy shelduck Tadorna ferruginea during trans-Himalayan migrations

USGS Publications Warehouse

Parr, N.; Bearhop, S.; Douglas, David C.; Takekawa, J.Y.; Prosser, Diann J.; Newman, S.H.; Perry, W.M.; Balachandran, S.; Witt, M.J.; Hou, Y.; Luo, Z.; Hawkes, L.A.

2017-01-01

Birds that migrate across high altitude mountain ranges are faced with the challenge of maintaining vigorous exercise in environments with limited oxygen. Ruddy shelducks are known to use wintering grounds south of the Tibetan Plateau at sea level and breeding grounds north of Himalayan mountain range. Therefore, it is likely these shelducks are preforming high altitude migrations. In this study we analyse satellite telemetry data collected from 15 ruddy shelduck from two populations wintering south of the Tibetan Plateau from 2007 to 2011. During north and south migrations ruddy shelduck travelled 1481 km (range 548–2671 km) and 1238 km (range 548–2689 km) respectively. We find mean maximum altitudes of birds in flight reached 5590 m (range of means 4755–6800 m) and mean maximum climb rates of 0.45 m s–1 (range 0.23–0.74 m s–1). The ruddy shelduck is therefore an extreme high altitude migrant that has likely evolved a range of physiological adaptations in order to complete their migrations.

Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system.

PubMed

Kuhn, A; Bauman, D; Darras, H; Aron, S

2017-10-01

Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.

Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs

PubMed Central

Lü, Meng-Die; Han, Xu-Man; Ma, Yun-Fei; Irwin, David M.; Gao, Yun; Deng, Jia-Kun; Adeola, Adeniyi C.; Xie, Hai-Bing; Zhang, Ya-Ping

2016-01-01

A common phenotypic difference among domestic animals is variation in coat color. Six-white-point is a pigmentation pattern observed in varying pig breeds, which seems to have evolved through several different mechanistic pathways. Herein, we re-sequenced whole genomes of 31 Diannan small-ear pigs from China and found that the six-white-point coat color in Diannan small-ear pigs is likely regulated by polygenic loci, rather than by the MC1R locus. Strong associations were observed at three loci (EDNRB, CNTLN, and PINK1), which explain about 20 percent of the total coat color variance in the Diannan small-ear pigs. We found a mutation that is highly differentiated between six-white-point and black Diannan small-ear pigs, which is located in a conserved noncoding sequence upstream of the EDNRB gene and is a putative binding site of the CEBPB protein. This study advances our understanding of coat color evolution in Diannan small-ear pigs and expands our traditional knowledge of coat color being a monogenic trait. PMID:27270507

Inbreeding avoidance in rhesus macaques: whose choice?

PubMed

Manson, J H; Perry, S E

1993-03-01

Whether nonhuman primates avoid copulating with close kin living in their social group is controversial. If sexual aversion to relatives occurs, it should be stronger in females than in males because of females' greater investment in each offspring and hence greater costs resulting from less viable offspring. Data presented here show that adult male rhesus macaques breeding in their natal groups at Cayo Santiago experienced high copulatory success, but copulated less with females of their own matrilineages than with females of other matrilineages. Adult females were never observed to copulate with males of their own matrilineage during their fertile periods. Although natal males sometimes courted their relatives, examination of two measures of female mate choice showed that females chose unrelated natal males over male kin. Female aversion to male kin was specific to the sexual context; during the birth season, females did not discriminate against their male relatives in distributing grooming. Evolved inbreeding avoidance mechanisms probably produce different outcomes at Cayo Santiago than in wild rhesus macaque populations. Gender differences in sexual aversion to relatives may be partly responsible for differences between studies in reported frequency of copulations by related pairs.

