Science.gov

Sample records for persistence genetic variation

  1. Brief communication: Effect of nomadic subsistence practices on lactase persistence associated genetic variation in Kuwait.

    PubMed

    Hill, Sarah Catherine; Mohammad, Talal Ramadan; Kivisild, Toomas

    2013-09-01

    Lactase persistence (LP)-the ability to digest lactose in adulthood-is paradigmatic of Holocenic dietary change affecting the evolutionary trajectory of specific populations. Kuwait represents one location of high LP where the variation in associated genomic regions has not been examined. Here, we present new sequence data from a 427 bp amplicon 14 kb upstream of the LCT (lactase) gene for two Bedouin tribal populations, the Ajman and Mutran. We estimate the frequency of known LP associated alleles and discuss the impact of nomadic-pastoralism on the associated genetic variation. We observe high frequency (56% on average) of the -13,915*G allele in both tribes, which is consistent with the high prevalence of LP in Kuwait. Whilst LP associated alleles occur in Kuwait at a similar frequency to other regional populations, we suggest that the -13,915*G allele frequency among the Kuwaiti Bedouin may be higher than among non-Bedouin Kuwaitis, possibly due to greater historical reliance on milk consumption or genetic drift.

  2. Genetic variation of foot-and-mouth disease virus isolates recovered from persistently infected water buffalo (Bubalus bubalis).

    PubMed

    Barros, José Júnior F; Malirat, Viviana; Rebello, Moacyr A; Costa, Eliane V; Bergmann, Ingrid E

    2007-02-25

    Genetic variation of foot-and-mouth disease virus (FMDV) isolates, serotype O, recovered serially over a 1-year period from persistently infected buffalos was assessed. The persistent state was established experimentally with plaque-purified FMDV, strain O(1)Campos, in five buffalos (Bubalus bubalis). Viral isolates collected from esophageal-pharyngeal (EP) fluids for up to 71 weeks after infection were analyzed at different times by nucleotide sequencing and T(1) RNase oligonucleotide fingerprinting to assess variability in the VP1-coding region and in the complete genome, respectively. Genetic variation increased, although irregularly, with time after infection. The highest values observed for the VP1-coding region and for the whole genome were 2.5% and 1.8%, respectively. High rates of fixation of mutations were observed using both methodologies, reaching values of 0.65 substitutions per nucleotide per year (s/nt/y) and 0.44s/nt/y for nucleotide sequencing and oligonucleotide fingerprinting, respectively, when selected samples recovered at close time periods were analyzed. The data herein indicate that complex mixtures of genotypes may arise during FMDV type O persistent infection in water buffalos, which can act as viral reservoirs and also represent a potential source of viral variants. These results fit within the quasi-species dynamics described for FMDV, in which viral populations are constituted by related, non-identical genomes that evolve independently from each other, and may predominate at a given time.

  3. Antigenic and genetic variation in cytopathic hepatitis A virus variants arising during persistent infection: evidence for genetic recombination.

    PubMed Central

    Lemon, S M; Murphy, P C; Shields, P A; Ping, L H; Feinstone, S M; Cromeans, T; Jansen, R W

    1991-01-01

    Variants of hepatitis A virus (pHM175 virus) recovered from persistently infected green monkey kidney (BS-C-1) cells induced a cytopathic effect during serial passage in BS-C-1 or fetal rhesus kidney (FRhK-4) cells. Epitope-specific radioimmunofocus assays showed that this virus comprised two virion populations, one with altered antigenicity including neutralization resistance to monoclonal antibody K24F2, and the other with normal antigenic characteristics. Replication of the antigenic variant was favored over that of virus with the normal antigenic phenotype during persistent infection, while virus with the normal antigenic phenotype was selected during serial passage. Viruses of each type were clonally isolated; both were cytopathic in cell cultures and displayed a rapid replication phenotype when compared with the noncytopathic passage 16 (p16) HM175 virus which was used to establish the original persistent infection. The two cytopathic virus clones contained 31 and 34 nucleotide changes from the sequence of p16 HM175. Both shared a common 5' sequence (bases 30 to 1677), as well as sequence identity in the P2-P3 region (bases 3249 to 5303 and 6462 to 6781) and 3' terminus (bases 7272 to 7478). VP3, VP1, and 3Cpro contained different mutations in the two virus clones, with amino acid substitutions at residues 70 of VP3 and 197 and 276 of VP1 of the antigenic variant. These capsid mutations did not affect virion thermal stability. A comparison of the nearly complete genomic sequences of three clonally isolated cytopathic variants was suggestive of genetic recombination between these viruses during persistent infection and indicated that mutations in both 5' and 3' nontranslated regions and in the nonstructural proteins 2A, 2B, 2C, 3A, and 3Dpol may be related to the cytopathic phenotype. Images PMID:1705995

  4. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola.

    PubMed

    Coelho, Margarida; Sequeira, Fernando; Luiselli, Donata; Beleza, Sandra; Rocha, Jorge

    2009-04-21

    Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations. Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12%) and mtDNA (22%) Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%), which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals. Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus and the Khoe-San likely involved cattle herders from the

  5. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

    PubMed Central

    Coelho, Margarida; Sequeira, Fernando; Luiselli, Donata; Beleza, Sandra; Rocha, Jorge

    2009-01-01

    Background Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale). We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations. Results Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12%) and mtDNA (22%) Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%), which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals. Conclusion Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus and the Khoe-San likely

  6. Genetic variation during persistent reovirus infection: isolation of cold-sensitive and temperature-sensitive mutants from persistently infected L cells.

    PubMed

    Ahmed, R; Kauffman, R S; Fields, B N

    1983-11-01

    We have examined the evolution of reovirus in two independently established persistently infected (p.i.) cell lines. We found that reovirus undergoes extensive mutation during persistent infection in L cells. However, there was no consistent pattern of virus evolution; in one p.i. cell line temperature-sensitive (ts) mutants were selected, whereas cold-sensitive (cs) mutants were isolated from the second p.i. culture. Neither the cs nor the ts mutants isolated from the carrier cultures expressed their defect at 37 degrees, the temperature at which the p.i. cells were maintained, indicating that the cs and ts phenotypes were nonselected markers. These results emphasize the point that emergence of the ts or cs mutants during persistent infection only signifies that the virus has changed; it does not necessarily imply that the particular mutant is essential for the maintenance of the persistent infection. Given the high mutation rate of viruses, and the wide spectrum of viral mutants present in carrier cultures, it is essential to distinguish the relevant changes from those which may simply represent an epiphenomenon. In the accompanying paper (R. S. Kauffman, R. Ahmed, and B. N. Fields Virology, 130, 79-87, 1983), we show that by using a genetic approach, it is possible to identify the viral gene(s) which are critical for the maintenance of persistent reovirus infection.

  7. Will Climate Change, Genetic and Demographic Variation or Rat Predation Pose the Greatest Risk for Persistence of an Altitudinally Distributed Island Endemic?

    PubMed Central

    Simmons, Catherine Laura; Auld, Tony D.; Hutton, Ian; Baker, William J.; Shapcott, Alison

    2012-01-01

    Species endemic to mountains on oceanic islands are subject to a number of existing threats (in particular, invasive species) along with the impacts of a rapidly changing climate. The Lord Howe Island endemic palm Hedyscepe canterburyana is restricted to two mountains above 300 m altitude. Predation by the introduced Black Rat (Rattus rattus) is known to significantly reduce seedling recruitment. We examined the variation in Hedyscepe in terms of genetic variation, morphology, reproductive output and demographic structure, across an altitudinal gradient. We used demographic data to model population persistence under climate change predictions of upward range contraction incorporating long-term climatic records for Lord Howe Island. We also accounted for alternative levels of rat predation into the model to reflect management options for control. We found that Lord Howe Island is getting warmer and drier and quantified the degree of temperature change with altitude (0.9 °C per 100 m). For H. canterburyana, differences in development rates, population structure, reproductive output and population growth rate were identified between altitudes. In contrast, genetic variation was high and did not vary with altitude. There is no evidence of an upward range contraction as was predicted and recruitment was greatest at lower altitudes. Our models predicted slow population decline in the species and that the highest altitude populations are under greatest threat of extinction. Removal of rat predation would significantly enhance future persistence of this species. PMID:24832517

  8. Genetics and variation

    Treesearch

    John R. Jones; Norbert V. DeByle

    1985-01-01

    The broad genotypic variability in quaking aspen (Populus tremuloides Michx.), that results in equally broad phenotypic variability among clones is important to the ecology and management of this species. This chapter considers principles of aspen genetics and variation, variation in aspen over its range, and local variation among clones. For a more...

  9. Genetic engineering compared to natural genetic variations.

    PubMed

    Arber, Werner

    2010-11-30

    By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades.

  10. Lactose digestion and the evolutionary genetics of lactase persistence.

    PubMed

    Ingram, Catherine J E; Mulcare, Charlotte A; Itan, Yuval; Thomas, Mark G; Swallow, Dallas M

    2009-01-01

    It has been known for some 40 years that lactase production persists into adult life in some people but not in others. However, the mechanism and evolutionary significance of this variation have proved more elusive, and continue to excite the interest of investigators from different disciplines. This genetically determined trait differs in frequency worldwide and is due to cis-acting polymorphism of regulation of lactase gene expression. A single nucleotide polymorphism located 13.9 kb upstream from the lactase gene (C-13910 > T) was proposed to be the cause, and the -13910*T allele, which is widespread in Europe was found to be located on a very extended haplotype of 500 kb or more. The long region of haplotype conservation reflects a recent origin, and this, together with high frequencies, is evidence of positive selection, but also means that -13910*T might be an associated marker, rather than being causal of lactase persistence itself. Doubt about function was increased when it was shown that the original SNP did not account for lactase persistence in most African populations. However, the recent discovery that there are several other SNPs associated with lactase persistence in close proximity (within 100 bp), and that they all reside in a piece of sequence that has enhancer function in vitro, does suggest that they may each be functional, and their occurrence on different haplotype backgrounds shows that several independent mutations led to lactase persistence. Here we provide access to a database of worldwide distributions of lactase persistence and of the C-13910*T allele, as well as reviewing lactase molecular and population genetics and the role of selection in determining present day distributions of the lactase persistence phenotype.

  11. Cryptic Genetic Variation in Evolutionary Developmental Genetics.

    PubMed

    Paaby, Annalise B; Gibson, Greg

    2016-06-13

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

  12. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    PubMed Central

    Paaby, Annalise B.; Gibson, Greg

    2016-01-01

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits. PMID:27304973

  13. GENETIC VARIATION AT AN IMMUNE SYSTEM LOCUS PROVIDES BOTH A GENERALIZED AND SPECIFIC STRESS INDICATOR: EFFECTS OF PERSISTENT, BIOACCUMULATIVE AND TOXIC CONTAIMINANT EXPOSURES ON AN ESTUARINE FISH POPULATION

    EPA Science Inventory

    The major histocompatibility complex (MHC) is a group of linked genes that mediates the adaptive immune response in vertebrates. Studies using mammals and birds have shown that environmental stressors can directly and indirectly produce genetic changes at MHC loci that can affect...

  14. GENETIC VARIATION AT AN IMMUNE SYSTEM LOCUS PROVIDES BOTH A GENERALIZED AND SPECIFIC STRESS INDICATOR: EFFECTS OF PERSISTENT, BIOACCUMULATIVE AND TOXIC CONTAIMINANT EXPOSURES ON AN ESTUARINE FISH POPULATION

    EPA Science Inventory

    The major histocompatibility complex (MHC) is a group of linked genes that mediates the adaptive immune response in vertebrates. Studies using mammals and birds have shown that environmental stressors can directly and indirectly produce genetic changes at MHC loci that can affect...

  15. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

  16. Molecular Darwinism: the contingency of spontaneous genetic variation.

    PubMed

    Arber, Werner

    2011-01-01

    The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

  17. Sex reduces genetic variation: a multidisciplinary review.

    PubMed

    Gorelick, Root; Heng, Henry H Q

    2011-04-01

    For over a century, the paradigm has been that sex invariably increases genetic variation, despite many renowned biologists asserting that sex decreases most genetic variation. Sex is usually perceived as the source of additive genetic variance that drives eukaryotic evolution vis-à-vis adaptation and Fisher's fundamental theorem. However, evidence for sex decreasing genetic variation appears in ecology, paleontology, population genetics, and cancer biology. The common thread among many of these disciplines is that sex acts like a coarse filter, weeding out major changes, such as chromosomal rearrangements (that are almost always deleterious), but letting minor variation, such as changes at the nucleotide or gene level (that are often neutral), flow through the sexual sieve. Sex acts as a constraint on genomic and epigenetic variation, thereby limiting adaptive evolution. The diverse reasons for sex reducing genetic variation (especially at the genome level) and slowing down evolution may provide a sufficient benefit to offset the famed costs of sex.

  18. Genetic variation and its maintenance

    SciTech Connect

    Roberts, D.F.; De Stefano, G.F.

    1986-01-01

    This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

  19. Collecting genetic variation on a small island

    Treesearch

    S. Kallow; C. Trivedi

    2017-01-01

    Genetic variation is the most powerful factor in ensuring the long term success of trees and forests in times of change. In order to protect against loss of genetic variation from threats, including pests and diseases and climate change, the Royal Botanic Gardens, Kew, is developing a national tree seed collection for the United Kingdom. This paper...

  20. Genetic Variations in Vesicoureteral Reflux Sequelae

    PubMed Central

    Hains, David S.; Schwaderer, Andrew L.

    2016-01-01

    Urinary tract infections (UTI) are a common condition in children. Vesicoureteral reflux (VUR) represents a common associated condition with childhood UTI. UTI susceptibility appears to have a genetic component based on family and UTI cohort studies. Targeted analysis of innate immune system genetic variations indicate that these variations are important in UTI susceptibility. In this overview, we discuss how current cohorts and genetic strategies can be implemented to discover new susceptibility loci in patients with UTI. PMID:26848692

  1. Genetic Variation in Cardiomyopathy and Cardiovascular Disorders.

    PubMed

    McNally, Elizabeth M; Puckelwartz, Megan J

    2015-01-01

    With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.

  2. The Genetic Contribution to Phenological Variation

    NASA Astrophysics Data System (ADS)

    Friedman, J. M.; Roelle, J. E.; Cade, B. S.

    2009-12-01

    Variation in phenology is often attributed to a changing climate. However, in wild populations some of the variation in phenology over space and time is a consequence of genetic variation. We used a common garden consisting of paired collections of native and introduced riparian trees sampled along a latitudinal gradient to explore the genetic component of latitudinal phenological variation. The garden in Fort Collins, Colorado (latitude 40.6°N), included 681 native plains cottonwood (Populus deltoides subsp. monilifera) and introduced saltcedar (Tamarix ramosissima, T. chinensis and hybrids) collected from 15 sites at 29.2-47.6°N in the central United States. In the common garden both species showed latitudinal variation in fall, but not spring, leaf phenology, demonstrating that the latitudinal gradient in fall phenology observed in the field reflects both genetic and climatic variation, while the latitudinal gradient in spring phenology observed in the field reflects climatic variation alone. In contrast, cold hardiness showed strong genetic variation in both fall and spring for both species. The latitudinal variation in fall phenology and cold hardiness of saltcedar appears to have evolved through hybridization and natural selection in the 150 years since introduction. We suggest that phenological networks observing wild populations include marked trees replicated in common gardens to distinguish genetic and environmental influences on phenology.

  3. Genetic Variation Sampled in Three California Oaks

    Treesearch

    Lawrence A. Riggs; Constance I. Millar; Diane L. Delany

    1991-01-01

    As a first step in acquiring genetic information about oak species indigenous to California's hardwood rangelands we drew on experience from both forest regeneration and species conservation and applied biochemical techniques for rapidly assaying patterns of genetic variation. In a study sponsored by the California Integrated Hardwood Range Management Program we...

  4. Genetic sources of population epigenomic variation.

    PubMed

    Taudt, Aaron; Colomé-Tatché, Maria; Johannes, Frank

    2016-06-01

    The field of epigenomics has rapidly progressed from the study of individual reference epigenomes to surveying epigenomic variation in populations. Recent studies in a number of species, from yeast to humans, have begun to dissect the cis- and trans-regulatory genetic mechanisms that shape patterns of population epigenomic variation at the level of single epigenetic marks, as well as at the level of integrated chromatin state maps. We show that this information is paving the way towards a more complete understanding of the heritable basis underlying population epigenomic variation. We also highlight important conceptual challenges when interpreting results from these genetic studies, particularly in plants, in which epigenomic variation can be determined both by genetic and epigenetic inheritance.

  5. Genetic Variations Involved in Vitamin E Status

    PubMed Central

    Borel, Patrick; Desmarchelier, Charles

    2016-01-01

    Vitamin E (VE) is the generic term for four tocopherols and four tocotrienols that exhibit the biological activity of α-tocopherol. VE status, which is usually estimated by measuring fasting blood VE concentration, is affected by numerous factors, such as dietary VE intake, VE absorption efficiency, and VE catabolism. Several of these factors are in turn modulated by genetic variations in genes encoding proteins involved in these factors. To identify these genetic variations, two strategies have been used: genome-wide association studies and candidate gene association studies. Each of these strategies has its advantages and its drawbacks, nevertheless they have allowed us to identify a list of single nucleotide polymorphisms associated with fasting blood VE concentration and α-tocopherol bioavailability. However, much work remains to be done to identify, and to replicate in different populations, all the single nucleotide polymorphisms involved, to assess the possible involvement of other kind of genetic variations, e.g., copy number variants and epigenetic modifications, in order to establish a reliable list of genetic variations that will allow us to predict the VE status of an individual by knowing their genotype in these genetic variations. Yet, the potential usefulness of this area of research is exciting with regard to personalized nutrition and for future clinical trials dedicated to assessing the biological effects of the various isoforms of VE. PMID:27983595

  6. Community Engagement about Genetic Variation Research

    PubMed Central

    Christensen, Kurt D.; Metosky, Susan; Rudofsky, Gayle; Deignan, Kathleen P.; Martinez, Hulda; Johnson-Moore, Penelope; Citrin, Toby

    2012-01-01

    Abstract The aim of this article is to describe the methods and effectiveness of the Public Engagement in Genetic Variation and Haplotype Mapping Issues (PEGV) Project, which engaged a community in policy discussion about genetic variation research. The project implemented a 6-stage community engagement model in New Rochelle, New York. First, researchers recruited community partners. Second, the project team created community oversight. Third, focus groups discussed concerns generated by genetic variation research. Fourth, community dialogue sessions addressed focus group findings and developed policy recommendations. Fifth, a conference was held to present these policy recommendations and to provide a forum for HapMap (haplotype mapping) researchers to dialogue directly with residents. Finally, findings were disseminated via presentations and papers to the participants and to the wider community beyond. The project generated a list of proposed guidelines for genetic variation research that addressed the concerns of New Rochelle residents. Project team members expressed satisfaction with the engagement model overall but expressed concerns about how well community groups were utilized and what segment of the community actually engaged in the project. The PEGV Project represents a model for researchers to engage the general public in policy development about genetic research. There are benefits of such a process beyond the desired genetic research. (Population Health Management 2012;15:78–89) PMID:21815821

  7. The population genetic theory of hidden variation and genetic robustness.

    PubMed

    Hermisson, Joachim; Wagner, Günter P

    2004-12-01

    One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype.

  8. Genetic variation, predator–prey interactions and food web structure

    PubMed Central

    Moya-Laraño, Jordi

    2011-01-01

    Food webs are networks of species that feed on each other. The role that within-population phenotypic and genetic variation plays in food web structure is largely unknown. Here, I show via simulation how variation in two key traits, growth rates and phenology, by influencing the variability of body sizes present through time, can potentially affect several structural parameters in the direction of enhancing food web persistence: increased connectance, decreased interaction strengths, increased variation among interaction strengths and increased degree of omnivory. I discuss other relevant traits whose variation could affect the structure of food webs, such as morphological and additional life-history traits, as well as animal personalities. Furthermore, trait variation could also contribute to the stability of food web modules through metacommunity dynamics. I propose future research to help establish a link between within-population variation and food web structure. If appropriately established, such a link could have important consequences for biological conservation, as it would imply that preserving (functional) genetic variation within populations could ensure the preservation of entire communities. PMID:21444316

  9. A global reference for human genetic variation.

    PubMed

    Auton, Adam; Brooks, Lisa D; Durbin, Richard M; Garrison, Erik P; Kang, Hyun Min; Korbel, Jan O; Marchini, Jonathan L; McCarthy, Shane; McVean, Gil A; Abecasis, Gonçalo R

    2015-10-01

    The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

  10. A global reference for human genetic variation

    PubMed Central

    2016-01-01

    The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. PMID:26432245

  11. Genetic diversity of lactase persistence in East African populations.

    PubMed

    Hassan, Hisham Y; van Erp, Anke; Jaeger, Martin; Tahir, Hanan; Oosting, Marije; Joosten, Leo A B; Netea, Mihai G

    2016-01-04

    The expression of lactase which digests lactose from milk in humans is generally lost after weaning, but selected mutations influencing the promoter of the lactase gene have spread into the human populations. This is considered a classical example of gene-culture co-evolution, and several studies suggested that the lactase gene has been under strong directional evolutionary selective pressure in the past 5000 to 10,000 years. In the present study we investigated the distribution of three gene variants leading to lactase persistence in 12 different East African populations as well as one European population. Our results show that with the exception of Copts and Nilotic populations who are fully lactose non-persistent, the majority of populations of East Africa show at least partly lactose persistence, with both ethnic and socio-economic aspects playing an important role in the distribution of genetic variants. In this study, the variants C/G-13907 and T/G-13915, which are the major variants among the nomadic Arabs in the Arabia and Beja of East Africa, showed remarkable frequencies in Sudanese populations, especially those of pastoralists, in line with the historical links and bidirectional migration of nomadic populations between Arabia and East Africa. The C/T-13910 variant, generally associated with European populations is uniquely present among the Fulani. These data indicate that a combination of socio-economic, ethnic and evolutionary factors converged to shape the genetic structure of lactase persistence in East African populations.

  12. A brief history of genetic variation analysis.

    PubMed

    Ahmadian, Afshin; Lundeberg, Joakim

    2002-05-01

    As the human genome sequence is determined, there is an emerging need for the analysis of human sequence variations as genetic markers in diagnosis, linkage and association studies, cancer research, and pharmacogenomics. There are several different techniques and approaches for detecting these genetic variations, and here we review some of these techniques and their application fields. However, all the techniques have advantages and disadvantages, andfactors such as laboratory instrumentation, personnel experience, required accuracy, required throughput, and cost often have to be taken into account before selecting a method.

  13. Genetic variation in cultivated Rheum tanguticum populations

    PubMed Central

    Hu, Yanping; Xie, Xiaolong; Wang, Li; Zhang, Huaigang; Yang, Jian; Li, Yi

    2014-01-01

    To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, HB = 0.3231, I = 0.3812) and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA) showed that more genetic variation was found within populations (76.1%) than among them (23.9%). This was supported by the coefficient of gene differentiation (Gst = 0.2742) and Bayesian analysis (θB = 0.1963). The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686). UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3). A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum. PMID:25249777

  14. The probability of parallel genetic evolution from standing genetic variation.

    PubMed

    MacPherson, A; Nuismer, S L

    2017-02-01

    Parallel evolution is often assumed to result from repeated adaptation to novel, yet ecologically similar, environments. Here, we develop and analyse a mathematical model that predicts the probability of parallel genetic evolution from standing genetic variation as a function of the strength of phenotypic selection and constraints imposed by genetic architecture. Our results show that the probability of parallel genetic evolution increases with the strength of natural selection and effective population size and is particularly likely to occur for genes with large phenotypic effects. Building on these results, we develop a Bayesian framework for estimating the strength of parallel phenotypic selection from genetic data. Using extensive individual-based simulations, we show that our estimator is robust across a wide range of genetic and evolutionary scenarios and provides a useful tool for rigorously testing the hypothesis that parallel genetic evolution is the result of adaptive evolution. An important result that emerges from our analyses is that existing studies of parallel genetic evolution frequently rely on data that is insufficient for distinguishing between adaptive evolution and neutral evolution driven by random genetic drift. Overcoming this challenge will require sampling more populations and the inclusion of larger numbers of loci.

  15. Genetic basis of persister tolerance to aminoglycosides in Escherichia coli.

    PubMed

    Shan, Yue; Lazinski, David; Rowe, Sarah; Camilli, Andrew; Lewis, Kim

    2015-04-07

    Persisters are dormant variants that form a subpopulation of drug-tolerant cells largely responsible for the recalcitrance of chronic infections. However, our understanding of the genetic basis of antibiotic tolerance remains incomplete. In this study, we applied transposon sequencing (Tn-Seq) to systematically investigate the mechanism of aminoglycoside tolerance in Escherichia coli. We constructed a highly saturated transposon library that covered the majority of E. coli genes and promoter regions and exposed a stationary-phase culture to a lethal dose of gentamicin. Tn-Seq was performed to evaluate the survival of each mutant to gentamicin exposure. We found that the disruption of several distinct pathways affected gentamicin tolerance. We identified 105 disrupted gene/promoter regions with a more than 5-fold reduction in gentamicin tolerance and 37 genes with a more than 5-fold increased tolerance. Functional cluster analysis suggests that deficiency in motility and amino acid synthesis significantly diminished persisters tolerant to gentamicin, without changing the MIC. Amino acid auxotrophs, including serine, threonine, glutamine, and tryptophan auxotrophs, exhibit strongly decreased tolerance to gentamicin, which cannot be restored by supplying the corresponding amino acids to the culture. Interestingly, supplying these amino acids to wild-type E. coli sensitizes stationary-phase cells to gentamicin, possibly through the inhibition of amino acid synthesis. In addition, we found that the deletion of amino acid synthesis genes significantly increases gentamicin uptake in stationary phase, while the deletion of flagellar genes does not affect gentamicin uptake. We conclude that activation of motility and amino acid biosynthesis contributes to the formation of persisters tolerant to gentamicin. Persisters are responsible for the recalcitrance of chronic infections to antibiotics. The pathways of persister formation in E. coli are redundant, and our understanding

  16. Relating Human Genetic Variation to Variation in Drug Responses

    PubMed Central

    Madian, Ashraf G.; Wheeler, Heather E.; Jones, Richard Baker; Dolan, M. Eileen

    2012-01-01

    Although sequencing a single human genome was a monumental effort a decade ago, more than one thousand genomes have now been sequenced. The task ahead lies in transforming this information into personalized treatment strategies that are tailored to the unique genetics of each individual. One important aspect of personalized medicine is patient-to-patient variation in drug response. Pharmacogenomics addresses this issue by seeking to identify genetic contributors to human variation in drug efficacy and toxicity. Here, we present a summary of the current status of this field, which has evolved from studies of single candidate genes to comprehensive genome-wide analyses. Additionally, we discuss the major challenges in translating this knowledge into a systems-level understanding of drug physiology with the ultimate goal of developing more effective personalized clinical treatment strategies. PMID:22840197

  17. Genetic variation of contact dermatitis in broilers.

    PubMed

    Ask, B

    2010-05-01

    This study aimed to investigate the presence of genetic variation in footpad dermatitis (FPD) and hock burns (HB) and the possibility to genetically select against these. A field trial including 10 commercial broiler lines (n = 102 to 265) was carried out at 2 Dutch farms. Footpad dermatitis and HB were subjectively scored at approximately 4, 5, and 7 wk on a scale from 0 through 5. Genetic parameters were estimated in 2 lines based on a larger data set. The overall agreement of repeated FPD and HB scores was high (0.66 to 0.86) and the scoring system was, therefore, considered reliable. Kendall's tau between left and right scores was lower than 1 (FPD: 0.73 and HB: 0.57), and both left and right FPD and HB must, therefore, be evaluated. High prevalences of FPD, but also HB, were achieved in the field trial, but lower prevalences may be sufficient for genetic evaluations and would be less detrimental to welfare. Genetic variation between and within lines was present for both FPD and HB as indicated by between-line differences and heritabilities, and selection against FPD and HB is, therefore, possible. It is important that selection is done against both FPD and HB, and such selection should not have a negative influence on the genetic improvement in BW. In contrast, continued selection for increased BW while ignoring FPD in the breeding goal is likely to lead to an increased propensity to develop FPD in broilers.

  18. Ecological release exposes genetically based niche variation.

    PubMed

    Emery, Nancy C; Ackerly, D D

    2014-09-01

    The evolutionary trajectories of ecological niches have profound impacts on community, population and speciation dynamics, yet the underlying causes of niche lability vs. stasis are poorly understood. Here, we conducted a field experiment to quantify the effects of competition and, conversely, competitive release on the microevolutionary processes driving microhabitat niche evolution in an annual plant population restricted to California vernal pool wetlands. Removing competitors generated a strong increase in mean fitness, the exposure of genetically based niche variation and directional selection for niche evolution in the experimental population. In contrast, genetic variation in the microhabitat niche and directional selection for niche evolution were not detected in individuals growing with competitors. These results indicate that ecological opportunity (here, the removal of competitors) can trigger the immediate expression of latent, heritable niche variation that is necessary for rapid evolutionary responses; conversely, competitors may restrict niche evolution, contributing to niche conservatism in saturated communities. © 2014 John Wiley & Sons Ltd/CNRS.

  19. The nature of genetic variation among viruses.

    PubMed

    Purcell, R H; Miller, R H

    1991-01-01

    Genetic variation among viruses may seem unimportant and academic--related only to pedagogical classification of things--but accurate determination of genetic relationships can have important implications, from characterizing the molecular basis of attenuation of viral vaccines to furthering knowledge about origins of viruses and even of life itself. It can even help to establish priority in the discovery of viruses when properly applied. The purpose of this brief review is to demonstrate how viruses change and what implications these changes can have on the delicate balance between the viral parasite and its host. Examples will be drawn from the hepatitis viruses when possible.

  20. Genetic specificity of a plant–insect food web: Implications for linking genetic variation to network complexity

    PubMed Central

    Barbour, Matthew A.; Fortuna, Miguel A.; Bascompte, Jordi; Nicholson, Joshua R.; Julkunen-Tiitto, Riitta; Jules, Erik S.; Crutsinger, Gregory M.

    2016-01-01

    Theory predicts that intraspecific genetic variation can increase the complexity of an ecological network. To date, however, we are lacking empirical knowledge of the extent to which genetic variation determines the assembly of ecological networks, as well as how the gain or loss of genetic variation will affect network structure. To address this knowledge gap, we used a common garden experiment to quantify the extent to which heritable trait variation in a host plant determines the assembly of its associated insect food web (network of trophic interactions). We then used a resampling procedure to simulate the additive effects of genetic variation on overall food-web complexity. We found that trait variation among host-plant genotypes was associated with resistance to insect herbivores, which indirectly affected interactions between herbivores and their insect parasitoids. Direct and indirect genetic effects resulted in distinct compositions of trophic interactions associated with each host-plant genotype. Moreover, our simulations suggest that food-web complexity would increase by 20% over the range of genetic variation in the experimental population of host plants. Taken together, our results indicate that intraspecific genetic variation can play a key role in structuring ecological networks, which may in turn affect network persistence. PMID:26858398

  1. Genetic and environmental stress, and the persistence of populations.

    PubMed

    Bijlsma, R; Bundgaard, J; Boerema, A C; Van Putten, W F

    1997-01-01

    Many populations of endangered species have to cope both with stressful and deteriorating environmental conditions (mostly the primary cause of the endangerment) and with an increase in homozygosity due to genetic drift and/or inbreeding in small isolated populations. The latter will result in genetic stress often accompanied by a decrease in fitness (inbreeding depression). We have studied the consequences of genetic stress, under optimal as well as stressful environmental conditions, for the fitness and persistence of small populations using Drosophila melanogaster as a model system. The results show that, already under optimal environmental conditions, an increase in homozygosity or inbreeding both impairs fitness and increases the extinction risk of populations significantly. Under environmental stress, however, these effects become greatly enhanced. More important, the results show that the impact of environmental stress becomes significantly greater for higher inbreeding levels. This explicitly demonstrates that genetic and environmental stress are not independent but can act synergistically. This apparent interaction may have important consequences for the conservation of endangered species.

  2. The capture of heritable variation for genetic quality through social competition.

    PubMed

    Wolf, Jason B; Harris, W Edwin; Royle, Nick J

    2008-09-01

    In theory, females of many species choose mates based on traits that are indicators of male genetic quality. A fundamental question in evolutionary biology is why genetic variation for such indicator traits persists despite strong persistent selection imposed by female preference, which is known as the lek paradox. One potential solution to the lek paradox suggests that the traits that are targets of mate choice should evolve condition-dependent expression and that condition should have a large genetic variance. Condition is expected to exhibit high genetic variance because it is affected by a large number of physiological processes and hence, condition-dependent traits should 'capture' variation contributed by a large number of loci. We suggest that a potentially important cause of variation in condition is competition for limited resources. Here, we discuss a pair of models to analyze the evolutionary genetics of traits affected by success in social competition for resources. We show that competition can contribute to genetic variation of 'competition-dependent' traits that have fundamentally different evolutionary properties than other sources of variation. Competition dependence can make traits honest indicators of genetic quality by revealing the relative competitive ability of males, can provide a component of heritable variation that does not contribute to trait evolution, and can help maintain heritable variation under directional selection. Here we provide a general introduction to the concept of competition dependence and briefly introduce two models to demonstrate the potential evolutionary consequences of competition-dependent trait expression.

  3. The dynamics of genetic and morphological variation on volcanic islands

    PubMed Central

    Gübitz, Thomas; Thorpe, Roger S; Malhotra, Anita

    2005-01-01

    Oceanic archipelagos of volcanic origin have been important in the study of evolution because they provide repeated natural experiments allowing rigorous tests of evolutionary hypotheses. Ongoing volcanism on these islands may, however, affect the evolutionary diversification of species. Analysis of population structure and phylogeographic patterns in island populations can provide insight into evolutionary dynamics on volcanic islands. We analysed genetic and morphological variation in the gecko Tarentola boettgeri on the island of Gran Canaria and compared it with Tarentola delalandii on Tenerife, a neighbouring volcanic island of similar age but distinctly different geological past. Intraspecific divergence of mitochondrial haplotypes indicates long-term persistence of Tarentola on each island, with a phylogeographic signal left by older volcanic events. More recent volcanic eruptions (approximately 0.2 million years ago on Tenerife, approximately 2.2 million years ago on Gran Canaria) have left a signature of population expansion in the population genetic structure, the strength of which depends on the time since the last major volcanic eruption on each island. While these stochastic events have left traces in morphological variation in Tenerife, in Gran Canaria geographical variation was solely associated with environmental variables. This suggests that historically caused patterns in morphology may be overwritten by natural selection within 2 million years. PMID:15870037

  4. Genetic Basis of Persister Tolerance to Aminoglycosides in Escherichia coli

    PubMed Central

    Shan, Yue; Lazinski, David; Rowe, Sarah; Camilli, Andrew

    2015-01-01

    ABSTRACT Persisters are dormant variants that form a subpopulation of drug-tolerant cells largely responsible for the recalcitrance of chronic infections. However, our understanding of the genetic basis of antibiotic tolerance remains incomplete. In this study, we applied transposon sequencing (Tn-Seq) to systematically investigate the mechanism of aminoglycoside tolerance in Escherichia coli. We constructed a highly saturated transposon library that covered the majority of E. coli genes and promoter regions and exposed a stationary-phase culture to a lethal dose of gentamicin. Tn-Seq was performed to evaluate the survival of each mutant to gentamicin exposure. We found that the disruption of several distinct pathways affected gentamicin tolerance. We identified 105 disrupted gene/promoter regions with a more than 5-fold reduction in gentamicin tolerance and 37 genes with a more than 5-fold increased tolerance. Functional cluster analysis suggests that deficiency in motility and amino acid synthesis significantly diminished persisters tolerant to gentamicin, without changing the MIC. Amino acid auxotrophs, including serine, threonine, glutamine, and tryptophan auxotrophs, exhibit strongly decreased tolerance to gentamicin, which cannot be restored by supplying the corresponding amino acids to the culture. Interestingly, supplying these amino acids to wild-type E. coli sensitizes stationary-phase cells to gentamicin, possibly through the inhibition of amino acid synthesis. In addition, we found that the deletion of amino acid synthesis genes significantly increases gentamicin uptake in stationary phase, while the deletion of flagellar genes does not affect gentamicin uptake. We conclude that activation of motility and amino acid biosynthesis contributes to the formation of persisters tolerant to gentamicin. PMID:25852159

  5. Genetics of sprouting: effects of long-term persistence in fire-prone ecosystems.

    PubMed

    Premoli, Andrea C; Steinke, Lina

    2008-09-01

    Fire functional traits (postfire resprouting and seeding) are considered to be adaptations for persisting in fire-prone environments. Although ecological and evolutionary consequences of sprouting have been extensively discussed, within-species genetic variability and structure are unknown. Here we report levels and distribution patterns of genetic polymorphisms in postfire stands of the predominant sprouter Nothofagus antarctica. Fresh foliage of 50 individuals was collected following a spatially explicit sampling design for isozyme analysis from two replicates of each of four habitat types inhabited by the species in northwestern Patagonia, Argentina: matorral, high elevation, forest, and temporally flooded basins. Average polymorphism per population ranged from 44% to 78% and mean gene diversity per site H(S )varied from 0.187 to 0.274. These results show that sprouter populations hold considerable genetic variation. Significant genetic structure over short distances (< 50 m) was found at all locations. Ancient fine-scale genetic structure is preserved by occasional seedling establishment that results in high co-ancestry coefficients. Sprouter populations growing in suboptimal habitats such as matorral, high elevation or basins consist of pairs of heterozygous genets that occur at larger spatial scales as a result of micro-environmental heterogeneity and/or local competition between near neighbour genotypes. In contrast, homozygous pairs of individuals for distinct isozyme loci occurred at larger spatial scales in forest stands. This indicates that biparental inbreeding due to local propagule establishment may take place to some extent in sprouters growing under favourable conditions. Our results show that sprouters follow a long-lasting genet persistence strategy which most probably is selected under unpredictable disturbance regimes, such as fire.

  6. Genetic variation in healthy oldest-old.

    PubMed

    Halaschek-Wiener, Julius; Amirabbasi-Beik, Mahsa; Monfared, Nasim; Pieczyk, Markus; Sailer, Christian; Kollar, Anita; Thomas, Ruth; Agalaridis, Georgios; Yamada, So; Oliveira, Lisa; Collins, Jennifer A; Meneilly, Graydon; Marra, Marco A; Madden, Kenneth M; Le, Nhu D; Connors, Joseph M; Brooks-Wilson, Angela R

    2009-08-14

    Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that enhance their ability to avoid disease and prolong lifespan. Healthy aging is a complex phenotype likely to be affected by both genetic and environmental factors. We sequenced 24 candidate healthy aging genes in DNA samples from 47 healthy individuals aged eighty-five years or older (the 'oldest-old'), to characterize genetic variation that is present in this exceptional group. These healthy seniors were never diagnosed with cancer, cardiovascular disease, pulmonary disease, diabetes, or Alzheimer disease. We re-sequenced all exons, intron-exon boundaries and selected conserved non-coding sequences of candidate genes involved in aging-related processes, including dietary restriction (PPARG, PPARGC1A, SIRT1, SIRT3, UCP2, UCP3), metabolism (IGF1R, APOB, SCD), autophagy (BECN1, FRAP1), stem cell activation (NOTCH1, DLL1), tumor suppression (TP53, CDKN2A, ING1), DNA methylation (TRDMT1, DNMT3A, DNMT3B) Progeria syndromes (LMNA, ZMPSTE24, KL) and stress response (CRYAB, HSPB2). We detected 935 variants, including 848 single nucleotide polymorphisms (SNPs) and 87 insertion or deletions; 41% (385) were not recorded in dbSNP. This study is the first to present a comprehensive analysis of genetic variation in aging-related candidate genes in healthy oldest-old. These variants and especially our novel polymorphisms are valuable resources to test for genetic association in models of disease susceptibility or resistance. In addition, we propose an innovative tagSNP selection strategy that combines variants identified through gene re-sequencing- and HapMap-derived SNPs.

  7. Genetic Variation in Healthy Oldest-Old

    PubMed Central

    Halaschek-Wiener, Julius; Amirabbasi-Beik, Mahsa; Monfared, Nasim; Pieczyk, Markus; Sailer, Christian; Kollar, Anita; Thomas, Ruth; Agalaridis, Georgios; Yamada, So; Oliveira, Lisa; Collins, Jennifer A.; Meneilly, Graydon; Marra, Marco A.; Madden, Kenneth M.; Le, Nhu D.; Connors, Joseph M.; Brooks-Wilson, Angela R.

    2009-01-01

    Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that enhance their ability to avoid disease and prolong lifespan. Healthy aging is a complex phenotype likely to be affected by both genetic and environmental factors. We sequenced 24 candidate healthy aging genes in DNA samples from 47 healthy individuals aged eighty-five years or older (the ‘oldest-old’), to characterize genetic variation that is present in this exceptional group. These healthy seniors were never diagnosed with cancer, cardiovascular disease, pulmonary disease, diabetes, or Alzheimer disease. We re-sequenced all exons, intron-exon boundaries and selected conserved non-coding sequences of candidate genes involved in aging-related processes, including dietary restriction (PPARG, PPARGC1A, SIRT1, SIRT3, UCP2, UCP3), metabolism (IGF1R, APOB, SCD), autophagy (BECN1, FRAP1), stem cell activation (NOTCH1, DLL1), tumor suppression (TP53, CDKN2A, ING1), DNA methylation (TRDMT1, DNMT3A, DNMT3B) Progeria syndromes (LMNA, ZMPSTE24, KL) and stress response (CRYAB, HSPB2). We detected 935 variants, including 848 single nucleotide polymorphisms (SNPs) and 87 insertion or deletions; 41% (385) were not recorded in dbSNP. This study is the first to present a comprehensive analysis of genetic variation in aging-related candidate genes in healthy oldest-old. These variants and especially our novel polymorphisms are valuable resources to test for genetic association in models of disease susceptibility or resistance. In addition, we propose an innovative tagSNP selection strategy that combines variants identified through gene re-sequencing- and HapMap-derived SNPs. PMID:19680556

  8. Do Coinfections Maintain Genetic Variation in Parasites?

    PubMed

    Seppälä, Otto; Jokela, Jukka

    2016-12-01

    Host individuals are often infected with multiple, potentially interacting parasite species and genotypes. Such coinfections have consequences for epidemiology, disease severity, and evolution of parasite virulence. As fitness effects of coinfection can be specific to interacting parasite genotypes, coinfections may induce high fitness variation among parasite genotypes. We argue that such interactions can be an important mechanism maintaining genetic variation in parasite traits such as infectivity and virulence. We also argue that such interactions may slow coevolutionary dynamics between hosts and parasites. This is because, instead of depending only on host genotype, parasite fitness may be determined by average infection success across all coinfection scenarios. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Genetic basis of metabolome variation in yeast.

    PubMed

    Breunig, Jeffrey S; Hackett, Sean R; Rabinowitz, Joshua D; Kruglyak, Leonid

    2014-03-01

    Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

  10. Genetic Basis of Metabolome Variation in Yeast

    PubMed Central

    Breunig, Jeffrey S.; Hackett, Sean R.; Rabinowitz, Joshua D.; Kruglyak, Leonid

    2014-01-01

    Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism. PMID:24603560

  11. Using the Genetics Concept Assessment to document persistent conceptual difficulties in undergraduate genetics courses.

    PubMed

    Smith, Michelle K; Knight, Jennifer K

    2012-05-01

    To help genetics instructors become aware of fundamental concepts that are persistently difficult for students, we have analyzed the evolution of student responses to multiple-choice questions from the Genetics Concept Assessment. In total, we examined pretest (before instruction) and posttest (after instruction) responses from 751 students enrolled in six genetics courses for either majors or nonmajors. Students improved on all 25 questions after instruction, but to varying degrees. Notably, there was a subgroup of nine questions for which a single incorrect answer, called the most common incorrect answer, was chosen by >20% of students on the posttest. To explore response patterns to these nine questions, we tracked individual student answers before and after instruction and found that particular conceptual difficulties about genetics are both more likely to persist and more likely to distract students than other incorrect ideas. Here we present an analysis of the evolution of these incorrect ideas to encourage instructor awareness of these genetics concepts and provide advice on how to address common conceptual difficulties in the classroom.

  12. Genetic and metabolic determinants of human epigenetic variation.

    PubMed

    Haggarty, Paul

    2015-07-01

    Epigenetics has emerged in recent years as one of the most important biological mechanisms linking exposures across the life course to long-term health. This article reviews recent developments in our understanding of the metabolic and genetic determinants of epigenetic variation in human populations. Epigenetic status is influenced by a range of environmental exposures, including diet and nutrition, social status, the early emotional environment, and infertility and its treatment. The period around conception is particularly sensitive to environmental exposures with evidence for effects on epigenetic imprinting within the offspring. Epigenetic status is also influenced by genotype, and genetic variation in methylene tetrahydrofolate reductase, and the DNA methytransferase and ten-eleven translocation methylcytosine dioxygenase proteins has been linked to the epigenetic status, biological function and disease. Epigenetics is at the heart of a series of feedback loops linking the environment to the human genome in a way that allows crosstalk between the genome and the environment it exists within. It offers the potential for modification of adverse epigenetic states resulting from events/exposures at earlier life stages. We need to better understand the nutritional programming of epigenetic states, the persistence of these marks in time and their effect on biological function and health in current and future generations.

  13. Intraspecific genetic variation and competition interact to influence niche expansion

    PubMed Central

    Agashe, Deepa; Bolnick, Daniel I.

    2010-01-01

    Theory and empirical evidence show that intraspecific competition can drive selection favouring the use of novel resources (i.e. niche expansion). The evolutionary response to such selection depends on genetic variation for resource use. However, while genetic variation might facilitate niche expansion, genetically diverse groups may also experience weaker competition, reducing density-dependent selection on resource use. Therefore, genetic variation for fitness on different resources could directly facilitate, or indirectly retard, niche expansion. To test these alternatives, we factorially manipulated both the degree of genetic variation and population density in flour beetles (Tribolium castaneum) exposed to both novel and familiar food resources. Using stable carbon isotope analysis, we measured temporal change and individual variation in beetle diet across eight generations. Intraspecific competition and genetic variation acted on different components of niche evolution: competition facilitated niche expansion, while genetic variation increased individual variation in niche use. In addition, genetic variation and competition together facilitated niche expansion, but all these impacts were temporally variable. Thus, we show that the interaction between genetic variation and competition can also determine niche evolution at different time scales. PMID:20462902

  14. Genetic variation in pea seed globulin composition.

    PubMed

    Tzitzikas, Emmanouil N; Vincken, Jean-Paul; de Groot, Jolan; Gruppen, Harry; Visser, Richard G F

    2006-01-25

    A quantitative characterization of seeds from 59 pea (Pisum sativum L.) lines and relative taxa with various external characteristics and wide geographical origin was performed to explore the genetic variation of pea concerning its starch and protein contents and globulin composition. Pea lines, which produce round, wrinkled, flat, and round-dimpled seeds, have starch as the major reserve, with an average content of 46%. Protein content varied from 13.7 to 30.7% of the seed dry matter, with an overall average of 22.3%. Densitometric quantification of the individual globulins (legumin, vicilin, convicilin, and globulin-related proteins) based on SDS-PAGE gels showed no lines lacking any particular globulin. Among the lines tested, variation was shown in both their total globulins content and their globulin composition. The total globulin content ranged from 49.2 to 81.8% of the total pea protein extract (TPPE). Legumin content varied between 5.9 and 24.5% of the TPPE. Vicilin was the most abundant protein of pea, and its content varied between 26.3 and 52.0% of the TPPE. Both processed and nonprocessed vicilins occurred. The processed vicilin was the predominant one, with values between 17.8 and 40.8%, whereas the nonprocessed ones constituted between 3.1 and 13.5% of the TPPE. Convicilin was the least abundant globulin, and its content ranged from 3.9 to 8.3%. Finally, the globulin-related proteins were present in amounts ranging from 2.8 to 17.3%. They were less abundant in comparison with legumin and vicilin, but they showed the largest relative variation of the four globulin classes. Correlations between the different external characteristics and globulin composition were determined. Comparison with soybean showed that pea lines show more variety in the abundance of globulin proteins, enabling a wider range of food application.

  15. Persisting variation in testing and reporting Clostridium difficile cases

    PubMed Central

    Parekh, Sejal; Dabrowski, Hannah; Petkar, Hawabibee

    2015-01-01

    Previous evidence suggested a significant variation in the testing algorithms used across the United Kingdom for the diagnosis of Clostridium difficile infection (CDI) and new national guidelines were issued in 2012. The main aim of this paper was to explore if such variation in testing and reporting is still present, to compare the management of CDI cases, and to investigate if there is any significant variation in the antibiotic policies among different hospitals. Using London hospitals as a sample, results show that there is still a wide variation of testing methods and reporting used, making comparisons difficult. It is likely that the overall variability in practices would be greater at a national and, even more, at international level. The relationship between broad-spectrum antibiotics and C. difficile incidence and alternative approaches in antibiotic guidelines may require further studies. PMID:26877769

  16. Demographic variation, reintroduction, and persistence of an island duck (Anas laysanensis)

    USGS Publications Warehouse

    Reynolds, Michelle H.; Weiser, Emily; Jamieson, Ian; Hatfield, Jeffrey S.

    2013-01-01

    Population variation in life history can be important for predicting successful establishment and persistence of reintroduced populations of endangered species. The Laysan duck (Anas laysanensis) is an endangered bird native to the Hawaiian Archipelago that was extirpated from most islands after the introduction of mammalian predators. Laysan ducks were restricted to a single remote island, Laysan Island (4.1 km2), for nearly 150 years. Since the species is not known to disperse between distant Hawaiian Islands today, 42 wild birds from Laysan Island were translocated to another mammalian predator-free low-lying atoll (Midway Atoll; 6.0 km2) to reduce extinction risk. We explored how variation in demography influences establishment and longer-term retention of genetic diversity (rare alleles) for reintroductions of this species. We observed dramatic differences in population growth between the source (λ = 1.18) and reintroduced (λ = 3.28) population. The number of eggs hatched at Midway Atoll was greater than at Laysan Island, however, we found no difference in hatching success (proportion of clutch hatched) between populations. Adult females produced 3 times as many fledglings per breeding year on Midway Atoll compared to Laysan Island. We estimated population abundance of both populations until 2010 and applied a Gompertz model with a Bayesian approach to infer density dependence, process variation, observation error, and carrying capacity for the Laysan Island and Midway Atoll populations. The carrying capacity from the Gompertz model for Midway Atoll (K = 883 ± 210 SD) was estimated to be greater than that of Laysan Island (K = 598 ± 76 SD). Translocations with small numbers of founders and no immigration can create population bottlenecks, leading to loss of genetic variation over time, and potentially reducing the reintroduced population's viability or its potential to serve as a source for future translocations. Therefore, we

  17. Antigenic variation: Molecular and genetic mechanisms of relapsing disease

    SciTech Connect

    Cruse, J.M.; Lewis, R.E.

    1987-01-01

    This book contains 10 chapters. They are: Contemporary Concepts of Antigenic Variation; Antigenic Variation in the Influenza Viruses; Mechanisms of Escape of Visna Lentiviruses from Immunological Control; A Review of Antigenic Variation by the Equine Infectious Anemia Virus; Biologic and Molecular Variations in AIDS Retrovirus Isolates; Rabies Virus Infection: Genetic Mutations and the Impact on Viral Pathogenicity and Immunity; Immunobiology of Relapsing Fever; Antigenic Variation in African Trypanosomes; Antigenic Variation and Antigenic Diversity in Malaria; and Mechanisms of Immune Evasion in Schistosomiasis.

  18. Genetic variation in resistance to ionizing radiation

    SciTech Connect

    Ayala, F.J.

    1991-06-24

    We proposed an investigation of genetically-determined individual differences in sensitivity to ionizing radiation. The model organism is Drosophila melanogaster. The gene coding for Cu,Zn superoxide dismutase (SOD) is the target locus, but the effects of variation in other components of the genome that modulate SOD levels are also taken into account. SOD scavenges oxygen radicals generated during exposure to ionizing radiation. It has been shown to protect against ionizing radiation damage to DNA, viruses, bacteria, mammalian cells, whole mice, and Drosophila. Two alleles, S and F, are commonly found in natural populations of D. melanogaster; in addition we have isolated from a natural population null'' (CA1) mutant that yields only 3.5% of normal SOD activity. The S, F, and CA1 alleles provide an ideal model system to investigate SOD-dependent radioresistance, because each allele yields different levels of SOD, so that S > F >> CA1. The roles of SOD level in radioresistance are being investigated in a series of experiments that measure the somatic and germ-line effects of increasing doses of ionizing radiation. In addition, we have pursued an unexpected genetic event-namely the nearly simultaneous transformation of several lines homozygous for the SOD null'' allele into predominately S lines. Using specifically designed probes and DNA amplification by means of the Tag polymerase chain reaction (PCR) we have shown that (1) the null allele was still present in the transformed lines, but was being gradually replaced by the S allele as a consequence of natural selection; and (2) that the transformation was due to the spontaneous deletion of a 0.68 Kb truncated P-element, the insertion of which is characteristic of the CA1 null allele.

  19. Modeling genetic inheritance of copy number variations

    PubMed Central

    Wang, Kai; Chen, Zhen; Tadesse, Mahlet G.; Glessner, Joseph; Grant, Struan F. A.; Hakonarson, Hakon; Bucan, Maja

    2008-01-01

    Copy number variations (CNVs) are being used as genetic markers or functional candidates in gene-mapping studies. However, unlike single nucleotide polymorphism or microsatellite genotyping techniques, most CNV detection methods are limited to detecting total copy numbers, rather than copy number in each of the two homologous chromosomes. To address this issue, we developed a statistical framework for intensity-based CNV detection platforms using family data. Our algorithm identifies CNVs for a family simultaneously, thus avoiding the generation of calls with Mendelian inconsistency while maintaining the ability to detect de novo CNVs. Applications to simulated data and real data indicate that our method significantly improves both call rates and accuracy of boundary inference, compared to existing approaches. We further illustrate the use of Mendelian inheritance to infer SNP allele compositions in each of the two homologous chromosomes in CNV regions using real data. Finally, we applied our method to a set of families genotyped using both the Illumina HumanHap550 and Affymetrix genome-wide 5.0 arrays to demonstrate its performance on both inherited and de novo CNVs. In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs. PMID:18832372

  20. A Longitudinal Behavioral Genetic Analysis of Task Persistence

    ERIC Educational Resources Information Center

    Deater-Deckard, Kirby; Petrill, Stephen A.; Thompson, Lee A.; DeThorne, Laura S.

    2006-01-01

    Change in task persistence was assessed in two annual assessments using teachers', testers', and observers' ratings. Participants included 79 monozygotic and 116 same-sex dizygotic twin pairs who were in Kindergarten or 1st grade (4.3 to 7.9 years old) at the initial assessment. Task persistence was widely distributed and higher among older…

  1. Unusually low levels of genetic variation among Giardia lamblia isolates.

    PubMed

    Teodorovic, Smilja; Braverman, John M; Elmendorf, Heidi G

    2007-08-01

    Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite.

  2. Genetics

    USDA-ARS?s Scientific Manuscript database

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  3. Landscape location affects genetic variation of Canada lynx (Lynx canadensis)

    Treesearch

    M. K. Schwartz; L. S. Mills; Y. Ortega; L. F. Ruggiero; F. W. Allendorf

    2003-01-01

    The effect of a population's location on the landscape on genetic variation has been of interest to population genetics for more than half a century. However, most studies do not consider broadscale biogeography when interpreting genetic data. In this study, we propose an operational definition of a peripheral population, and then explore whether peripheral...

  4. Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding the LCT gene.

    PubMed

    De Fanti, Sara; Sazzini, Marco; Giuliani, Cristina; Frazzoni, Federica; Sarno, Stefania; Boattini, Alessio; Marasco, Elena; Mantovani, Vilma; Franceschi, Claudio; Moral, Pedro; Garagnani, Paolo; Luiselli, Donata

    2015-12-01

    Although genetic variants related to lactase persistence in European populations were supposed to have firstly undergone positive selection in farmers from the Balkans and Central Europe, demographic and evolutionary dynamics that subsequently shaped the distribution of this adaptive trait across the continent have still to be elucidated. To deepen the knowledge about potential routes of diffusion of lactase persistence to Western Europe we investigated variation at a large genomic region surrounding the LCT gene along the Italian peninsula, a geographical area that played a key role in population movements responsible for Neolithic diffusion across Europe. By genotyping 40 highly selected SNPs in more than 400 Italian individuals we described gradients of nucleotide and haplotype variation potentially related to lactase persistence and compared them with those observed in several European and Mediterranean human groups. Multiple migratory events responsible for earlier introduction of the examined alleles in Italy than in Northern European regions could be invoked. Different demic processes occurred along the western and eastern sides of the peninsula were also inferred via linkage disequilibrium and population structure analyses. The appreciable genetic continuum observed between people from Northern or Central-Western Italy and Central European populations suggested a local arrival of lactase persistence-related variants mainly via overland routes. On the contrary, diversity of Central-Eastern and Southern Italian groups entailed also gene flow from South-Eastern Mediterranean regions, in accordance to the earlier entrance of the Neolithic in Southern Italy via maritime population movements along the Mediterranean coastlines. © 2015 Wiley Periodicals, Inc.

  5. Genetic variation of Mycobacterium tuberculosis circulating in Kharkiv Oblast, Ukraine

    PubMed Central

    2011-01-01

    Background A persistent increase of tuberculosis cases has recently been noted in the Ukraine. The reported incidence of drug-resistant isolates of M. tuberculosis is growing steadily; however, data on the genetic variation of isolates of M. tuberculosis circulating in northern Ukraine and on the spectrum and frequency of occurrence of mutations determining resistance to the principal anti-tuberculosis drugs isoniazid and rifampicin have not yet been reported. Methods Isolates of M. tuberculosis from 98 tuberculosis patients living in Kharkiv Oblast (Ukraine) were analyzed using VNTR- and RFLP-IS6110-typing methods. Mutations associated with resistance to rifampicin and isoniazid were detected by RFLP-PCR methods, and also confirmed by sequencing. Results We identified 75 different genetic profiles. Thirty four (34%) isolates belonged to the Beijing genotype and 23 (23%) isolates belonged to the LAM family. A cluster of isolates belonging to the LAM family had significant genetic heterogeneity, indicating that this family had an ancient distribution and circulation in this geographical region. Moreover, we found a significant percentage of the isolates (36%) belonged to as yet unidentified families of M. tuberculosis or had individual non-clustering genotypes. Mutations conferring rifampicin and isoniazid resistance were detected in 49% and 54% isolates, respectively. Mutations in codon 531 of the rpoB gene and codon 315 of the katG gene were predominant among drug-resistant isolates. An association was found for belonging to the LAM strain family and having multiple drug resistance (R = 0.27, p = 0.0059) and also for the presence of a mutation in codon 531 of the rpoB gene and belonging to the Beijing strain family (R = 0.2, p = 0.04). Conclusions Transmission of drug-resistant isolates seems to contribute to the spread of resistant TB in this oblast. The Beijing genotype and LAM genotype should be seen as a major cause of drug resistant TB in this region. PMID

  6. A Cross-Sectional Behavioral Genetic Analysis of Task Persistence in the Transition to Middle Childhood

    ERIC Educational Resources Information Center

    Deater-Deckard, Kirby; Petrill, Stephen A.; Thompson, Lee A.; DeThorne, Laura S.

    2005-01-01

    Task persistence, measured by a composite score of independent teacher, tester and observer reports, was examined using behavioral genetic analysis. Participants included 92 monozygotic and 137 same-sex dizygotic twin pairs in Kindergarten or 1st grade (4.3 to 7.9 years old). Task persistence was widely distributed, higher among older children,…

  7. Elevational patterns of genetic variation in the cosmopolitan moss Bryum argenteum (Bryaceae).

    PubMed

    Pisa, Sergio; Werner, Olaf; Vanderpoorten, Alain; Magdy, Mahmoud; Ros, Rosa M

    2013-10-01

    The Baas Becking tenet posits that 'everything is everywhere, but the environment selects' to explain cosmopolitan distributions in highly vagile taxa. Bryophyte species show wider distributions than vascular plants and include examples of truly cosmopolitan ranges, which have been interpreted as a result of high dispersal capacities and ecological plasticity. In the current study, we documented patterns of genetic structure and diversity in the cosmopolitan moss Bryum argenteum along an elevational gradient to determine if genetic diversity and structure is homogenized by intense migrations in the lack of ecological differentiation. • 60 specimens were collected in the Sierra Nevada Mountains (Spain) between 100 and 2870 m and sequenced for ITS and rps4. Comparative analyses, genetic diversity estimators, and Mantel's tests were employed to determine the relationship between genetic variation, elevation, and geographic distance and to look for signs of demographic shifts. • Genetic diversity peaked above 1900 m and no signs of demographic shifts were detected at any elevation. There was a strong phylogenetic component in elevational variation. Genetic variation was significantly correlated with elevation, but not with geographic distance. • The results point to the long-term persistence of Bryum argenteum in a range that was glaciated during the Late Pleistocene. Evidence for an environmentally driven pattern of genetic differentiation suggests adaptive divergence. This supports the Baas Becking tenet and indicates that ecological specialization might play a key role in explaining patterns of genetic structure in cosmopolitan mosses.

  8. Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation

    PubMed Central

    Badyaev, Alexander V

    2005-01-01

    Extreme environments are closely associated with phenotypic evolution, yet the mechanisms behind this relationship are poorly understood. Several themes and approaches in recent studies significantly further our understanding of the importance that stress-induced variation plays in evolution. First, stressful environments modify (and often reduce) the integration of neuroendocrinological, morphological and behavioural regulatory systems. Second, such reduced integration and subsequent accommodation of stress-induced variation by developmental systems enables organismal ‘memory’ of a stressful event as well as phenotypic and genetic assimilation of the response to a stressor. Third, in complex functional systems, a stress-induced increase in phenotypic and genetic variance is often directional, channelled by existing ontogenetic pathways. This accounts for similarity among individuals in stress-induced changes and thus significantly facilitates the rate of adaptive evolution. Fourth, accumulation of phenotypically neutral genetic variation might be a common property of locally adapted and complex organismal systems, and extreme environments facilitate the phenotypic expression of this variance. Finally, stress-induced effects and stress-resistance strategies often persist for several generations through maternal, ecological and cultural inheritance. These transgenerational effects, along with both the complexity of developmental systems and stressor recurrence, might facilitate genetic assimilation of stress-induced effects. Accumulation of phenotypically neutral genetic variance by developmental systems and phenotypic accommodation of stress-induced effects, together with the inheritance of stress-induced modifications, ensure the evolutionary persistence of stress–response strategies and provide a link between individual adaptability and evolutionary adaptation. PMID:16024341

  9. Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity.

    PubMed

    Tarone, A M; McIntyre, L M; Harshman, L G; Nuzhdin, S V

    2012-10-01

    One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular network, with the Yolk protein 1-3 (Yp) genes as the most downstream target. Our analyses reveal that genetic variation in expression for genes known to be upstream in the pathway explains variation in downstream targets. Relationships differ between the two sexes, and each Yp has a distinct transcriptional pattern. Yp expression is significantly negatively correlated with longevity, an important life history trait, for both males and females.

  10. The Genetics of Canine Skull Shape Variation

    PubMed Central

    Schoenebeck, Jeffrey J.; Ostrander, Elaine A.

    2013-01-01

    A dog’s craniofacial diversity is the result of continual human intervention in natural selection, a process that began tens of thousands of years ago. To date, we know little of the genetic underpinnings and developmental mechanisms that make dog skulls so morphologically plastic. In this Perspectives, we discuss the origins of dog skull shapes in terms of history and biology and highlight recent advances in understanding the genetics of canine skull shapes. Of particular interest are those molecular genetic changes that are associated with the development of distinct breeds. PMID:23396475

  11. Genetic variation in natural honeybee populations, Apis mellifera capensis

    NASA Astrophysics Data System (ADS)

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  12. Genetic variation in natural honeybee populations, Apis mellifera capensis.

    PubMed

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  13. Genetic variation among white croaker populations

    NASA Astrophysics Data System (ADS)

    Han, Zhiqiang; Gao, Tianxiang; Zhuang, Zhimeng; Tang, Qisheng

    2008-02-01

    To investigate the genetic structures and differentiation of different wild populations of white croaker ( Pennahia argentata), horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 loci, of which eleven were polymorphic. The percentage of polymorphic loci of white croaker populations varied from 6.67% to 53.33%; the mean observed and expected heterozygosity ranged from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The expected heterozygosity revealed a low genetic variability for white croaker in comparison with other marine fishes. The genetic distances between populations ranged from 0.00005 to 0.00026. A weak differentiation was observed within each clade and between clades; and no significant differences in gene frequencies among populations were observed in white croaker. Among the five populations, three Chinese populations showed more genetic diversity than that in Japanese populations.

  14. Genetic variation in social influence on mate preferences.

    PubMed

    Rebar, Darren; Rodríguez, Rafael L

    2013-07-22

    Patterns of phenotypic variation arise in part from plasticity owing to social interactions, and these patterns contribute, in turn, to the form of selection that shapes the variation we observe in natural populations. This proximate-ultimate dynamic brings genetic variation in social environments to the forefront of evolutionary theory. However, the extent of this variation remains largely unknown. Here, we use a member of the Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae) to assess how mate preferences are influenced by genetic variation in the social environment. We used full-sibling split-families as 'treatment' social environments, and reared focal females alongside each treatment family, describing the mate preferences of the focal females. With this method, we detected substantial genetic variation in social influence on mate preferences. The mate preferences of focal females varied according to the treatment families along with which they grew up. We discuss the evolutionary implications of the presence of such genetic variation in social influence on mate preferences, including potential contributions to the maintenance of genetic variation, the promotion of divergence, and the adaptive evolution of social effects on fitness-related traits.

  15. Genetic variation and constraints on the evolution of defense against spittlebug (Philaenus spumarius) herbivory in Mimulus guttatus.

    PubMed

    Ivey, C T; Carr, D E; Eubanks, M D

    2009-03-01

    Plants mediate carbon into most ecosystems and are thus under persistent attack by diverse enemies. The evolution of defense against such assaults will depend on the availability of genetic variation, as well as the costs and constraints on defense. We estimated the magnitude of genetic variation for defense against spittlebug (Philaenus spumarius) herbivory in Mimulus guttatus using a diallel cross-grown in a greenhouse. Except for flowering time, additive genetic variation for the plant traits we measured was negligible, regardless of herbivory environment. In contrast, nonadditive genetic variation contributed significantly to all plant traits measured. We found significant additive genetic variation among plants for biomass of adult spittlebugs, suggesting heritability for resistance to herbivory. The other putative resistance trait measured, spittlebug maturation time, was not significantly heritable. We found no evidence for significant genetic variation for tolerance to herbivory except for a small non-nuclear paternal contribution to tolerance for flower number. Additive genetic correlations indicated that more resistant plant genotypes (in terms of adult spittlebug biomass) were also smaller in the absence of spittlebugs, suggesting a potential cost of resistance to herbivory. We found no other significant genetic correlations indicating a cost of defense, nor did we find evidence for a tradeoff between resistance and tolerance to herbivory. Overall, these results suggest the future adaptive evolution of tolerance to spittlebugs in this population will be limited primarily by available genetic variation, whereas the future evolution of antibiosis resistance may be constrained by allocation costs of resistance.

  16. Genetic variation in adaptability and pleiotropy in budding yeast

    PubMed Central

    Mitchell, James Kameron; Bloom, Joshua S; Kruglyak, Leonid

    2017-01-01

    Evolution can favor organisms that are more adaptable, provided that genetic variation in adaptability exists. Here, we quantify this variation among 230 offspring of a cross between diverged yeast strains. We measure the adaptability of each offspring genotype, defined as its average rate of adaptation in a specific environmental condition, and analyze the heritability, predictability, and genetic basis of this trait. We find that initial genotype strongly affects adaptability and can alter the genetic basis of future evolution. Initial genotype also affects the pleiotropic consequences of adaptation for fitness in a different environment. This genetic variation in adaptability and pleiotropy is largely determined by initial fitness, according to a rule of declining adaptability with increasing initial fitness, but several individual QTLs also have a significant idiosyncratic role. Our results demonstrate that both adaptability and pleiotropy are complex traits, with extensive heritable differences arising from naturally occurring variation. PMID:28826486

  17. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

    USGS Publications Warehouse

    Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

    2015-01-01

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already

  18. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout.

    PubMed

    Kovach, Ryan P; Muhlfeld, Clint C; Wade, Alisa A; Hand, Brian K; Whited, Diane C; DeHaan, Patrick W; Al-Chokhachy, Robert; Luikart, Gordon

    2015-02-06

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4-7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = -0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already

  19. Genetic variation and the de novo assembly of human genomes

    PubMed Central

    Chaisson, Mark J. P.; Wilson, Richard K.; Eichler, Evan E.

    2016-01-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. PMID:26442640

  20. Explaining additional genetic variation in complex traits

    PubMed Central

    Robinson, Matthew R.; Wray, Naomi R.; Visscher, Peter M.

    2015-01-01

    Genome-wide association studies (GWAS) have provided valuable insights into the genetic basis of complex traits, discovering >6000 variants associated with >500 quantitative traits and common complex diseases in humans. The associations identified so far represent only a fraction of those which influence phenotype, as there are likely to be very many variants across the entire frequency spectrum, each of which influences multiple traits, with only a small average contribution to the phenotypic variance. This presents a considerable challenge to further dissection of the remaining unexplained genetic variance within populations, which limits our ability to predict disease risk, identify new drug targets, improve and maintain food sources, and understand natural diversity. This challenge will be met within the current framework through larger sample size, better phenotyping including recording of non-genetic risk factors, focused study designs, and an integration of multiple sources of phenotypic and genetic information. The current evidence supports the application of quantitative genetic approaches, and we argue that one should retain simpler theories until simplicity can be traded for greater explanatory power. PMID:24629526

  1. Heredity vs. Environment: The Effects of Genetic Variation with Age

    ERIC Educational Resources Information Center

    Gourlay, N.

    1978-01-01

    Major problems in the field are presented through a brief review of Burt's work and a critical account of the Hawaiian and British schools of biometrical genetics. The merits and demerits of Christopher Jencks' study are also discussed. There follows an account of the principle of genetic variation with age, a new concept to the…

  2. Heredity vs. Environment: The Effects of Genetic Variation with Age

    ERIC Educational Resources Information Center

    Gourlay, N.

    1978-01-01

    Major problems in the field are presented through a brief review of Burt's work and a critical account of the Hawaiian and British schools of biometrical genetics. The merits and demerits of Christopher Jencks' study are also discussed. There follows an account of the principle of genetic variation with age, a new concept to the…

  3. A multivariate analysis of genetic variation in the advertisement call of the gray treefrog, Hyla versicolor.

    PubMed

    Welch, Allison M; Smith, Michael J; Gerhardt, H Carl

    2014-06-01

    Genetic variation in sexual displays is crucial for an evolutionary response to sexual selection, but can be eroded by strong selection. Identifying the magnitude and sources of additive genetic variance underlying sexually selected traits is thus an important issue in evolutionary biology. We conducted a quantitative genetics experiment with gray treefrogs (Hyla versicolor) to investigate genetic variances and covariances among features of the male advertisement call. Two energetically expensive traits showed significant genetic variation: call duration, expressed as number of pulses per call, and call rate, represented by its inverse, call period. These two properties also showed significant genetic covariance, consistent with an energetic constraint to call production. Combining the genetic variance-covariance matrix with previous estimates of directional sexual selection imposed by female preferences predicts a limited increase in call duration but no change in call rate despite significant selection on both traits. In addition to constraints imposed by the genetic covariance structure, an evolutionary response to sexual selection may also be limited by high energetic costs of long-duration calls and by preferences that act most strongly against very short-duration calls. Meanwhile, the persistence of these preferences could be explained by costs of mating with males with especially unattractive calls. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  4. Genetic variation in the east Midlands.

    PubMed

    Mastana, S S; Sokol, R J

    1998-01-01

    According to history, the population of the British Isles derives its genepool from a succession of invaders and immigrants. The settlement pattern of these invaders gave rise to a patchwork of genepools, shown in previous genetic surveys. Specimens from 1117 blood donors of regionally subdivided East Midlands (Derbyshire, Nottinghamshire and Leicestershire) were analysed for 18 conventional genetic systems (blood groups, serum proteins and red cell enzymes), according to place of residence. Significant differences exist among the five geographically defined sub-populations, and it is argued that these are derived from the historical settlement of continental European populations in the region, especially the Danes and the Vikings.

  5. The contribution of additive genetic variation to personality variation: heritability of personality.

    PubMed

    Dochtermann, Ned A; Schwab, Tori; Sih, Andrew

    2015-01-07

    Individual animals frequently exhibit repeatable differences from other members of their population, differences now commonly referred to as 'animal personality'. Personality differences can arise, for example, from differences in permanent environmental effects--including parental and epigenetic contributors--and the effect of additive genetic variation. Although several studies have evaluated the heritability of behaviour, less is known about general patterns of heritability and additive genetic variation in animal personality. As overall variation in behaviour includes both the among-individual differences that reflect different personalities and temporary environmental effects, it is possible for personality to be largely genetically influenced even when heritability of behaviour per se is quite low. The relative contribution of additive genetic variation to personality variation can be estimated whenever both repeatability and heritability are estimated for the same data. Using published estimates to address this issue, we found that approximately 52% of animal personality variation was attributable to additive genetic variation. Thus, while the heritability of behaviour is often moderate or low, the heritability of personality is much higher. Our results therefore (i) demonstrate that genetic differences are likely to be a major contributor to variation in animal personality and (ii) support the phenotypic gambit: that evolutionary inferences drawn from repeatability estimates may often be justified.

  6. The contribution of additive genetic variation to personality variation: heritability of personality

    PubMed Central

    Dochtermann, Ned A.; Schwab, Tori; Sih, Andrew

    2015-01-01

    Individual animals frequently exhibit repeatable differences from other members of their population, differences now commonly referred to as ‘animal personality’. Personality differences can arise, for example, from differences in permanent environmental effects―including parental and epigenetic contributors―and the effect of additive genetic variation. Although several studies have evaluated the heritability of behaviour, less is known about general patterns of heritability and additive genetic variation in animal personality. As overall variation in behaviour includes both the among-individual differences that reflect different personalities and temporary environmental effects, it is possible for personality to be largely genetically influenced even when heritability of behaviour per se is quite low. The relative contribution of additive genetic variation to personality variation can be estimated whenever both repeatability and heritability are estimated for the same data. Using published estimates to address this issue, we found that approximately 52% of animal personality variation was attributable to additive genetic variation. Thus, while the heritability of behaviour is often moderate or low, the heritability of personality is much higher. Our results therefore (i) demonstrate that genetic differences are likely to be a major contributor to variation in animal personality and (ii) support the phenotypic gambit: that evolutionary inferences drawn from repeatability estimates may often be justified. PMID:25392476

  7. Population-level genetic variation and climate change in a biodiversity hotspot.

    PubMed

    Schierenbeck, Kristina A

    2017-01-01

    Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant-insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California's plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species.

  8. Influence of barriers to movement on within-watershed genetic variation of coastal cutthroat trout

    USGS Publications Warehouse

    Wofford, John E.B.; Gresswell, Robert E.; Banks, Michael A.

    2005-01-01

    Because human land use activities often result in increased fragmentation of aquatic and terrestrial habitats, a better understanding of the effects of fragmentation on the genetic heterogeneity of animal populations may be useful for effective management. We used eight microsatellites to examine the genetic structure of coastal cutthroat trout (Oncorhynchus clarki clarki) in Camp Creek, an isolated headwater stream in western Oregon. Our objectives were to determine if coastal cutthroat trout were genetically structured within streams and to assess the effects of natural and anthropogenic barriers on coastal cutthroat trout genetic variation. Fish sampling occurred at 10 locations, and allele frequencies differed significantly among all sampling sections. Dispersal barriers strongly influenced coastal cutthroat trout genetic structure and were associated with reduced genetic diversity and increased genetic differentiation. Results indicate that Camp Creek coastal cutthroat trout exist as many small, partially independent populations that are strongly affected by genetic drift. In headwater streams, barriers to movement can result in genetic and demographic isolation leading to reduced coastal cutthroat trout genetic diversity, and potentially compromising long-term population persistence. When habitat fragmentation eliminates gene flow among small populations, similar results may occur in other species.

  9. P450 GENETIC VARIATION: IMPLICATIONS FOR ENVIRONMENTAL AND WORKPLACE EXPOSURE

    EPA Science Inventory

    The Cytochrome P450 array detoxifies many chemicals by catalyzing the conversion of mostly hydrophobic chemicals into more hydrophilic forms that can subsequently be excreted by the body. Human genetic variation in the genes for these enzymes produces wide variations in the abili...

  10. P450 GENETIC VARIATION: IMPLICATIONS FOR ENVIRONMENTAL AND WORKPLACE EXPOSURE

    EPA Science Inventory

    The Cytochrome P450 array detoxifies many chemicals by catalyzing the conversion of mostly hydrophobic chemicals into more hydrophilic forms that can subsequently be excreted by the body. Human genetic variation in the genes for these enzymes produces wide variations in the abili...

  11. Intracortical bone remodeling variation shows strong genetic effects.

    PubMed

    Havill, L M; Allen, M R; Harris, J A K; Levine, S M; Coan, H B; Mahaney, M C; Nicolella, D P

    2013-11-01

    Intracortical microstructure influences crack propagation and arrest within bone cortex. Genetic variation in intracortical remodeling may contribute to mechanical integrity and, therefore, fracture risk. Our aim was to determine the degree to which normal population-level variation in intracortical microstructure is due to genetic variation. We examined right femurs from 101 baboons (74 females, 27 males; aged 7-33 years) from a single, extended pedigree to determine osteon number, osteon area (On.Ar), haversian canal area, osteon population density, percent osteonal bone (%On.B), wall thickness (W.Th), and cortical porosity (Ct.Po). Through evaluation of the covariance in intracortical properties between pairs of relatives, we quantified the contribution of additive genetic effects (heritability [h (2)]) to variation in these traits using a variance decomposition approach. Significant age and sex effects account for 9 % (Ct.Po) to 21 % (W.Th) of intracortical microstructural variation. After accounting for age and sex, significant genetic effects are evident for On.Ar (h (2) = 0.79, p = 0.002), %On.B (h (2) = 0.82, p = 0.003), and W.Th (h (2) = 0.61, p = 0.013), indicating that 61-82 % of the residual variation (after accounting for age and sex effects) is due to additive genetic effects. This corresponds to 48-75 % of the total phenotypic variance. Our results demonstrate that normal, population-level variation in cortical microstructure is significantly influenced by genes. As a critical mediator of crack behavior in bone cortex, intracortical microstructural variation provides another mechanism through which genetic variation may affect fracture risk.

  12. The evolution of human genetic and phenotypic variation in Africa.

    PubMed

    Campbell, Michael C; Tishkoff, Sarah A

    2010-02-23

    Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.

  13. A model for monitoring of Hsp90-buffered genetic variations

    NASA Astrophysics Data System (ADS)

    Kozeko, Liudmyla

    Genetic material of terrestrial organisms can be considerably injured by cosmic rays and UV-radiation in the space environment. Organisms onboard are also exposed to the entire complex of negative physical factors which can generate genetic variations and affect morphogenesis. However, species phenotypes must be robust to genetic variation, requiring "buffering" systems to ensure normal development. The molecular chaperone Hsp90 can serve as such "a buffer". It is important in the maturation and conformational regulation of a diverse set of signal transducers. The requirement of many principal regulatory proteins for Hsp90 renders entire metabolic pathways sensitive to impairment of its function. So inhibition of Hsp90 function can open cryptic genetic variations and produce morphological changes. In this paper, we present a model for monitoring of cryptic Hsp90-buffered genetic variations arising during exposure to space and spaceflight factors. This model has been developed with Arabidopsis thaliana seeds gathered in natural habitats with high anthropogenic pressure and wild type (Col-0) seeds subjected to negative influences (UV, heavy metals) experimentally. The phenotypic traits of early seedlings grown under reduction of Hsp90 activity were characterized to estimate Hsp90-buffered genetic variations. Geldanamycin was used as an inhibitor of Hsp90 function.

  14. Multiple capacitors for natural genetic variation in Drosophila melanogaster.

    PubMed

    Takahashi, Kazuo H

    2013-03-01

    Cryptic genetic variation (CGV) or a standing genetic variation that is not ordinarily expressed as a phenotype is released when the robustness of organisms is impaired under environmental or genetic perturbations. Evolutionary capacitors modulate the amount of genetic variation exposed to natural selection and hidden cryptically; they have a fundamental effect on the evolvability of traits on evolutionary timescales. In this study, I have demonstrated the effects of multiple genomic regions of Drosophila melanogaster on CGV in wing shape. I examined the effects of 61 genomic deficiencies on quantitative and qualitative natural genetic variation in the wing shape of D. melanogaster. I have identified 10 genomic deficiencies that do not encompass a known candidate evolutionary capacitor, Hsp90, exposing natural CGV differently depending on the location of the deficiencies in the genome. Furthermore, five genomic deficiencies uncovered qualitative CGV in wing morphology. These findings suggest that CGV in wing shape of wild-type D. melanogaster is regulated by multiple capacitors with divergent functions. Future analysis of genes encompassed by these genomic regions would help elucidate novel capacitor genes and better understand the general features of capacitors regarding natural genetic variation.