Genetic basis of sexual dimorphism in the threespine stickleback Gasterosteus aculeatus

PubMed Central

Leinonen, T; Cano, J M; Merilä, J

2011-01-01

Sexual dimorphism (SD) in morphological, behavioural and physiological features is common, but the genetics of SD in the wild has seldom been studied in detail. We investigated the genetic basis of SD in morphological traits of threespine stickleback (Gasterosteus aculeatus) by conducting a large breeding experiment with fish from an ancestral marine population that acts as a source of morphological variation. We also examined the patterns of SD in a set of 38 wild populations from different habitats to investigate the relationship between the genetic architecture of SD of the marine ancestral population in relation to variation within and among natural populations. The results show that genetic architecture in terms of heritabilities, additive genetic variances and covariances (as well as correlations) is very similar in the two sexes in spite of the fact that many of the traits express significant SD. Furthermore, population differences in threespine stickleback body shape and armour SD appear to have evolved despite constraints imposed by genetic architecture. This implies that constraints for the evolution of SD imposed by strong genetic correlations are not as severe and absolute as commonly thought. PMID:20700139

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

PubMed

Mancini, Giordano; Gargani, Maria; Chillemi, Giovanni; Nicolazzi, Ezequiel Luis; Marsan, Paolo Ajmone; Valentini, Alessio; Pariset, Lorraine

2014-02-01

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.

Genetic variation in the endangered Southwestern Willow Flycatcher

USGS Publications Warehouse

Busch, Joseph; Miller, Mark P.; Paxton, E.H.; Sogge, M.K.; Keim, Paul

2000-01-01

The Southwestern Willow Flycatcher (Empidonax traillii extimus) is an endangered Neotropical migrant that breeds in isolated remnants of dense riparian habitat in the southwestern United States. We estimated genetic variation at 20 breeding sites of the Southwestern Willow Flycatcher (290 individuals) using 38 amplified fragment length polymorphisms (AFLPs). Our results suggest that considerable genetic diversity exists within the subspecies and within local breeding sites. Statistical analyses of genetic variation revealed only slight, although significant, differentiation among breeding sites (Mantel's r = 0.0705, P < 0.0005; θ = 0.0816, 95% CI = 0.0608 to 0.1034; ΦST = 0.0458, P < 0.001). UPGMA cluster analysis of the AFLP markers indicates that extensive gene flow has occurred among breeding sites. No one site stood out as being genetically unique or isolated. Therefore, the small level of genetic structure that we detected may not be biologically significant. Ongoing field studies are consistent with this conclusion. Of the banded birds that were resighted or recaptured in Arizona during the 1996 to 1998 breeding seasons, one-third moved between breeding sites and two-thirds were philopatric. Low differentiation may be the result of historically high rangewide diversity followed by recent geographic isolation of breeding sites, although observational data indicate that gene flow is a current phenomenon. Our data suggest that breeding groups of E. t. extimus act as a metapopulation.

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure.

PubMed

Druml, T; Baumung, R; Sölkner, J

2009-10-01

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.

A Genetic Analysis of Taoyuan Pig and Its Phylogenetic Relationship to Eurasian Pig Breeds

PubMed Central

Li, Kuan-Yi; Li, Kuang-Ti; Cheng, Chun-Chun; Chen, Chia-Hsuan; Hung, Chien-Yi; Ju, Yu-Ten

2015-01-01

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan’s early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value (FIS) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high FST values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes. PMID:25656199

Timing of initial arrival at the breeding site predicts age at first reproduction in a long-lived migratory bird

PubMed Central

Becker, Peter H.; Dittmann, Tobias; Ludwigs, Jan-Dieter; Limmer, Bente; Ludwig, Sonja C.; Bauch, Christina; Braasch, Alexander; Wendeln, Helmut

2008-01-01

In long-lived vertebrates, individuals generally visit potential breeding areas or populations during one or more seasons before reproducing for the first time. During these years of prospecting, they select a future breeding site, colony, or mate and improve various skills and their physical condition to meet the requirements of reproduction. One precondition of successful reproduction is arrival in time on the breeding grounds. Here, we study the intricate links among the date of initial spring arrival, body mass, sex, and the age of first breeding in the common tern Sterna hirundo, a long-lived migratory colonial seabird. The study is based on a unique, individual-based, long-term dataset of sexed birds, marked with transponders, which allow recording their individual arrival, overall attendance, and clutch initiation remotely and automatically year by year over the entire lifetime at the natal colony site. We show that the seasonal date of initial arrival at the breeding grounds predicts the individual age at first reproduction, which mostly occurs years later. Late first-time arrivals remain delayed birds throughout subsequent years. Our findings reveal that timing of arrival at the site of reproduction and timing of reproduction itself are coherent parameters of individual quality, which are linked with the prospects of the breeding career and may have consequences for fitness. PMID:18711134

Predicting breed composition using breed frequencies of 50,000 markers from the U.S. Meat Animal Research Center 2,000 bull project

USDA-ARS?s Scientific Manuscript database

Knowledge of breed composition can be useful in multiple aspects of cattle production, and can be critical for analyzing the results of whole genome wide association studies (GWAS) currently being conducted around the world. We examine the feasibility and accuracy of using genotype data from the mo...