  15. Ecologically relevant genetic variation from a non-Arabidopsis perspective.

    PubMed

    Karrenberg, Sophie; Widmer, Alex

    2008-04-01

    Ecologically relevant genetic variation occurs in genes harbouring alleles that are adaptive in some environments but not in others. Analysis of this type of genetic variation in model organisms has made substantial progress, and is now being expanded to other species in order to better cover the diversity of plant life. Recent advances in connecting ecological and molecular studies in non-model species have been made with regard to edaphic and climatic adaptation, plant reproduction, life-history parameters and biotic interactions. New research avenues that increase biological complexity and ecological relevance by integrating ecological experiments with population genetic and functional genomic approaches provide new insights into the genetic basis of ecologically relevant variation.

  16. Genetic variation and pharmacogenomics: concepts, facts, and challenges.

    PubMed

    Hoehe, Margret R; Kroslak, Thomas

    2004-03-01

    The analysis of genetic variation in candidate genes is an issue of central importance in pharmacogenomics. The specific approaches taken will have a critical impact on the successful identification of disease genes, the molecular correlates of drug response, and the establishment of meaningful relationships between genetic variants and phenotypes of biomedical and pharmaceutical importance in general. Against a historical background, this article distinguishes different approaches to candidate gene analysis, reflecting different stages in human genome research. Only recently has it become feasible to analyze genetic variation systematically at the ultimate level of resolution, ie, the DNA sequence. In this context, the importance of haplotype-based approaches to candidate gene analysis has at last been recognized; the determination of the specific combinations of variants for each of the two sequences of a gene defined as a haplotype is essential. An up-to-date summary of such maximum resolution data on the amount, nature, and structure of genetic variation in candidate genes will be given. These data demonstrate abundant gene sequence and haplotype diversity. Numerous individually different forms of a gene may exist. This presents major challenges to the analysis of relationships between genetic variation, gene function, and phenotype. First solutions seem within reach. The implications of naturally occurring variation for pharmacogenomics and "personalized" medicine are now evident. Future approaches to the identification, evaluation, and prioritization of drug targets, the optimization of clinical trials, and the development of efficient therapies must be based on in-depth knowledge of candidate gene variation as an essential prerequisite.

  17. Phase Variation Mediates Reductions in Expression of Surface Proteins during Persistent Meningococcal Carriage

    PubMed Central

    Alamro, Mohamed; Bidmos, Fadil A.; Chan, Hannah; Oldfield, Neil J.; Newton, Emma; Bai, Xilian; Aidley, Jack; Care, Rory; Mattick, Claire; Turner, David P. J.; Neal, Keith R.; Ala'Aldeen, Dlawer A. A.; Feavers, Ian; Borrow, Ray

    2014-01-01

    Asymptomatic and persistent colonization of the upper respiratory tract by Neisseria meningitidis occurs despite elicitation of adaptive immune responses against surface antigens. A putative mechanism for facilitating host persistence of this bacterial commensal and pathogen is alterations in expression of surface antigens by simple sequence repeat (SSR)-mediated phase variation. We investigated how often phase variation occurs during persistent carriage by analyzing the SSRs of eight loci in multiple isolates from 21 carriers representative of 1 to 6 months carriage. Alterations in repeat number were detected by a GeneScan analysis and occurred at 0.06 mutations/gene/month of carriage. The expression states were determined by Western blotting and two genes, fetA and nadA, exhibited trends toward low expression states. A critical finding from our unique examination of combinatorial expression states, “phasotypes,” was for significant reductions in expression of multiple phase-variable surface proteins during persistent carriage of some strains. The immune responses in these carriers were examined by measuring variant-specific PorA IgG antibodies, capsular group Y IgG antibodies and serum bactericidal activity in concomitant serum samples. Persistent carriage was associated with high levels of specific IgG antibodies and serum bactericidal activity while recent strain acquisition correlated with a significant induction of antibodies. We conclude that phase-variable genes are driven into lower expression states during long-term persistent meningococcal carriage, in part due to continuous exposure to antibody-mediated selection, suggesting localized hypermutation has evolved to facilitate host persistence. PMID:24686058

  18. Genetic Variations Leading to Familial Dilated Cardiomyopathy

    PubMed Central

    Cho, Kae Won; Lee, Jongsung; Kim, Youngjo

    2016-01-01

    Cardiomyopathy is a major cause of death worldwide. Based on pathohistological abnormalities and clinical manifestation, cardiomyopathies are categorized into several groups: hypertrophic, dilated, restricted, arrhythmogenic right ventricular, and unclassified. Dilated cardiomyopathy, which is characterized by dilation of the left ventricle and systolic dysfunction, is the most severe and prevalent form of cardiomyopathy and usually requires heart transplantation. Its etiology remains unclear. Recent genetic studies of single gene mutations have provided significant insights into the complex processes of cardiac dysfunction. To date, over 40 genes have been demonstrated to contribute to dilated cardiomyopathy. With advances in genetic screening techniques, novel genes associated with this disease are continuously being identified. The respective gene products can be classified into several functional groups such as sarcomere proteins, structural proteins, ion channels, and nuclear envelope proteins. Nuclear envelope proteins are emerging as potential molecular targets in dilated cardiomyopathy. Because they are not directly associated with contractile force generation and transmission, the molecular pathways through which these proteins cause cardiac muscle disorder remain unclear. However, nuclear envelope proteins are involved in many essential cellular processes. Therefore, integrating apparently distinct cellular processes is of great interest in elucidating the etiology of dilated cardiomyopathy. In this mini review, we summarize the genetic factors associated with dilated cardiomyopathy and discuss their cellular functions. PMID:27802374

  19. Genetic variation within the Lidia bovine breed.

    PubMed

    Cañón, J; Tupac-Yupanqui, I; García-Atance, M A; Cortés, O; García, D; Fernández, J; Dunner, S

    2008-08-01

    The results of an exhaustive data collection from a bovine population with a low level of exchangeability, the Lidia breed, are presented. A total of 1683 individuals from 79 herds were sampled and genetic diversity within and among lineages was assessed using 24 microsatellite loci on 22 different chromosomes. Expected heterozygosity ranged between 0.46 and 0.68 per lineage and there was significant inbreeding in the lineages, which included several farms [mean F(IS) = 0.11, bootstrap 95% confidence interval (0.09, 0.14)], mainly because of the high genetic divergence between herds within those lineages. High genetic differentiation between lineages was also found with a mean F(ST) of 0.18 [bootstrap 95% confidence interval (0.17, 0.19)], and all pairwise values, which ranged from 0.07 to 0.35, were highly significant. The relationships among lineages showed weak statistical support. Nonetheless, lineages were highly discrete when analysed using correspondence analysis and a great proportion of the individuals were correctly assigned to their own lineage when performing standard assignment procedures.

  20. Genetic Variations Leading to Familial Dilated Cardiomyopathy.

    PubMed

    Cho, Kae Won; Lee, Jongsung; Kim, Youngjo

    2016-10-01

    Cardiomyopathy is a major cause of death worldwide. Based on pathohistological abnormalities and clinical manifestation, cardiomyopathies are categorized into several groups: hypertrophic, dilated, restricted, arrhythmogenic right ventricular, and unclassified. Dilated cardiomyopathy, which is characterized by dilation of the left ventricle and systolic dysfunction, is the most severe and prevalent form of cardiomyopathy and usually requires heart transplantation. Its etiology remains unclear. Recent genetic studies of single gene mutations have provided significant insights into the complex processes of cardiac dysfunction. To date, over 40 genes have been demonstrated to contribute to dilated cardiomyopathy. With advances in genetic screening techniques, novel genes associated with this disease are continuously being identified. The respective gene products can be classified into several functional groups such as sarcomere proteins, structural proteins, ion channels, and nuclear envelope proteins. Nuclear envelope proteins are emerging as potential molecular targets in dilated cardiomyopathy. Because they are not directly associated with contractile force generation and transmission, the molecular pathways through which these proteins cause cardiac muscle disorder remain unclear. However, nuclear envelope proteins are involved in many essential cellular processes. Therefore, integrating apparently distinct cellular processes is of great interest in elucidating the etiology of dilated cardiomyopathy. In this mini review, we summarize the genetic factors associated with dilated cardiomyopathy and discuss their cellular functions.

  1. Pigeonetics takes flight: evolution, development, and genetics of intraspecific variation

    PubMed Central

    Domyan, Eric T.; Shapiro, Michael D.

    2017-01-01

    Intensive artificial selection over thousands of years has produced hundreds of varieties of domestic pigeon. As Charles Darwin observed, the morphological differences among breeds can rise to the magnitude of variation typically observed among different species. Nevertheless, different pigeon varieties are interfertile, thereby enabling forward genetic and genomic approaches to identify genes that underlie derived traits. Building on classical genetic studies of pigeon variation, recent molecular investigations find a spectrum of coding and regulatory alleles controlling derived traits, including plumage color, feather growth polarity, and limb identity. Developmental and genetic analyses of pigeons are revealing the molecular basis of variation in a classic example of extreme intraspecific diversity, and have the potential to nominate genes that control variation among other birds and vertebrates in general. PMID:27847323

  2. Cryptic genetic variation in natural populations: a predictive framework.

    PubMed

    Ledón-Rettig, Cris C; Pfennig, David W; Chunco, Amanda J; Dworkin, Ian

    2014-11-01

    Understanding how populations respond to rapid environmental change is critical both for preserving biodiversity and for human health. An increasing number of studies have shown that genetic variation that has no discernable effect under common ecological conditions can become amplified under stressful or novel conditions, suggesting that environmental change per se can provide the raw materials for adaptation. Indeed, the release of such hidden, or "cryptic," genetic variants has been increasingly viewed as playing a general and important role in allowing populations to respond to rapid environmental change. However, additional studies have suggested that there is a balance between cryptic genetic variants that are potentially adaptive in future environments and genetic variants that are deleterious. In this article, we begin by discussing how population and environmental parameters-such as effective population size and the historical frequency and strength of selection under inducing conditions-influence relative amounts of cryptic genetic variation among populations and the overall phenotypic effects of such variation. The amount and distribution of cryptic genetic variation will, in turn, determine the likelihood that cryptic variants, once expressed, will be adaptive or maladaptive during environmental transitions. We then present specific approaches for measuring these parameters in natural populations. Finally, we discuss one natural system that will be conducive to testing whether populations that vary in these parameters harbor different amounts, or types, of cryptic genetic variation. Generally, teasing apart how population and environmental parameters influence the accumulation of cryptic genetic variation will help us to understand how populations endure and adapt (or fail to adapt) to natural environmental change and anthropogenic disturbance.

  3. Spatial Variations in Drought Persistence in the South-Central U.S.

    NASA Astrophysics Data System (ADS)

    Leasor, Z. T.; Quiring, S. M.

    2016-12-01

    Drought is one of the most prominent climatic hazards in the south-central United States. This study examines spatial variations in meteorological drought persistence using high-resolution PRISM gridded precipitation data from 1900-2015. The Standardized Precipitation Index (SPI) is used to represent meteorological drought conditions. The study region covers Texas, Oklahoma, and Kansas. Droughts are first divided into different severity categories using the classification employed by the U.S. National Drought Monitor. The frequency and duration of each drought event is determined and this is used to calculate drought persistence. Our results indicate that drought persistence in the south-central U.S. varies as a function of drought severity. In addition, drought persistence also varies substantially over space and time. The probability of drought termination is a function of drought severity, geographic location and time of the year. In addition, there is evidence that drought persistence is influenced by global teleconnections and land-atmosphere interactions. The results of this drought persistence climatology can benefit seasonal forecasting and the current understanding of drought recovery.

  4. Genetic architecture of natural variation in visual senescence in Drosophila.

    PubMed

    Carbone, Mary Anna; Yamamoto, Akihiko; Huang, Wen; Lyman, Rachel A; Meadors, Tess Brune; Yamamoto, Ryoan; Anholt, Robert R H; Mackay, Trudy F C

    2016-10-25

    Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span.

  5. Genetic architecture of natural variation in visual senescence in Drosophila

    PubMed Central

    Carbone, Mary Anna; Yamamoto, Akihiko; Huang, Wen; Lyman, Rachel A.; Meadors, Tess Brune; Yamamoto, Ryoan; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2016-01-01

    Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span. PMID:27791033

  6. Genetic Variation in an Individual Human Exome

    PubMed Central

    Ng, Pauline C.; Levy, Samuel; Huang, Jiaqi; Stockwell, Timothy B.; Walenz, Brian P.; Li, Kelvin; Axelrod, Nelson; Busam, Dana A.; Strausberg, Robert L.; Venter, J. Craig

    2008-01-01

    There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ∼12,500 variants that affect the protein coding portion of an individual's genome. We identified ∼10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ∼15–20% are rare in the human population. We predict ∼1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ∼700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ∼12,500 nonsilent coding variants by ∼8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation. PMID:18704161

  7. Genetic variation in an individual human exome.

    PubMed

    Ng, Pauline C; Levy, Samuel; Huang, Jiaqi; Stockwell, Timothy B; Walenz, Brian P; Li, Kelvin; Axelrod, Nelson; Busam, Dana A; Strausberg, Robert L; Venter, J Craig

    2008-08-15

    There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's 'exome,' which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the approximately 12,500 variants that affect the protein coding portion of an individual's genome. We identified approximately 10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which approximately 15-20% are rare in the human population. We predict approximately 1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the approximately 700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of approximately 12,500 nonsilent coding variants by approximately 8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.

  8. Persistence

    NASA Astrophysics Data System (ADS)

    Moore, John W.

    1998-11-01

    Eudora Welty, the famous writer, was once asked what should be done by society or government to encourage young writers. Her response, which surprised the questioner, and me when I heard it, was "Nothing". Welty contended that a person who was really a writer would be persistent enough to overcome whatever obstacles were in the way, needing no interference or support from others.

  9. Lactase non-persistence is directed by DNA variation-dependent epigenetic aging

    PubMed Central

    Labrie, Viviane; Buske, Orion J; Oh, Edward; Jeremian, Richie; Ptak, Carolyn; Gasiūnas, Giedrius; Maleckas, Almantas; Petereit, Rūta; Žvirbliene, Aida; Adamonis, Kęstutis; Kriukienė, Edita; Koncevičius, Karolis; Gordevičius, Juozas; Nair, Akhil; Zhang, Aiping; Ebrahimi, Sasha; Oh, Gabriel; Šikšnys, Virginijus; Kupčinskas, Limas; Brudno, Michael; Petronis, Arturas

    2016-01-01

    Inability to digest lactose due to lactase non-persistence is a common trait in adult mammals, with the exception of certain human populations that exhibit lactase persistence. It is not clear how the lactase gene can be dramatically downregulated with age in most individuals, but remains active in some. We performed a comprehensive epigenetic study of the human and mouse intestine using chromosome-wide DNA modification profiling and targeted bisulfite sequencing. Epigenetically-controlled regulatory elements were found to account for the differences in lactase mRNA levels between individuals, intestinal cell types and species. The importance of these regulatory elements in modulating lactase mRNA levels was confirmed by CRISPR-Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, as lactase persistence- and non-persistence-DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors facilitate a gradual accumulation of epigenetic changes with age to affect phenotypic outcome. PMID:27159559

  10. Artificial Selection Reveals High Genetic Variation in Phenology at the Trailing Edge of a Species Range.

    PubMed

    Sheth, Seema Nayan; Angert, Amy Lauren

    2016-02-01

    Species responses to climate change depend on the interplay of migration and adaptation, yet we know relatively little about the potential for adaptation. Genetic adaptations to climate change often involve shifts in the timing of phenological events, such as flowering. If populations at the edge of a species range have lower genetic variation in phenological traits than central populations, then their persistence under climate change could be threatened. To test this hypothesis, we performed artificial selection experiments using the scarlet monkeyflower (Mimulus cardinalis) and compared genetic variation in flowering time among populations at the latitudinal center, northern edge, and southern edge of the species range. We also assessed whether selection on flowering time yielded correlated responses in functional traits, potentially representing a cost associated with early or late flowering. Contrary to prediction, southern populations exhibited greater responses to selection on flowering time than central or northern populations. Further, selection for early flowering resulted in correlated increases in specific leaf area and leaf nitrogen, whereas selection for late flowering led to decreases in these traits. These results provide critical insights about how spatial variation in the potential for adaptation may affect population persistence under changing climates.

  11. Intraspecific genetic variation and species coexistence in plant communities

    PubMed Central

    Ehlers, Bodil K.; Damgaard, Christian F.; Laroche, Fabien

    2016-01-01

    Many studies report that intraspecific genetic variation in plants can affect community composition and coexistence. However, less is known about which traits are responsible and the mechanisms by which variation in these traits affect the associated community. Focusing on plant–plant interactions, we review empirical studies exemplifying how intraspecific genetic variation in functional traits impacts plant coexistence. Intraspecific variation in chemical and architectural traits promotes species coexistence, by both increasing habitat heterogeneity and altering competitive hierarchies. Decomposing species interactions into interactions between genotypes shows that genotype × genotype interactions are often intransitive. The outcome of plant–plant interactions varies with local adaptation to the environment and with dominant neighbour genotypes, and some plants can recognize the genetic identity of neighbour plants if they have a common history of coexistence. Taken together, this reveals a very dynamic nature of coexistence. We outline how more traits mediating plant–plant interactions may be identified, and how future studies could use population genetic surveys of genotype distribution in nature and methods from trait-based ecology to better quantify the impact of intraspecific genetic variation on plant coexistence. PMID:26790707

  12. Intraspecific genetic variation and species coexistence in plant communities.

    PubMed

    Ehlers, Bodil K; Damgaard, Christian F; Laroche, Fabien

    2016-01-01

    Many studies report that intraspecific genetic variation in plants can affect community composition and coexistence. However, less is known about which traits are responsible and the mechanisms by which variation in these traits affect the associated community. Focusing on plant-plant interactions, we review empirical studies exemplifying how intraspecific genetic variation in functional traits impacts plant coexistence. Intraspecific variation in chemical and architectural traits promotes species coexistence, by both increasing habitat heterogeneity and altering competitive hierarchies. Decomposing species interactions into interactions between genotypes shows that genotype × genotype interactions are often intransitive. The outcome of plant-plant interactions varies with local adaptation to the environment and with dominant neighbour genotypes, and some plants can recognize the genetic identity of neighbour plants if they have a common history of coexistence. Taken together, this reveals a very dynamic nature of coexistence. We outline how more traits mediating plant-plant interactions may be identified, and how future studies could use population genetic surveys of genotype distribution in nature and methods from trait-based ecology to better quantify the impact of intraspecific genetic variation on plant coexistence. © 2016 The Author(s).

  13. Evolutionary response when selection and genetic variation covary across environments.

    PubMed

    Wood, Corlett W; Brodie, Edmund D

    2016-10-01

    Although models of evolution usually assume that the strength of selection on a trait and the expression of genetic variation in that trait are independent, whenever the same ecological factor impacts both parameters, a correlation between the two may arise that accelerates trait evolution in some environments and slows it in others. Here, we address the evolutionary consequences and ecological causes of a correlation between selection and expressed genetic variation. Using a simple analytical model, we show that the correlation has a modest effect on the mean evolutionary response and a large effect on its variance, increasing among-population or among-generation variation in the response when positive, and diminishing variation when negative. We performed a literature review to identify the ecological factors that influence selection and expressed genetic variation across traits. We found that some factors - temperature and competition - are unlikely to generate the correlation because they affected one parameter more than the other, and identified others - most notably, environmental novelty - that merit further investigation because little is known about their impact on one of the two parameters. We argue that the correlation between selection and genetic variation deserves attention alongside other factors that promote or constrain evolution in heterogeneous landscapes.

  14. Patterns of genetic variation in US federal bison herds.

    PubMed

    Halbert, Natalie D; Derr, James N

    2008-12-01

    Like many wide-ranging mammals, American bison (Bison bison) have experienced significant range contraction over the past two centuries and are maintained in artificially isolated populations. A basic understanding of the distribution of genetic variation among populations is necessary to facilitate long-term germplasm preservation and species conservation. The 11 herds maintained within the US federal system are a critically important source of germplasm for bison conservation, as they include many of the oldest herds in the USA and have served as a primary resource for the establishment of private and public herds worldwide. In this study, we used a panel of 51 nuclear markers to investigate patterns of neutral genetic variation among these herds. Most of these herds have maintained remarkably high levels of variation despite the severe bottleneck suffered in the late 1800s. However, differences were noted in the patterns of variation and levels of differentiation among herds, which were compared with historical records of establishment, supplementation, herd size, and culling practices. Although some lineages have been replicated across multiple herds within the US federal system, other lineages with high levels of genetic variation exist in isolated herds and should be considered targets for the establishment of satellite herds. From this and other studies, it is clear that the genetic variation represented in the US federal system is unevenly distributed among National Park Service and Fish and Wildlife Service herds, and that these resources must be carefully managed to ensure long-term species conservation.

  15. Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior.

    PubMed

    Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R H; Mackay, Trudy F C

    2015-07-07

    Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics.

  16. Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior

    PubMed Central

    Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics. PMID:26100892

  17. TEMPLE: analysing population genetic variation at transcription factor binding sites.

    PubMed

    Litovchenko, Maria; Laurent, Stefan

    2016-11-01

    Genetic variation occurring at the level of regulatory sequences can affect phenotypes and fitness in natural populations. This variation can be analysed in a population genetic framework to study how genetic drift and selection affect the evolution of these functional elements. However, doing this requires a good understanding of the location and nature of regulatory regions and has long been a major hurdle. The current proliferation of genomewide profiling experiments of transcription factor occupancies greatly improves our ability to identify genomic regions involved in specific DNA-protein interactions. Although software exists for predicting transcription factor binding sites (TFBS), and the effects of genetic variants on TFBS specificity, there are no tools currently available for inferring this information jointly with the genetic variation at TFBS in natural populations. We developed the software Transcription Elements Mapping at the Population LEvel (TEMPLE), which predicts TFBS, evaluates the effects of genetic variants on TFBS specificity and summarizes the genetic variation occurring at TFBS in intraspecific sequence alignments. We demonstrate that TEMPLE's TFBS prediction algorithms gives identical results to PATSER, a software distribution commonly used in the field. We also illustrate the unique features of TEMPLE by analysing TFBS diversity for the TF Senseless (SENS) in one ancestral and one cosmopolitan population of the fruit fly Drosophila melanogaster. TEMPLE can be used to localize TFBS that are characterized by strong genetic differentiation across natural populations. This will be particularly useful for studies aiming to identify adaptive mutations. TEMPLE is a java-based cross-platform software that easily maps the genetic diversity at predicted TFBSs using a graphical interface, or from the Unix command line.

  18. Selection Transforms the Landscape of Genetic Variation Interacting with Hsp90

    PubMed Central

    Geiler-Samerotte, Kerry A.; Zhu, Yuan O.; Goulet, Benjamin E.; Hall, David W.; Siegal, Mark L.

    2016-01-01

    The protein-folding chaperone Hsp90 has been proposed to buffer the phenotypic effects of mutations. The potential for Hsp90 and other putative buffers to increase robustness to mutation has had major impact on disease models, quantitative genetics, and evolutionary theory. But Hsp90 sometimes contradicts expectations for a buffer by potentiating rapid phenotypic changes that would otherwise not occur. Here, we quantify Hsp90’s ability to buffer or potentiate (i.e., diminish or enhance) the effects of genetic variation on single-cell morphological features in budding yeast. We corroborate reports that Hsp90 tends to buffer the effects of standing genetic variation in natural populations. However, we demonstrate that Hsp90 tends to have the opposite effect on genetic variation that has experienced reduced selection pressure. Specifically, Hsp90 tends to enhance, rather than diminish, the effects of spontaneous mutations and recombinations. This result implies that Hsp90 does not make phenotypes more robust to the effects of genetic perturbation. Instead, natural selection preferentially allows buffered alleles to persist and thereby creates the false impression that Hsp90 confers greater robustness. PMID:27768682

  19. Stochastic and compensatory effects limit persistence of variation in body mass of young caribou

    USGS Publications Warehouse

    Dale, B.W.; Adams, L.G.; Collins, W.B.; Joly, Kyle; Valkenburg, P.; Tobey, R.

    2008-01-01

    Nutritional restriction during growth can have short- and long-term effects on fitness; however, animals inhabiting uncertain environments may exhibit adaptations to cope with variation in food availability. We examined changes in body mass in free-ranging female caribou (Rangifer tarandus) by measuring mass at birth and at 4, 11, and 16 months of age to evaluate the relative importance of seasonal nutrition to growth, the persistence of cohort-specific variation in body mass through time, and compensatory growth of individuals. Relative mean body mass of cohorts did not persist through time. Compensatory growth of smaller individuals was not observed in summer; however, small calves exhibited more positive change in body mass than did large calves. Compensation occurred during periods of nutritional restriction (winter) rather than during periods of rapid growth (summer) thus differing from the conventional view of compensatory growth. ?? 2008 American Society of Mammalogists.

  20. Genetic variation of St. Louis encephalitis virus.

    PubMed

    May, Fiona J; Li, Li; Zhang, Shuliu; Guzman, Hilda; Beasley, David W C; Tesh, Robert B; Higgs, Stephen; Raj, Pushker; Bueno, Rudy; Randle, Yvonne; Chandler, Laura; Barrett, Alan D T

    2008-08-01

    St. Louis encephalitis virus (SLEV) has been regularly isolated throughout the Americas since 1933. Previous phylogenetic studies involving 62 isolates have defined seven major lineages (I-VII), further divided into 14 clades. In this study, 28 strains isolated in Texas in 1991 and 2001-2003, and three older, previously unsequenced strains from Jamaica and California were sequenced over the envelope protein gene. The inclusion of these new sequences, and others published since 2001, has allowed better delineation of the previously published SLEV lineages, in particular the clades of lineage II. Phylogenetic analysis of 106 isolates identified 13 clades. All 1991 and 2001-2003 isolates from Nueces, Jefferson and Harris Counties (Texas Gulf Coast) group in clade IIB with other isolates from these counties isolated during the 1980s and 1990s. This lack of evidence for introduction of novel strains into the Texas Gulf Coast over a long period of time is consistent with overwintering of SLEV in this region. Two El Paso isolates, both from 2002, group in clade VA with recent Californian isolates from 1998-2001 and some South American strains with a broad temporal range. Overall, these data are consistent with multiple introductions of SLEV from South America into North America, and provide support for the hypothesis that in most situations, SLEV circulates within a locality, with occasional incursions from other areas. Finally, SLEV has much lower nucleotide (10.1 %) and amino acid variation (2.8 %) than other members of the Japanese encephalitis virus complex (maximum variation 24.6 % nucleotide and 11.8 % amino acid).

  1. Genetic variation of St. Louis encephalitis virus

    PubMed Central

    May, Fiona J.; Li, Li; Zhang, Shuliu; Guzman, Hilda; Beasley, David W. C.; Tesh, Robert B.; Higgs, Stephen; Raj, Pushker; Bueno, Rudy; Randle, Yvonne; Chandler, Laura; Barrett, Alan D. T.

    2008-01-01

    St. Louis encephalitis virus (SLEV) has been regularly isolated throughout the Americas since 1933. Previous phylogenetic studies involving 62 isolates have defined seven major lineages (I–VII), further divided into 14 clades. In this study, 28 strains isolated in Texas in 1991 and 2001–2003, and three older, previously unsequenced strains from Jamaica and California were sequenced over the envelope protein gene. The inclusion of these new sequences, and others published since 2001, has allowed better delineation of the previously published SLEV lineages, in particular the clades of lineage II. Phylogenetic analysis of 106 isolates identified 13 clades. All 1991 and 2001–2003 isolates from Nueces, Jefferson and Harris Counties (Texas Gulf Coast) group in clade IIB with other isolates from these counties isolated during the 1980s and 1990s. This lack of evidence for introduction of novel strains into the Texas Gulf Coast over a long period of time is consistent with overwintering of SLEV in this region. Two El Paso isolates, both from 2002, group in clade VA with recent Californian isolates from 1998–2001 and some South American strains with a broad temporal range. Overall, these data are consistent with multiple introductions of SLEV from South America into North America, and provide support for the hypothesis that in most situations, SLEV circulates within a locality, with occasional incursions from other areas. Finally, SLEV has much lower nucleotide (10.1 %) and amino acid variation (2.8 %) than other members of the Japanese encephalitis virus complex (maximum variation 24.6 % nucleotide and 11.8 % amino acid). PMID:18632961

  2. Genetic variation and a fitness tradeoff in the tolerance of gray treefrog (Hyla versicolor) tadpoles to the insecticide carbaryl.

    PubMed

    Semlitsch, R D; Bridges, C M; Welch, A M

    2000-10-01

    One of the major unanswered questions in the study of global amphibian declines is why only some species or populations suffer declines. A possible explanation is that species and populations vary in the genetic basis of their tolerance to environmental stress such as chemical contamination. The presence of genetic variation in tolerance to chemicals and in fitness traits of amphibians is essential for persistence of species populations through survival and successful reproduction in contaminated environments. We tested for the presence of genetic variation in the tolerance of amphibian larvae to the insecticide carbaryl using gray treefrog tadpoles (Hyla versicolor). We also assessed whether tolerance of tadpoles is negatively associated with larval performance traits directly related to adult fitness, thereby providing a test of the "cost of tolerance" hypothesis. Our results demonstrate significant variation in tolerance of tadpoles to the insecticide carbaryl within a single population of the gray treefrog, Hyla versicolor. Our half-sibship design indicates that variation among sires explains a significant amount of the variation in chemical tolerance thereby suggesting a heritability genetic basis. Our results also indicate the presence of a fitness tradeoff with tolerance to the chemical carbaryl being negatively correlated, or traded off, with survival of tadpoles reared in the field in the absence of the chemical. Knowledge of genetic tradeoffs with chemical tolerance under realistic environmental conditions will be important for predicting the rate of adaptation and potential for persistence of species. Finally, the partitioning of environmental and genetic variation in tolerance to chemicals is critical to identifying which species are most susceptible, the amount of genetic variance present, the potential for adaptation to contaminants, and the presence of fitness tradeoffs. Such information is necessary to clearly understand the persistence of

  3. Genetic variation and linkage disequilibrium in Bacillus anthracis.

    PubMed

    Zwick, Michael E; Thomason, Maureen Kiley; Chen, Peter E; Johnson, Henry R; Sozhamannan, Shanmuga; Mateczun, Alfred; Read, Timothy D

    2011-01-01

    We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.

  4. Cordova: Web-based management of genetic variation data

    PubMed Central

    Ephraim, Sean S.; Anand, Nikhil; DeLuca, Adam P.; Taylor, Kyle R.; Kolbe, Diana L.; Simpson, Allen C.; Azaiez, Hela; Sloan, Christina M.; Shearer, A. Eliot; Hallier, Andrea R.; Casavant, Thomas L.; Scheetz, Todd E.; Smith, Richard J. H.; Braun, Terry A.

    2014-01-01

    Summary: Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician–scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Availability and implementation: Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Contact: sean.ephraim@gmail.com or terry-braun@uiowa.edu PMID:25123904

  5. Genetic and epigenetic variation of transposable elements in Arabidopsis.

    PubMed

    Underwood, Charles J; Henderson, Ian R; Martienssen, Robert A

    2017-04-01

    Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution. Copyright © 2017. Published by Elsevier Ltd.

  6. Assortative mating by fitness and sexually antagonistic genetic variation.

    PubMed

    Arnqvist, Göran

    2011-07-01

    Recent documentations of sexually antagonistic genetic variation in fitness have spurred an interest in the mechanisms that may act to maintain such variation in natural populations. Using individual-based simulations, I show that positive assortative mating by fitness increases the amount of sexually antagonistic genetic variance in fitness, primarily by elevating the equilibrium frequency of heterozygotes, over most of the range of sex-specific selection and dominance. Further, although the effects of assortative mating by fitness on the protection conditions of polymorphism in sexually antagonistic loci were relatively minor, it widens the protection conditions under most reasonable scenarios (e.g., under heterozygote superiority when fitness is averaged across the sexes) but can also somewhat narrow the protection conditions under other circumstances. The near-ubiquity of assortative mating in nature suggests that it may contribute to upholding standing sexually antagonistic genetic variation in fitness.

  7. Temporal Variation of Chemical Persistence in a Swedish Lake Assessed by Benchmarking.

    PubMed

    Zou, Hongyan; Radke, Michael; Kierkegaard, Amelie; McLachlan, Michael S

    2015-08-18

    Chemical benchmarking was used to investigate the temporal variation of the persistence of chemical contaminants in a Swedish lake. The chemicals studied included 12 pharmaceuticals, an artificial sweetener, and an X-ray contrast agent. Measurements were conducted in late spring, late autumn, and winter. The transformation half-life in the lake could be quantified for 7 of the chemicals. It ranged from several days to hundreds of days. For 5 of the chemicals (bezafibrate, climbazole, diclofenac, furosemide, and hydrochlorothiazide), the measured persistence was lower in late spring than in late autumn. This may have been caused by lower temperatures and/or less irradiation during late autumn. The seasonality in chemical persistence contributed to changes in chemical concentrations in the lake during the year. The impact of seasonality of persistence was compared with the impact of other important variables determining concentrations in the lake: chemical inputs and water flow/dilution. The strongest seasonal variability in chemical concentration in lake water was observed for hydrochlorothiazide (over a factor of 10), and this was attributable to the seasonality in its persistence.

  8. Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

    PubMed Central

    Lewis, Jeffrey A.; Broman, Aimee T.; Will, Jessica; Gasch, Audrey P.

    2014-01-01

    Natural variation in gene expression is pervasive within and between species, and it likely explains a significant fraction of phenotypic variation between individuals. Phenotypic variation in acute systemic responses can also be leveraged to reveal physiological differences in how individuals perceive and respond to environmental perturbations. We previously found extensive variation in the transcriptomic response to acute ethanol exposure in two wild isolates and a common laboratory strain of Saccharomyces cerevisiae. Many expression differences persisted across several modules of coregulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. Here, we conducted expression QTL mapping of the ethanol response in two strain crosses to identify the genetic basis for these differences. To understand systemic differences, we focused on “hotspot” loci that affect many transcripts in trans. Candidate causal regulators contained within hotspots implicate upstream regulators as well as downstream effectors of the ethanol response. Overlap in hotspot targets revealed additive genetic effects of trans-acting loci as well as “epi-hotspots,” in which epistatic interactions between two loci affected the same suites of downstream targets. One epi-hotspot implicated interactions between Mkt1p and proteins linked to translational regulation, prompting us to show that Mkt1p localizes to P bodies upon ethanol stress in a strain-specific manner. Our results provide a glimpse into the genetic architecture underlying natural variation in a stress response and present new details on how yeast respond to ethanol stress. PMID:24970865

  9. Genetic variation in resistance to ionizing radiation

    SciTech Connect

    Ayala, F.J.

    1992-01-01

    Results of an investigation of the gene coding for Cu, Zn superoxide dismutase (Sod) in Drosophila melanogaster seeking to understand the enzyme's role in cell protection against ionizing radiation are reported. Components of the investigation include molecular characterization of the gene; measuring the response of different genotypes to increasing levels of radiation; and investigation of the processes that maintain the Sod polymorphism in populations. While two alleles, S and F, are commonly found at the Sod locus in natural populations of D. melanogaster we have isolated from a natural population a null (CA1) mutant that yields only 3.5% of normal SOD activity. The S, F, and CA1 alleles provide a model system to investigate SOD-dependent radioresistance, because each allele yields different levels of SOD, so that S > F >> CAl. The radioprotective effects of SOD can be established by showing protective effects for the various genotypes that correspond to those inequalities. Because the allele variants studied are derived from natural populations, the proposed investigation avoids problems that arise when mutants obtained my mutagenesis are used. Moreover, each allele is studied in multiple genetic backgrounds, so that we correct for effects attributable to other loci by randomizing these effects.

  10. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

    PubMed Central

    Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

    2013-01-01

    Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

  11. GEMINI: integrative exploration of genetic variation and genome annotations.

    PubMed

    Paila, Umadevi; Chapman, Brad A; Kirchner, Rory; Quinlan, Aaron R

    2013-01-01

    Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.

  12. Genetic variation in the natriuretic peptide system and heart failure.

    PubMed

    Lanfear, David E

    2010-05-01

    Heart failure (HF) is a modern epidemic and is one of the few cardiovascular diseases which is increasing in prevalence. The growing importance of the Natriuretic Peptide (NP) system in HF is well recognized. Laboratory tests for B-type Natriuretic Peptide (BNP) have proven value as diagnostic and prognostic tools in HF and are now part of routine clinical care. Furthermore, recombinant atrial natriuretic peptide (ANP) (carperitide) and BNP (nesiritide) and are approved HF therapies in Japan and the US, respectively and additional natriuretic peptides (e.g., CNP, urodilatin, and designer NPs) are under investigation for use in HF. Common genetic sequence variants are increasingly being recognized as determinants of disease risk or drug response and may help explain a portion of the inter-individual variation in the human NP system. This review describes current knowledge of NP system genetic variation as it pertains to HF as well as ongoing studies and where the field is expected to progress in the near future. To briefly summarize, NP system genetic variants have been associated with alterations in gene expression, NP levels, and cardiovascular disease. The next step forward will include specific investigations into how this genetic variation can advance 'Personalized Medicine', such as whether they impact the utility of diagnostic BNP testing or effectiveness of therapeutic NP infusion. This is already in progress, with pharmacogenetic studies of nesiritide currently underway. We expect that within 5 years there should be a reasonable idea of whether NP system genetic variation will have important clinical implications.

  13. Genetic Variations of Tyrosine Hydroxylase in the Pathogenesis of Hypertension

    PubMed Central

    Lee, Yu Ho; Kim, Yang Gyun; Moon, Ju-Young; Kim, Jin Sug; Jeong, Kyung-Hwan; Lee, Tae Won; Ihm, Chun-Gyoo

    2016-01-01

    One of the major pathophysiological features of primary hypertension is an inappropriate activation of the sympathetic nervous system, which is mediated by excessive synthesis and secretion of catecholamine into the blood. Tyrosine hydroxylase (TH), a rate-limiting enzyme in the synthesis of catecholamine, has been highlighted because genetic variations of TH could alter the activity of the sympathetic nervous system activity and subsequently contribute to the pathogenesis of hypertension. Here, we discuss the role of TH as a regulator of sympathetic activity and review several studies that investigated the relationship between genetic variations of TH and hypertension. PMID:28275384

  14. Genetics of the dentofacial variation in human malocclusion

    PubMed Central

    Moreno Uribe, L. M.; Miller, S. F.

    2015-01-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes. PMID:25865537

  15. Genetics of the dentofacial variation in human malocclusion.

    PubMed

    Moreno Uribe, L M; Miller, S F

    2015-04-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes.

  16. Genetic variation in steelhead of Oregon and northern California

    USGS Publications Warehouse

    Reisenbichler, R.R.; McIntyre, J.D.; Solazzi, M.F.; Landino, S.W

    1992-01-01

    Steelhead Oncorhynchus mykiss from various sites between the Columbia River and the Mad River, California, were genetically characterized at 10 protein-coding loci or pairs of loci by starch gel electrophoresis. Fish from coastal streams differed from fish east of the Cascade Mountains and from fish of the Willamette River (a tributary of the Columbia River, west of the Cascade Mountains). Coastal steelhead from the northern part of the study area differed from those in the southern part. Genetic differentiation within and among drainages was not statistically significant; however, gene diversity analysis and the life history of steelhead suggested that fish from different drainages should be considered as separate populations. Genetic variation among fish in separate drainages was similar to that reported in northwestern Washington and less than that reported in British Columbia. Allele frequencies varied significantly among year-classes. Genetic variation within samples accounted for 98.3% of the total genetic variation observed in this study. Most hatchery populations differed from wild populations, suggesting that conservation of genetic diversity among and within wild populations could be facilitated by altering hatchery programs.

  17. Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

    NASA Astrophysics Data System (ADS)

    Maier, E.; Buckenmaier, A.; Tollrian, R.; Nürnberger, B.

    2012-06-01

    In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.

  18. Interactions of chemical carcinogens and genetic variation in hepatocellular carcinoma

    PubMed Central

    Zhang, Yu-Jing

    2010-01-01

    In the etiology of hepatocellular carcinoma (HCC), in addition to hepatitis B virus and hepatitis C virus infections, chemical carcinogens also play important roles. For example, aflatoxin B1 (AFB1) epoxide reacts with guanine in DNA and can lead to genetic changes. In HCC, the tumor suppressor gene p53 codon 249 mutation is associated with AFB1 exposure and mutations in the K-ras oncogene are related to vinyl chloride exposure. Numerous genetic alterations accumulate during the process of hepatocarcinogenesis. Chemical carcinogen DNA-adduct formation is the basis for these genetic changes and also a molecular marker which reflects exposure level and biological effects. Metabolism of chemical carcinogens, including their activation and detoxification, also plays a key role in chemical hepatocarcinogenesis. Cytochrome p450 enzymes, N-acetyltransferases and glutathione S-transferases are involved in activating and detoxifying chemical carcinogens. These enzymes are polymorphic and genetic variation influences biological response to chemical carcinogens. This genetic variation has been postulated to influence the variability in risk for HCC observed both within and across populations. Ongoing studies seek to fully understand the mechanisms by which genetic variation in response to chemical carcinogens impacts on HCC risk. PMID:21160980

  19. Persistent longitudinal variations in 8 years of CIPS/AIM polar mesospheric clouds

    NASA Astrophysics Data System (ADS)

    Liu, Xiao; Yue, Jia; Xu, Jiyao; Yuan, Wei; Russell, James M.; Hervig, M. E.; Nakamura, Takuji

    2016-07-01

    The Cloud Imaging and Particle Size (CIPS) instrument on the Aeronomy of Ice in the Mesosphere (AIM) satellite provides an opportunity to study the longitudinal variation in polar mesospheric cloud (PMC). We examined the longitudinal variation in PMC albedo using 8 years (2007-2014) of observations from the CIPS instrument. The results show that the PMC albedo in the Southern Hemisphere (SH), especially in the latitude band of 80°S-85°S, is persistently low ( 65% relative to the rest of the hemisphere) within 60°W to 150°W longitude. In the Northern Hemisphere (NH), however, PMC albedo is found to be relatively zonally asymmetry. Harmonic analyses show that the persistent longitudinal variation in the SH PMC albedo is due to zonal wave numbers 1 through 4 (WN1-WN4) processes with minima in the longitude range of 60°W-150°W. The influence of temperature and H2O on the longitudinal variation of the PMC albedo is discussed based on results obtained using a simple 0-D PMC model and temperature from the Microwave Limb Sounder (MLS) and the Sounding of the Atmosphere with Broadband Emission Radiometry (SABER) and H2O from MLS. The modeled region of low ice mass in the SH is generally consistent with that of low PMC albedo seen in CIPS. Tidal analyses using the SABER temperatures indicate that the nonmigrating semidiurnal tides with modes of S0, W1, and E1 might be the main drivers of the persistent longitudinal variations of PMC albedo in the SH. Nonmigrating tides are much weaker in the NH and consistent with the observed lack of longitudinal variability in PMC albedo.

  20. Widespread evidence for non-additive genetic variation in Cloninger's and Eysenck's personality dimensions using a twin plus sibling design.

    PubMed

    Keller, Matthew C; Coventry, William L; Heath, Andrew C; Martin, Nicholas G

    2005-11-01

    Studies using the classical twin design often conclude that most genetic variation underlying personality is additive in nature. However, studies analyzing only twins are very limited in their ability to detect non-additive genetic variation and are unable to detect sources of variation unique to twins, which can mask non-additive genetic variation. The current study assessed 9672 MZ and DZ twin individuals and 3241 of their siblings to investigate the environmental and genetic architecture underlying eight dimensions of personality: four from Eysenck's Personality Questionnaire and four from Cloninger's Temperament and Character Inventory. Broad-sense heritability estimates from best-fitting models were two to three times greater than the narrow-sense heritability estimates for Harm Avoidance, Novelty Seeking, Reward Dependence, Persistence, Extraversion, and Neuroticism. This genetic non-additivity could be due to dominance, additive-by-additive epistasis, or to additive genetic effects combined with higher-order epistasis. Environmental effects unique to twins were detected for both Lie and Psychoticism but accounted for little overall variation. Our results illustrate the increased sensitivity afforded by extending the classical twin design to include siblings, and may provide clues to the evolutionary origins of genetic variation underlying personality.

  1. Persistence of genetic variants of the arctic fox strain of Rabies virus in southern Ontario.

    PubMed

    Nadin-Davis, Susan A; Muldoon, Frances; Wandeler, Alexander I

    2006-01-01

    Genetic-variant analysis of rabies viruses provides the most sensitive epidemiologic tool for following the spread and persistence of these viruses in their wildlife hosts. Since its introduction by a southern epizootic movement that began in the far north, the arctic fox (AFX) strain of Rabies virus has been enzootic in Ontario for almost 50 y. Prior genetic studies identified 4 principal genetic variants (ONT.T1 to ONT.T4) that were localized to different regions of the province; furthermore, these viruses could be distinguished from the variant circulating in northern regions of Quebec, Newfoundland, and arctic zones, ARC.T5. Despite an intensive provincial control program undertaken over the last decade that involved aerial distribution of baits laden with rabies vaccine to combat fox rabies throughout the enzootic zone of Ontario, pockets of rabies activity persist. Re-evaluation of the genetic characteristics of the viral variants circulating in these areas of persistence has been undertaken. These data demonstrate that the recent outbreaks are, with 1 exception, due to persistence of the regional variant first identified in the area in the early 1990s. In contrast, the disease in the Georgian Bay area is a consequence of the incursion of a variant previously found further south. An outbreak that occurred in northern Ontario north and west of North Bay and in the neighboring border areas of Quebec in 2000-2001 was due to renewed incursion of the ARC.T5 variant from more northerly areas.

  2. Genetic Variation of Bordetella pertussis in Austria.

    PubMed

    Wagner, Birgit; Melzer, Helen; Freymüller, Georg; Stumvoll, Sabine; Rendi-Wagner, Pamela; Paulke-Korinek, Maria; Repa, Andreas; Mooi, Frits R; Kollaritsch, Herwig; Mittermayer, Helmut; Kessler, Harald H; Stanek, Gerold; Steinborn, Ralf; Duchêne, Michael; Wiedermann, Ursula

    2015-01-01

    In Austria, vaccination coverage against Bordetella pertussis infections during infancy is estimated at around 90%. Within the last years, however, the number of pertussis cases has increased steadily, not only in children but also in adolescents and adults, indicating both insufficient herd immunity and vaccine coverage. Waning immunity in the host and/or adaptation of the bacterium to the immunised hosts could contribute to the observed re-emergence of pertussis. In this study we therefore addressed the genetic variability in B. pertussis strains from several Austrian cities. Between the years 2002 and 2008, 110 samples were collected from Vienna (n = 32), Linz (n = 63) and Graz (n = 15) by nasopharyngeal swabs. DNA was extracted from the swabs, and bacterial sequence polymorphisms were examined by MLVA (multiple-locus variable number of tandem repeat analysis) (n = 77), by PCR amplification and conventional Sanger sequencing of the polymorphic regions of the prn (pertactin) gene (n = 110), and by amplification refractory mutation system quantitative PCR (ARMS-qPCR) (n = 110) to directly address polymorphisms in the genes encoding two pertussis toxin subunits (ptxA and ptxB), a fimbrial adhesin (fimD), tracheal colonisation factor (tcfA), and the virulence sensor protein (bvgS). Finally, the ptxP promoter region was screened by ARMS-qPCR for the presence of the ptxP3 allele, which has been associated with elevated production of pertussis toxin. The MLVA analysis revealed the highest level of polymorphisms with an absence of MLVA Type 29, which is found outside Austria. Only Prn subtypes Prn1/7, Prn2 and Prn3 were found with a predominance of the non-vaccine type Prn2. The analysis of the ptxA, ptxB, fimD, tcfA and bvgS polymorphisms showed a genotype mixed between the vaccine strain Tohama I and a clinical isolate from 2006 (L517). The major part of the samples (93%) displayed the ptxP3 allele. The consequences for the vaccination strategy are discussed.

  3. Genetic Variation of Bordetella pertussis in Austria

    PubMed Central

    Wagner, Birgit; Melzer, Helen; Freymüller, Georg; Stumvoll, Sabine; Rendi-Wagner, Pamela; Paulke-Korinek, Maria; Repa, Andreas; Mooi, Frits R.; Kollaritsch, Herwig; Kessler, Harald H.; Stanek, Gerold; Steinborn, Ralf; Duchêne, Michael; Wiedermann, Ursula

    2015-01-01

    In Austria, vaccination coverage against Bordetella pertussis infections during infancy is estimated at around 90%. Within the last years, however, the number of pertussis cases has increased steadily, not only in children but also in adolescents and adults, indicating both insufficient herd immunity and vaccine coverage. Waning immunity in the host and/or adaptation of the bacterium to the immunised hosts could contribute to the observed re-emergence of pertussis. In this study we therefore addressed the genetic variability in B. pertussis strains from several Austrian cities. Between the years 2002 and 2008, 110 samples were collected from Vienna (n = 32), Linz (n = 63) and Graz (n = 15) by nasopharyngeal swabs. DNA was extracted from the swabs, and bacterial sequence polymorphisms were examined by MLVA (multiple-locus variable number of tandem repeat analysis) (n = 77), by PCR amplification and conventional Sanger sequencing of the polymorphic regions of the prn (pertactin) gene (n = 110), and by amplification refractory mutation system quantitative PCR (ARMS-qPCR) (n = 110) to directly address polymorphisms in the genes encoding two pertussis toxin subunits (ptxA and ptxB), a fimbrial adhesin (fimD), tracheal colonisation factor (tcfA), and the virulence sensor protein (bvgS). Finally, the ptxP promoter region was screened by ARMS-qPCR for the presence of the ptxP3 allele, which has been associated with elevated production of pertussis toxin. The MLVA analysis revealed the highest level of polymorphisms with an absence of MLVA Type 29, which is found outside Austria. Only Prn subtypes Prn1/7, Prn2 and Prn3 were found with a predominance of the non-vaccine type Prn2. The analysis of the ptxA, ptxB, fimD, tcfA and bvgS polymorphisms showed a genotype mixed between the vaccine strain Tohama I and a clinical isolate from 2006 (L517). The major part of the samples (93%) displayed the ptxP3 allele. The consequences for the vaccination strategy are discussed. PMID

  4. Androgens and doping tests: genetic variation and pit-falls

    PubMed Central

    Rane, Anders; Ekström, Lena

    2012-01-01

    The large variation in disposition known for most drugs is also true for anabolic androgenic steroids. Genetic factors are probably the single most important cause of this variation. Further, there are reasons to believe that there is a corresponding variation in efficacy of doping agents. Doped individuals employ a large variety of doping strategies in respect of choice of substance, dose, dose interval, duration of treatment and use of other drugs for enforcement of effects or correction of side effects. Metabolic steps up-stream and down-stream of testosterone are genetically variable and contribute substantially to the variation in disposition of testosterone, the most common doping agent in sports and in society. Large inter- and intra-ethnic variation in testosterone glucuronidation and excretion is described as well as the pit-falls in evaluation of testosterone doping test results. The hydrolysis and bioactivation of testosterone enanthate is also genetically variable yielding a 2–3 fold variation in excretion rate and serum concentration, thereby implicating a substantial variation in ‘efficacy’ of testosterone. Given this situation it is logical to adopt the new findings in the doping control programme. The population based cut-off level for the testosterone : epitestosterone ratio should be replaced by a Bayesian interpretation of consecutive tests in the same individual. When combined with the above genetic information the sensitivity of the test is considerably improved. The combination of the three approaches should reduce the rate of falsely negative or positive results and the number of expensive follow-up tests, stipulated by the World Anti-Doping Agency. PMID:22506612

  5. Effects of Genetic Drift and Gene Flow on the Selective Maintenance of Genetic Variation

    PubMed Central

    Star, Bastiaan; Spencer, Hamish G.

    2013-01-01

    Explanations for the genetic variation ubiquitous in natural populations are often classified by the population–genetic processes they emphasize: natural selection or mutation and genetic drift. Here we investigate models that incorporate all three processes in a spatially structured population, using what we call a construction approach, simulating finite populations under selection that are bombarded with a steady stream of novel mutations. As expected, the amount of genetic variation compared to previous models that ignored the stochastic effects of drift was reduced, especially for smaller populations and when spatial structure was most profound. By contrast, however, for higher levels of gene flow and larger population sizes, the amount of genetic variation found after many generations was greater than that in simulations without drift. This increased amount of genetic variation is due to the introduction of slightly deleterious alleles by genetic drift and this process is more efficient when migration load is higher. The incorporation of genetic drift also selects for fitness sets that exhibit allele-frequency equilibria with larger domains of attraction: they are “more stable.” Moreover, the finiteness of populations strongly influences levels of local adaptation, selection strength, and the proportion of allele-frequency vectors that can be distinguished from the neutral expectation. PMID:23457235

  6. Genetic Parameters for Milk Yield and Lactation Persistency Using Random Regression Models in Girolando Cattle.

    PubMed

    Canaza-Cayo, Ali William; Lopes, Paulo Sávio; da Silva, Marcos Vinicius Gualberto Barbosa; de Almeida Torres, Robledo; Martins, Marta Fonseca; Arbex, Wagner Antonio; Cobuci, Jaime Araujo

    2015-10-01

    A total of 32,817 test-day milk yield (TDMY) records of the first lactation of 4,056 Girolando cows daughters of 276 sires, collected from 118 herds between 2000 and 2011 were utilized to estimate the genetic parameters for TDMY via random regression models (RRM) using Legendre's polynomial functions whose orders varied from 3 to 5. In addition, nine measures of persistency in milk yield (PSi) and the genetic trend of 305-day milk yield (305MY) were evaluated. The fit quality criteria used indicated RRM employing the Legendre's polynomial of orders 3 and 5 for fitting the genetic additive and permanent environment effects, respectively, as the best model. The heritability and genetic correlation for TDMY throughout the lactation, obtained with the best model, varied from 0.18 to 0.23 and from -0.03 to 1.00, respectively. The heritability and genetic correlation for persistency and 305MY varied from 0.10 to 0.33 and from -0.98 to 1.00, respectively. The use of PS7 would be the most suitable option for the evaluation of Girolando cattle. The estimated breeding values for 305MY of sires and cows showed significant and positive genetic trends. Thus, the use of selection indices would be indicated in the genetic evaluation of Girolando cattle for both traits.

  7. Surviving in isolation: genetic variation, bottlenecks and reproductive strategies in the Canarian endemic Limonium macrophyllum (Plumbaginaceae).

    PubMed

    Jiménez, Ares; Weigelt, Barbara; Santos-Guerra, Arnoldo; Caujapé-Castells, Juli; Fernández-Palacios, José María; Conti, Elena

    2017-02-01

    Oceanic archipelagos are typically rich in endemic taxa, because they offer ideal conditions for diversification and speciation in isolation. One of the most remarkable evolutionary radiations on the Canary Islands comprises the 16 species included in Limonium subsection Nobiles, all of which are subject to diverse threats, and legally protected. Since many of them are single-island endemics limited to one or a few populations, there exists a risk that a loss of genetic variation might limit their long-term survival. In this study, we used eight newly developed microsatellite markers to characterize the levels of genetic variation and inbreeding in L. macrophyllum, a species endemic to the North-east of Tenerife that belongs to Limonium subsection Nobiles. We detected generally low levels of genetic variation over all populations (H T = 0.363), and substantial differentiation among populations (F ST = 0.188; R ST = 0.186) coupled with a negligible degree of inbreeding (F = 0.042). Obligate outcrossing may have maintained L. macrophyllum relatively unaffected by inbreeding despite the species' limited dispersal ability and the genetic bottlenecks likely caused by a prolonged history of grazing. Although several factors still constitute a risk for the conservation of L. macrophyllum, the lack of inbreeding and the recent positive demographic trends observed in the populations of this species are factors that favour its future persistence.

  8. Most genetic risk for autism resides with common variation

    PubMed Central

    Gaugler, Trent; Klei, Lambertus; Sanders, Stephan J.; Bodea, Corneliu A.; Goldberg, Arthur P.; Lee, Ann B.; Mahajan, Milind; Manaa, Dina; Pawitan, Yudi; Reichert, Jennifer; Ripke, Stephan; Sandin, Sven; Sklar, Pamela; Svantesson, Oscar; Reichenberg, Abraham; Hultman, Christina M.; Devlin, Bernie

    2014-01-01

    A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (henceforth autism) the nature of its allelic spectrum is uncertain. Individual risk genes have been identified from rare variation, especially de novo mutations1–8. From this evidence one might conclude that rare variation dominates its allelic spectrum, yet recent studies show that common variation, individually of small effect, has substantial impact en masse9,10. At issue is how much of an impact relative to rare variation. Using a unique epidemiological sample from Sweden, novel methods that distinguish total narrow-sense heritability from that due to common variation, and by synthesizing results from other studies, we reach several conclusions about autism’s genetic architecture: its narrow-sense heritability is ≈54% and most traces to common variation; rare de novo mutations contribute substantially to individuals’ liability; still their contribution to variance in liability, 2.6%, is modest compared to heritable variation. PMID:25038753

  9. Obesity, hypertension and genetic variation in the TIGER Study

    USDA-ARS?s Scientific Manuscript database

    Obesity and hypertension are multifactoral conditions in which the onset and severity of the conditions are influenced by the interplay of genetic and environmental factors. We hypothesize that multiple genes and environmental factors account for a significant amount of variation in BMI and blood pr...

  10. Genetic architecture of flowering time variation in Brachypodium distachyon

    USDA-ARS?s Scientific Manuscript database

    The transition to reproductive development is a crucial step of a plant’s life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a non-domesticated c...

  11. Genetic variation in the widespread lichenicolous fungus Marchandiomyces corallinus.

    PubMed

    Molina, M Carmen; DePriest, Paula T; Lawrey, James D

    2005-01-01

    The lichenicolous basidiomycete Marchandiomyces corallinus is widely distributed in North America and Europe, where it commonly is found on a variety of lichens. Theoretically either of these characteristics, a wide geographic range or generalized host ecology, could provide opportunities for genetic differentiation within this species. To determine how genetic variation is partitioned in M. corallinus, 12 fungal isolates were obtained from locations in North America and Europe; at two locations, in Washington County, Maine, and on the Isle of Mull in Scotland, fungi also were isolated from different lichen hosts. Vegetative mycelial compatibility tests were used to determine compatibility groupings from among the isolates; in addition, several PCR amplification products (RAPD, nuITS rDNA) were obtained for each isolate. A number of distinct compatibility groups were recognizable based on geography, not host ecology. In addition compatible isolates always were restricted to either North America or Europe. However RAPD markers indicated that compatible isolates are not always genetically identical. The presence of sequence heterozygosity at specific positions indicated that the isolates are heterokaryotic and a number of distinct haplotypes could be identified based on ITS variation at three separate locations. This type of genetic variation in these fungi suggests that sexual recombination is possible and that genetic differentiation has taken place recently as a result of geographic isolation, not host switching.

  12. When Does Frequency-Independent Selection Maintain Genetic Variation?

    PubMed

    Novak, Sebastian; Barton, Nicholas H

    2017-10-01

    Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear. Copyright © 2017 by the Genetics Society of America.

  13. Genetic Variation in Populations of a Tropical Mysid, Mysidium gracile

    NASA Astrophysics Data System (ADS)

    Chapina, R.; Ramos-Chavez, J.; Walsh, E.

    2016-02-01

    Genetic diversity allows organisms to adapt to environmental factors such as climate change and ocean acidification. Greater genetic diversity among organisms allows a higher probability of adaptation to changing environments. The mysid Mysidium gracile is a shrimp-like crustacean that aggregates into swarms near coral reefs. They are important in reef systems since they occupy an important intermediate level of marine food webs by transferring energy from planktonic species to reef fishes. Thus, there is concern regarding the tolerance of reef- associated organisms to climatic changes and overall coral reef health. The objective of this study is to determine the level of genetic variation within and among Caribbean M. gracile populations. Mysids from 7 islands were collected and preserved for genetic analysis. The CO1 gene was amplified and sequenced for 100 mysids representing 14 swarms. Haplotype diversity was determined using DnaSP5.0. Twenty- three haplotypes were detected with a haplotype diversity of 0.94, thus indicating a high level of haplotypic variation. Mysids from two populations shared a haplotype, implying that there is potential gene flow between these populations. Mysids from additional swarms are in process of being characterized. Overall, these results show that there is substantial genetic variation within and among mysid populations that may allow them to adapt environmental factors.

  14. Permanence or change? The meaning of genetic variation

    PubMed Central

    Salzano, Francisco M.

    2000-01-01

    Selected aspects of the evolutionary process and more specifically of the genetic variation are considered, with an emphasis in studies performed by my group. One key aspect of evolution seems to be the concomitant occurrence of dichotomic, contradictory (dialect) processes. Genetic variation is structured, and the dynamics of change at one level is not necessarily paralleled by that in another. The pathogenesis-related protein superfamily can be cited as an example in which permanence (the maintenance of certain key genetic features) coexists with change (modifications that led to different functions in different classes of organisms). Relationships between structure and function are exemplified by studies with hemoglobin Porto Alegre. The genetic structure of tribal populations may differ in important aspects from that of industrialized societies. Evolutionary histories also may differ when considered through the investigation of patrilineal or matrilineal lineages. Global evaluations taking into consideration all of these aspects are needed if we really want to understand the meaning of genetic variation. PMID:10805790

  15. The Evolution of Human Genetic and Phenotypic Variation in Africa

    PubMed Central

    Campbell, Michael C.

    2010-01-01

    Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations. PMID:20178763

  16. Unique genetic variation at a species' rear edge is under threat from global climate change.

    PubMed

    Provan, Jim; Maggs, Christine A

    2012-01-07

    Global climate change is having a significant effect on the distributions of a wide variety of species, causing both range shifts and population extinctions. To date, however, no consensus has emerged on how these processes will affect the range-wide genetic diversity of impacted species. It has been suggested that species that recolonized from low-latitude refugia might harbour high levels of genetic variation in rear-edge populations, and that loss of these populations could cause a disproportionately large reduction in overall genetic diversity in such taxa. In the present study, we have examined the distribution of genetic diversity across the range of the seaweed Chondrus crispus, a species that has exhibited a northward shift in its southern limit in Europe over the last 40 years. Analysis of 19 populations from both sides of the North Atlantic using mitochondrial single nucleotide polymorphisms (SNPs), sequence data from two single-copy nuclear regions and allelic variation at eight microsatellite loci revealed unique genetic variation for all marker classes in the rear-edge populations in Iberia, but not in the rear-edge populations in North America. Palaeodistribution modelling and statistical testing of alternative phylogeographic scenarios indicate that the unique genetic diversity in Iberian populations is a result not only of persistence in the region during the last glacial maximum, but also because this refugium did not contribute substantially to the recolonization of Europe after the retreat of the ice. Consequently, loss of these rear-edge populations as a result of ongoing climate change will have a major effect on the overall genetic diversity of the species, particularly in Europe, and this could compromise the adaptive potential of the species as a whole in the face of future global warming.

  17. Persistent high paleosecular variation activity in southern hemisphere for at least 10 000 years

    NASA Astrophysics Data System (ADS)

    Constable, Catherine; Korte, Monika; Panovska, Sanja

    2016-11-01

    Direct observations of the geomagnetic field show that secular variation is strong in the Atlantic hemisphere, and comparatively reduced in the Pacific region. The dipole has been decaying since at least 1840 AD, driven by growth and migration of reverse flux patches in the southern hemisphere. We investigate whether anything like this modern pattern of geomagnetic secular variation persists and can be detected in global paleomagnetic field models. Synthesis of results from two new time-varying spherical harmonic models shows that geographically distinct geomagnetic secular variation extends to at least 10 000 BP. The models use the same database but differ in methodology, leading to some regional differences in results. Consistent large-scale surface features include strong average fields in the northern hemisphere and weaker fields with greater overall variability in the south. Longitudinal structure is present, with weaker average fields in the western Pacific than in the east, and prominent negative inclination anomalies extending beneath Indonesia, across Africa and to Brazil, but weaker anomalies in the central Pacific. Marginally positive inclination anomalies occur west of the Americas. Paleosecular variation activity peaks at high southern latitudes, and there is a pattern of reduced activity at equatorial and mid-latitudes beneath the Pacific. Although the dipole has exhibited both growth and decay over the interval 0-10 000 BP, our results show that geomagnetic paleosecular variation is preferentially focused in similar geographic regions to secular variation seen in the modern field.

  18. Sex-specific genetic effects influence variation in body composition.

    PubMed

    Zillikens, M C; Yazdanpanah, M; Pardo, L M; Rivadeneira, F; Aulchenko, Y S; Oostra, B A; Uitterlinden, A G; Pols, H A P; van Duijn, C M

    2008-12-01

    Despite well-known sex differences in body composition it is not known whether sex-specific genetic or environmental effects contribute to these differences. We assessed body composition in 2,506 individuals, from a young Dutch genetic isolate participating in the Erasmus Rucphen Family study, by dual-energy X-ray absorptiometry and anthropometry. We used variance decomposition procedures to partition variation of body composition into genetic and environmental components common to both sexes and to men and women separately and calculated the correlation between genetic components in men and women. After accounting for age, sex and inbreeding, heritability ranged from 0.39 for fat mass index to 0.84 for height. We found sex-specific genetic effects for fat percentage (fat%), lean mass, lean mass index (LMI) and fat distribution, but not for BMI and height. Genetic correlations between sexes were significantly different from 1 for fat%, lean mass, LMI, android fat, android:gynoid fat ratio and WHR, indicating that there are sex-specific genes contributing to variation of these traits. Genetic variance was significantly higher in women for the waist, hip and thigh circumference and WHR, implying that genes account for more variance of fat distribution in women than in men. Environmental variance was significantly higher in men for the android:gynoid fat ratio. Sex-specific genetic effects underlie sexual dimorphism in several body composition traits. The findings are relevant for studies on the relationship of body composition with common diseases like cardiovascular disease and type 2 diabetes and for genetic association studies.

  19. The Expression of Additive and Nonadditive Genetic Variation under Stress

    PubMed Central

    Blows, M. W.; Sokolowski, M. B.

    1995-01-01

    Experimental lines of Drosophila melanogaster derived from a natural population, which had been isolated in the laboratory for ~70 generations, were crossed to determine if the expression of additive, dominance and epistatic genetic variation in development time and viability was associated with the environment. No association was found between the level of additive genetic effects and environmental value for either trait, but nonadditive genetic effects increased at both extremes of the environmental range for development time. The expression of high levels of dominance and epistatic genetic variation at environmental extremes may be a general expectation for some traits. The disruption of the epistatic gene complexes in the parental lines resulted in hybrid breakdown toward faster development and there was some indication of hybrid breakdown toward higher viability. A combination of genetic drift and natural selection had therefore resulted in different epistatic gene complexes being selected after ~70 generations from a common genetic base. After crossing, the hybrid populations were observed for 10 generations. Epistasis contributed on average 12 hr in development time. Fluctuating asymmetry in sternopleural bristle number also evolved in the hybrid populations, decreasing by >18% in the first seven generations after hybridization. PMID:7672585

  20. Genetic integration of molar cusp size variation in baboons.

    PubMed

    Koh, Christina; Bates, Elizabeth; Broughton, Elizabeth; Do, Nicholas T; Fletcher, Zachary; Mahaney, Michael C; Hlusko, Leslea J

    2010-06-01

    Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the nonoccluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar. Copyright 2009 Wiley-Liss, Inc.

  1. Genetic integration of molar cusp size variation in baboons

    PubMed Central

    Koh, Christina; Bates, Elizabeth; Broughton, Elizabeth; Do, Nicholas T.; Fletcher, Zachary; Mahaney, Michael C.; Hlusko, Leslea J.

    2010-01-01

    Many studies of primate diversity and evolution rely on dental morphology for insight into diet, behavior, and phylogenetic relationships. Consequently, variation in molar cusp size has increasingly become a phenotype of interest. In 2007 we published a quantitative genetic analysis of mandibular molar cusp size variation in baboons. Those results provided more questions than answers, as the pattern of genetic integration did not fit predictions from odontogenesis. To follow up, we expanded our study to include data from the maxillary molar cusps. Here we report on these later analyses, as well as inter-arch comparisons with the mandibular data. We analyzed variation in two-dimensional maxillary molar cusp size using data collected from a captive pedigreed breeding colony of baboons, Papio hamadryas, housed at the Southwest National Primate Research Center. These analyses show that variation in maxillary molar cusp size is heritable and sexually dimorphic. We also estimated additive genetic correlations between cusps on the same crown, homologous cusps along the tooth row, and maxillary and mandibular cusps. The pattern for maxillary molars yields genetic correlations of one between the paracone-metacone and protocone-hypocone. Bivariate analyses of cuspal homologues on adjacent teeth yield correlations that are high or not significantly different from one. Between dental arcades, the non-occluding cusps consistently yield high genetic correlations, especially the metaconid-paracone and metaconid-metacone. This pattern of genetic correlation does not immediately accord with the pattern of development and/or calcification, however these results do follow predictions that can be made from the evolutionary history of the tribosphenic molar. PMID:20034010

  2. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    USGS Publications Warehouse

    Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  3. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

    PubMed

    Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon

    2016-02-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics. © 2015 John Wiley & Sons Ltd.

  4. Differential Regulation of Cryptic Genetic Variation Shapes the Genetic Interactome Underlying Complex Traits

    PubMed Central

    Yadav, Anupama; Dhole, Kaustubh

    2016-01-01

    Cryptic genetic variation (CGV) refers to genetic variants whose effects are buffered in most conditions but manifest phenotypically upon specific genetic and environmental perturbations. Despite having a central role in adaptation, contribution of CGV to regulation of quantitative traits is unclear. Instead, a relatively simplistic architecture of additive genetic loci is known to regulate phenotypic variation in most traits. In this paper, we investigate the regulation of CGV and its implication on the genetic architecture of quantitative traits at a genome-wide level. We use a previously published dataset of biparental recombinant population of Saccharomyces cerevisiae phenotyped in 34 diverse environments to perform single locus, two-locus, and covariance mapping. We identify loci that have independent additive effects as well as those which regulate the phenotypic manifestation of other genetic variants (variance QTL). We find that whereas additive genetic variance is predominant, a higher order genetic interaction network regulates variation in certain environments. Despite containing pleiotropic loci, with effects across environments, these genetic networks are highly environment specific. CGV is buffered under most allelic combinations of these networks and perturbed only in rare combinations resulting in high phenotypic variance. The presence of such environment specific genetic networks is the underlying cause of abundant gene–environment interactions. We demonstrate that overlaying identified molecular networks on such genetic networks can identify potential candidate genes and underlying mechanisms regulating phenotypic variation. Such an integrated approach applied to human disease datasets has the potential to improve the ability to predict disease predisposition and identify specific therapeutic targets. PMID:28172852

  5. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection.

    PubMed

    Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E

    2017-03-10

    Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set (TS) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of

  6. Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection

    PubMed Central

    Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E.

    2017-01-01

    Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents (Np), but little is known about how Np affects genomic selection (GS) in RS, especially the persistency of prediction accuracy (rg,g^) and genetic gain. Synthetics were simulated by intermating Np= 2–32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA) and subjected to multiple cycles of GS. We determined rg,g^ and genetic gain across 30 cycles for different training set (TS) sizes, marker densities, and generations of recombination before model training. Contributions to rg,g^ and genetic gain from pedigree relationships, as well as from cosegregation and LDA between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of rg,g^ was high for small Np, where predominantly cosegregation contributed to rg,g^, but also for large Np, where LDA replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to rg,g^ for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size (NTS) and higher marker density improved persistency of rg,g^ and hence genetic gain, but additional recombinations could not increase genetic gain. PMID:28064189

  7. The genetics of phenotypic plasticity. X. Variation versus uncertainty

    PubMed Central

    Scheiner, Samuel M; Holt, Robert D

    2012-01-01

    Despite the apparent advantages of adaptive plasticity, it is not common. We examined the effects of variation and uncertainty on selection for plasticity using an individual-based computer simulation model. In the model, the environment consisted of a linear gradient of 50 demes with dispersal occurring either before or after selection. Individuals consisted of multiple loci whose phenotypic expression either are affected (plastic) or are not affected (nonplastic) by the environment. Typically, evolution occurred first as genetic differentiation, which was then replaced by the evolution of adaptive plasticity, opposite to the evolutionary trend that is often assumed. Increasing dispersal rates selected for plasticity, if selection occurred before dispersal. If selection occurred after dispersal, the highest plasticity was at intermediate dispersal rates. Temporal variation in the environment occurring after development, but before selection, favored the evolution of plasticity. With dispersal before selection, such temporal variation resulted in hyperplasticity, with a reaction norm much steeper than the optimum. This effect was enhanced with negative temporal autocorrelation and can be interpreted as representing a form of bet hedging. As the number of nonplastic loci increased, plasticity was disfavored due to an increase in the uncertainty of the genomic environment. This effect was reversed with temporal variation. Thus, variation and uncertainty affect whether or not plasticity is favored with different sources of variation—arising from the amount and timing of dispersal, from temporal variation, and even from the genetic architecture underlying the phenotype—having contrasting, interacting, and at times unexpected effects. PMID:22837824

  8. Interhemispheric comparison of recruitment to intertidal communities: pattern persistence and scales of variation.

    PubMed

    Navarrete, Sergio A; Broitman, Bernardo R; Menge, Bruce A

    2008-05-01

    Recruitment variation can be a major source of fluctuation in populations and communities, making it difficult to generalize results. Determining the scales of variation and whether spatial patterns in the supply of individuals are persistent over time can provide insight into spatial generality and the application of conservation and metacommunity models. We examined these issues using eight-year-long data sets of monthly recruitment of intertidal mussels (Mytilus spp., Perumytilus purpuratus, Semimytilus algosus, Brachidontes granulata) and barnacles (Balanus glandula, Chthamalus dalli, Jehlius cirratus, Notochthamalus scabrosus) at sites spanning > 900 km along the coasts of Oregon-northern California (OR-NCA, 45.47-39.43 degrees N) and central Chile (CC, 29.5-34.65 degrees S). We evaluated four general "null" hypotheses: that despite different phylogenies and great spatial separation of these taxa, their similar life history strategies and environmental settings lead to similar patterns of recruitment (1) between hemispheres, (2) in time, (3) in space, and (4) at larger and smaller spatial scales. Hypothesis 1 was rejected: along the OR-NCA coast, rates of recruitment were between two and three orders of magnitude higher, and patterns of seasonality were generally stronger and more coherent across space and time than along CC. Surprisingly, however, further analysis revealed regularities in both time and space for all species, supporting hypotheses 2 and 3. Temporal decorrelation scales were 1-3 months, and characteristic spatial scales of recruitment were approximately 250 km. Contrary to hypothesis 4, for the ecologically dominant species in both hemispheres, recruitment was remarkably persistent at larger mesoscales (kilometers) but was highly stochastic at smaller microscales (meters). Across species, increased recruitment variation at large scales was positively associated with increased persistence. Our results have several implications. Although the two

  9. Genetic Variations Strongly Influence Phenotypic Outcome in the Mouse Retina

    PubMed Central

    Jelcick, Austin S.; Yuan, Yang; Leehy, Barrett D.; Cox, Lakeisha C.; Silveira, Alexandra C.; Qiu, Fang; Schenk, Sarah; Sachs, Andrew J.; Morrison, Margaux A.; Nystuen, Arne M.; DeAngelis, Margaret M.; Haider, Neena B.

    2011-01-01

    Variation in genetic background can significantly influence the phenotypic outcome of both disease and non-disease associated traits. Additionally, differences in temporal and strain specific gene expression can also contribute to phenotypes in the mammalian retina. This is the first report of microarray based cross-strain analysis of gene expression in the retina investigating genetic background effects. Microarray analyses were performed on retinas from the following mouse strains: C57BL6/J, AKR/J, CAST/EiJ, and NOD.NON-H2-nb1 at embryonic day 18.5 (E18.5) and postnatal day 30.5 (P30.5). Over 3000 differentially expressed genes were identified between strains and developmental stages. Differential gene expression was confirmed by qRT-PCR, Western blot, and immunohistochemistry. Three major gene networks were identified that function to regulate retinal or photoreceptor development, visual perception, cellular transport, and signal transduction. Many of the genes in these networks are implicated in retinal diseases such as bradyopsia, night-blindness, and cone-rod dystrophy. Our analysis revealed strain specific variations in cone photoreceptor cell patterning and retinal function. This study highlights the substantial impact of genetic background on both development and function of the retina and the level of gene expression differences tolerated for normal retinal function. These strain specific genetic variations may also be present in other tissues. In addition, this study will provide valuable insight for the development of more accurate models for human retinal diseases. PMID:21779340

  10. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae.

    PubMed

    Wang, Li; Li, Jing; Zhao, Jing; He, Chaoying

    2015-01-01

    Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops.

  11. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae

    PubMed Central

    Wang, Li; Li, Jing; Zhao, Jing; He, Chaoying

    2015-01-01

    Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops. PMID:25918515

  12. Developmental and Genetic Origins of Murine Long Bone Length Variation

    PubMed Central

    Sanger, Thomas J.; Norgard, Elizabeth A.; Pletscher, L. Susan; Bevilacqua, Michael; Brooks, Victoria R.; Sandell, Linda M.; Cheverud, James M.

    2011-01-01

    If we wish to understand whether development influences the rate or direction of morphological evolution, we must first understand the developmental bases of morphological variation within species. However, quantitative variation in adult morphology is the product of molecular and cellular processes unfolding from embryonic development through juvenile growth to maturity. The Atchley-Hall model provides a useful framework for dissecting complex morphologies into their component parts as a way of determining which developmental processes contribute to variation in adult form. We have examined differences in postnatal allometry and the patterns of genetic correlation between age-specific traits for 10 recombinant inbred strains of mice generated from an intercross of LG/J and SM/J. Long bone length is closely tied to body size, but variation in adult morphology is more closely tied to differences in growth rate between 3 and 5 weeks of age. These analyses show that variation generated during early development is overridden by variation generated later in life. To more precisely determine the cellular processes generating this variation we then examined the cellular dynamics of long bone growth plates at the time of maximum elongation rate differences in the parent strains. Our analyses revealed that variation in long bone length is the result of faster elongation rates of the LG/J stain. The developmental bases for these differences in growth rate involve the rate of cell division and chondrocyte hypertrophy in the growth plate. PMID:21328530

  13. Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions

    PubMed Central

    Zan, Yanjun; Shen, Xia; Forsberg, Simon K. G.; Carlborg, Örjan

    2016-01-01

    An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant’s extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population. PMID:27226169

  14. Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

    USGS Publications Warehouse

    Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

    2007-01-01

    Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

  15. Human genetic variation: new challenges and opportunities for doping control.

    PubMed

    Schneider, Angela J; Fedoruk, Matthew N; Rupert, Jim L

    2012-01-01

    Sport celebrates differences in competitors that lead to the often razor-thin margins between victory and defeat. The source of this variation is the interaction between the environment in which the athletes develop and compete and their genetic make-up. However, a darker side of sports may also be genetically influenced: some anti-doping tests are affected by the athlete's genotype. Genetic variation is an issue that anti-doping authorities must address as more is learned about the interaction between genotype and the responses to prohibited practices. To differentiate between naturally occurring deviations in indirect blood and urine markers from those potentially caused by doping, the "biological-passport" program uses intra-individual variability rather than population values to establish an athlete's expected physiological range. The next step in "personalized" doping control may be the inclusion of genetic data, both for the purposes of documenting an athlete's responses to doping agents and doping-control assays as well facilitating athlete and sample identification. Such applications could benefit "clean" athletes but will come at the expense of risks to privacy. This article reviews the instances where genetics has intersected with doping control, and briefly discusses the potential role, and ethical implications, of genotyping in the struggle to eliminate illicit ergogenic practices.

  16. Additive and nonadditive genetic variation in avian personality traits.

    PubMed

    van Oers, K; Drent, P J; de Jong, G; van Noordwijk, A J

    2004-11-01

    Individuals of all vertebrate species differ consistently in their reactions to mildly stressful challenges. These typical reactions, described as personalities or coping strategies, have a clear genetic basis, but the structure of their inheritance in natural populations is almost unknown. We carried out a quantitative genetic analysis of two personality traits (exploration and boldness) and the combination of these two traits (early exploratory behaviour). This study was carried out on the lines resulting from a two-directional artificial selection experiment on early exploratory behaviour (EEB) of great tits (Parus major) originating from a wild population. In analyses using the original lines, reciprocal F(1) and reciprocal first backcross generations, additive, dominance, maternal effects ands sex-dependent expression of exploration, boldness and EEB were estimated. Both additive and dominant genetic effects were important determinants of phenotypic variation in exploratory behaviour and boldness. However, no sex-dependent expression was observed in either of these personality traits. These results are discussed with respect to the maintenance of genetic variation in personality traits, and the expected genetic structure of other behavioural and life history traits in general.