Health and Behavioral Survey of over 8000 Finnish Cats

PubMed Central

Vapalahti, Katariina; Virtala, Anna-Maija; Joensuu, Tara A.; Tiira, Katriina; Tähtinen, Jaana; Lohi, Hannes

2016-01-01

A comprehensive feline health survey was conducted to reveal breed-specific inheritable diseases in Finnish pedigree cats for genetic research. Prevalence of 19 disease categories and 227 feline diseases were defined in a study population of 8175 cats belonging to 30 breeds. Dental and oral diseases, with a prevalence of 28%, and dental calculus and gingivitis (21 and 8%, respectively) were the most prevalent disease category and diseases among all cats and in most of the breeds. An exception was Korats, which were more often affected by the diseases of the respiratory tract (23%) and asthma (19%). Other prevalent disease categories affected various organ systems, such as the skin (12%), the urinary system (12%), the digestive tract (11%), eyes (10%), the musculoskeletal system (10%), and genitals of female cats (17%). Prevalent health or developmental issues included repetitive vomiting (4%), tail kink (4%), feline odontoclastic resorption lesion (4%), urinary tract infections (4%), as well as cesarean section (6%) and stillborn kittens (6%) among female cats. We found 57 breed-specific conditions by Fisher’s exact tests and logistic regression analyses, including 32 previously described and 19 new breed-specific diseases. The genetic defect has already been found in six of them: polycystic kidney disease, progressive retinal atrophy, hypertrophic cardiomyopathy, and three types of tail malformations. Behavioral profiling revealed breed-specific traits, such as an increased human avoidance in British Short and Longhairs and a higher level of aggression in Turkish vans. Our epidemiological study reveals the overall health profile in Finnish pure and mixed breed cats and identifies many breed-specific conditions without molecular identity for genetic research. PMID:27622188

Agriculture modifies the seasonal decline of breeding success in a tropical wild bird population

PubMed Central

Cartwright, Samantha J; Nicoll, Malcolm A C; Jones, Carl G; Tatayah, Vikash; Norris, Ken

2014-01-01

Habitat conversion for agriculture is a major driver of biodiversity loss, but our understanding of the demographic processes involved remains poor. We typically investigate the impacts of agriculture in isolation even though populations are likely to experience multiple, concurrent changes in the environment (e.g. land and climate change). Drivers of environmental change may interact to affect demography, but the mechanisms have yet to be explored fully in wild populations. Here, we investigate the mechanisms linking agricultural land use with breeding success using long-term data for the formerly Critically Endangered Mauritius kestrel Falco punctatus, a tropical forest specialist that also occupies agricultural habitats. We specifically focused on the relationship between breeding success, agriculture and the timing of breeding because the latter is sensitive to changes in climatic conditions (spring rainfall) and enables us to explore the interactive effects of different (land and climate) drivers of environmental change. Breeding success, measured as egg survival to fledging, declines seasonally in this population, but we found that the rate of this decline became increasingly rapid as the area of agriculture around a nest site increased. If the relationship between breeding success and agriculture was used in isolation to estimate the demographic impact of agriculture, it would significantly under-estimate breeding success in dry (early) springs and over-estimate breeding success in wet (late) springs. Analysis of prey delivered to nests suggests that the relationship between breeding success and agriculture might be due, in part, to spatial variation in the availability of native, arboreal geckos. Synthesis and applications. Agriculture modifies the seasonal decline in breeding success in this population. As springs are becoming wetter in our study area and since the kestrels breed later in wetter springs, the impact of agriculture on breeding success will become worse over time. Our results suggest that forest restoration designed to reduce the detrimental impacts of agriculture on breeding may also help reduce the detrimental effects of breeding late due to wetter springs. Our results therefore highlight the importance of considering the interactive effects of environmental change when managing wild populations. PMID:25558086

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Wolf (Canis lupus) Generation Time and Proportion of Current Breeding Females by Age.