  17. Genetic Architectures of Quantitative Variation in RNA Editing Pathways.

    PubMed

    Gu, Tongjun; Gatti, Daniel M; Srivastava, Anuj; Snyder, Elizabeth M; Raghupathy, Narayanan; Simecek, Petr; Svenson, Karen L; Dotu, Ivan; Chuang, Jeffrey H; Keller, Mark P; Attie, Alan D; Braun, Robert E; Churchill, Gary A

    2016-02-01

    RNA editing refers to post-transcriptional processes that alter the base sequence of RNA. Recently, hundreds of new RNA editing targets have been reported. However, the mechanisms that determine the specificity and degree of editing are not well understood. We examined quantitative variation of site-specific editing in a genetically diverse multiparent population, Diversity Outbred mice, and mapped polymorphic loci that alter editing ratios globally for C-to-U editing and at specific sites for A-to-I editing. An allelic series in the C-to-U editing enzyme Apobec1 influences the editing efficiency of Apob and 58 additional C-to-U editing targets. We identified 49 A-to-I editing sites with polymorphisms in the edited transcript that alter editing efficiency. In contrast to the shared genetic control of C-to-U editing, most of the variable A-to-I editing sites were determined by local nucleotide polymorphisms in proximity to the editing site in the RNA secondary structure. Our results indicate that RNA editing is a quantitative trait subject to genetic variation and that evolutionary constraints have given rise to distinct genetic architectures in the two canonical types of RNA editing. Copyright © 2016 by the Genetics Society of America.

  18. Genetic Variation in the Chemical Components of Eucalyptus globulus Wood

    PubMed Central

    Stackpole, Desmond J.; Vaillancourt, René E.; Alves, Ana; Rodrigues, José; Potts, Brad M.

    2011-01-01

    Despite the ecological and economic importance of lignin and other wood chemical components, there are few studies of the natural genetic variation that exists within plant species and its adaptive significance. We used models developed from near infra-red spectroscopy to study natural genetic variation in lignin content and monomer composition (syringyl-to-guaiacyl ratio [S/G]) as well as cellulose and extractives content, using a 16-year-old field trial of an Australian tree species, Eucalyptus globulus. We sampled 2163 progenies of 467 native trees from throughout the native geographic range of the species. The narrow-sense heritability of wood chemical traits (0.25–0.44) was higher than that of growth (0.15), but less than wood density (0.51). All wood chemical traits exhibited significant broad-scale genetic differentiation (QST = 0.34–0.43) across the species range. This differentiation exceeded that detected with putatively neutral microsatellite markers (FST = 0.09), arguing that diversifying selection has shaped population differentiation in wood chemistry. There were significant genetic correlations among these wood chemical traits at the population and additive genetic levels. However, population differentiation in the S/G ratio of lignin in particular was positively correlated with latitude (R2 = 76%), which may be driven by either adaptation to climate or associated biotic factors. PMID:22384327

  19. Lactase persistence-related genetic variant: population substructure and health outcomes

    PubMed Central

    Smith, George Davey; Lawlor, Debbie A; Timpson, Nic J; Baban, Jamil; Kiessling, Matt; Day, Ian N M; Ebrahim, Shah

    2009-01-01

    Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T−13910 variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60–79 years from 23 towns across Britain. We found an overall frequency of 0.253 for the C (lactase non-persistence) allele, but with considerable gradients of decreasing frequency from the south to the north and from the east to the west of Britain for this allele. Daily sunlight was positively related to C (non-persistence) allele prevalence. However, sunlight exposure and latitude are strongly correlated, and it was not possible to identify which is the primary factor statistically underlying the distribution of lactase persistence. The C/T−13910 variant (rs4988235) was not related to drinking milk or bone health (although drinking milk itself was protective of bone health), and was essentially unrelated to a wide range of other lifestyle, health and demographic characteristics. One exception was general health being rated as being poor or fair, for which there was an odds ratio of 1.38 (1.04, 1.84) for women homozygous for the C allele; on adjustment for latitude and longitude of place of birth, this attenuated to 1.19 (0.87, 1.64). The lactase persistence variant could contribute to the examination of data for the existence of, and then statistical control for, population substructure in genetic association studies. PMID:18797476

  20. Lactase persistence-related genetic variant: population substructure and health outcomes.

    PubMed

    Smith, George Davey; Lawlor, Debbie A; Timpson, Nic J; Baban, Jamil; Kiessling, Matt; Day, Ian N M; Ebrahim, Shah

    2009-03-01

    Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T(-13910) variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60-79 years from 23 towns across Britain. We found an overall frequency of 0.253 for the C (lactase non-persistence) allele, but with considerable gradients of decreasing frequency from the south to the north and from the east to the west of Britain for this allele. Daily sunlight was positively related to C (non-persistence) allele prevalence. However, sunlight exposure and latitude are strongly correlated, and it was not possible to identify which is the primary factor statistically underlying the distribution of lactase persistence. The C/T(-13910) variant (rs4988235) was not related to drinking milk or bone health (although drinking milk itself was protective of bone health), and was essentially unrelated to a wide range of other lifestyle, health and demographic characteristics. One exception was general health being rated as being poor or fair, for which there was an odds ratio of 1.38 (1.04, 1.84) for women homozygous for the C allele; on adjustment for latitude and longitude of place of birth, this attenuated to 1.19 (0.87, 1.64). The lactase persistence variant could contribute to the examination of data for the existence of, and then statistical control for, population substructure in genetic association studies.

  1. Using soil seed banks to assess temporal patterns of genetic variation in invasive plant populations

    PubMed Central

    Fennell, Mark; Gallagher, Tommy; Vintro, Luis Leon; Osborne, Bruce

    2014-01-01

    Most research on the genetics of invasive plant species has focused on analyzing spatial differences among existing populations. Using a long-established Gunnera tinctoria population from Ireland, we evaluated the potential of using plants derived from seeds associated with different soil layers to track genetic variation through time. This species and site were chosen because (1) G. tinctoria produces a large and persistent seed bank; (2) it has been present in this locality, Sraheens, for ∼90 years; (3) the soil is largely undisturbed; and (4) the soil's age can be reliably determined radiometrically at different depths. Amplified fragment length polymorphic markers (AFLPs) were used to assess differences in the genetic structure of 75 individuals sampled from both the standing population and from four soil layers, which spanned 18 cm (estimated at ∼90 years based on 210Pb and 137Cs dating). While there are difficulties in interpreting such data, including accounting for the effects of selection, seed loss, and seed migration, a clear pattern of lower total allele counts, percentage polymorphic loci, and genetic diversity was observed in deeper soils. The greatest percentage increase in the measured genetic variables occurred prior to the shift from the lag to the exponential range expansion phases and may be of adaptive significance. These findings highlight that seed banks in areas with long-established invasive populations can contain valuable genetic information relating to invasion processes and as such, should not be overlooked. PMID:24967082

  2. Mobilizing diversity: transposable element insertions in genetic variation and disease

    PubMed Central

    2010-01-01

    Transposable elements (TEs) comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source of genetic variation and, in rare cases, these events cause mutations that lead to disease. Yet, the extent to which these elements impact their host genomes is not completely understood. This review will summarize our current understanding of the mechanisms underlying transposon regulation and the contribution of TE insertions to genetic diversity in the germline and in somatic cells. Finally, traditional methods and emerging technologies for identifying transposon insertions will be considered. PMID:20813032

  3. Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation

    PubMed Central

    Flori, Laurence; Gao, Yu; Laloë, Denis; Lemonnier, Gaëtan; Leplat, Jean-Jacques; Teillaud, Angélique; Cossalter, Anne-Marie; Laffitte, Joëlle; Pinton, Philippe; de Vaureix, Christiane; Bouffaud, Marcel; Mercat, Marie-José; Lefèvre, François; Oswald, Isabelle P.; Bidanel, Jean-Pierre; Rogel-Gaillard, Claire

    2011-01-01

    Background Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. Methodology/Principal Findings Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA) and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10), phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.10.4) heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. Conclusions/Significance Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection

  4. Genetic mapping of variation in spatial learning in the mouse.

    PubMed

    Steinberger, Daniela; Reynolds, David S; Ferris, Pushpindar; Lincoln, Rachael; Datta, Susmita; Stanley, Joanna; Paterson, Andrea; Dawson, Gerard R; Flint, Jonathan

    2003-03-15

    Inbred strains of mice are known to differ in their performance in the Morris water maze task, a test of spatial discrimination and place navigation in rodents, but the genetic basis of individual variation in spatial learning is unknown. We have mapped genetic effects that contribute to the difference between two strains, DBA/2 and C57BL6/J, using an F2 intercross and methods to detect quantitative trait loci (QTL). We found two QTL, one on chromosome 4 and one on chromosome 12, that influence behavior in the probe trial of the water maze (genome-wide significance p = 0.017 and 0.015, respectively). By including tests of avoidance conditioning and behavior in a novel environment, we show that the QTL on chromosomes 4 and 12 specifically influence variation in spatial learning. QTL that influence differences in fearful behavior (on chromosomes 1, 3, 7, 15, and 19) operate while mice are trained in the water maze apparatus.

  5. The African Genome Variation Project shapes medical genetics in Africa

    PubMed Central

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2014-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible. PMID:25470054

  6. Increased Extinction Potential of Insular Fish Populations with Reduced Life History Variation and Low Genetic Diversity

    PubMed Central

    Hellmair, Michael; Kinziger, Andrew P.

    2014-01-01

    Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species. PMID:25409501

  7. Basic principles and laboratory analysis of genetic variation.

    PubMed

    Gonzalez-Bosquet, Jesus; Chanock, Stephen J

    2011-01-01

    With the draft of the human genome and advances in technology, the approach toward mapping complex diseases and traits has changed. Human genetics has evolved into the study of the genome as a complex structure harbouring clues for multifaceted disease risk with the majority still unknown. The discovery of new candidate regions by genome-wide association studies (GWAS) has changed strategies for the study of genetic predisposition. More genome-wide, "agnostic" approaches, with increasing numbers of participants from high-quality epidemiological studies are for the first time replicating results in different settings. However, new-found regions (which become the new candidate "genes") require extensive follow-up and investigation of their functional significance. Understanding the true effect of genetic variability on the risk of complex diseases is paramount. The importance of designing high-quality studies to assess environmental contributions, as well as the interactions between genes and exposures, cannot be stressed enough. This chapter will address the basic issues of genetic variation, including population genetics, as well as analytical platforms and tools needed to investigate the contribution of genetics to human diseases and traits.

  8. Rapid loss of genetic variation in an endangered possum.

    PubMed

    Mitrovski, P; Hoffmann, A A; Heinze, D A; Weeks, A R

    2008-02-23

    The endangered mountain pygmy possum is the only Australian marsupial that hibernates under snow cover. Most of its alpine habitat was burnt by a rare fire in 2003, and habitat loss and disturbance have also occurred owing to ski resort development. Here we show that there has been a rapid loss of genetic variation following habitat loss associated with resort development, but no detectable loss of alleles or decrease in heterozygosity following the fire.

  9. Genetic Variation of Echinococcus canadensis (G7) in Mexico

    PubMed Central

    Rodriguez-Prado, Ulises; Jimenez-Gonzalez, Diego Emiliano; Avila, Guillermina; Gonzalez, Armando E.; Martinez-Flores, Williams Arony; Mondragon de la Peña, Carmen; Hernandez-Castro, Rigoberto; Romero-Valdovinos, Mirza; Flisser, Ana; Martinez-Hernandez, Fernando; Maravilla, Pablo; Martinez-Maya, Jose Juan

    2014-01-01

    We evaluated the genetic variation of Echinococcus G7 strain in larval and adult stages using a fragment of the mitochondrial cox1 gen. Viscera of pigs, bovines, and sheep and fecal samples of dogs were inspected for cystic and canine echinococcosis, respectively; only pigs had hydatid cysts. Bayesian inferences grouped the sequences in an E. canadensis G7 cluster, suggesting that, in Mexico, this strain might be mainly present. Additionally, the population genetic and network analysis showed that E. canadensis in Mexico is very diverse and has probably been introduced several times from different sources. Finally, a scarce genetic differentiation between G6 (camel strain) and G7 (pig strain) populations was identified. PMID:25266350

  10. Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

    DOE PAGES

    Woods, Daniel P.; Bednarek, Ryland; Bouché, Frédéric; ...

    2016-10-14

    The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time.more » A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.« less

  11. Genetic Architectures of Quantitative Variation in RNA Editing Pathways

    PubMed Central

    Gu, Tongjun; Gatti, Daniel M.; Srivastava, Anuj; Snyder, Elizabeth M.; Raghupathy, Narayanan; Simecek, Petr; Svenson, Karen L.; Dotu, Ivan; Chuang, Jeffrey H.; Keller, Mark P.; Attie, Alan D.; Braun, Robert E.; Churchill, Gary A.

    2016-01-01

    RNA editing refers to post-transcriptional processes that alter the base sequence of RNA. Recently, hundreds of new RNA editing targets have been reported. However, the mechanisms that determine the specificity and degree of editing are not well understood. We examined quantitative variation of site-specific editing in a genetically diverse multiparent population, Diversity Outbred mice, and mapped polymorphic loci that alter editing ratios globally for C-to-U editing and at specific sites for A-to-I editing. An allelic series in the C-to-U editing enzyme Apobec1 influences the editing efficiency of Apob and 58 additional C-to-U editing targets. We identified 49 A-to-I editing sites with polymorphisms in the edited transcript that alter editing efficiency. In contrast to the shared genetic control of C-to-U editing, most of the variable A-to-I editing sites were determined by local nucleotide polymorphisms in proximity to the editing site in the RNA secondary structure. Our results indicate that RNA editing is a quantitative trait subject to genetic variation and that evolutionary constraints have given rise to distinct genetic architectures in the two canonical types of RNA editing. PMID:26614740

  12. Ecological and genetic basis of metapopulation persistence of the Glanville fritillary butterfly in fragmented landscapes

    PubMed Central

    Hanski, Ilkka; Schulz, Torsti; Wong, Swee Chong; Ahola, Virpi; Ruokolainen, Annukka; Ojanen, Sami P.

    2017-01-01

    Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size. The Pgi genotypes are associated with dispersal rate and hence with colonizations and extinctions. Associations between Pgi genotypes, population turnover and metapopulation size reflect eco-evolutionary dynamics, which may be a common feature in species inhabiting patch networks with unstable local dynamics. PMID:28211463

  13. Ecological and genetic basis of metapopulation persistence of the Glanville fritillary butterfly in fragmented landscapes.

    PubMed

    Hanski, Ilkka; Schulz, Torsti; Wong, Swee Chong; Ahola, Virpi; Ruokolainen, Annukka; Ojanen, Sami P

    2017-02-17

    Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size. The Pgi genotypes are associated with dispersal rate and hence with colonizations and extinctions. Associations between Pgi genotypes, population turnover and metapopulation size reflect eco-evolutionary dynamics, which may be a common feature in species inhabiting patch networks with unstable local dynamics.

  14. A Simple Genetic Architecture Underlies Morphological Variation in Dogs

    PubMed Central

    Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

    2010-01-01

    Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species. PMID:20711490

  15. A simple genetic architecture underlies morphological variation in dogs.

    PubMed

    Boyko, Adam R; Quignon, Pascale; Li, Lin; Schoenebeck, Jeffrey J; Degenhardt, Jeremiah D; Lohmueller, Kirk E; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G; vonHoldt, Bridgett M; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G; Castelhano, Marta; Mosher, Dana S; Sutter, Nathan B; Johnson, Gary S; Novembre, John; Hubisz, Melissa J; Siepel, Adam; Wayne, Robert K; Bustamante, Carlos D; Ostrander, Elaine A

    2010-08-10

    Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (< or = 3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

  16. Patterns of molecular genetic variation among cat breeds.

    PubMed

    Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

    2008-01-01

    Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

  17. Genetic variation in insulin-induced kinase signaling

    PubMed Central

    Wang, Isabel Xiaorong; Ramrattan, Girish; Cheung, Vivian G

    2015-01-01

    Individual differences in sensitivity to insulin contribute to disease susceptibility including diabetes and metabolic syndrome. Cellular responses to insulin are well studied. However, which steps in these response pathways differ across individuals remains largely unknown. Such knowledge is needed to guide more precise therapeutic interventions. Here, we studied insulin response and found extensive individual variation in the activation of key signaling factors, including ERK whose induction differs by more than 20-fold among our subjects. This variation in kinase activity is propagated to differences in downstream gene expression response to insulin. By genetic analysis, we identified cis-acting DNA variants that influence signaling response, which in turn affects downstream changes in gene expression and cellular phenotypes, such as protein translation and cell proliferation. These findings show that polymorphic differences in signal transduction contribute to individual variation in insulin response, and suggest kinase modulators as promising therapeutics for diseases characterized by insulin resistance. PMID:26202599

  18. A new way to measure milk yield persistency: a genetic point of view with application to Gyr (Bos indicus) cattle.

    PubMed

    Pereira, Rodrigo Junqueira; Ayres, Denise Rocha; El Faro, Lenira; Vercesi Filho, Aníbal Eugênio; Verneque, Rui da Silva; de Albuquerque, Lucia Galvão

    2015-11-01

    The objective of this work was to estimate genetic parameters for a measure of persistency of milk yield and to evaluate its association with 305-d cumulative milk yield and lactation length. 12 346 records from 8202 dairy Gyr cows including lactations up to fifth calving were used. The measure of persistency was obtained from one of the parameters of a quadratic model that describes the cumulative yield across lactation as a function of days in milk. A three-trait multivariate analysis was done. Heritability and repeatability for persistency were 0.08 and 0.21, respectively. Deviance Information Criterion provided evidence that the additive genetic covariance between the measure of persistency studied and 305-d cumulative yield is zero. Genetic correlations between persistency and lactation length were 0.50 and 0.27 for first or all lactations, respectively. Milk yield persistency as measured in this study has low heritability. Selection for persistency can increase lactation length. The measure of milk yield persistency studied here is genetically independent of total milk yield and can be included in routine genetic evaluations of dairy cattle.

  19. Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors.

    PubMed

    Schradin, Carsten

    2013-05-19

    Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation.

  20. Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors

    PubMed Central

    Schradin, Carsten

    2013-01-01

    Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation. PMID:23569294

  1. A cat's tale: the impact of genetic restoration on Florida panther population dynamics and persistence.

    PubMed

    Hostetler, Jeffrey A; Onorato, David P; Jansen, Deborah; Oli, Madan K

    2013-05-01

    1. Genetic restoration has been suggested as a management tool for mitigating detrimental effects of inbreeding depression in small, inbred populations, but the demographic mechanisms underlying population-level responses to genetic restoration remain poorly understood. 2. We studied the dynamics and persistence of the endangered Florida panther Puma concolor coryi population and evaluated the potential influence of genetic restoration on population growth and persistence parameters. As part of the genetic restoration programme, eight female Texas pumas P. c. stanleyana were released into Florida panther habitat in southern Florida in 1995. 3. The overall asymptotic population growth rate (λ) was 1.04 (5th and 95th percentiles: 0.95-1.14), suggesting an increase in the panther population of approximately 4% per year. Considering the effects of environmental and demographic stochasticities and density-dependence, the probability that the population will fall below 10 panthers within 100 years was 0.072 (0-0.606). 4. Our results suggest that the population would have declined at 5% per year (λ = 0.95; 0.83-1.08) in the absence of genetic restoration. Retrospective life table response experiment analysis revealed that the positive effect of genetic restoration on survival of kittens was primarily responsible for the substantial growth of the panther population that would otherwise have been declining. 5. For comparative purposes, we also estimated probability of quasi-extinction under two scenarios - implementation of genetic restoration and no genetic restoration initiative - using the estimated abundance of panthers in 1995, the year genetic restoration was initiated. Assuming no density-dependence, the probability that the panther population would fall below 10 panthers by 2010 was 0.098 (0.002-0.332) for the restoration scenario and 0.445 (0.032-0.944) for the no restoration scenario, providing further evidence that the panther population would have faced a

  2. Variation in the Management of Infants Hospitalized for Bronchiolitis Persists After the 2006 AAP Bronchiolitis Guidelines

    PubMed Central

    Florin, Todd A.; Byczkowski, Terri; Ruddy, Richard M.; Zorc, Joseph J.; Test, Matthew; Shah, Samir S.

    2014-01-01

    Objective To describe variation across US pediatric hospitals in the utilization of resources not recommended for routine use by the AAP guideline for infants hospitalized with bronchiolitis and to examine the association between resource utilization and disposition outcomes. Study design We conducted a cross-sectional study of infants ≤12 months hospitalized for bronchiolitis from 2007-2012 at 42 hospitals contributing data to the Pediatric Health Information System. Patients with asthma were excluded. The primary outcome was hospital-level variation in utilization of five resources not recommended for routine use: albuterol, racemic epinephrine, corticosteroids, chest radiography and antibiotics. We also examined the association of resource utilization with length of stay (LOS) and readmission. Results 64,994 hospitalizations were analyzed. After adjustment for patient characteristics, albuterol (median, 52.4%; range, 3.5%-81%), racemic epinephrine (20.1%; 0.6%-78.8%), and chest radiography (54.9%; 24.1%-76.7%) had the greatest variation across hospitals. Utilization of albuterol, racemic epinephrine, and antibiotics did not change significantly over time compared with small decreases in corticosteroid (3.3%) and chest radiography (8.6%) use over the study period. Utilization of each resource was significantly associated with increased LOS without concomitant decreased odds of readmission. Conclusions Substantial use and variation in five resources not recommended for routine use by the AAP bronchiolitis guideline persists with increased utilization associated with increased LOS without the benefit of decreased readmission. Future work should focus on developing processes that can be widely disseminated and easily implemented to minimize unwarranted practice variation when evidence and guidelines exist. PMID:25015578

  3. Genetic variation in paternal investment in a seed beetle.

    PubMed

    Savalli; Fox

    1998-10-01

    Males of many species invest resources in their offspring. For paternal investment to evolve, it must exhibit heritable variation. Using a standard half-sibling quantitative genetic design, we investigated whether genetic variation in male ejaculate size, a trait that affects female fecundity and copulation duration, are present in the seed beetle Callosobruchus maculatus. Ejaculate size was estimated as the amount of weight lost by males during mating. Dams, but not sires, had significant effects on their sons' absolute ejaculate size (both replicates) and relative ejaculate size (proportion of body weight; one replicate only), explaining 21-25% of the variance in absolute ejaculate size and 8-16% of the variance in relative ejaculate size. These results suggest either a large maternal effect on ejaculate size or sex-linkage of loci that affect the variation in ejaculate size. The proportion of phenotypic variance explained by sex- linkage (assuming no maternal effects) was 42 and 49% (ejaculate size) and 17 and 31% (relative ejaculate size) in the two replicates. These results indicate that male paternal investment can respond to selection, and that it may be able to do so especially rapidly because sex-linked traits have the potential to evolve much more quickly than autosomal traits. There were only weak negative correlations between ejaculate size and mating duration, contrary to what we predicted. There was additive genetic variation in female copulation duration, but not in male copulation duration, suggesting that copulation duration is under female control. Copyright 1998 The Association for the Study of Animal Behaviour.

  4. Reproductive Flexibility: Genetic Variation, Genetic Costs and Long-Term Evolution in a Collembola

    PubMed Central

    Tully, Thomas; Ferrière, Régis

    2008-01-01

    In a variable yet predictable world, organisms may use environmental cues to make adaptive adjustments to their phenotype. Such phenotypic flexibility is expected commonly to evolve in life history traits, which are closely tied to Darwinian fitness. Yet adaptive life history flexibility remains poorly documented. Here we introduce the collembolan Folsomia candida, a soil-dweller, parthenogenetic (all-female) microarthropod, as a model organism to study the phenotypic expression, genetic variation, fitness consequences and long-term evolution of life history flexibility. We demonstrate that collembola have a remarkable adaptive ability for adjusting their reproductive phenotype: when transferred from harsh to good conditions (in terms of food ration and crowding), a mother can fine-tune the number and the size of her eggs from one clutch to the next. The comparative analysis of eleven clonal populations of worldwide origins reveals (i) genetic variation in mean egg size under both good and bad conditions; (ii) no genetic variation in egg size flexibility, consistent with convergent evolution to a common physiological limit; (iii) genetic variation of both mean reproductive investment and reproductive investment flexibility, associated with a reversal of the genetic correlation between egg size and clutch size between environmental conditions ; (iv) a negative genetic correlation between reproductive investment flexibility and adult lifespan. Phylogenetic reconstruction shows that two life history strategies, called HIFLEX and LOFLEX, evolved early in evolutionary history. HIFLEX includes six of our 11 clones, and is characterized by large mean egg size and reproductive investment, high reproductive investment flexibility, and low adult survival. LOFLEX (the other five clones) has small mean egg size and low reproductive investment, low reproductive investment flexibility, and high adult survival. The divergence of HIFLEX and LOFLEX could represent different

  5. Patterns of genetic variation across inversions: geographic variation in the In(2L)t inversion in populations of Drosophila melanogaster from eastern Australia.

    PubMed

    Kennington, W Jason; Hoffmann, Ary A

    2013-05-20

    Chromosomal inversions are increasingly being recognized as important in adaptive shifts and are expected to influence patterns of genetic variation, but few studies have examined genetic patterns in inversion polymorphisms across and within populations. Here, we examine genetic variation at 20 microsatellite loci and the alcohol dehydrogenase gene (Adh) located within and near the In(2L)t inversion of Drosophila melanogaster at three different sites along a latitudinal cline on the east coast of Australia. We found significant genetic differentiation between the standard and inverted chromosomal arrangements at each site as well as significant, but smaller differences among sites in the same arrangement. Genetic differentiation between pairs of sites was higher for inverted chromosomes than standard chromosomes, while inverted chromosomes had lower levels of genetic variation even well away from inversion breakpoints. Bayesian clustering analysis provided evidence of genetic exchange between chromosomal arrangements at each site. The strong differentiation between arrangements and reduced variation in the inverted chromosomes are likely to reflect ongoing selection at multiple loci within the inverted region. They may also reflect lower effective population sizes of In(2L)t chromosomes and colonization of Australia, although there was no consistent evidence of a recent bottleneck and simulations suggest that differences between arrangements would not persist unless rates of gene exchange between them were low. Genetic patterns therefore support the notion of selection and linkage disequilibrium contributing to inversion polymorphisms, although more work is needed to determine whether there are spatially varying targets of selection within this inversion. They also support the idea that the allelic content within an inversion can vary between geographic locations.

  6. Patterns of genetic variation across inversions: geographic variation in the In(2L)t inversion in populations of Drosophila melanogaster from eastern Australia

    PubMed Central

    2013-01-01

    Background Chromosomal inversions are increasingly being recognized as important in adaptive shifts and are expected to influence patterns of genetic variation, but few studies have examined genetic patterns in inversion polymorphisms across and within populations. Here, we examine genetic variation at 20 microsatellite loci and the alcohol dehydrogenase gene (Adh) located within and near the In(2L)t inversion of Drosophila melanogaster at three different sites along a latitudinal cline on the east coast of Australia. Results We found significant genetic differentiation between the standard and inverted chromosomal arrangements at each site as well as significant, but smaller differences among sites in the same arrangement. Genetic differentiation between pairs of sites was higher for inverted chromosomes than standard chromosomes, while inverted chromosomes had lower levels of genetic variation even well away from inversion breakpoints. Bayesian clustering analysis provided evidence of genetic exchange between chromosomal arrangements at each site. Conclusions The strong differentiation between arrangements and reduced variation in the inverted chromosomes are likely to reflect ongoing selection at multiple loci within the inverted region. They may also reflect lower effective population sizes of In(2L)t chromosomes and colonization of Australia, although there was no consistent evidence of a recent bottleneck and simulations suggest that differences between arrangements would not persist unless rates of gene exchange between them were low. Genetic patterns therefore support the notion of selection and linkage disequilibrium contributing to inversion polymorphisms, although more work is needed to determine whether there are spatially varying targets of selection within this inversion. They also support the idea that the allelic content within an inversion can vary between geographic locations. PMID:23688159

  7. Comparative RNA sequencing reveals substantial genetic variation in endangered primates.

    PubMed

    Perry, George H; Melsted, Páll; Marioni, John C; Wang, Ying; Bainer, Russell; Pickrell, Joseph K; Michelini, Katelyn; Zehr, Sarah; Yoder, Anne D; Stephens, Matthew; Pritchard, Jonathan K; Gilad, Yoav

    2012-04-01

    Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success.

  8. Comparative RNA sequencing reveals substantial genetic variation in endangered primates

    PubMed Central

    Perry, George H.; Melsted, Páll; Marioni, John C.; Wang, Ying; Bainer, Russell; Pickrell, Joseph K.; Michelini, Katelyn; Zehr, Sarah; Yoder, Anne D.; Stephens, Matthew; Pritchard, Jonathan K.; Gilad, Yoav

    2012-01-01

    Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success. PMID:22207615

  9. Genetic variation in personality traits explains genetic overlap between borderline personality features and substance use disorders.

    PubMed

    Few, Lauren R; Grant, Julia D; Trull, Timothy J; Statham, Dixie J; Martin, Nicholas G; Lynskey, Michael T; Agrawal, Arpana

    2014-12-01

    To examine the genetic overlap between borderline personality features (BPF) and substance use disorders (SUDs) and the extent to which variation in personality traits contributes to this covariance. Genetic structural equation modelling was used to partition the variance in and covariance between personality traits, BPF and SUDs into additive genetic, shared and individual-specific environmental factors. All participants were registered with the Australian Twin Registry. A total of 3127 Australian adult twins participated in the study. Diagnoses of DSM-IV alcohol and cannabis abuse/dependence (AAD; CAD) and nicotine dependence (ND) were derived via computer-assisted telephone interview. BPF and five-factor model personality traits were derived via self-report questionnaires. Personality traits, BPF and substance use disorders were partially influenced by genetic factors with heritability estimates ranging from 0.38 (neuroticism; 95% confidence interval: 0.30-0.45) to 0.78 (CAD; 95% confidence interval: 0.67-0.86). Genetic and individual-specific environmental correlations between BPF and SUDs ranged from 0.33 to 0.56 (95% CI = 0.19-0.74) and 0.19-0.32 (95% CI = 0.06-0.43), respectively. Overall, there was substantial support for genetic influences that were specific to AAD, ND and CAD (30.76-68.60%). Finally, genetic variation in personality traits was responsible for 11.46% (extraversion for CAD) to 59.30% (neuroticism for AAD) of the correlation between BPF and SUDs. Both genetic and individual-specific environmental factors contribute to comorbidity between borderline personality features and substance use disorders. A substantial proportion of this comorbidity can be attributed to variation in normal personality traits, particularly neuroticism. © 2014 Society for the Study of Addiction.

  10. Genetic variation in personality traits explains genetic overlap between borderline personality features and substance use disorders

    PubMed Central

    Few, Lauren R.; Grant, Julia D; Trull, Timothy J.; Statham, Dixie J.; Martin, Nicholas G.; Lynskey, Michael T.; Agrawal, Arpana

    2014-01-01

    Aims To examine the genetic overlap between borderline personality features (BPF) and substance use disorders (SUDs) and the extent to which variation in personality traits contributes to this covariance. Design Genetic structural equation modelling was used to partition the variance in and covariance between personality traits, BPF, and SUDs into additive genetic, shared, and individual-specific environmental factors. Setting All participants were registered with the Australian Twin Registry. Participants A total of 3,127 Australian adult twins participated in the study. Measurements Diagnoses of DSM-IV alcohol and cannabis abuse/dependence (AAD; CAD), and nicotine dependence (ND) were derived via computer-assisted telephone interview. BPF and five-factor model personality traits were derived via self-report questionnaires. Findings Genetic factors were responsible for 49% (95%CI: 42%–55%) of the variance in BPF, 38–42% (95%CI range: 32%–49%) for personality traits and 47% (95%CI: 17%–77%), 54% (95%CI: 43%–64%), and 78% (67%–86%) for ND, AAD and CAD, respectively. Genetic and individual-specific environmental correlations between BPF and SUDs ranged from .33–.56 (95%CI range: .19–.74) and .19–.32 (95%CI range: .06–.43), respectively. Overall, there was substantial support for genetic influences that were specific to AAD, ND and CAD (31%–69%). Finally, genetic variation in personality traits was responsible for 11% (Extraversion for CAD) to 59% (Neuroticism for AAD) of the correlation between BPF and SUDs. Conclusions Both genetic and individual-specific environmental factors contribute to comorbidity between borderline personality features and substance use disorders. A substantial proportion of this comorbidity can be attributed to variation in normal personality traits, particularly Neuroticism. PMID:25041562

  11. Occurrence, genetic diversity, and persistence of enterococci in a Lake Superior watershed.

    PubMed

    Ran, Qinghong; Badgley, Brian D; Dillon, Nicholas; Dunny, Gary M; Sadowsky, Michael J

    2013-05-01

    In 2012, the U.S. EPA suggested that coastal and Great Lakes states adopt enterococci as an alternative indicator for the monitoring of recreational water quality. Limited information, however, is available about the presence and persistence of enterococci in Lake Superior. In this study, the density, species composition, and persistence of enterococci in sand, sediment, water, and soil samples were examined at two sites in a Lake Superior watershed from May to September over a 2-year period. The genetic diversity of Enterococcus faecalis isolates collected from environmental samples was also studied by using the horizontal, fluorophore-enhanced repetitive PCR DNA fingerprinting technique. Results obtained by most-probable-number analyses indicated that enterococci were present in 149 (94%) of 159 samples and their densities were generally higher in the summer than in the other months examined. The Enterococcus species composition displayed spatial and temporal changes, with the dominant species being E. hirae, E. faecalis, E. faecium, E. mundtii, and E. casseliflavus. DNA fingerprint analyses indicated that the E. faecalis population in the watershed was genetically diverse and changed spatially and temporally. Moreover, some DNA fingerprints reoccurred over multiple sampling events. Taken together, these results suggest that some enterococci are able to persist and grow in the Lake Superior watershed, especially in soil, for a prolonged time after being introduced.

  12. Temporal variation of genetic composition in Atlantic salmon populations from the Western White Sea Basin: influence of anthropogenic factors?

    PubMed Central

    2013-01-01

    Background Studies of the temporal patterns of population genetic structure assist in evaluating the consequences of demographic and environmental changes on population stability and persistence. In this study, we evaluated the level of temporal genetic variation in 16 anadromous and 2 freshwater salmon populations from the Western White Sea Basin (Russia) using samples collected between 1995 and 2008. To assess whether the genetic stability was affected by human activity, we also evaluated the effect of fishing pressure on the temporal genetic variation in this region. Results We found that the genetic structure of salmon populations in this region was relatively stable over a period of 1.5 to 2.5 generations. However, the level of temporal variation varied among geographical regions: anadromous salmon of the Kola Peninsula exhibited a higher stability compared to that of the anadromous and freshwater salmon from the Karelian White Sea coast. This discrepancy was most likely attributed to the higher census, and therefore effective, population sizes of the populations inhabiting the rivers of the Kola Peninsula compared to salmon of the Karelian White Sea coast. Importantly, changes in the genetic diversity observed in a few anadromous populations were best explained by the increased level of fishing pressure in these populations rather than environmental variation or the negative effects of hatchery escapees. The observed population genetic patterns of isolation by distance remained consistent among earlier and more recent samples, which support the stability of the genetic structure over the period studied. Conclusions Given the increasing level of fishing pressure in the Western White Sea Basin and the higher level of temporal variation in populations exhibiting small census and effective population sizes, further genetic monitoring in this region is recommended, particularly on populations from the Karelian rivers. PMID:24053319

  13. Genetic variation in domestic reindeer and wild caribou in Alaska

    USGS Publications Warehouse

    Cronin, M.; Renecker, L.; Pierson, Barbara J.; Patton, J.C.

    1995-01-01

    Reindeer were introduced into Alaska 100 years ago and have been maintained as semidomestic livestock. They have had contact with wild caribou herds, including deliberate cross-breeding and mixing in the wild. Reindeer have considerable potential as a domestic animal for meat or velvet antler production, and wild caribou are important to subsistence and sport hunters. Our objective was to quantify the genetic relationships of reindeer and caribou in Alaska. We identified allelic variation among five herds of wild caribou and three herds of reindeer with DNA sequencing and restriction enzymes for three loci: a DQA locus of the major histocompatibility complex (Rata-DQA1), k-casein and the D-loop of mitochondrial DNA. These loci are of interest because of their potential influence on domestic animal performance and the fitness of wild populations. There is considerable genetic variation in reindeer and caribou for all three loci, including five, three and six alleles for DQA, k-casein and D-loop respectively. Most alleles occur in both reindeer and caribou, which may be the result of recent common ancestry or genetic introgression in either direction. However, allele frequencies differ considerably between reindeer and caribou, which suggests that gene flow has been limited.

  14. Standing genetic variation in host preference for mutualist microbial symbionts

    PubMed Central

    Simonsen, Anna K.; Stinchcombe, John R.

    2014-01-01

    Many models of mutualisms show that mutualisms are unstable if hosts lack mechanisms enabling preferential associations with mutualistic symbiotic partners over exploitative partners. Despite the theoretical importance of mutualism-stabilizing mechanisms, we have little empirical evidence to infer their evolutionary dynamics in response to exploitation by non-beneficial partners. Using a model mutualism—the interaction between legumes and nitrogen-fixing soil symbionts—we tested for quantitative genetic variation in plant responses to mutualistic and exploitative symbiotic rhizobia in controlled greenhouse conditions. We found significant broad-sense heritability in a legume host's preferential association with mutualistic over exploitative symbionts and selection to reduce frequency of associations with exploitative partners. We failed to detect evidence that selection will favour the loss of mutualism-stabilizing mechanisms in the absence of exploitation, as we found no evidence for a fitness cost to the host trait or indirect selection on genetically correlated traits. Our results show that genetic variation in the ability to preferentially reduce associations with an exploitative partner exists within mutualisms and is under selection, indicating that micro-evolutionary responses in mutualism-stabilizing traits in the face of rapidly evolving mutualistic and exploitative symbiotic bacteria can occur in natural host populations. PMID:25355477

  15. Conservation genetics and geographic patterns of genetic variation of the endangered officinal herb Fritillaria pallidiflora

    Treesearch

    Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaolong Jiang; Mingli Zhang

    2015-01-01

    Fritillaria pallidiflora is an endangered officinal herb distributed in the Tianshan Mountains of northwestern China. We examined its phylogeography to study evolutionary processes and suggest implications for conservation. Six haplotypes were detected based on three chloroplast non-coding spacers (psbA-trnH, rps16, and trnS-trnG); genetic variation mainly occurred...

  16. Conservation genetics and geographic patterns of genetic variation of the vulnerable officinal herb Fritillaria walujewii (Liliaceae)

    Treesearch

    Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaojun Shi; Xiaolong Jiang

    2015-01-01

    The Chinese herb Fritillaria walujewii Regel is an important officinal species that is vulnerable because of over-harvesting. Here, we examined the geographic pattern of genetic variation across the species entire range, to study its evolution process and give implication needed for the conservation. Nine haplotypes were detected on the basis of three chloroplast...

  17. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations.

    PubMed

    Porth, Ilga; Klápště, Jaroslav; Skyba, Oleksandr; Lai, Ben S K; Geraldes, Armando; Muchero, Wellington; Tuskan, Gerald A; Douglas, Carl J; El-Kassaby, Yousry A; Mansfield, Shawn D

    2013-02-01

    The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.

  18. Natural variation in populations of persistently colonizing bacteria affect human host cell phenotype.

    PubMed

    Aras, Rahul A; Lee, Yongchan; Kim, Sung-Kook; Israel, Dawn; Peek, Richard M; Blaser, Martin J

    2003-08-15

    The highly diverse bacterium Helicobacter pylori, which persistently colonizes the human stomach, provides models to study the role of genome plasticity in host adaptation. Within H. pylori populations from 2 colonized individuals, intragenomic recombination between cagA DNA repeat sequences leads to deletion or duplication of tyrosine phosphorylation sites in the CagA protein, which is injected by a type IV secretion system into host cells. Experimental coculture of gastric epithelial cells with the strains containing these naturally occurring CagA phosphorylation site variants induced markedly divergent host cell morphologic responses. Mutants were constructed in which a phosphorylation site was either added or deleted in the expressed CagA protein; coculture studies confirmed that the naturally occurring differences in CagA phosphorylation are responsible for the observed phenotypic variation. These findings indicate that within an individual host, intragenomic recombination between H. pylori repetitive DNA produces strain variants differing in their signals to host cells.