PubMed

Mech, L David; Barber-Meyer, Shannon M; Erb, John

2016-01-01

Information is sparse about aspects of female wolf (Canis lupus) breeding in the wild, including age of first reproduction, mean age of primiparity, generation time, and proportion of each age that breeds in any given year. We studied these subjects in 86 wolves (113 captures) in the Superior National Forest (SNF), Minnesota (MN), during 1972-2013 where wolves were legally protected for most of the period, and in 159 harvested wolves from throughout MN wolf range during 2012-2014. Breeding status of SNF wolves were assessed via nipple measurements, and wolves from throughout MN wolf range, by placental scars. In the SNF, proportions of currently breeding females (those breeding in the year sampled) ranged from 19% at age 2 to 80% at age 5, and from throughout wolf range, from 33% at age 2 to 100% at age 7. Excluding pups and yearlings, only 33% to 36% of SNF females and 58% of females from throughout MN wolf range bred in any given year. Generation time for SNF wolves was 4.3 years and for MN wolf range, 4.7 years. These findings will be useful in modeling wolf population dynamics and in wolf genetic and dog-domestication studies.

Microsatellite-based phylogeny of Indian domestic goats

PubMed Central

Rout, Pramod K; Joshi, Manjunath B; Mandal, Ajoy; Laloe, D; Singh, Lalji; Thangaraj, Kumarasamy

2008-01-01

Background The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones. Results The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The DA measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution. Conclusion Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information. PMID:18226239

Geographic distribution of haplotype diversity at the bovine casein locus

PubMed Central

Jann, Oliver C; Ibeagha-Awemu, Eveline M; Özbeyaz, Ceyhan; Zaragoza, Pilar; Williams, John L; Ajmone-Marsan, Paolo; Lenstra, Johannes A; Moazami-Goudarzi, Katy; Erhardt, Georg

2004-01-01

The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed. PMID:15040901

Wolf (Canis lupus) generation time and proportion of current breeding females by age

USGS Publications Warehouse

Mech, L. David; Barber-Meyer, Shannon M.; Erb, John

2016-01-01

Information is sparse about aspects of female wolf (Canis lupus) breeding in the wild, including age of first reproduction, mean age of primiparity, generation time, and proportion of each age that breeds in any given year. We studied these subjects in 86 wolves (113 captures) in the Superior National Forest (SNF), Minnesota (MN), during 1972–2013 where wolves were legally protected for most of the period, and in 159 harvested wolves from throughout MN wolf range during 2012–2014. Breeding status of SNF wolves were assessed via nipple measurements, and wolves from throughout MN wolf range, by placental scars. In the SNF, proportions of currently breeding females (those breeding in the year sampled) ranged from 19% at age 2 to 80% at age 5, and from throughout wolf range, from 33% at age 2 to 100% at age 7. Excluding pups and yearlings, only 33% to 36% of SNF females and 58% of females from throughout MN wolf range bred in any given year. Generation time for SNF wolves was 4.3 years and for MN wolf range, 4.7 years. These findings will be useful in modeling wolf population dynamics and in wolf genetic and dog-domestication studies.

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

PubMed Central

Pirault, Pauline; Danvy, Sophy; Verrier, Etienne; Leroy, Grégoire

2013-01-01

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges. PMID:23630596

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

PubMed Central

Browett, Sam; McHugo, Gillian; Richardson, Ian W.; Magee, David A.; Park, Stephen D. E.; Fahey, Alan G.; Kearney, John F.; Correia, Carolina N.; Randhawa, Imtiaz A. S.; MacHugh, David E.

2018-01-01

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland. PMID:29520297

A genetic dissection of breed composition and performance enhancement in the Alaskan sled dog