  19. Temporal variation in copepod abundance and composition in a strong, persistent coastal upwelling zone

    NASA Astrophysics Data System (ADS)

    Fontana, Rachel E.; Elliott, Meredith L.; Largier, John L.; Jahncke, Jaime

    2016-03-01

    Zooplankton abundance and species composition provide information on environmental variability in the ocean. While zooplankton time series span the west coast of North America, less data exist off north-central California. Here, we investigated a zooplankton time series, focusing specifically on copepods, collected within the Gulf of the Farallones-Cordell Bank area (37.5° to 38.5°N) from 2004 to 2009. Impacted by seasonally strong, persistent upwelling, this study area is located downstream of a major upwelling center (Point Arena). We found copepod abundance and species composition differed significantly, particularly between the first three years (2004-2006) and the latter three years (2007-2009) of the study. These changes were mainly observed as changes in abundance of boreal copepod species, Pseudocalanus mimus and Acartia longiremis. These taxa showed increasing abundances for the latter three years of the study (2007-2009). During the first three years of the time series, environmental measurements in the region showed lower alongshore wind stress, weaker upwelling, minimal surface alongshore flow, and warmer surface ocean temperatures. Temporal variations in copepod abundance and species composition correlated with several of these environmental measurements (e.g., surface cross-shore and alongshore flows, upwelling, and alongshore wind stress), indicating environmental forcing of primary consumers and ecosystem productivity in this strong, persistent upwelling zone.

  20. Peak and Persistent Excess of Genetic Diversity Following an Abrupt Migration Increase

    PubMed Central

    Alcala, Nicolas; Streit, Daniela; Goudet, Jérôme; Vuilleumier, Séverine

    2013-01-01

    Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population’s demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations. PMID:23307901

  1. Persistence of naturally occurring and genetically modified Choristoneura fumiferana nucleopolyhedroviruses in outdoor aquatic microcosms.

    PubMed

    Holmes, Stephen B; Fick, William E; Kreutzweiser, David P; Ebling, Peter M; England, Laura S; Trevors, Jack T

    2008-10-01

    To assess the persistence of genetically modified and naturally occurring baculoviruses in an aquatic environment, replicate (three) outdoor, aquatic microcosms were spiked with spruce budworm viruses [Ireland strain of Choristoneura fumiferana multiple nucleopolyhedrovirus (CfMNPV) and the recombinant CfMNPVegt(-)/lacZ(+)] at a rate of 1.86 x 10(10) occlusion bodies (OBs) m(-2) of surface area. The presence of virus in water samples collected at various times after inoculation was determined by PCR amplification of baculoviral DNA extracted from OBs. Although UV radiation rapidly degrades baculoviruses under natural conditions, both viruses persisted above the level of detection (>100 OBs 450 microL(-1) of natural pond water) for at least 1 year post-inoculation, with little difference between the viruses in their patterns of persistence. The present microcosm study suggests that occlusion bodies of baculoviruses can persist in the flocculent layer of natural ponds. On disturbance, OBs could re-enter the main water column and thus be available for transport to new locations. Implications for environmental risk assessment are discussed.

  2. A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence.

    PubMed

    Kim, Jee-Hyun; O'Brien, Kathryn M; Sharma, Ritu; Boshoff, Helena I M; Rehren, German; Chakraborty, Sumit; Wallach, Joshua B; Monteleone, Mercedes; Wilson, Daniel J; Aldrich, Courtney C; Barry, Clifton E; Rhee, Kyu Y; Ehrt, Sabine; Schnappinger, Dirk

    2013-11-19

    Antibacterial drug development suffers from a paucity of targets whose inhibition kills replicating and nonreplicating bacteria. The latter include phenotypically dormant cells, known as persisters, which are tolerant to many antibiotics and often contribute to failure in the treatment of chronic infections. This is nowhere more apparent than in tuberculosis caused by Mycobacterium tuberculosis, a pathogen that tolerates many antibiotics once it ceases to replicate. We developed a strategy to identify proteins that Mycobacterium tuberculosis requires to both grow and persist and whose inhibition has the potential to prevent drug tolerance and persister formation. This strategy is based on a tunable dual-control genetic switch that provides a regulatory range spanning three orders of magnitude, quickly depletes proteins in both replicating and nonreplicating mycobacteria, and exhibits increased robustness to phenotypic reversion. Using this switch, we demonstrated that depletion of the nicotinamide adenine dinucleotide synthetase (NadE) rapidly killed Mycobacterium tuberculosis under conditions of standard growth and nonreplicative persistence induced by oxygen and nutrient limitation as well as during the acute and chronic phases of infection in mice. These findings establish the dual-control switch as a robust tool with which to probe the essentiality of Mycobacterium tuberculosis proteins under different conditions, including those that induce antibiotic tolerance, and NadE as a target with the potential to shorten current tuberculosis chemotherapies.

  3. Prostate Cancer Genetics: Variation by Race, Ethnicity, and Geography.

    PubMed

    Rebbeck, Timothy R

    2017-01-01

    Prostate cancer rates vary substantially by race, ethnicity, and geography. These disparities can be explained by variation in access to screening and treatment, variation in exposure to prostate cancer risk factors, and variation in the underlying biology of prostate carcinogenesis (including genomic propensity of some groups to develop biologically aggressive disease). It is clear that access to screening and access to treatment are critical influencing factors of prostate cancer rates; yet, even among geographically diverse populations with similar access to care (eg, low- and medium-income countries), African descent men have higher prostate cancer rates and poorer prognosis. To date, the proportion of prostate cancer that can be explained by environmental exposures is small, and the effect of these factors across different racial, ethnic, or geographical populations is poorly understood. In contrast, prostate cancer has one of the highest heritabilities of all major cancers. Numerous genetic susceptibility markers have been identified from family-based studies, candidate gene association studies, and genome-wide association studies. Some prostate cancer loci, including the risk loci found at chromosome 8q24, have consistent effects in all groups studied to date. However, replication of many susceptibility loci across race, ethnicity, and geography remains limited, and additional studies in certain populations (particularly in men of African descent) are needed to better understand the underlying genetic basis of prostate cancer.

  4. The African Genome Variation Project shapes medical genetics in Africa

    NASA Astrophysics Data System (ADS)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  5. The African Genome Variation Project shapes medical genetics in Africa.

    PubMed

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  6. Genetic Etiology in Cases of Recovered and Persistent Stuttering in an Unselected, Longitudinal Sample of Young Twins

    ERIC Educational Resources Information Center

    Dworzynski, Katharina; Remington, Anna; Rijsdijk, Fruhling; Howell, Peter; Plomin, Robert

    2007-01-01

    Purpose: The contribution of genetic factors in the persistence of and early recovery from stuttering was assessed. Method: Data from the Twins Early Development Study were employed. Parental reports regarding stuttering were collected at ages 2, 3, 4, and 7 years, and were used to classify speakers into recovered and persistent groups. Of 12,892…

  7. Genetic Etiology in Cases of Recovered and Persistent Stuttering in an Unselected, Longitudinal Sample of Young Twins

    ERIC Educational Resources Information Center

    Dworzynski, Katharina; Remington, Anna; Rijsdijk, Fruhling; Howell, Peter; Plomin, Robert

    2007-01-01

    Purpose: The contribution of genetic factors in the persistence of and early recovery from stuttering was assessed. Method: Data from the Twins Early Development Study were employed. Parental reports regarding stuttering were collected at ages 2, 3, 4, and 7 years, and were used to classify speakers into recovered and persistent groups. Of 12,892…

  8. Soft sweeps: molecular population genetics of adaptation from standing genetic variation.

    PubMed

    Hermisson, Joachim; Pennings, Pleuni S

    2005-04-01

    A population can adapt to a rapid environmental change or habitat expansion in two ways. It may adapt either through new beneficial mutations that subsequently sweep through the population or by using alleles from the standing genetic variation. We use diffusion theory to calculate the probabilities for selective adaptations and find a large increase in the fixation probability for weak substitutions, if alleles originate from the standing genetic variation. We then determine the parameter regions where each scenario-standing variation vs. new mutations-is more likely. Adaptations from the standing genetic variation are favored if either the selective advantage is weak or the selection coefficient and the mutation rate are both high. Finally, we analyze the probability of "soft sweeps," where multiple copies of the selected allele contribute to a substitution, and discuss the consequences for the footprint of selection on linked neutral variation. We find that soft sweeps with weaker selective footprints are likely under both scenarios if the mutation rate and/or the selection coefficient is high.

  9. Genetic variation in Echinacea angustifolia along a climatic gradient.

    PubMed

    Still, D W; Kim, D-H; Aoyama, N

    2005-09-01

    Echinacea angustifolia is a widespread species distributed throughout the Great Plains region of North America. Genetic differentiation among populations was investigated along a 1500 km north-south climatic gradient in North America, a region with no major geographical barriers. The objective of the study was to determine if genetic differentiation of populations could be explained by an isolation-by-distance model or by associations with climatic parameters known to affect plant growth and survival. Historical climatic data were used to define the nature of the climatic gradient and AFLP markers were used to establish patterns of population genetic differentiation among ten Echinacea populations collected from North Dakota to Oklahoma. A total of 1290 fragments were scored using six EcoRI/MseI and three PstI/MseI primer combinations. Assessment of the correlation between climatic, genetic and geographic distances was assessed by Mantel and partial Mantel tests. PstI/MseI combinations produced significantly fewer fragments, but a larger percentage was unique compared with EcoRI/MseI markers. Using estimates of F(ST), populations in Oklahoma and southern Kansas were identified as the most divergent from the other populations. Both the neighbour-joining tree and principal co-ordinate analysis clustered the populations in a north-south spatial orientation. About 60% of the genetic variation was found within populations, 20% among populations and the remaining 20% was partitioned among groups that were defined by the topology of the neighbour-joining tree. Significant support was found for the isolation-by-distance model independent of the effects of annual mean precipitation, but not from annual mean temperature and freeze-free days. Echinacea angustifolia populations exhibit genetic divergence along a north-south climatic gradient. The data support an isolation-by-distance restriction in gene flow that is independent of annual mean precipitation.

  10. How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations.

    PubMed

    Schneider, Ralf F; Meyer, Axel

    2017-01-01

    There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.

  11. Genetic variation in Bactericera cockerelli (Hemiptera: Triozidae) from Mexico.

    PubMed

    Lopez, Beatriz; Favela, Susana; Ponce, Gustavo; Foroughbakhch, Rahim; Flores, Adriana E

    2013-04-01

    Bactericera cockerelli (Sulc) is a significant pest of several solanacious crops in Mexico and the United States since 1970. In 2001 significant outbreaks of outstanding importance were observed for the first time in areas where infestations of this insect were historically rare. Molecular studies revealed that this was because of the development of a new biotype of B. cockerelli that had become adapted to south-western United States, further demonstrating that this genetic differentiation was reflected in the survival, development cycle, fertility, and growth rate of both the native biotype as well as the one recently reported. To determine genetic variation in populations of B. cockerelli from Mexico, inter simple sequence repeat were used. Results showed that populations of B. cockerelli from central and northeastern Mexico (Guanajuato, Morelos, Estado de Mexico, and Nuevo Leon states) are genetically similar, meanwhile B. cockerelli from northwest, southwest, and southeast of the country (Sinaloa, Michoacan, and Oaxaca states) are genetically distinct from each other and from the rest of the populations included in the study.

  12. Genetic Variation and HIV-Associated Neurologic Disease

    PubMed Central

    Nonnemacher, Michael R.; Wigdahl, Brian

    2014-01-01

    HIV-associated neurologic disease continues to be a significant complication in the era of highly active antiretroviral therapy. A substantial subset of the HIV-infected population shows impaired neuropsychological performance as a result of HIV-mediated neuroinflammation and eventual central nervous system (CNS) injury. CNS compartmentalization of HIV, coupled with the evolution of genetically isolated populations in the CNS, is responsible for poor prognosis in patients with AIDS, warranting further investigation and possible additions to the current therapeutic strategy. This chapter reviews key advances in the field of neuropathogenesis and studies that have highlighted how molecular diversity within the HIV genome may impact HIV-associated neurologic disease. We also discuss the possible functional implications of genetic variation within the viral promoter and possibly other regions of the viral genome, especially in the cells of monocyte–macrophage lineage, which are arguably key cellular players in HIV-associated CNS disease. PMID:23809924

  13. Genetic and epigenetic variation of human populations: An adaptive tale.

    PubMed

    Quintana-Murci, Lluis

    2016-01-01

    The evolutionary history of modern humans means much more than their demographic past. It includes the way in which humans have had to genetically adapt to the different environments they have encountered-nutritional, climatic or pathogenic-as well as the different epigenetic responses elicited by such environmental cues. Detecting how natural selection has affected human genome variability has proven to be a powerful tool to delineate genes and biological functions having played a key role in human adaptation, a variation which can also be involved in phenotypes of medical relevance. This article reviews several examples that illustrate well how different environmental pressures, particularly those imposed by pathogens and infectious diseases, have shaped the patterns of genetic and epigenetic variability currently observed in human populations. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  14. Fatty acid metabolism: Implications for diet, genetic variation, and disease

    PubMed Central

    Suburu, Janel; Gu, Zhennan; Chen, Haiqin; Chen, Wei; Zhang, Hao; Chen, Yong Q.

    2014-01-01

    Cultures across the globe, especially Western societies, are burdened by chronic diseases such as obesity, metabolic syndrome, cardiovascular disease, and cancer. Several factors, including diet, genetics, and sedentary lifestyle, are suspected culprits to the development and progression of these health maladies. Fatty acids are primary constituents of cellular physiology. Humans can acquire fatty acids by de novo synthesis from carbohydrate or protein sources or by dietary consumption. Importantly, regulation of their metabolism is critical to sustain balanced homeostasis, and perturbations of such can lead to the development of disease. Here, we review de novo and dietary fatty acid metabolism and highlight recent advances in our understanding of the relationship between dietary influences and genetic variation in fatty acid metabolism and their role in chronic diseases. PMID:24511462

  15. Morphological, physiological, and genetic variation between metallicolous and nonmetallicolous populations of Dianthus carthusianorum.

    PubMed

    Wójcik, Małgorzata; Dresler, Sławomir; Jawor, Emilia; Kowalczyk, Krzysztof; Tukiendorf, Anna

    2013-01-01

    Waste deposits produced by metal mining and smelting activities provide extremely difficult habitats for plant colonization and growth. Therefore, plants spontaneously colonizing such areas represent a very interesting system for studying evolution of plant adaptation and population differentiation between contaminated and noncontaminated environments. In this study, two populations of Dianthus carthusianorum, one originating from Zn-Pb waste deposit (a metallicolous population, M) and the other from unpolluted soil (a nonmetallicolous population, NM), were analyzed in respect of their morphological and physiological traits as well as genetic markers. It was found that the plants inhabiting the waste heap differed significantly from the NM plants in terms of leaf size and shape, and these differences were persistent between the first generation of the plants of both populations cultivated under uniform, controlled laboratory conditions. In contrast with the evident morphological differences, no significant differentiation between the populations regarding the physiological traits measured (accumulation of proline, anthocyanins, chlorophyll, carotenoids) was found. These traits can be regarded as neither population specific nor stress markers. The genetic variability was analyzed using 17 random amplified polymorphic DNA (RAPD) and four inter simple sequence repeat (ISSR) markers; this proved that the differentiation between the M and NM populations exists also at the genetic level. Analysis of molecular variance (AMOVA) showed that 24% of the total genetic diversity resided among populations, while 76% - within the populations. However, no significant differences in intrapopulation genetic diversity (Hj) between the M and NM populations of D. carthusianorum was found, which contradicts the theory that acquisition of adaptation mechanisms to adverse, isolated growth habitats is related to reduction in genetic diversity. Distinct genetic differences between the two

  16. Genetic variation in Asiatic lions and Indian tigers.

    PubMed

    Shankaranarayanan, P; Banerjee, M; Kacker, R K; Aggarwal, R K; Singh, L

    1997-08-01

    Previous reports have suggested that Asiatic lions and tigers are highly inbred and exhibit very low levels of genetic variation. Our analyses on these species have shown much higher degrees of polymorphism than reported. Randomly amplified polymorphic DNA (RAPD) analysis of 38 Asiatic lions, which exist as a single population in the Gir Forest Sanctuary in India, shows an average heterozygosity of 25.82% with four primers. Sperm motility studies by our colleagues corroborate this data. In Indian tigers, microsatellite analysis of five CA repeat loci and multilocus fingerprinting using Bkm 2(8) probe on a population of 22 individuals revealed a heterozygosity of 22.65%. Microsatellite analysis of loci Fca 77 and Fca 126 revealed polymorphism amongst the Asiatic x African lion hybrids, which has enabled us to use these as markers to discriminate the pure Asiatic lions from the hybrids. A similar analysis was used to identify hybrids of Indian and Siberian tigers through polymerase chain reaction (PCR) amplification of hair samples. To ascertain the variation which existed before the population bottleneck at the turn of the present century, microsatellite analysis was performed on 50- to 125-year-old skin samples from museum specimens. Our results show similar levels of genetic variability as in the present population (21.01%). This suggests that low genetic variability may be the characteristic feature of these species and not the result of intensive inbreeding. DNA fingerprinting studies of Asiatic lions and tigers have helped in identifying individuals with high genetic variability which can be used for conservation breeding programs.

  17. Geographic variation and genetic structure in Spotted Owls

    USGS Publications Warehouse

    Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

    2001-01-01

    We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

  18. Variation in metabolic enzyme activity of persistent Haemophilus influenzae in respiratory tracts of patients with cystic fibrosis.

    PubMed

    Möller, L V; Grasselier, H; Dankert, J; van Alphen, L

    1996-08-01

    Haemophilus influenzae organisms were isolated from sputum specimens prospectively collected from 40 patients with cystic fibrosis during 2 years to study variations in the metabolic enzyme activities of persistent H. influenzae strains as determined by biotyping. In total, 97 distinct H. influenzae strains without variations in their major outer membrane protein (MOMP) patterns and 73 MOMP variants derived from 30 of these distinct strains were obtained. Twelve distinct strains and 42 MOMP variant strains were isolated at multiple time points during the study period, indicating the persistence of these strains. Among the 54 persistent H. influenzae strains, 22 (41%) strains with stable MOMP compositions showed random variations in biotypes. In 39 of 103 (38%) H. influenzae strains, biotype changes coincided with MOMP variations. Biotype variations were the result of both the loss and the acquisition of enzyme activities. The results of the study indicate that changes in metabolic enzyme activity occur randomly during the persistence of H. influenzae organisms in cystic fibrosis patients, irrespective of MOMP variations.

  19. Intraspecific Variation among Social Insect Colonies: Persistent Regional and Colony-Level Differences in Fire Ant Foraging Behavior.

    PubMed

    Bockoven, Alison A; Wilder, Shawn M; Eubanks, Micky D

    2015-01-01

    Individuals vary within a species in many ecologically important ways, but the causes and consequences of such variation are often poorly understood. Foraging behavior is among the most profitable and risky activities in which organisms engage and is expected to be under strong selection. Among social insects there is evidence that within-colony variation in traits such as foraging behavior can increase colony fitness, but variation between colonies and the potential consequences of such variation are poorly documented. In this study, we tested natural populations of the red imported fire ant, Solenopsis invicta, for the existence of colony and regional variation in foraging behavior and tested the persistence of this variation over time and across foraging habitats. We also reared single-lineage colonies in standardized environments to explore the contribution of colony lineage. Fire ants from natural populations exhibited significant and persistent colony and regional-level variation in foraging behaviors such as extra-nest activity, exploration, and discovery of and recruitment to resources. Moreover, colony-level variation in extra-nest activity was significantly correlated with colony growth, suggesting that this variation has fitness consequences. Lineage of the colony had a significant effect on extra-nest activity and exploratory activity and explained approximately half of the variation observed in foraging behaviors, suggesting a heritable component to colony-level variation in behavior.

  20. Intraspecific Variation among Social Insect Colonies: Persistent Regional and Colony-Level Differences in Fire Ant Foraging Behavior

    PubMed Central

    Bockoven, Alison A.; Wilder, Shawn M.; Eubanks, Micky D.

    2015-01-01

    Individuals vary within a species in many ecologically important ways, but the causes and consequences of such variation are often poorly understood. Foraging behavior is among the most profitable and risky activities in which organisms engage and is expected to be under strong selection. Among social insects there is evidence that within-colony variation in traits such as foraging behavior can increase colony fitness, but variation between colonies and the potential consequences of such variation are poorly documented. In this study, we tested natural populations of the red imported fire ant, Solenopsis invicta, for the existence of colony and regional variation in foraging behavior and tested the persistence of this variation over time and across foraging habitats. We also reared single-lineage colonies in standardized environments to explore the contribution of colony lineage. Fire ants from natural populations exhibited significant and persistent colony and regional-level variation in foraging behaviors such as extra-nest activity, exploration, and discovery of and recruitment to resources. Moreover, colony-level variation in extra-nest activity was significantly correlated with colony growth, suggesting that this variation has fitness consequences. Lineage of the colony had a significant effect on extra-nest activity and exploratory activity and explained approximately half of the variation observed in foraging behaviors, suggesting a heritable component to colony-level variation in behavior. PMID:26197456

  1. Genetic variations and head and neck cancer risks.

    PubMed

    Masood, Nosheen; Yasmin, Azra; Kayani, Mahmood Akhtar

    2014-01-01

    Variations in CYP1A1, GSTM1, GSTT1 and GSTP1 in head and neck cancer have been frequently found in literature. But these studies give an overview of these genetic variations in different populations. The current mini review focus on the analysis of these genetic variations at DNA, mRNA and protein levels in the same study group. Eight publications were reviewed on the same study samples yielding results at DNA, mRNA and protein levels. At DNA level, CYP1A1 showed significantly higher mutations in head and neck cancer patients compared to controls at g.2842A>C and g.2842_2843insT. GSTM1 and GSTT1 showed deletion polymorphisms and heterozygous deletion confers protection against cancer. Mutations were also found in GSTP1 at g.2848A>T, g.2849G>A, g.1074delC and g.1466delC. mRNA and protein expressional analysis revealed underexpression of CYP1A1, loss or underexpression of GSTM1 and GSTT1 and overexpression of GSTP1. In addition an unusual intronic variant of GSTP1 mRNA was also found, retaining the intronic portion between exons. The current review gives a complete study overview regarding CYP1A1, GSTM1, GSTT1 and GSTP1 variations at DNA, mRNA and protein levels in head and neck cancer. The review is helpful in designing a new experiment or gene therapy for head and neck cancer patients.

  2. Genetic variation in a human odorant receptor alters odour perception.

    PubMed

    Keller, Andreas; Zhuang, Hanyi; Chi, Qiuyi; Vosshall, Leslie B; Matsunami, Hiroaki

    2007-09-27

    Human olfactory perception differs enormously between individuals, with large reported perceptual variations in the intensity and pleasantness of a given odour. For instance, androstenone (5alpha-androst-16-en-3-one), an odorous steroid derived from testosterone, is variously perceived by different individuals as offensive ("sweaty, urinous"), pleasant ("sweet, floral") or odourless. Similar variation in odour perception has been observed for several other odours. The mechanistic basis of variation in odour perception between individuals is unknown. We investigated whether genetic variation in human odorant receptor genes accounts in part for variation in odour perception between individuals. Here we show that a human odorant receptor, OR7D4, is selectively activated in vitro by androstenone and the related odorous steroid androstadienone (androsta-4,16-dien-3-one) and does not respond to a panel of 64 other odours and two solvents. A common variant of this receptor (OR7D4 WM) contains two non-synonymous single nucleotide polymorphisms (SNPs), resulting in two amino acid substitutions (R88W, T133M; hence 'RT') that severely impair function in vitro. Human subjects with RT/WM or WM/WM genotypes as a group were less sensitive to androstenone and androstadienone and found both odours less unpleasant than the RT/RT group. Genotypic variation in OR7D4 accounts for a significant proportion of the valence (pleasantness or unpleasantness) and intensity variance in perception of these steroidal odours. Our results demonstrate the first link between the function of a human odorant receptor in vitro and odour perception.

  3. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader

    PubMed Central

    Li, Shou-Li; Vasemägi, Anti; Ramula, Satu

    2016-01-01

    Background and Aims Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. Methods Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. Key Results It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (QST) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F′ST), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. Conclusions The study suggests that although genetic

  4. Placental genetic variations in circadian clock-related genes increase the risk of placental abruption

    PubMed Central

    Qiu, Chunfang; Gelaye, Bizu; Denis, Marie; Tadesse, Mahlet G; Enquobahrie, Daniel A; Ananth, Cande V; Pacora, Percy N; Salazar, Manuel; Sanchez, Sixto E; Williams, Michelle A

    2016-01-01

    The genetic architecture of placental abruption (PA) remains poorly understood. We examined variations in SNPs of circadian clock-related genes in placenta with PA risk. We also explored placental and maternal genomic contributions to PA risk. Placental genomic DNA samples were isolated from 280 PA cases and 244 controls. Genotyping was performed using the Illumina Cardio-MetaboChip. We examined 116 SNPs in 13 genes known to moderate circadian rhythms. Logistic regression models were fit to estimate odds ratios (ORs). The combined effect of multiple SNPs on PA risk was estimated using a weighted genetic risk score. We examined independent and joint associations of wGRS derived from placental and maternal genomes with PA. Seven SNPs in five genes (ARNTL2, CRY2, DEC1, PER3 and RORA), in the placental genome, were associated with PA risk. Each copy of the minor allele (G) of a SNP in the RORA gene (rs2899663) was associated with a 30% reduced odds of PA (95% CI 0.52-0.95). The odds of PA increased with increasing placental-wGRS (Ptrend<0.001). The ORs were 1.00, 2.16, 3.24 and 4.48 across quartiles. Associations persisted after the maternal-wGRS was included in the model. There was evidence of an additive contribution of placental and maternal genetic contributions to PA risk. Participants with placental- and maternal-wGRS in the highest quartile, compared with those in the lowest quartile, had a 15.57-fold (95% CI 3.34-72.60) increased odds of PA. Placental variants in circadian clock-related genes are associated with PA risk; and the association persists after control of genetic variants in the maternal genome. PMID:27186326

  5. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.

    PubMed

    Sun, Guangyun; McGarvey, Stephen T; Bayoumi, Riad; Mulligan, Connie J; Barrantes, Ramiro; Raskin, Salmo; Zhong, Yixi; Akey, Joshua; Chakraborty, Ranajit; Deka, Ranjan

    2003-01-01

    We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended.

  6. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development

    PubMed Central

    Pires, Nuno D.; Bemer, Marian; Müller, Lena M.; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

    2016-01-01

    Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict. PMID:26811909

  7. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

    PubMed

    Pires, Nuno D; Bemer, Marian; Müller, Lena M; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

    2016-01-01

    Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

  8. Global genetic variations predict brain response to faces.

    PubMed

    Dickie, Erin W; Tahmasebi, Amir; French, Leon; Kovacevic, Natasa; Banaschewski, Tobias; Barker, Gareth J; Bokde, Arun; Büchel, Christian; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Gallinat, Juergen; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lawrence, Claire; Mann, Karl; Martinot, Jean-Luc; Nees, Frauke; Nichols, Thomas; Lathrop, Mark; Loth, Eva; Pausova, Zdenka; Rietschel, Marcela; Smolka, Michal N; Ströhle, Andreas; Toro, Roberto; Schumann, Gunter; Paus, Tomáš

    2014-08-01

    Face expressions are a rich source of social signals. Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼ 500,000 single nucleotide polymorphisms. Using genomic-relationship-matrix restricted maximum likelihood (GREML), we related this global genetic variance to that in the brain response to facial expressions, as assessed with functional magnetic resonance imaging (fMRI) in a community-based sample of adolescents (n = 1,620). Brain response to facial expressions was measured in 25 regions constituting a face network, as defined previously. In 9 out of these 25 regions, common genetic variance explained a significant proportion of phenotypic variance (40-50%) in their response to ambiguous facial expressions; this was not the case for angry facial expressions. Across the network, the strength of the genotype-phenotype relationship varied as a function of the inter-individual variability in the number of functional connections possessed by a given region (R(2) = 0.38, p<0.001). Furthermore, this variability showed an inverted U relationship with both the number of observed connections (R2 = 0.48, p<0.001) and the magnitude of brain response (R(2) = 0.32, p<0.001). Thus, a significant proportion of the brain response to facial expressions is predicted by common genetic variance in a subset of regions constituting the face network. These regions show the highest inter-individual variability in the number of connections with other network nodes, suggesting that the genetic model captures variations across the adolescent brains in co-opting these regions into the face network.

  9. Global Genetic Variations Predict Brain Response to Faces

    PubMed Central

    Dickie, Erin W.; Tahmasebi, Amir; French, Leon; Kovacevic, Natasa; Banaschewski, Tobias; Barker, Gareth J.; Bokde, Arun; Büchel, Christian; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Gallinat, Juergen; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lawrence, Claire; Mann, Karl; Martinot, Jean-Luc; Nees, Frauke; Nichols, Thomas; Lathrop, Mark; Loth, Eva; Pausova, Zdenka; Rietschel, Marcela; Smolka, Michal N.; Ströhle, Andreas; Toro, Roberto; Schumann, Gunter; Paus, Tomáš

    2014-01-01

    Face expressions are a rich source of social signals. Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼500,000 single nucleotide polymorphisms. Using genomic-relationship-matrix restricted maximum likelihood (GREML), we related this global genetic variance to that in the brain response to facial expressions, as assessed with functional magnetic resonance imaging (fMRI) in a community-based sample of adolescents (n = 1,620). Brain response to facial expressions was measured in 25 regions constituting a face network, as defined previously. In 9 out of these 25 regions, common genetic variance explained a significant proportion of phenotypic variance (40–50%) in their response to ambiguous facial expressions; this was not the case for angry facial expressions. Across the network, the strength of the genotype-phenotype relationship varied as a function of the inter-individual variability in the number of functional connections possessed by a given region (R2 = 0.38, p<0.001). Furthermore, this variability showed an inverted U relationship with both the number of observed connections (R2 = 0.48, p<0.001) and the magnitude of brain response (R2 = 0.32, p<0.001). Thus, a significant proportion of the brain response to facial expressions is predicted by common genetic variance in a subset of regions constituting the face network. These regions show the highest inter-individual variability in the number of connections with other network nodes, suggesting that the genetic model captures variations across the adolescent brains in co-opting these regions into the face network. PMID:25122193

  10. Genetic variation in retinal vascular patterning predicts variation in pial collateral extent and stroke severity

    PubMed Central

    Prabhakar, Pranay; Zhang, Hua; Chen, De; Faber, James E.

    2015-01-01

    The presence of a native collateral circulation in tissues lessens injury in occlusive vascular diseases. However, differences in genetic background cause wide variation in collateral number and diameter in mice, resulting in large variation in protection. Indirect estimates of collateral perfusion suggest wide variation also exists in humans. Unfortunately, methods used to obtain these estimates are invasive and not widely available. We sought to determine if differences in genetic background in mice result in variation in branch-patterning of the retinal arterial circulation, and if these differences predict strain-dependent differences in pial collateral extent and severity of ischemic stroke. Retinal patterning metrics, collateral extent, and infarct volume were obtained for 10 strains known to differ widely in collateral extent. Multivariate regression was conducted and model performance assessed using K-fold cross-validation. Twenty-one metrics varied with strain (p<0.01). Ten metrics (eg, bifurcation angle, lacunarity, optimality) predicted collateral number and diameter across 7 regression models, with the best model closely predicting (p<0.0001) number (± 1.2-3.4 collaterals, K-fold R2=0.83-0.98), diameter (± 1.2-1.9μm, R2=0.73-0.88) and infarct volume (± 5.1 mm3, R2=0.85-0.87). These metrics obtained for the middle cerebral artery tree in a subset of the above strains also predicted (p<0.0001) collateral number and diameter and diameter, although with less strength (K-fold R2=0.61-0.78) and 0.60-0.86, respectively). Thus, differences in arterial branch-patterning in the retina and the MCA trees are specified by genetic background and predict variation in collateral extent and stroke severity. If also true in human retina, and since genetic variation in cerebral collaterals extends to other tissues at least in mice, a similar “retinal predictor index” could serve as a non-or minimally invasive biomarker for collateral extent in brain and other

  11. Genetics of Brazil nut (Bertholletia excelsa Humb. & Bonpl.: Lecythidaceae) : 1. Genetic variation in natural populations.

    PubMed

    Buckley, D P; O'Malley, D M; Apsit, V; Prance, G T; Bawa, K S

    1988-12-01

    We provide an estimate of genetic variation within and between two populations of Bertholletia excelsa (Brazil nut), a large canopy tree found in the rain forests of South America. Average heterozygosity is 0.190, and 54.3% of the sampled loci are polymorphic. The population structure deviates significantly from Hardy-Weinberg expectations for Fest2 and Pgm2 (F =0.405 and 0.443, respectively) in one population, and highly significantly (F=-0.341) for Gdh in the other population. Although allele frequencies of the two populations differ significantly for Aat2, Est5, Mdh1, and Mdh2B, Nei's coefficient of gene differentiation (Gst) indicates that the between-population component (Dst) of genic diversity represents only 3.75% of the size of the within-population component (Hs). The implications of these findings in terms of conservation genetics are that much of the genetic diversity of this species may be preserved within one or a few populations. However, such populations must be very large because it appears that the large amount of genetic variation in Brazil nut populations is maintained by extensive gene flow and bonds of mating over a large area. The genetic architecture of Bertholletia excelsa is similar to that expected for an extensively diploidized paleopolyploid species.

  12. FINDbase: a worldwide database for genetic variation allele frequencies updated

    PubMed Central

    Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I.; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F.; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P.

    2011-01-01

    Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding. PMID:21113021

  13. Genetic variation in radiation-induced cell death.

    PubMed

    Smirnov, Denis A; Brady, Lauren; Halasa, Krzysztof; Morley, Michael; Solomon, Sonia; Cheung, Vivian G

    2012-02-01

    Radiation exposure through environmental, medical, and occupational settings is increasingly common. While radiation has harmful effects, it has utility in many applications such as radiotherapy for cancer. To increase the efficacy of radiation treatment and minimize its risks, a better understanding of the individual differences in radiosensitivity and the molecular basis of radiation response is needed. Here, we integrated human genetic and functional genomic approaches to study the response of human cells to radiation. We measured radiation-induced changes in gene expression and cell death in B cells from normal individuals. We found extensive individual variation in gene expression and cellular responses. To understand the genetic basis of this variation, we mapped the DNA sequence variants that influence expression response to radiation. We also identified radiation-responsive genes that regulate cell death; silencing of these genes by small interfering RNA led to an increase in radiation-induced cell death in human B cells, colorectal and prostate cancer cells. Together these results uncovered DNA variants that contribute to radiosensitivity and identified genes that can be targeted to increase the sensitivity of tumors to radiation.

  14. Variation in the peacock's train shows a genetic component.

    PubMed

    Petrie, Marion; Cotgreave, Peter; Pike, Thomas W

    2009-01-01

    Female peafowl (Pavo cristatus) show a strong mating preference for males with elaborate trains. This, however, poses something of a paradox because intense directional selection should erode genetic variation in the males' trains, so that females will no longer benefit by discriminating among males on the basis of these traits. This situation is known as the 'lek paradox', and leads to the theoretical expectation of low heritability in the peacock's train. We used two independent breeding experiments, involving a total of 42 sires and 86 of their male offspring, to estimate the narrow sense heritabilities of male ornaments and other morphometric traits. Contrary to expectation, we found significant levels of heritability in a trait known to be used by females during mate choice (train length), while no significant heritabilities were evident for other, non-fitness related morphological traits (tarsus length, body weight or spur length). This study adds to the building body of evidence that high levels of additive genetic variance can exist in secondary sexual traits under directional selection, but further emphasizes the main problem of what maintains this variation.

  15. HPA Axis Genetic Variation, Cortisol, and Psychosis in Major Depression

    PubMed Central

    Schatzberg, Alan F.; Keller, Jennifer; Tennakoon, Lakshika; Lembke, Anna; Williams, Gordon; Kraemer, Fredric B.; Sarginson, Jane E.; Lazzeroni, Laura C.; Murphy, Greer M.

    2013-01-01

    Genetic variation underlying hypothalamic pituitary adrenal (HPA) axis over-activity in healthy controls and patients with severe forms of major depression has not been well explored but could explain risk for cortisol dysregulation. 95 participants were studied: 40 patients with psychotic major depression (PMD); 26 patients with nonpsychotic major depression (NPMD); and 29 healthy controls (HC). Collection of genetic material was added one third of the way into a larger study on cortisol, cognition, and psychosis in major depression. Subjects were assessed using the Brief Psychiatric Rating Scale, the Hamilton Depression Rating Scale and the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders. Blood was collected hourly for determination of cortisol from 6pm to 9am and for the assessment of alleles for 6 genes involved in HPA Axis regulation. Two of the 6 genes contributed significantly to cortisol levels, psychosis measures or depression severity. After accounting for age, depression, and psychosis, and medication status, only allelic variation for the glucocorticoid receptor gene (GR) accounted for significant variance for mean cortisol levels from 6pm to 1am (r2=.317) and from 1am to 9am (r2=.194). Interestingly, neither depression severity nor psychosis predicted cortisol variance. In addition, GR and corticotropin-releasing hormone receptor 1 (CRH-R1) contributed significantly to psychosis measures and CRH-R1 contributed significantly to depression severity rating. PMID:24166410

  16. FINDbase: a worldwide database for genetic variation allele frequencies updated.

    PubMed

    Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2011-01-01

    Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft's PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding.

  17. Genetic Variation in Virulence among Chalkbrood Strains Infecting Honeybees

    PubMed Central

    Vojvodic, Svjetlana; Jensen, Annette B.; Markussen, Bo; Eilenberg, Jørgen; Boomsma, Jacobus J.

    2011-01-01

    Ascosphaera apis causes chalkbrood in honeybees, a chronic disease that reduces the number of viable offspring in the nest. Although lethal for larvae, the disease normally has relatively low virulence at the colony level. A recent study showed that there is genetic variation for host susceptibility, but whether Ascosphaera apis strains differ in virulence is unknown. We exploited a recently modified in vitro rearing technique to infect honeybee larvae from three colonies with naturally mated queens under strictly controlled laboratory conditions, using four strains from two distinct A. apis clades. We found that both strain and colony of larval origin affected mortality rates. The strains from one clade caused 12–14% mortality while those from the other clade induced 71–92% mortality. Larvae from one colony showed significantly higher susceptibility to chalkbrood infection than larvae from the other two colonies, confirming the existence of genetic variation in susceptibility across colonies. Our results are consistent with antagonistic coevolution between a specialized fungal pathogen and its host, and suggest that beekeeping industries would benefit from more systematic monitoring of this chronic stress factor of their colonies. PMID:21966406

  18. Identification of common genetic variation that modulates alternative splicing.

    PubMed

    Hull, Jeremy; Campino, Susana; Rowlands, Kate; Chan, Man-Suen; Copley, Richard R; Taylor, Martin S; Rockett, Kirk; Elvidge, Gareth; Keating, Brendan; Knight, Julian; Kwiatkowski, Dominic

    2007-06-01

    Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs). In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.

  19. Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients.

    PubMed

    Renders, N; Licciardello, L; IJsseldijk, C; Sijmons, M; van Alphen, L; Verbrugh, H; van Belkum, A

    1999-04-01

    Serial sputum isolates of Haemophilus influenzae (n = 69) were obtained from eight patients suffering from cystic fibrosis. For two of these patients all strains were analysed for polymorphism in the major outer membrane protein profile. For all patients the strains were genetically characterised by random amplification of polymorphic DNA analysis. All strains were included in a survey for polymorphism in regions containing moieties of repetitive DNA as well. A single locus containing trinucleotide repeat units, three loci harbouring tetranucleotides, one region comprising pentanucleotide units and two hexanucleotide repeat unit-containing loci were analysed for repeat number variability. Most of the regions were previously shown to be directly adjacent to or even within virulence genes. All regions behaved as genuine variable number of tandem repeat loci in the sense that genetic polymorphism based on the presence of varying numbers of repeat units could be demonstrated among different strains. Interestingly, several of the repeats showed variation in the absence of the variability as assessed by major outer membrane protein or random amplification of polymorphic DNA analysis. These observations indicate that the repeat loci may vary independently from major chromosomal polymorphism. Consequently, H. influenzae appears to modify its virulence gene regions of the chromosome during persistent colonisation of the lung in cystic fibrosis patients.

  20. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model.

    PubMed

    Gailing, Oliver; Vornam, Barbara; Leinemann, Ludger; Finkeldey, Reiner

    2009-12-01

    With the increasing availability of sequence information at putatively important genes or regulatory regions, the characterization of adaptive genetic diversity and their association with phenotypic trait variation becomes feasible for many non-model organisms such as forest trees. Especially in predominantly outcrossing forest tree populations with large effective size, a high genetic variation in relevant genes is maintained, that is the raw material for the adaptation to changing and variable environments, and likewise for plant breeding. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe as dominant tree species in many forests and grow under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes, we are now able to test the functional importance of single nucleotide polymorphisms (SNPs) by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Here, we report on quantitative trait locus (QTL), candidate gene and association mapping approaches that are applicable to characterize gene markers and SNPs associated with variation in adaptive traits, such as bud burst, drought resistance and other traits showing selective responses to environmental change and stress. Because genome-wide association mapping studies are not feasible because of the enormous amount of SNP markers required in outcrossing trees with high recombination rates, the success of such an approach depends largely on the reasonable selection of candidate genes.