PubMed Central

2010-01-01

Background The Alaskan sled dog offers a rare opportunity to investigate the development of a dog breed based solely on performance, rather than appearance, thus setting the breed apart from most others. Several established breeds, many of which are recognized by the American Kennel Club (AKC), have been introduced into the sled dog population to enhance racing performance. We have used molecular methods to ascertain the constitutive breeds used to develop successful sled dog lines, and in doing so, determined the breed origins of specific performance-related behaviors. One hundred and ninety-nine Alaskan sled dogs were genotyped using 96 microsatellite markers that span the canine genome. These data were compared to that from 141 similarly genotyped purebred dog breeds. Sled dogs were evaluated for breed composition based on a variety of performance phenotypes including speed, endurance and work ethic, and the data stratified based on population structure. Results We observe that the Alaskan sled dog has a unique molecular signature and that the genetic profile is sufficient for identifying dogs bred for sprint versus distance. When evaluating contributions of existing breeds we find that the Alaskan Malamute and Siberian Husky contributions are associated with enhanced endurance; Pointer and Saluki are associated with enhanced speed and the Anatolian Shepherd demonstrates a positive influence on work ethic. Conclusion We have established a genetic breed profile for the Alaskan sled dog, identified profile variance between sprint and distance dogs, and established breeds associated with enhanced performance attributes. These data set the stage for mapping studies aimed at finding genes that are associated with athletic attributes integral to the high performing Alaskan sled dog. PMID:20649949

Fasting urinary calcium-to-creatinine and oxalate-to-creatinine ratios in dogs with calcium oxalate urolithiasis and breed-matched controls.

PubMed

Furrow, E; Patterson, E E; Armstrong, P J; Osborne, C A; Lulich, J P

2015-01-01

Hypercalciuria and hyperoxaluria are risk factors for calcium oxalate (CaOx) urolithiasis, but breed-specific reports of urinary metabolites and their relationship with stone status are lacking. To compare urinary metabolites (calcium and oxalate) and blood ionized calcium (iCa) concentrations between CaOx stone formers and breed-matched stone-free controls for the Miniature Schnauzer, Bichon Frise, and Shih Tzu breeds. Forty-seven Miniature Schnauzers (23 cases and 24 controls), 27 Bichons Frise (14 cases and 13 controls), and 15 Shih Tzus (7 cases and 8 controls). Prospective study. Fasting spot urinary calcium-to-creatinine and oxalate-to-creatinine ratios (UCa/Cr and UOx/Cr, respectively) and blood iCa concentrations were measured and compared between cases and controls within and across breeds. Regression models were used to test the effect of patient and environmental factors on these variables. UCa/Cr was higher in cases than controls for each of the 3 breeds. In addition to stone status, being on a therapeutic food designed to prevent CaOx stone recurrence was associated with higher UCa/Cr. UOx/Cr did not differ between cases and controls for any of the breeds. Blood iCa was higher in cases than controls in the Miniature Schnauzer and Bichon Frise breeds and had a moderate correlation with UCa/Cr. Hypercalciuria is associated with CaOx stone status in the Miniature Schnauzer, Bichon Frise, and Shih Tzu breeds. UOx/Cr did not correlate with stone status in these 3 breeds. These findings may influence breed-specific stone prevention recommendations. Copyright © 2015 by the American College of Veterinary Internal Medicine.

Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

PubMed

Rochus, Christina M; Johansson, Anna M

2017-01-01

Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

Toxicity of DDT to Japanese quail as influenced by body weight, breeding condition, and sex

USGS Publications Warehouse

Gish, C.D.; Chura, N.J.

1970-01-01

Controlled experiments were utilized to simulate the stresses on wild birds of breeding condition and of weight loss due to migration. Light conditions in the laboratory were manipulated to produce Japanese quail (Coturnix coturnix japonica) in breeding condition and not in breeding condition. Within each of these groups, some birds were partially starved before dosage and some were fully fed. Birds were then fed dietary levels of 0, 700, 922, 1214, or 1600 ppm dry weight of p,p?-DDT for a period of 20 days or until death. Birds partially starved before dosage were more susceptible to DDT intoxication than nonstarved ones, and birds not in breeding condition were slightly more so than birds in breeding condition. Similarly, males died earlier than females, and the birds of the lighter weight strain used in the second half of the study died earlier than the birds of the heavier strain used in the first half. The heavier birds of each sex not only survived longer than lighter individuals receiving the same treatments, but they also lost a greater proportion of their weight before death. During the early portion of the dosage period, females in breeding condition were less sensitive to DDT than were females not in breeding condition and males. After 10 days on dosage, however, the cumulative mortality of females in breeding condition rapidly approached that of males and of females not in breeding condition. Food restriction prior to dosage, strains of quail, breeding conditions, and sexes resulted in weight differences and a corresponding accentuation or delay of the effects of the different levels of DDT.