  1. Natural variation and genetic covariance in adult hippocampal neurogenesis

    SciTech Connect

    Kempermann, Gerd; Chesler, Elissa J; Lu, Lu; Williams, Robert; Gage, Fred

    2006-01-01

    Adult hippocampal neurogenesis is highly variable and heritable among laboratory strains of mice. Adult neurogenesis is also remarkably plastic and can be modulated by environment and activity. Here, we provide a systematic quantitative analysis of adult hippocampal neurogenesis in two large genetic reference panels of recombinant inbred strains (BXD and AXB?BXA, n ? 52 strains). We combined data on variation in neurogenesis with a new transcriptome database to extract a set of 190 genes with expression patterns that are also highly variable and that covary with rates of (i) cell proliferation, (ii) cell survival, or the numbers of surviving (iii) new neurons, and (iv) astrocytes. Expression of a subset of these neurogenesis-associated transcripts was controlled in cis across the BXD set. These self-modulating genes are particularly interesting candidates to control neurogenesis. Among these were musashi (Msi1h) and prominin1?CD133 (Prom1), both of which are linked to stem-cell maintenance and division. Twelve neurogenesis-associated transcripts had significant cis-acting quantitative trait loci, and, of these, six had plausible biological association with adult neurogenesis (Prom1, Ssbp2, Kcnq2, Ndufs2, Camk4, and Kcnj9). Only one cis- cting candidate was linked to both neurogenesis and gliogenesis, Rapgef6, a downstream target of ras signaling. The use of genetic reference panels coupled with phenotyping and global transcriptome profiling thus allowed insight into the complexity of the genetic control of adult neurogenesis.

  2. Functional significance of genetic variation underlying limb bone diaphyseal structure

    PubMed Central

    Wallace, Ian J.; Middleton, Kevin M.; Lublinsky, Svetlana; Kelly, Scott A.; Judex, Stefan; Garland, Theodore; Demes, Brigitte

    2010-01-01

    Limb bone diaphyseal structure is frequently used to infer hominin activity levels from skeletal remains, an approach based on the well-documented ability of bone to adjust to its loading environment during life. However, diaphyseal structure is also determined in part by genetic factors. This study investigates the possibility that genetic variation underlying diaphyseal structure is influenced by the activity levels of ancestral populations and might also have functional significance in an evolutionary context. We adopted an experimental evolution approach and tested for differences in femoral diaphyseal structure in one-week-old mice from a line that had been artificially selected (45 generations) for high voluntary wheel running and unselected controls. As adults, selected mice are significantly more active on wheels and in home cages, and have thicker diaphyses. Structural differences at one week can be assumed to primarily reflect the effects of selective breeding rather than direct mechanical stimuli, given that the onset of locomotion in mice is shortly after day seven. We hypothesized that if genetically determined diaphyseal structure reflects the activity patterns of members of a lineage, then selected animals will have relatively larger diaphyseal dimensions at one week compared to controls. The results provide strong support for this hypothesis and suggest that limb bone cross sections may not always only reflect the activity levels of particular fossil individuals, but also convey an evolutionary signal providing information about hominin activity in the past. PMID:20310061

  3. HSP90 Shapes the Consequences of Human Genetic Variation.

    PubMed

    Karras, Georgios I; Yi, Song; Sahni, Nidhi; Fischer, Máté; Xie, Jenny; Vidal, Marc; D'Andrea, Alan D; Whitesell, Luke; Lindquist, Susan

    2017-02-23

    HSP90 acts as a protein-folding buffer that shapes the manifestations of genetic variation in model organisms. Whether HSP90 influences the consequences of mutations in humans, potentially modifying the clinical course of genetic diseases, remains unknown. By mining data for >1,500 disease-causing mutants, we found a strong correlation between reduced phenotypic severity and a dominant (HSP90 ≥ HSP70) increase in mutant engagement by HSP90. Examining the cancer predisposition syndrome Fanconi anemia in depth revealed that mutant FANCA proteins engaged predominantly by HSP70 had severely compromised function. In contrast, the function of less severe mutants was preserved by a dominant increase in HSP90 binding. Reducing HSP90's buffering capacity with inhibitors or febrile temperatures destabilized HSP90-buffered mutants, exacerbating FA-related chemosensitivities. Strikingly, a compensatory FANCA somatic mutation from an "experiment of nature" in monozygotic twins both prevented anemia and reduced HSP90 binding. These findings provide one plausible mechanism for the variable expressivity and environmental sensitivity of genetic diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Evaluation of genetic variation among wild rice populations in Cambodia

    PubMed Central

    Orn, Chhourn; Shishido, Rieko; Akimoto, Masahiro; Ishikawa, Ryo; Htun, Than Myint; Nonomura, Ken-Ichi; Koide, Yohei; Sarom, Men; Vang, Seng; Sophany, Sakhan; Makara, Ouk; Ishii, Takashige

    2015-01-01

    A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources. PMID:26719746

  5. Origins of Shared Genetic Variation in African Cichlids

    PubMed Central

    Loh, Yong-Hwee E.; Bezault, Etienne; Muenzel, Frauke M.; Roberts, Reade B.; Swofford, Ross; Barluenga, Marta; Kidd, Celeste E.; Howe, Aimee E.; Di Palma, Federica; Lindblad-Toh, Kerstin; Hey, Jody; Seehausen, Ole; Salzburger, Walter; Kocher, Thomas D.; Streelman, J. Todd

    2013-01-01

    Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ∼160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa. PMID:23275489

  6. Clinically Relevant Genetic Variations in Drug Metabolizing Enzymes

    PubMed Central

    Pinto, Navin; Dolan, M. Eileen

    2011-01-01

    In the field of pharmacogenetics, we currently have a few markers to guide physicians as to the best course of therapy for patients. For the most part, these genetic variants are within a drug metabolizing enzyme that has a large effect on the degree or rate at which a drug is converted to its metabolites. For many drugs, response and toxicity are multi-genic traits and understanding relationships between a patient's genetic variation in drug metabolizing enzymes and the efficacy and/or toxicity of a medication offers the potential to optimize therapies. This review will focus on variants in drug metabolizing enzymes with predictable and relatively large impacts on drug efficacy and/or toxicity; some of these drug/gene variant pairs have impacted drug labels by the United States Food and Drug Administration. The challenges in identifying genetic markers and implementing clinical changes based on known markers will be discussed. In addition, the impact of next generation sequencing in identifying rare variants will be addressed. PMID:21453273

  7. Genetic analyses of smoking initiation, persistence, quantity, and age-at-onset of regular cigarette use in Brazilian families: the Baependi Heart Study.

    PubMed

    Horimoto, Andréa R V R; Oliveira, Camila M; Giolo, Suely R; Soler, Júlia P; de Andrade, Mariza; Krieger, José E; Pereira, Alexandre C

    2012-01-30

    The purpose of this study was to estimate the genetic influences on the initiation of cigarette smoking, the persistence, quantity and age-at-onset of regular cigarette use in Brazilian families. The data set consisted of 1,694 individuals enrolled in the Baependi Heart Study. The heritability and the heterogeneity in genetic and environmental variance components by gender were estimated from variance components approaches, using the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package. The mixed-effects Cox model was used for the genetic analysis of the age-at onset of regular cigarette use. The heritability estimates were high (> 50%) for smoking initiation and were intermediate, ranging from 23.4 to 31.9%, for smoking persistence and quantity. Significant evidence for heterogeneity in variance components by gender was observed for smoking initiation and age-at-onset of regular cigarette use. Genetic factors play an important role in the interindividual variation of these phenotypes in females, while in males there is a predominant environmental component, which could be explained by greater social influences in the initiation of tobacco use. Significant heritabilities were observed in smoking phenotypes for both males and females from the Brazilian population. These data add to the literature and are concordant with the notion of significant biological determination in smoking behavior. Samples from the Baependi Heart Study may be valuable for the mapping of genetic loci that modulate this complex biological trait.

  8. Genetic variation in natural populations of Populus tremuloide

    SciTech Connect

    Cheliak, W.M.

    1980-01-01

    Vegetative reproduction results in a mosaic of clones throughout the extensive natural range of this species. An electrophoretic survey of 26 loci in 222 trees from seven natural populations in Alberta demonstrated great variability. Average observed population heterozygosity was 0.52 with an average of 2.3 alleles per locus; 84% of the loci were polymorphic. A model (for a finite population with neutral alleles) was developed to investigate the effects of partial vegetative reproduction on the amount of variation in a population. Results of the survey conformed to those predicted by the model for a population with a rate of sexual establishment greater than 1/N, where N is the population size. The model states that under these conditions, vegetative reproduction has no effect on the population. Therefore, the high level of observed variation is not an artifact of the mode of natural reproduction. These results support conclusions about high population variability based on phenotypic measurements and also suggest a genetic basis for this variation, rather than simply phenotypic plasticity.

  9. Genetics in endocrinology: genetic variation in deiodinases: a systematic review of potential clinical effects in humans.

    PubMed

    Verloop, Herman; Dekkers, Olaf M; Peeters, Robin P; Schoones, Jan W; Smit, Johannes W A

    2014-09-01

    Iodothyronine deiodinases represent a family of selenoproteins involved in peripheral and local homeostasis of thyroid hormone action. Deiodinases are expressed in multiple organs and thyroid hormone affects numerous biological systems, thus genetic variation in deiodinases may affect multiple clinical endpoints. Interest in clinical effects of genetic variation in deiodinases has clearly increased. We aimed to provide an overview for the role of deiodinase polymorphisms in human physiology and morbidity. In this systematic review, studies evaluating the relationship between deiodinase polymorphisms and clinical parameters in humans were eligible. No restrictions on publication date were imposed. The following databases were searched up to August 2013: Pubmed, EMBASE (OVID-version), Web of Science, COCHRANE Library, CINAHL (EbscoHOST-version), Academic Search Premier (EbscoHOST-version), and ScienceDirect. Deiodinase physiology at molecular and tissue level is described, and finally the role of these polymorphisms in pathophysiological conditions is reviewed. Deiodinase type 1 (D1) polymorphisms particularly show moderate-to-strong relationships with thyroid hormone parameters, IGF1 production, and risk for depression. D2 variants correlate with thyroid hormone levels, insulin resistance, bipolar mood disorder, psychological well-being, mental retardation, hypertension, and risk for osteoarthritis. D3 polymorphisms showed no relationship with inter-individual variation in serum thyroid hormone parameters. One D3 polymorphism was associated with risk for osteoarthritis. Genetic deiodinase profiles only explain a small proportion of inter-individual variations in serum thyroid hormone levels. Evidence suggests a role of genetic deiodinase variants in certain pathophysiological conditions. The value for determination of deiodinase polymorphism in clinical practice needs further investigation.

  10. Genetic variation in Pinus strobiformis growth and drought tolerance from southwestern US populations.

    PubMed

    Goodrich, Betsy A; Waring, Kristen M; Kolb, Thomas E

    2016-10-01

    The persistence of some tree species is threatened by combinations of novel abiotic and biotic stressors. To examine the hypothesis that Pinus strobiformis Engelm., a tree threatened by an invasive forest pathogen and a changing climate, exhibits intraspecific genetic variation in adaptive traits, we conducted a common garden study of seedlings at one location with two watering regimes using 24 populations. Four key findings emerged: (i) growth and physiological traits were low to moderately differentiated among populations but differentiation was high for some traits in water-stressed populations; (ii) seedlings from warmer climates grew larger, had higher stomatal density and were more water-use efficient (as measured by the carbon isotope ratio) than populations from colder climates; (iii) seedlings from the northern edge of the species' distribution had lower water-use efficiency, higher stomatal conductance, slower growth and longer survival in a lethal drought experiment compared with seedlings from more southern populations; and (iv) based on non-metric multidimensional scaling analyses, populations clustered into southern and northern groups, which did not correspond to current seed transfer zones. Our discovery of a clinal geographic pattern of genetic variation in adaptive traits of P. strobiformis seedlings will be useful in developing strategies to maintain the species during ongoing climate change and in the face of an invasive pathogen. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. GENETIC ASSOCIATION ANALYSIS OF COPY NUMBER VARIATION (CNVs) IN HUMAN DISEASE PATHOGENESIS

    PubMed Central

    Ionita-Laza, Iuliana; Rogers, Angela J.; Lange, Christoph; Raby, Benjamin A.; Lee, Charles

    2009-01-01

    Structural genetic variation, including copy number variation (CNV), constitutes a substantial fraction of total genetic variability and the importance of structural genetic variants in modulating human disease is increasingly being recognized. Early successes in identifying disease-associated CNVs via a candidate gene approach mandate that future disease association studies need to include structural genetic variation. Such analyses should not rely on previously developed methodologies that were designed to evaluate single nucleotide polymorphisms (SNPs). Instead, development of novel technical, statistical, and epidemiologic methods will be necessary to optimally capture this newly-appreciated form of genetic variation in a meaningful manner. PMID:18822366

  12. Biomonitoring the spatial and historical variations of persistent organic pollutants (POPs) in an industrial region.

    PubMed

    Odabasi, Mustafa; Falay, Ezgi Ozgunerge; Tuna, Gizem; Altiok, Hasan; Kara, Melik; Dumanoglu, Yetkin; Bayram, Abdurrahman; Tolunay, Doganay; Elbir, Tolga

    2015-02-17

    Several persistent organic pollutants (POPs) like polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), polychlorinated naphthalenes (PCNs), and polybrominated diphenyl ethers (PBDEs) were measured in needle, branch, bark, and tree ring samples in pine samples collected at 27 sites (21 industrial, 6 background) in Aliaga industrial region in Turkey. Soil, litter, and air samples were also collected to investigate the relationships between the air and soil, litter, and tree components. Concentrations decreased with distance from the sources and the lowest ones were measured at background sites. The spatial distribution of POPs indicated that the major sources in the region are the iron-steel, ship-breaking, petrochemical plants and the petroleum refinery. Significant correlations between the air concentrations and, soil, litter, and tree components indicated the interaction of these compartments with air. Observed increasing trends of POPs in the tree-ring samples were representative for the variations in anthropogenic emissions and resulting atmospheric concentrations in Aliaga region. These results indicated that tree components, litter and soil could be used to determine the spatial variations while tree rings could be used to investigate the historical trends of atmospheric POPs in a region. POP amounts (mg/ha) stored in different tree components, litter, and soil were also inventoried. Among the tree components, generally, the highest amounts were stored in the stem followed by needles. For the overall inventory, the highest amounts were stored in soil for PCNs, PBDEs, and PCBs while highest PAH amounts were stored in trees, indicating that in addition to soil, vegetation is also an important reservoir for POPs.

  13. Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense

    PubMed Central

    Joseph, Bindu; Corwin, Jason A.; Kliebenstein, Daniel J.

    2015-01-01

    Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype. PMID:25569687

  14. Genetic variation in the nuclear and organellar genomes modulates stochastic variation in the metabolome, growth, and defense.

    PubMed

    Joseph, Bindu; Corwin, Jason A; Kliebenstein, Daniel J

    2015-01-01

    Recent studies are starting to show that genetic control over stochastic variation is a key evolutionary solution of single celled organisms in the face of unpredictable environments. This has been expanded to show that genetic variation can alter stochastic variation in transcriptional processes within multi-cellular eukaryotes. However, little is known about how genetic diversity can control stochastic variation within more non-cell autonomous phenotypes. Using an Arabidopsis reciprocal RIL population, we showed that there is significant genetic diversity influencing stochastic variation in the plant metabolome, defense chemistry, and growth. This genetic diversity included loci specific for the stochastic variation of each phenotypic class that did not affect the other phenotypic classes or the average phenotype. This suggests that the organism's networks are established so that noise can exist in one phenotypic level like metabolism and not permeate up or down to different phenotypic levels. Further, the genomic variation within the plastid and mitochondria also had significant effects on the stochastic variation of all phenotypic classes. The genetic influence over stochastic variation within the metabolome was highly metabolite specific, with neighboring metabolites in the same metabolic pathway frequently showing different levels of noise. As expected from bet-hedging theory, there was more genetic diversity and a wider range of stochastic variation for defense chemistry than found for primary metabolism. Thus, it is possible to begin dissecting the stochastic variation of whole organismal phenotypes in multi-cellular organisms. Further, there are loci that modulate stochastic variation at different phenotypic levels. Finding the identity of these genes will be key to developing complete models linking genotype to phenotype.

  15. Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci.

    Treesearch

    P. Spruell; A.R. Hemmingsen; P.J. Howell; N. Kanda; F.W. Allendorf

    2003-01-01

    We describe the genetic population structure of 65 bull trout (Salvelinus confluentus) populations from the northwestern United States using four microsatellite loci. The distribution of genetic variation as measured by microsatellites is consistent with previous allozyme and mitochondrial DNA analysis. There is relatively little genetic variation...

  16. Longitudinal analysis of Plasmodium falciparum genetic variation in Turbo, Colombia: implications for malaria control and elimination.

    PubMed

    Chenet, Stella M; Taylor, Jesse E; Blair, Silvia; Zuluaga, Lina; Escalante, Ananias A

    2015-09-22

    Malaria programmes estimate changes in prevalence to evaluate their efficacy. In this study, parasite genetic data was used to explore how the demography of the parasite population can inform about the processes driving variation in prevalence. In particular, how changes in treatment and population movement have affected malaria prevalence in an area with seasonal malaria. Samples of Plasmodium falciparum collected over 8 years from a population in Turbo, Colombia were genotyped at nine microsatellite loci and three drug-resistance loci. These data were analysed using several population genetic methods to detect changes in parasite genetic diversity and population structure. In addition, a coalescent-based method was used to estimate substitution rates at the microsatellite loci. The estimated mean microsatellite substitution rates varied between 5.35 × 10(-3) and 3.77 × 10(-2) substitutions/locus/month. Cluster analysis identified six distinct parasite clusters, five of which persisted for the full duration of the study. However, the frequencies of the clusters varied significantly between years, consistent with a small effective population size. Malaria control programmes can detect re-introductions and changes in transmission using rapidly evolving microsatellite loci. In this population, the steadily decreasing diversity and the relatively constant effective population size suggest that an increase in malaria prevalence from 2004 to 2007 was primarily driven by local rather than imported cases.

  17. Persistent genetic signatures of historic climatic events in an Antarctic octopus.

    PubMed

    Strugnell, J M; Watts, P C; Smith, P J; Allcock, A L

    2012-06-01

    Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase 1 gene to examine genetic structure in the direct-developing, endemic Southern Ocean octopod Pareledone turqueti sampled from a broad range of areas that circumvent Antarctica. We find that, unusually for a species with poor dispersal potential, P. turqueti has a circumpolar distribution and is also found off the islands of South Georgia and Shag Rocks. The overriding pattern of spatial genetic structure can be explained by hydrographic (with ocean currents both facilitating and hindering gene flow) and bathymetric features. The Antarctic Peninsula region displays a complex population structure, consistent with its varied topographic and oceanographic influences. Genetic similarities between the Ross and Weddell Seas, however, are interpreted as a persistent historic genetic signature of connectivity during the hypothesized Pleistocene West Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two major lineages within P. turqueti, a continental lineage and a sub-Antarctic lineage, that diverged in the mid-Pliocene with no subsequent gene flow. Both lineages survived subsequent major glacial cycles. Our data are indicative of potential refugia at Shag Rocks and South Georgia and also around the Antarctic continent within the Ross Sea, Weddell Sea and off Adélie Land. The mean age of mtDNA diversity within these main continental lineages coincides with Pleistocene glacial cycles.

  18. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus.

    PubMed

    Chen, Jinhui; Xie, Jianbo; Chen, Beibei; Quan, Mingyang; Li, Ying; Li, Bailian; Zhang, Deqiang

    2016-10-01

    Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  19. Genetic Variation of the Endangered Gentiana lutea L. var. aurantiaca (Gentianaceae) in Populations from the Northwest Iberian Peninsula

    PubMed Central

    González-López, Oscar; Polanco, Carlos; György, Zsuzsanna; Pedryc, Andrzej; Casquero, Pedro A.

    2014-01-01

    Gentiana lutea L. (G. lutea L.) is an endangered plant, patchily distributed along the mountains of Central and Southern Europe. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variation in this species within and among populations of G. lutea L. var. aurantiaca of the Cantabrian Mountains (Northwest Iberian Peninsula). Samples of G. lutea L. collected at different locations of the Pyrenees and samples of G. lutea L. subsp. vardjanii of the Dolomites Alps were also analyzed for comparison. Using nine ISSR primers, 106 bands were generated, and 89.6% of those were polymorphic. The populations from the Northwest Iberian Peninsula were clustered in three different groups, with a significant correlation between genetic and geographic distances. Gentiana lutea L. var. aurantiaca showed 19.8% private loci and demonstrated a remarkable level of genetic variation, both among populations and within populations; those populations with the highest level of isolation show the lowest genetic variation within populations. The low number of individuals, as well as the observed genetic structure of the analyzed populations makes it necessary to protect them to ensure their survival before they are too small to persist naturally. PMID:24905405

  20. Genetic variation of the endangered Gentiana lutea L. var. aurantiaca (Gentianaceae) in populations from the Northwest Iberian Peninsula.

    PubMed

    González-López, Oscar; Polanco, Carlos; György, Zsuzsanna; Pedryc, Andrzej; Casquero, Pedro A

    2014-06-05

    Gentiana lutea L. (G. lutea L.) is an endangered plant, patchily distributed along the mountains of Central and Southern Europe. In this study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic variation in this species within and among populations of G. lutea L. var. aurantiaca of the Cantabrian Mountains (Northwest Iberian Peninsula). Samples of G. lutea L. collected at different locations of the Pyrenees and samples of G. lutea L. subsp. vardjanii of the Dolomites Alps were also analyzed for comparison. Using nine ISSR primers, 106 bands were generated, and 89.6% of those were polymorphic. The populations from the Northwest Iberian Peninsula were clustered in three different groups, with a significant correlation between genetic and geographic distances. Gentiana lutea L. var. aurantiaca showed 19.8% private loci and demonstrated a remarkable level of genetic variation, both among populations and within populations; those populations with the highest level of isolation show the lowest genetic variation within populations. The low number of individuals, as well as the observed genetic structure of the analyzed populations makes it necessary to protect them to ensure their survival before they are too small to persist naturally.

  1. The 1001 Arabidopsis DNA Methylomes: An Important Resource for Studying Natural Genetic, Epigenetic, and Phenotypic Variation.

    PubMed

    Lang, Zhaobo; Xie, Shaojun; Zhu, Jian-Kang

    2016-11-01

    Intraspecific phenotypic diversity is controlled by natural genetic and epigenetic variation. Kawakatsu et al. recently sequenced the DNA methylomes of a global collection of over 1000 Arabidopsis accessions, and have thereby provided a comprehensive resource for studying natural genetic and epigenetic variation as well as the association of such variation with phenotypic diversity.

  2. Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

    SciTech Connect

    Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

    2004-02-25

    The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

  3. Human copy number variation and complex genetic disease.

    PubMed

    Girirajan, Santhosh; Campbell, Catarina D; Eichler, Evan E

    2011-01-01

    Copy number variants (CNVs) play an important role in human disease and population diversity. Advancements in technology have allowed for the analysis of CNVs in thousands of individuals with disease in addition to thousands of controls. These studies have identified rare CNVs associated with neuropsychiatric diseases such as autism, schizophrenia, and intellectual disability. In addition, copy number polymorphisms (CNPs) are present at higher frequencies in the population, show high diversity in copy number, sequence, and structure, and have been associated with multiple phenotypes, primarily related to immune or environmental response. However, the landscape of copy number variation still remains largely unexplored, especially for smaller CNVs and those embedded within complex regions of the human genome. An integrated approach including characterization of single nucleotide variants and CNVs in a large number of individuals with disease and normal genomes holds the promise of thoroughly elucidating the genetic basis of human disease and diversity.

  4. Genetic variation in alkaloid accumulation in leaves of Nicotiana *

    PubMed Central

    Sun, Bo; Zhang, Fen; Zhou, Guo-jun; Chu, Guo-hai; Huang, Fang-fang; Wang, Qiao-mei; Jin, Li-feng; Lin, Fu-cheng; Yang, Jun

    2013-01-01

    Alkaloids are plant secondary metabolites that are widely distributed in Nicotiana species and contribute greatly to the quality of tobacco leaves. Some alkaloids, such as nornicotine and myosmine, have adverse effects on human health. To reduce the content of harmful alkaloids in tobacco leaves through conventional breeding, a genetic study of the alkaloid variation among different genotypes is required. In this study, alkaloid profiles in leaves of five Nicotiana tabacum cultivars and Nicotiana tomentosiformis were investigated. Six alkaloids were identified from all six genotypes via gas chromatograph-mass spectrometry (GC-MS). Significant differences in alkaloid content were observed both among different leaf positions and among cultivars. The contents of nornicotine and myosmine were positively and significantly correlated (R 2=0.881), and were also separated from those of other alkaloids by clustering. Thus, the genotype plays a major role in alkaloid accumulation, indicating a high potential for manipulation of alkaloid content through traditional breeding. PMID:24302710

  5. Genetic variation in alkaloid accumulation in leaves of Nicotiana.

    PubMed

    Sun, Bo; Zhang, Fen; Zhou, Guo-jun; Chu, Guo-hai; Huang, Fang-fang; Wang, Qiao-mei; Jin, Li-feng; Lin, Fu-cheng; Yang, Jun

    2013-12-01

    Alkaloids are plant secondary metabolites that are widely distributed in Nicotiana species and contribute greatly to the quality of tobacco leaves. Some alkaloids, such as nornicotine and myosmine, have adverse effects on human health. To reduce the content of harmful alkaloids in tobacco leaves through conventional breeding, a genetic study of the alkaloid variation among different genotypes is required. In this study, alkaloid profiles in leaves of five Nicotiana tabacum cultivars and Nicotiana tomentosiformis were investigated. Six alkaloids were identified from all six genotypes via gas chromatograph-mass spectrometry (GC-MS). Significant differences in alkaloid content were observed both among different leaf positions and among cultivars. The contents of nornicotine and myosmine were positively and significantly correlated (R(2)=0.881), and were also separated from those of other alkaloids by clustering. Thus, the genotype plays a major role in alkaloid accumulation, indicating a high potential for manipulation of alkaloid content through traditional breeding.

  6. Exploiting genomics and natural genetic variation to decode macrophage enhancers

    PubMed Central

    Romanoski, Casey E.; Link, Verena M.; Heinz, Sven; Glass, Christopher K.

    2015-01-01

    The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease. PMID:26298065

  7. Independent natural genetic variation of punishment- versus relief-memory

    PubMed Central

    Appel, Mirjam; Kocabey, Samet; Savage, Sinead; König, Christian

    2016-01-01

    A painful event establishes two opponent memories: cues that are associated with pain onset are remembered negatively, whereas cues that coincide with the relief at pain offset acquire positive valence. Such punishment- versus relief-memories are conserved across species, including humans, and the balance between them is critical for adaptive behaviour with respect to pain and trauma. In the fruit fly, Drosophila melanogaster as a study case, we found that both punishment- and relief-memories display natural variation across wild-derived inbred strains, but they do not covary, suggesting a considerable level of dissociation in their genetic effectors. This provokes the question whether there may be heritable inter-individual differences in the balance between these opponent memories in man, with potential psycho-clinical implications. PMID:28003518

  8. Investigation of Genetic Variation Underlying Central Obesity amongst South Asians.

    PubMed

    Scott, William R; Zhang, Weihua; Loh, Marie; Tan, Sian-Tsung; Lehne, Benjamin; Afzal, Uzma; Peralta, Juan; Saxena, Richa; Ralhan, Sarju; Wander, Gurpreet S; Bozaoglu, Kiymet; Sanghera, Dharambir K; Elliott, Paul; Scott, James; Chambers, John C; Kooner, Jaspal S

    2016-01-01

    South Asians are 1/4 of the world's population and have increased susceptibility to central obesity and related cardiometabolic disease. Knowledge of genetic variants affecting risk of central obesity is largely based on genome-wide association studies of common SNPs in Europeans. To evaluate the contribution of DNA sequence variation to the higher levels of central obesity (defined as waist hip ratio adjusted for body mass index, WHR) among South Asians compared to Europeans we carried out: i) a genome-wide association analysis of >6M genetic variants in 10,318 South Asians with focused analysis of population-specific SNPs; ii) an exome-wide association analysis of ~250K SNPs in protein-coding regions in 2,637 South Asians; iii) a comparison of risk allele frequencies and effect sizes of 48 known WHR SNPs in 12,240 South Asians compared to Europeans. In genome-wide analyses, we found no novel associations between common genetic variants and WHR in South Asians at P<5x10-8; variants showing equivocal association with WHR (P<1x10-5) did not replicate at P<0.05 in an independent cohort of South Asians (N = 1,922) or in published, predominantly European meta-analysis data. In the targeted analyses of 122,391 population-specific SNPs we also found no associations with WHR in South Asians at P<0.05 after multiple testing correction. Exome-wide analyses showed no new associations between genetic variants and WHR in South Asians, either individually at P<1.5x10-6 or grouped by gene locus at P<2.5x10-6. At known WHR loci, risk allele frequencies were not higher in South Asians compared to Europeans (P = 0.77), while effect sizes were unexpectedly smaller in South Asians than Europeans (P<5.0x10-8). Our findings argue against an important contribution for population-specific or cosmopolitan genetic variants underlying the increased risk of central obesity in South Asians compared to Europeans.

  9. Patterns of Genetic Variation Within and Between Gibbon Species

    PubMed Central

    Kim, Sung K.; Carbone, Lucia; Becquet, Celine; Mootnick, Alan R.; de Jong, Pieter J.; Wall, Jeffrey D.

    2011-01-01

    Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5–6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ∼60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations. PMID:21368318

  10. Ecology and genetic variation of Amblyomma tonelliae in Argentina.

    PubMed

    Tarragona, E L; Mangold, A J; Mastropaolo, M; Guglielmone, A A; Nava, S

    2015-09-01

    The ecology of Amblyomma tonelliae (Ixodida: Ixodidae), including its seasonal distribution and the development periods of each stage, was investigated during a study carried out over two consecutive years in northwestern Argentina. In addition, the genetic variation of this tick was studied through analyses of 16S rDNA sequences. Amblyomma tonelliae has a 1-year lifecycle characterized by a long pre-moult period in larvae with no development of morphogenetic diapause. Larvae peak in abundance during late autumn and early winter; nymphs peak in abundance in spring, and adults do so from late spring to early summer. Amblyomma tonelliae shows a marked ecological preference for the driest areas of the Chaco ecoregion. In analyses of 16S rDNA sequences in genes from different populations of A. tonelliae, values for nucleotide diversity and the average number of nucleotide differences showed genetic diversity within this species to be low. No significant differences were found in comparisons among populations. © 2015 The Royal Entomological Society.

  11. Genetic variation of germination cold tolerance in Japanese rice germplasm

    PubMed Central

    Bosetti, Fátima; Montebelli, Camila; Novembre, Ana Dionísia L.C.; Chamma, Helena Pescarin; Pinheiro, José Baldin

    2012-01-01

    Low temperatures at the initial stages of rice development prevent fast germination and seedling establishment and may cause significant productivity losses. In order to develop rice cultivars exhibiting cold tolerance, it is necessary to investigate genetic resources, providing basic knowledge to allow the introduction of genes involved in low temperature germination ability from accessions into elite cultivars. Japanese rice accessions were evaluated at the germination under two conditions: 13°C for 28 days (cold stress) and 28°C for seven days (optimal temperature). The traits studied were coleoptile and radicle length under optimal temperature, coleoptile and radicle length under cold and percentage of the reduction in coleptile and radicle length due to low temperature. Among the accessions studied, genetic variation for traits related to germination under low temperatures was observed and accessions exhibiting adequate performance for all investigated traits were identified. The use of multivariate analysis allowed the identification of the genotypes displaying cold tolerance by smaller reductions in coleoptile and radicle lenght in the presence of cold and high vigour, by higher coleoptile and radicle growth under cold. PMID:23226080

  12. A first assessment of genetic variation in Welwitschia mirabilis Hook.

    PubMed

    Jacobson, K M; Lester, E

    2003-01-01

    Welwitschia mirabilis is a monotypic member of the family Welwitchiaceae which, along with Ephedra and Gnetum species, comprises the gymnospermous order Gnetales. While the monophyly of this order is now widely accepted, the relationship of the Gnetales to other seed plants is still contentious. Despite the unique phylogenetic position of W. mirabilis and its extraordinary physiological and anatomical adaptations, little is known about the plant's phylogeny or its current distribution in isolated locations throughout the Namib Desert. As a preliminary step in the design of an more extensive phylogeographic study, we analyzed 37 random amplified polymorphic DNA (RAPD) loci from 59 plants distributed among five sites separated by distances of 6-440 km. Cluster analysis and analysis of molecular variance (AMOVA) revealed significant levels of variation within and between populations and little evidence of inbreeding. Genetic differences between populations reflect the geographic distances separating them. Three of the populations formed discernable genetic clusters, suggesting that little gene flow occurs between populations separated by > or = 18 km. In contrast, gene flow is occurring between two populations separated by only 6 km, supporting previous observations that pollen dispersal is primarily local and that seeds are not readily wind-born over the large distances separating most W. mirabilis populations. As a working hypothesis, we propose that W. mirabilis had a continuous distribution across its current range as much as 105 million years ago, and that as a consequence of subsequent drying trends and physical disturbance, populations became progressively isolated, accounting for their current distribution.

  13. Genetic variation in the dopamine pathway and smoking cessation.

    PubMed

    David, Sean P; Munafò, Marcus R

    2008-09-01

    Twin and family studies have established that genetic factors account for much of the variation in tobacco dependence. Therefore, identification of genetic variants predictive of successful smoking cessation has implications for the future prospect of personalized smoking cessation therapies. Converging data implicate the dopamine pathway as an important neural substrate for tobacco dependence. Several candidate genes within the dopamine pathway (e.g., DRD2 and COMT) have been reported to be associated with the efficacy of bupropion and nicotine replacement therapy, and others (e.g., SLC6A3 and DRD4) have been reported to be associated with smoking cessation independent of pharmacotherapy. However, few of these candidate genes are present within regions of suggestive or significant linkage or overlap with genome-wide linkage or association studies of tobacco dependence or smoking cessation. Future studies should seek to replicate genome-wide association analyses with individual-level genotyping, and use better-defined smoking cessation phenotypes. Once robust evidence for association is established, which may take several more years, further research into the likely cost-effectiveness, feasibility and acceptability of personalized medicine for smoking cessation will be necessary before it can be translated into practice.

  14. Floral variation and floral genetics in basal angiosperms.

    PubMed

    Soltis, Pamela S; Brockington, Samuel F; Yoo, Mi-Jeong; Piedrahita, Ana; Latvis, Maribeth; Moore, Michael J; Chanderbali, Andre S; Soltis, Douglas E

    2009-01-01

    Recent advances in phylogeny reconstruction and floral genetics set the stage for new investigations of the origin and diversification of the flower. We review the current state of angiosperm phylogeny, with an emphasis on basal lineages. With the surprising inclusion of Hydatellaceae with Nymphaeales, recent studies support the topology of Amborella sister to all other extant angiosperms, with Nymphaeales and then Austrobaileyales as subsequent sisters to all remaining angiosperms. Notable modifications from most recent analyses are the sister relationships of Chloranthaceae with the magnoliids and of Ceratophyllaceae with eudicots. We review "trends" in floral morphology and contrast historical, intuitive interpretations with explicit character-state reconstructions using molecular-based trees, focusing on (1) the size, number, and organization of floral organs; (2) the evolution of the perianth; (3) floral symmetry; and (4) floral synorganization. We provide summaries of those genes known to affect floral features that contribute to much of floral diversity. Although most floral genes have not been investigated outside of a few model systems, sufficient information is emerging to identify candidate genes for testing specific hypotheses in nonmodel plants. We conclude with a set of evo-devo case studies in which floral genetics have been linked to variation in floral morphology.

  15. Patterns of genetic variation within and between Gibbon species.

    PubMed

    Kim, Sung K; Carbone, Lucia; Becquet, Celine; Mootnick, Alan R; Li, David Jiang; de Jong, Pieter J; Wall, Jeffrey D

    2011-08-01

    Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.

  16. Genetic variation for egg production, egg quality and bone strength in selected and traditional breeds of laying fowl.

    PubMed

    Hocking, P M; Bain, M; Channing, C E; Fleming, R; Wilson, S

    2003-07-01

    1. A multi-breed experiment was conducted with 25 commercial and traditional lines of laying fowl to determine the extent of between-breed genetic variation for adult body weight, sexual maturity, rate of lay, egg weight and egg composition to 55 weeks of age. The genetic variability for bone strength and eggshell strength was determined at 55 weeks of age and a comparison of commercially selected and traditional breeds was performed. 2. The proportion of the total variation that was associated with breed or line of origin was high (> 0.8) for body weight, sexual maturity and shell colour; moderately high (0.4 to 0.7) for rate of lay, early and late egg weight, weights of egg yolk, albumen and shell at 55 weeks; and low (< 0.4) for egg weight at 42 to 45 weeks, albumen quality and the number of egg inclusions. 3. There were no detectable differences between breed within category (traditional and commercial lines) for rate of lay, and estimates of breed variation for egg weight and egg components were substantially decreased within category compared with the overall analysis. 4. Commercial lines displayed earlier sexual maturity, greater rates and persistency of lay, and higher egg weights at earlier (32 to 35 weeks) and later (52 to 55 weeks) ages. At 55 weeks, the larger eggs from commercial birds contained more albumen of higher quality and paler yolks of similar weight to those from traditional breeds. The relative weight of the eggshell was similar in both categories. 5. There was considerable genetic variation between commercial lines for bone density and a moderate proportion of genetic variability for bone strength. Commercial lines had very weak bones compared with traditional lines but there was relatively little genetic variation for eggshell strength. The results suggest that eggshell quality is maintained in genetically selected lines at the expense of bone strength and bone radiographic density.

  17. Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops.

    PubMed

    Yan, Juan; Song, Zhihong; Xu, Qin; Kang, Lifang; Zhu, Caiyun; Xing, Shilai; Liu, Wei; Greimler, Josef; Züst, Tobias; Li, Jianqiang; Sang, Tao

    2017-08-22

    The use of transcriptome data in the study of the population genetics of a species can capture faint signals of both genetic variation and expression variation and can provide a broad picture of a species' genomic response to environmental conditions. In this study, we characterized the genetic and expression diversity of Miscanthus lutarioriparius by comparing more than 16,225 transcripts obtained from 78 individuals, belonging to 10 populations distributed across the species' entire geographic range. We only observed a low level of nucleotide diversity (π = 0.000434) among the transcriptome data of these populations, which is consistent with highly conserved sequences of functional elements and protein-coding genes captured with this method. Tests of population divergence using the transcriptome data were consistent with previous microsatellite data but proved to be more sensitive, particularly if gene expression variation was considered as well. For example, the analysis of expression data showed that genes involved in photosynthetic processes and responses to temperature or reactive oxygen species stimuli were significantly enriched in certain populations. This differential gene expression was primarily observed among populations and not within populations. Interestingly, nucleotide diversity was significantly negatively correlated with expression diversity within populations, while this correlation was positive among populations. This suggests that genetic and expression variation play separate roles in adaptation and population persistence. Combining analyses of genetic and gene expression variation represents a promising approach for studying the population genetics of wild species and may uncover both adaptive and nonadaptive processes. © 2017 John Wiley & Sons Ltd.

  18. Genetic and phenotypic intra-species variation in Candida albicans

    PubMed Central

    Hirakawa, Matthew P.; Martinez, Diego A.; Sakthikumar, Sharadha; Anderson, Matthew Z.; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M.; Greenberg, Joshua M.; Berman, Judith

    2015-01-01

    Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity. PMID:25504520

  19. Transformation of natural genetic variation into Haemophilus influenzae genomes.

    PubMed

    Mell, Joshua Chang; Shumilina, Svetlana; Hall, Ira M; Redfield, Rosemary J

    2011-07-01

    Many bacteria are able to efficiently bind and take up double-stranded DNA fragments, and the resulting natural transformation shapes bacterial genomes, transmits antibiotic resistance, and allows escape from immune surveillance. The genomes of many competent pathogens show evidence of extensive historical recombination between lineages, but the actual recombination events have not been well characterized. We used DNA from a clinical isolate of Haemophilus influenzae to transform competent cells of a laboratory strain. To identify which of the ~40,000 polymorphic differences had recombined into the genomes of four transformed clones, their genomes and their donor and recipient parents were deep sequenced to high coverage. Each clone was found to contain ~1000 donor polymorphisms in 3-6 contiguous runs (8.1±4.5 kb in length) that collectively comprised ~1-3% of each transformed chromosome. Seven donor-specific insertions and deletions were also acquired as parts of larger donor segments, but the presence of other structural variation flanking 12 of 32 recombination breakpoints suggested that these often disrupt the progress of recombination events. This is the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, connecting experimental studies of transformation with the high levels of natural genetic variation found in isolates of the same species.

  20. Genetic variation in aggregation behaviour and interacting phenotypes in Drosophila

    PubMed Central

    Philippe, Anne-Sophie; Jeanson, Raphael; Pasquaretta, Cristian; Rebaudo, Francois; Sueur, Cedric; Mery, Frederic

    2016-01-01

    Aggregation behaviour is the tendency for animals to group together, which may have important consequences on individual fitness. We used a combination of experimental and simulation approaches to study how genetic variation and social environment interact to influence aggregation dynamics in Drosophila. To do this, we used two different natural lines of Drosophila that arise from a polymorphism in the foraging gene (rovers and sitters). We placed groups of flies in a heated arena. Flies could freely move towards one of two small, cooler refuge areas. In groups of the same strain, sitters had a greater tendency to aggregate. The observed behavioural variation was based on only two parameters: the probability of entering a refuge and the likelihood of choosing a refuge based on the number of individuals present. We then directly addressed how different strains interact by mixing rovers and sitters within a group. Aggregation behaviour of each line was strongly affected by the presence of the other strain, without changing the decision rules used by each. Individuals obeying local rules shaped complex group dynamics via a constant feedback loop between the individual and the group. This study could help to identify the circumstances under which particular group compositions may improve individual fitness through underlying aggregation mechanisms under specific environmental conditions. PMID:27009219

  1. Genetic and phenotypic intra-species variation in Candida albicans.

    PubMed

    Hirakawa, Matthew P; Martinez, Diego A; Sakthikumar, Sharadha; Anderson, Matthew Z; Berlin, Aaron; Gujja, Sharvari; Zeng, Qiandong; Zisson, Ethan; Wang, Joshua M; Greenberg, Joshua M; Berman, Judith; Bennett, Richard J; Cuomo, Christina A

    2015-03-01

    Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity.

  2. Genetic Variation among Endosymbionts of Widely Distributed Vestimentiferan Tubeworms

    PubMed Central

    Di Meo, Carol A.; Wilbur, Ami E.; Holben, William E.; Feldman, Robert A.; Vrijenhoek, Robert C.; Cary, S. Craig

    2000-01-01

    Vestimentiferan tubeworms thriving in sulfidic deep-sea hydrothermal vents and cold seeps are constrained by their nutritional reliance on chemoautotrophic endosymbionts. In a recent phylogenetic study using 16S ribosomal DNA, we found that endosymbionts from vent and seep habitats form two distinct clades with little variation within each clade. In the present study, we used two different approaches to assess the genetic variation among biogeographically distinct vestimentiferan symbionts. DNA sequences were obtained for the noncoding, internal transcribed spacer (ITS) regions of the rRNA operons of symbionts associated with six different genera of vestimentiferan tubeworms. ITS sequences from endosymbionts of host genera collected from different habitats and widely distributed vent sites were surprisingly conserved. Because the ITS region was not sufficient for distinguishing endosymbionts from different habitats or locations, we used a DNA fingerprinting technique, repetitive-extragenic-palindrome PCR (REP-PCR), to reveal differences in the distribution of repetitive sequences in the genomes of the bacterial endosymbionts. Most of the endosymbionts displayed unique REP-PCR patterns. A cladogram generated from these fingerprints reflected relationships that may be influenced by a variety of factors, including host genera, geographic location, and bottom type. PMID:10653731

  3. Ethnic variation of genetic (idiopathic) generalized epilepsy in Malaysia.

    PubMed

    Lim, Kheng Seang; Ng, Ching Ching; Chan, Chung Kin; Foo, Wee Shean; Low, Joyce Siew Yong; Tan, Chong Tin

    2017-02-01

    Ethnic variation in epilepsy classification was reported in the Epilepsy Phenome/Genome Project. This study aimed to determine the ethnic variation in the prevalence of genetic (idiopathic) generalized epilepsy (GGE) and GGE with family history in a multi-ethnic Asian population in Malaysia. In this cross-sectional study, 392 patients with a clinical diagnosis of GGE were recruited in the neurology outpatient clinic, University of Malaya Medical Centre (UMMC), from January 2011 till April 2016. In our epilepsy cohort (n=2100), 18.7% were diagnosed to have GGE. Of those, 28.6% >(N=112) had family history of epilepsy with a mean age of seizure onset of 16.5 years old, and 42.0% had myoclonic seizures (N=47). The lifetime prevalence of epilepsy among first-degree relative of those with GGE and positive family history was 15.0%. Analysis according to ethnicity showed that Malaysian Chinese had the lowest percentage of GGE among those with epilepsy (12.3%), as compared with Indian and Malay (25.3% and 21.3%, p<0.001). In addition, 32.1% of these Indian patients with GGE had positive family history, which is more than the Malay (26.4%) and Chinese (27.5%) ethnic groups. Consanguineous marriage was noted in 5 Indian families with positive family history (9.6%). There was ethnic variation in the prevalence of GGE, whereby the Malaysian Chinese had the lowest percentage of GGE as compared with Indian and Malay. A substantial proportion of GGE had positive family history among the three ethnics groups. Copyright © 2016 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  4. Molecular and structural analysis of genetic variations in congenital cataract

    PubMed Central

    Kumar, Manoj; Agarwal, Tushar; Kaur, Punit; Kumar, Manoj; Khokhar,, Sudarshan

    2013-01-01

    Objective To determine the relative contributions of mutations in congenital cataract cases in an Indian population by systematic screening of genes associated with cataract. Methods We enrolled 100 congenital cataract cases presenting at the Dr. R. P. Centre for Ophthalmic Sciences, a tertiary research and referral hospital (AIIMS, New Delhi, India). Crystallin, alpha A (CRYAA), CRYAB, CRYGs, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, beaded filament structural protein 1 (BFSP1), gap function protein, alpha 3 (GJA3), GJA8, and heat shock transcription factor 4 gene genes were amplified. Protein structure differences analysis was performed using Discovery Studio (DS) 2.0. Results The mean age of the patients was 17.45±16.51 months, and the age of onset was 1.618±0.7181 months. Sequencing analysis of 14 genes identified 18 nucleotide variations. Fourteen variations were found in the crystallin genes, one in Cx-46 (GJA3), and three in BFSP1. Conclusions Congenital cataract shows marked clinical and genetic heterogeneity. Five nucleotide variations (CRYBA4:p.Y67N, CRYBB1:p.D85N, CRYBB1:p.E75K, CRYBB1:p.E155K, and GJA3:p.M1V) were predicted to be pathogenic. Variants in other genes might also be involved in maintaining lens development, growth, and transparency. The study confirms that the crystallin beta cluster on chromosome 22, Cx-46, and BFSP1 plays a major role in maintaining lens transparency. This study also expands the mutation spectrum of the genes associated with congenital cataract. PMID:24319337

  5. Selection of genetic variants of simian immunodeficiency virus in persistently infected rhesus monkeys.

    PubMed Central

    Burns, D P; Desrosiers, R C

    1991-01-01

    Genetic and antigenic variation may be one means by which lentiviruses that cause AIDS avoid elimination by host immune responses. Genetic variation in the envelope gene (env) was studied by comparing the nucleotide sequences of 27 clones obtained from two rhesus monkeys infected with molecularly cloned simian immunodeficiency virus. All 27 clones differed from each other and differed from the input clone in the gp120 (SU) portion of the envelope gene. Nucleotide substitutions were shown to accumulate with time at an average rate of 8.5 per 1,000 per year in SU. Surprisingly, the majority of nucleotide substitutions (81%) resulted in amino acid changes. Variation in SU was not random but occurred predominantly in five discrete regions. Within these variable regions, a remarkable 98% of the nucleotide substitutions changed the amino acid. These results demonstrate that extensive sequence variability accumulates in vivo after infection with molecularly cloned virus and that selection occurs in vivo for changes in distinct variable regions in env. PMID:2002545

  6. Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait specificity in Drosophila melanogaster.

    PubMed

    Takahashi, Kazuo H

    2015-11-01

    Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster and then investigated the trait specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist.

  7. Impact of genetic variation on synaptic protein levels in genetically diverse mice.

    PubMed

    Loos, Maarten; Li, Ka Wan; van der Schors, Roel; Gouwenberg, Yvonne; van der Loo, Rolinka; Williams, Robert W; Smit, August B; Spijker, Sabine

    2016-04-01

    The relative abundance of synaptic proteins shapes protein complex formation and is essential for synapse function and behavioral fitness. Here, we have used a panel of highly diverse inbred strains of mice-NOD/LtJ, A/J, 129S1/SvImJ, FVB/NJ, C57BL/6J, WSB/EiJ, PWK/PhJ, and CAST/EiJ-to quantify the effects of genetic variation on the synaptic proteome between strains. Using iTRAQ-based quantitative proteome analyses, we detected significant differences in ∼20% of 400 core synaptic proteins. Surprisingly, the differentially abundant proteins showed a modest range of variation across strains, averaging about 1.3-fold. Analysis of protein abundance covariation across the eight strains identified known protein-protein relations (proteins of Arp2/3 complex), as well as novel relations (e.g. Dlg family, Fscn1). Moreover, covariation of synaptic proteins was substantially tighter (∼fourfold more dense than chance level) than corresponding networks of synaptic transcripts (∼twofold more dense than chance). The tight stoichiometry and coherent synaptic protein covariation networks suggest more intense evolutionary selection at this level of molecular organization. In conclusion, genetic diversity in the mouse genome differentially affects the transcriptome and proteome, and only partially penetrates the synaptic proteome. Protein abundance correlation analyses in genetically divergent strains can complement protein-protein interaction network analyses, to provide insight into protein interactomes.

  8. Population Genetics of Euphydryas Butterflies. I. Genetic Variation and the Neutrality Hypothesis

    PubMed Central

    McKechnie, Stephen W.; Ehrlich, Paul R.; White, Raymond R.

    1975-01-01

    Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation presisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents. PMID:1205135

  9. Genetic Variations in SLCO Transporter Genes Contributing to Racial Disparity in Aggressiveness of Prostate Cancer

    DTIC Science & Technology

    2016-10-01

    AWARD NUMBER: W81XWH-14-1-0453 TITLE: Genetic Variations in SLCO Transporter Genes Contributing to Racial Disparity in Aggressiveness of...Sep 2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Genetic Variations in SLCO Transporter Genes Contributing to Racial Disparity in Aggressiveness...expected to (1) identify genetic variations in the genes of androgen transporters that are associated with the racial differences in prostate cancer

  10. Tracing Technological Development Trajectories: A Genetic Knowledge Persistence-Based Main Path Approach.

    PubMed

    Park, Hyunseok; Magee, Christopher L

    2017-01-01

    The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological trajectories but nonetheless have some limitations. They have high potential to miss some dominant patents from the identified main paths; nonetheless, the high network complexity of their main paths makes qualitative tracing of trajectories problematic. The proposed method searches backward and forward paths from the high-persistence patents which are identified based on a standard genetic knowledge persistence algorithm. We tested the new method by applying it to the desalination and the solar photovoltaic domains and compared the results to output from the same domains using a prior method. The empirical results show that the proposed method can dramatically reduce network complexity without missing any dominantly important patents. The main paths identified by our approach for two test cases are almost 10x less complex than the main paths identified by the existing approach. The proposed approach identifies all dominantly important patents on the main paths, but the main paths identified by the existing approach miss about 20% of dominantly important patents.

  11. Tracing Technological Development Trajectories: A Genetic Knowledge Persistence-Based Main Path Approach

    PubMed Central

    2017-01-01

    The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological trajectories but nonetheless have some limitations. They have high potential to miss some dominant patents from the identified main paths; nonetheless, the high network complexity of their main paths makes qualitative tracing of trajectories problematic. The proposed method searches backward and forward paths from the high-persistence patents which are identified based on a standard genetic knowledge persistence algorithm. We tested the new method by applying it to the desalination and the solar photovoltaic domains and compared the results to output from the same domains using a prior method. The empirical results show that the proposed method can dramatically reduce network complexity without missing any dominantly important patents. The main paths identified by our approach for two test cases are almost 10x less complex than the main paths identified by the existing approach. The proposed approach identifies all dominantly important patents on the main paths, but the main paths identified by the existing approach miss about 20% of dominantly important patents. PMID:28135304

  12. Quantifying how fine-grained environmental heterogeneity and genetic variation affect demography in an annual plant population.

    PubMed

    Latimer, Andrew M; Jacobs, Brooke S

    2012-11-01

    The ability of plant species to colonize new habitats and persist in changing environments depends on their ability to respond plastically to environmental variation and on the presence of genetic variation, thus allowing adaptation to new conditions. For invasive species in particular, the relationship between phenotypic trait expression, demography, and the quantitative genetic variation that is available to respond to selection are likely to be important determinants of the successful establishment and persistence of populations. However, the magnitude and sources of individual demographic variation in exotic plant populations remain poorly understood. How important is plasticity versus adaptability in populations of invasive species? Among environmental factors, is temperature, soil nutrients, or competition most influential, and at what scales and life stages do they affect the plants? To investigate these questions we planted seeds of the exotic annual plant Erodium brachycarpum into typical pasture habitat in a spatially nested design. Seeds were drawn from 30 inbred lines to enable quantification of genetic effects. Despite a positive population growth rate, a few plants (0.1 %) produced >50 % of the seeds, suggesting a low effective population size. Emergence and early growth varied by genotype, but as in previous studies on native plants, environmental effects greatly exceeded genetic effects, and survival was unrelated to genotype. Environmental influences shifted from microscale soil compaction and litter depth at emergence through to larger-scale soil nutrient gradients during growth and to competition during later survival and seed production. Temperature had no effect. Most demographic rates were positively correlated, but emergence was negatively correlated with other rates.

  13. Spatio-temporal dynamics of genetic variation in the Iberian lynx along its path to extinction reconstructed with ancient DNA.

    PubMed

    Casas-Marce, Mireia; Marmesat, Elena; Soriano, Laura; Martínez-Cruz, Begoña; Lucena, María; Nocete, Francisco; Rodríguez-Hidalgo, Antonio; Canals, Antoni; Nadal, Jordi; Detry, Cleia; Bernáldez-Sánchez, Eloísa; Fernández-Rodríguez, Carlos; Pérez-Ripoll, Manuel; Stiller, Mathias; Hofreiter, Michael; Rodríguez, Alejandro; Revilla, Eloy; Delibes, Miguel; Godoy, José A

    2017-08-29

    There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity amongst other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. Our study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Genetic rescue persists beyond first-generation outbreeding in small populations of a rare plant.

    PubMed

    Willi, Yvonne; van Kleunen, Mark; Dietrich, Stefan; Fischer, Markus

    2007-09-22

    Habitat fragmentation commonly causes genetic problems and reduced fitness when populations become small. Stocking small populations with individuals from other populations may enrich genetic variation and alleviate inbreeding, but such artificial gene flow is not commonly used in conservation owing to potential outbreeding depression. We addressed the role of long-term population size, genetic distance between populations and test environment for the performance of two generations of offspring from between-population crosses of the locally rare plant Ranunculus reptans L. Interpopulation outbreeding positively affected an aggregate measure of fitness, and the fitness superiority of interpopulation hybrids was maintained in the second offspring (F2) generation. Small populations benefited more strongly from interpopulation outbreeding. Genetic distance between crossed populations in neutral markers or quantitative characters was not important. These results were consistent under near-natural competition-free and competitive conditions. We conclude that the benefits of interpopulation outbreeding are likely to outweigh potential drawbacks, especially for populations that suffer from inbreeding.

  15. Dispersal and persistence of genetically modified oilseed rape around Japanese harbors.

    PubMed

    Kawata, Masaharu; Murakami, Kikuko; Ishikawa, Toyohisa

    2009-03-01

    The possibility of gene transfer from genetically modified oilseed rape (OSR) to its cultivated or wild relatives is of concern since its commercial cultivation, because of its potential weediness and impact on the environment. Introgression of modified genes can affect conservation of agricultural crops, because there are many cultivars and wild Brassicaceae that may cross with genetically modified OSR (Brassica napus) in Japan. Japan imports more than 2 million tons of OSR a year from Canada and other countries. Since volunteers of GM OSR were found around harbors in 2004, a lot of feral GM OSR was discovered in Japan. To consider the way how to keep domestic Brassicaceae from GM contamination, we surveyed and analyzed the dispersal and persistence of GM OSR around Japanese harbors. We present the cause and abundance of GM OSR in Japan by this paper. Survey of the feral OSR was performed several times a year at different seasons when domestic OSR either grows or does not around port areas. Detection of herbicide tolerance in feral B. napus was done by test papers that cross react with the modified gene product. Two kinds of herbicide tolerance (glyphosate and glufosinate) were tested. The feral B. napus were discovered around all 13 harbors that import rapeseeds from foreign countries. Genetically modified, herbicide-tolerant OSR were frequently found in the surveyed populations. Two kinds of herbicide-tolerant OSR (glyphosate- and glufosinate-tolerant) were discovered in a natural condition 40 km from port to an oil factory where 60,000 tons of OSR seed are processed a year. The cause of voluntary growth of OSR is seed spillage during transportation by trucks from harbors to oil factories and other processing facilities. Some of the feral OSR growing along the roadsides of transport paths exhibited perennial growth spilling their seeds around the places. Alteration of the generation of feral GM OSR was discovered for the first time in Japan as a result of this

  16. Foliar Nitrogen and Potassium Variation in Cottonwood as Affected by Genetic and Site Factors

    Treesearch

    James B. Baker; W. K. Randall

    1975-01-01

    Genetic and soil factors accounted for 49 percent of the variation in foliar N and 60 percent of the variation in foliar K among four good and four poor cottonwood clones grown on productive and unproductive soils in Mississippi. Variation in foliar N was associated primarily with the clone X soil interaction; variation in foliar K was related chiefly to clonal...

  17. Genetic and phenotypic variation of West Nile virus in New York, 2000-2003.

    PubMed

    Ebel, Gregory D; Carricaburu, Justin; Young, David; Bernard, Kristen A; Kramer, Laura D

    2004-10-01

    West Nile virus (WNV) strains circulating during the first five years of WNV transmission in New York were collected, partial nucleotide sequences were determined, and in vitro and in vivo phenotypic analyses of selected strains were undertaken to determine whether observed increases in the intensity of enzootic and epidemic transmission in New York State during 2002 and 2003 were associated with viral genetic changes. Functionally diverse regions of the WNV genome were also compared to determine whether some regions may be more or less variable than others. The complete envelope coding regions of 67 strains and fragments of the nonstructural protein 5 (NS5) and 3' noncoding regions of 39 strains collected during 2002 and 2003 were examined. West Nile virus in New York remains relatively genetically homogeneous. Viral genetic diversity was greater in 2002 and 2003 at both the nucleotide and amino acid levels than in previous years due to the emergence of a new WNV genotype in 2002. This genotype persisted and became dominant in 2003. Envelope and NS5 coding regions were approximately two-fold more likely than the 3' untranslated region to contain nucleotide substitutions, and the envelope region was approximately three-fold more likely to contain amino acid substitutions than the NS5 region. Variation was noted in in vivo mosquito transmission assays, but not in in vitro growth studies. Strains belonging to the epizootiologically dominant clade were transmitted after approximately two fewer days of extrinsic incubation, providing a possible mechanism for the dominance of this clade. The observed increase in the intensity of WNV transmission beginning in 2002 was associated with an increase in viral genetic diversity that was the result of the emergence of an additional phylogenetic clade. This genotype seems to possess an advantage over previously recognized WNV strains in mosquito transmission phenotype.

  18. SOCIAL ADVERSITY, GENETIC VARIATION, STREET CODE, AND AGGRESSION: A GENETICLLY INFORMED MODEL OF VIOLENT BEHAVIOR

    PubMed Central

    Simons, Ronald L.; Lei, Man Kit; Stewart, Eric A.; Brody, Gene H.; Beach, Steven R. H.; Philibert, Robert A.; Gibbons, Frederick X.

    2011-01-01

    Elijah Anderson (1997, 1999) argues that exposure to extreme community disadvantage, residing in “street” families, and persistent discrimination encourage many African Americans to develop an oppositional culture that he labels the “code of the street.” Importantly, while the adverse conditions described by Anderson increase the probability of adopting the code of the street, most of those exposed to these adverse conditions do not do so. The present study examines the extent to which genetic variation accounts for these differences. Although the diathesis-stress model guides most genetically informed behavior science, the present study investigates hypotheses derived from the differential susceptibility perspective (Belsky & Pluess, 2009). This model posits that some people are genetically predisposed to be more susceptible to environmental influence than others. An important implication of the model is that those persons most vulnerable to adverse social environments are the same ones who reap the most benefit from environmental support. Using longitudinal data from a sample of several hundred African American males, we examined the manner in which variants in three genes - 5-HTT, DRD4, and MAOA - modulate the effect of community and family adversity on adoption of the street code and aggression. We found strong support for the differential susceptibility perspective. When the social environment was adverse, individuals with these genetic variants manifested more commitment to the street code and aggression than those with other genotypes, whereas when adversity was low they demonstrated less commitment to the street code and aggression than those with other genotypes. PMID:23785260

  19. Human Papillomavirus 18 Genetic Variation and Cervical Cancer Risk Worldwide

    PubMed Central

    Chen, Alyce A.; Gheit, Tarik; Franceschi, Silvia

    2015-01-01

    ABSTRACT Human papillomavirus 18 (HPV18) is the second most carcinogenic HPV type, after HPV16, and it accounts for approximately 12% of squamous cell carcinoma (SCC) as well as 37% of adenocarcinoma (ADC) of the cervix worldwide. We aimed to evaluate the worldwide diversity and carcinogenicity of HPV18 genetic variants by sequencing the entire long control region (LCR) and the E6 open reading frame of 711 HPV18-positive cervical samples from 39 countries, taking advantage of the International Agency for Research on Cancer biobank. A total of 209 unique HPV18 sequence variants were identified that formed three phylogenetic lineages (A, B, and C). A and B lineages each divided into four sublineages, including a newly identified candidate B4 sublineage. The distribution of lineages varied by geographical region, with B and C lineages found principally in Africa. HPV18 (sub)lineages were compared between 453 cancer cases and 236 controls, as well as between 81 ADC and 160 matched SCC cases. In region-stratified analyses, there were no significant differences in the distribution of HPV18 variant lineages between cervical cancer cases and controls or between ADC and SCC. In conclusion, our findings do not support the role of HPV18 (sub)lineages for discriminating cancer risk or explaining why HPV18 is more strongly linked with ADC than SCC. IMPORTANCE This is the largest and most geographically/ethnically diverse study of the genetic variation of HPV18 to date, providing a comprehensive reference for phylogenetic classification of HPV18 sublineages for epidemiological and biological studies. PMID:26269181

  20. Ethnic differences in cancer risk resulting from genetic variation.

    PubMed

    Neuhausen, S L

    1999-12-01

    Ethnic differences in cancer incidence and mortality exist and are probably the result of genetic and epidemiological risk factors. Genetic differences caused by founder mutations are reviewed, with special emphasis on mutations in BRCA1 and BRCA2. Germline mutations in cancer susceptibility genes have been identified in individuals of all races and ethnic groups. Differences among ethnic groups for cancer risks have been recognized, and a proportion of the differences may be the result of founder mutations within these genes. The BRCA2 999del5 mutation in Iceland and the three BRCA1 and BRCA2 mutations in Ashkenazic Jews have been well characterized and were easy to study because the patient population and anonymous samples were readily available and ethnicity was known. Mutations in BRCA1 and BRCA2 probably account for approximately 3 to 10% of breast cancer in the general population and a much higher proportion in those with a strong family history of breast and ovarian cancers and in those of Ashkenazic Jewish descent. However, no overall increased risk of breast or ovarian cancers exists among Ashkenazic Jewish women compared with non-Jewish Caucasians. Some ethnic variation in cancer risk may be explained by founder mutations identified in cancer-predisposing genes. Knowledge acquired by studying the effect of a single mutation in a well defined population may be applied to larger, more heterogeneous populations. Individuals from all racial and ethnic groups carry deleterious mutations. Mutations are simply easier to find and characterize when identified in a specific ethnic group.

  1. Mine, Yours, Ours? Sharing Data on Human Genetic Variation

    PubMed Central

    Montinaro, Francesco; Capocasa, Marco; Sanna, Emanuele; Bisol, Giovanni Destro

    2012-01-01

    The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing. PMID:22679483

  2. Intersubtype Genetic Variation of HIV-1 Tat Exon 1.

    PubMed

    Roy, Chandra Nath; Khandaker, Irona; Oshitani, Hitoshi

    2015-06-01

    HIV-1 Tat is a regulatory protein that plays a pivotal role in viral transcription and replication. Our study aims to investigate the genetic variation of Tat exon 1 in all subtypes of HIV-1: A, B, C, D, F, G, H, J, and K. We performed phylogenetic, mutation, and selection pressure analyses on a total of 1,179 sequences of different subtypes of HIV-1 Tat obtained from the Los Alamos National Laboratory (LANL). The mean nucleotide divergences (%) among the analyzed sequences of subtypes A, B, C, D, F, G, H, J, and K were 88, 89, 90, 88, 86, 89, 88, 97, and 97, respectively. We revealed that subtype B evolved relatively faster than other subtypes. The second and fifth domains were found comparatively more variable among all subtypes. Site-by-site tests of positive selection revealed that several positions in all subtypes were under significant positive selection. Positively selected sites were found in the acidic domain at positions 3, 4, and 19, in the cysteine-rich domains at positions 24, 29, 32, and 36, in the core domain at position 40, and in the basic domain for the rest of the positions for all subtypes. Positions 58 and 68 in the basic domain were positively selected in subtypes A, B, C and B, C, F, respectively. We also observed high variability within positively selected sites in amino acid positions. Our study findings on HIV-1 Tat genetic variability may contribute to a better understanding of HIV-1 evolution as well as to the development of effective Tat-targeted therapeutics and vaccines.

  3. Genetic variation and recurrent parasitaemia in Peruvian Plasmodium vivax populations

    PubMed Central

    2014-01-01

    Background Plasmodium vivax is a predominant species of malaria in parts of South America and there is increasing resistance to drugs to treat infections by P. vivax. The existence of latent hypnozoites further complicates the ability to classify recurrent infections as treatment failures due to relapse, recrudescence of hyponozoites or re-infections. Antigen loci are putatively under natural selection and may not be an optimal molecular marker to define parasite haplotypes in paired samples. Putatively neutral microsatellite loci, however, offer an assessment of neutral haplotypes. The objective here was to assess the utility of neutral microsatellite loci to reconcile cases of recurrent parasitaemia in Amazonian P. vivax populations in Peru. Methods Patient blood samples were collected from three locations in or around Iquitos in the Peruvian Amazon. Five putatively neutral microsatellite loci were characterized from 445 samples to ascertain the within and amongst population variation. A total of 30 day 0 and day of recurrent parasitaemia samples were characterized at microsatellite loci and five polymorphic antigen loci for haplotype classification. Results The genetic diversity at microsatellite loci was consistent with neutral levels of variation measured in other South American P. vivax populations. Results between antigen and microsatellite loci for the 30 day 0 and day of recurrent parasitaemia samples were the same for 80% of the pairs. The majority of non-concordant results were the result of differing alleles at microsatellite loci. This analysis estimates that 90% of the paired samples with the same microsatellite haplotype are unlikely to be due to a new infection. Conclusions A population-level approach was used to yield a better estimate of the probability of a new infection versus relapse or recrudescence of homologous hypnozoites; hypnozoite activation was common for this cohort. Population studies are critical with the evaluation of genetic

  4. The genomic signature of parallel adaptation from shared genetic variation

    PubMed Central

    Roesti, Marius; Gavrilets, Sergey; Hendry, Andrew P.; Salzburger, Walter; Berner, Daniel

    2014-01-01

    Parallel adaptation is common and may often occur from shared genetic variation, but the genomic consequences of this process remain poorly understood. We first use individual-based simulations to demonstrate that comparisons among populations adapted in parallel from shared variation reveal a characteristic genomic signature around a selected locus: a low divergence valley centered at the locus and flanked by twin peaks of high divergence. This signature is initiated by the hitchhiking of haplotype tracts differing among derived populations in the broader neighborhood of the selected locus (driving the high divergence twin peaks) and shared haplotype tracts in the tight neighborhood of the locus (driving the low divergence valley). This initial hitchhiking signature is reinforced over time because the selected locus acts as a barrier to gene flow from the source to the derived populations, thus promoting divergence by drift in its close neighborhood. We next empirically confirm the peak-valley-peak signature by combining targeted and RAD sequence data at three candidate adaptation genes in multiple marine (source) and freshwater (derived) populations of threespine stickleback. Finally, we use a genome-wide screen for the peak-valley-peak signature to discover additional genome regions involved in parallel marine-freshwater divergence. Our findings offer a new explanation for heterogeneous genomic divergence and thus challenge the standard view that peaks in population divergence harbor divergently selected loci, and that low-divergence regions result from balancing selection or localized introgression. We anticipate that genome scans for peak-valley-peak divergence signatures will promote the discovery of adaptation genes in other organisms. PMID:24635356

  5. Impact of Genetic Variation in SORCS1 on Memory Retention

    PubMed Central

    Reitz, Christiane; Lee, Joseph H.; Rogers, Robert S.; Mayeux, Richard

    2011-01-01

    Objective We previously reported that genetic variants in SORCS1 increase the risk of AD, that over-expression of SorCS1 reduces γ-secretase activity and Aβ levels, and that SorCS1 suppression increases γ-secretase processing of APP and Aβ levels. We now explored the effect of variation in SORCS1 on memory. Methods We explored associations between SORCS1-SNPs and memory retention in the NIA-LOAD case control dataset (162 cases,670 controls) and a cohort of Caribbean Hispanics (549 cases,544 controls) using single marker and haplotype analyses. Results Three SNPs in intron 1, were associated with memory retention in the NIA-LOAD dataset or the Caribbean Hispanic dataset (rs10884402(A allele:β = −0.15,p = 0.008), rs7078098(C allele:β = 0.18,p = 0.007) and rs950809(C allele:β = 0.17,p = 0.008)) and all three SNPs were significant in a meta-analysis of both datasets (0.002Variation in intron 1 in SORCS1 is associated with memory changes in AD. PMID:22046233

  6. Moose body mass variation revisited: disentangling effects of environmental conditions and genetics.

    PubMed

    Herfindal, Ivar; Haanes, Hallvard; Solberg, Erling J; Røed, Knut H; Høgda, Kjell Arild; Sæther, Bernt-Erik

    2014-02-01

    Large-scale geographical variation in phenotypic traits within species is often correlated to local environmental conditions and population density. Such phenotypic variation has recently been shown to also be influenced by genetic structuring of populations. In ungulates, large-scale geographical variation in phenotypic traits, such as body mass, has been related to environmental conditions and population density, but little is known about the genetic influences. Research on the genetic structure of moose suggests two distinct genetic lineages in Norway, structured along a north-south gradient. This corresponds with many environmental gradients, thus genetic structuring provides an additional factor affecting geographical phenotypic variation in Norwegian moose. We investigated if genetic structure explained geographical variation in body mass in Norwegian moose while accounting for environmental conditions, age and sex, and if it captured some of the variance in body mass that previously was attributed to environmental factors. Genetic structuring of moose was the most important variable in explaining the geographic variation in body mass within age and sex classes. Several environmental variables also had strong explanatory power, related to habitat diversity, environmental seasonality and winter harshness. The results suggest that environmental conditions, landscape characteristics, and genetic structure should be evaluated together when explaining large-scale patterns in phenotypic characters or life history traits. However, to better understand the role of genetic and environmental effects on phenotypic traits in moose, an extended individual-based study of variation in fitness-related characters is needed, preferably in an area of convergence between different genetic lineages.

  7. Genetic origins of lactase persistence and the spread of pastoralism in Africa.

    PubMed

    Ranciaro, Alessia; Campbell, Michael C; Hirbo, Jibril B; Ko, Wen-Ya; Froment, Alain; Anagnostou, Paolo; Kotze, Maritha J; Ibrahim, Muntaser; Nyambo, Thomas; Omar, Sabah A; Tishkoff, Sarah A

    2014-04-03

    In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ~2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ~198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  8. Neanderthal-Derived Genetic Variation Shapes Modern Human Cranium and Brain.

    PubMed

    Gregory, Michael D; Kippenhan, J Shane; Eisenberg, Daniel P; Kohn, Philip D; Dickinson, Dwight; Mattay, Venkata S; Chen, Qiang; Weinberger, Daniel R; Saad, Ziad S; Berman, Karen F

    2017-07-24

    Before their disappearance from the fossil record approximately 40,000 years ago, Neanderthals, the ancient hominin lineage most closely related to modern humans, interbred with ancestors of present-day humans. The legacy of this gene flow persists through Neanderthal-derived variants that survive in modern human DNA; however, the neural implications of this inheritance are uncertain. Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology. First, as a validation of our approach, we demonstrate that a greater load of Neanderthal-derived genetic variants (higher "NeanderScore") is associated with skull shapes resembling those of known Neanderthal cranial remains, particularly in occipital and parietal bones. Next, we demonstrate convergent NeanderScore-related findings in the brain (measured by gray- and white-matter volume, sulcal depth, and gyrification index) that localize to the visual cortex and intraparietal sulcus. This work provides insights into ancestral human neurobiology and suggests that Neanderthal-derived genetic variation is neurologically functional in the contemporary population.

  9. Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus

    PubMed Central

    2013-01-01

    Background Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Results Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). Conclusions The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a

  10. Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus.

    PubMed

    Cidade, Fernanda W; Vigna, Bianca Bz; de Souza, Francisco Hd; Valls, José Francisco M; Dall'Agnol, Miguel; Zucchi, Maria I; de Souza-Chies, Tatiana T; Souza, Anete P

    2013-06-08

    Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species

  11. Inherited genetic variation and overall survival following follicular lymphoma

    PubMed Central

    Gibson, Todd M.; Wang, Sophia S.; Cerhan, James R.; Maurer, Matthew J.; Hartge, Patricia; Habermann, Thomas M.; Davis, Scott; Cozen, Wendy; Lynch, Charles F.; Severson, Richard K.; Rothman, Nathaniel; Chanock, Stephen J.; Morton, Lindsay M.

    2012-01-01

    Follicular lymphoma (FL) has variable progression and survival, and improved identification of patients at high risk for progression would aid in identifying patients most likely to benefit from alternative therapy. In a sample of 244 FL cases identified during a population-based case-control study of non-Hodgkin lymphoma (NHL), we examined 6,679 tag SNPs in 488 gene regions for associations with overall FL survival. Over a median follow-up of 89 months with 65 deaths in this preliminary study, we identified 5 gene regions (BMP7, GALNT12, DUSP2, GADD45B, and ADAM17) that were associated with overall survival from FL. Results did not meet the criteria for statistical significance after adjustment for multiple hypothesis testing. These results, which support a role for host factors in determining the variable progression of FL, serve as an initial examination that can inform future studies of genetic variation and FL survival. However, they require replication in independent populations, as well as assessment in rituximab-treated patients. PMID:22473939

  12. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader.

    PubMed

    Li, Shou-Li; Vasemägi, Anti; Ramula, Satu

    2016-01-01

    Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. The study suggests that although genetic variation may facilitate plant invasions by

  13. Interspecific variation in persistence of buried weed seeds follows trade-offs among physiological, chemical, and physical seed defenses.

    PubMed

    Davis, Adam S; Fu, Xianhui; Schutte, Brian J; Berhow, Mark A; Dalling, James W

    2016-10-01

    Soil seedbanks drive infestations of annual weeds, yet weed management focuses largely on seedling mortality. As weed seedbanks increasingly become reservoirs of herbicide resistance, species-specific seedbank management approaches will be essential to weed control. However, the development of seedbank management strategies can only develop from an understanding of how seed traits affect persistence.We quantified interspecific trade-offs among physiological, chemical, and physical traits of weed seeds and their persistence in the soil seedbank in a common garden study. Seeds of 11 annual weed species were buried in Savoy, IL, from 2007 through 2012. Seedling recruitment was measured weekly and seed viability measured annually. Seed physiological (dormancy), chemical (phenolic compound diversity and concentration; invertebrate toxicity), and physical traits (seed coat mass, thickness, and rupture resistance) were measured.Seed half-life in the soil (t0.5) showed strong interspecific variation (F10,30 = 15, p < .0001), ranging from 0.25 years (Bassia scoparia) to 2.22 years (Abutilon theophrasti). Modeling covariances among seed traits and seedbank persistence quantified support for two putative defense syndromes (physiological-chemical and physical-chemical) and highlighted the central role of seed dormancy in controlling seed persistence.A quantitative comparison between our results and other published work indicated that weed seed dormancy and seedbank persistence are linked across diverse environments and agroecosystems. Moreover, among seedbank-forming early successional plant species, relative investment in chemical and physical seed defense varies with seedbank persistence. Synthesis and applications. Strong covariance among weed seed traits and persistence in the soil seedbank indicates potential for seedbank management practices tailored to specific weed species. In particular, species with high t0.5 values tend to invest less in chemical defenses

  14. Analysis of host genetic diversity and viral entry as sources of between-host variation in viral load

    USGS Publications Warehouse

    Wargo, Andrew R.; Kell, Alison M.; Scott, Robert J.; Thorgaard, Gary H.; Kurath, Gael

    2012-01-01

    Little is known about the factors that drive the high levels of between-host variation in pathogen burden that are frequently observed in viral infections. Here, two factors thought to impact viral load variability, host genetic diversity and stochastic processes linked with viral entry into the host, were examined. This work was conducted with the aquatic vertebrate virus, Infectious hematopoietic necrosis virus (IHNV), in its natural host, rainbow trout. It was found that in controlled in vivo infections of IHNV, a suggestive trend of reduced between-fish viral load variation was observed in a clonal population of isogenic trout compared to a genetically diverse population of out-bred trout. However, this trend was not statistically significant for any of the four viral genotypes examined, and high levels of fish-to-fish variation persisted even in the isogenic trout population. A decrease in fish-to-fish viral load variation was also observed in virus injection challenges that bypassed the host entry step, compared to fish exposed to the virus through the natural water-borne immersion route of infection. This trend was significant for three of the four virus genotypes examined and suggests host entry may play a role in viral load variability. However, high levels of viral load variation also remained in the injection challenges. Together, these results indicate that although host genetic diversity and viral entry may play some role in between-fish viral load variation, they are not major factors. Other biological and non-biological parameters that may influence viral load variation are discussed.

  15. Analysis of host genetic diversity and viral entry as sources of between-host variation in viral load

    PubMed Central

    Wargo, Andrew R.; Kell, Alison M.; Scott, Robert J.; Thorgaard, Gary H.; Kurath, Gael

    2012-01-01

    Little is known about the factors that drive the high levels of between-host variation in pathogen burden that are frequently observed in viral infections. Here, two factors thought to impact viral load variability, host genetic diversity and stochastic processes linked with viral entry into the host, were examined. This work was conducted with the aquatic vertebrate virus, Infectious hematopoietic necrosis virus (IHNV), in its natural host, rainbow trout. It was found that in controlled in vivo infections of IHNV, a suggestive trend of reduced between-fish viral load variation was observed in a clonal population of isogenic trout compared to a genetically diverse population of out-bred trout. However, this trend was not statistically significant for any of the four viral genotypes examined, and high levels of fish-to-fish variation persisted even in the isogenic trout population. A decrease in fish-to-fish viral load variation was also observed in virus injection challenges that bypassed the host entry step, compared to fish exposed to the virus through the natural water-borne immersion route of infection. This trend was significant for three of the four virus genotypes examined and suggests host entry may play a role in viral load variability. However, high levels of viral load variation also remained in the injection challenges. Together, these results indicate that although host genetic diversity and viral entry may play some role in between-fish viral load variation, they are not major factors. Other biological and non-biological parameters that may influence viral load variation are discussed. PMID:22310066

  16. Levels of genetic variation in trees: influence of life history characteristics

    Treesearch

    J. L Hamrick; J. B. Milton; Y. B. Linhart

    1981-01-01

    In a previous study, levels of genetic variation, as measured by isozyme analyses, were compared for 113 taxa of vascular plants. Each species was classified for 12 life history and ecological traits and three measures of genetic variation were calculated. Plants with large ranges, high fecundities, an outcrossing mode of reproduction, wind pollination, a long...

  17. The genetic basis for variation in resistance to infection in the Drosophila melanogaster genetic reference panel

    PubMed Central

    Wang, Jonathan B.

    2017-01-01

    Individuals vary extensively in the way they respond to disease but the genetic basis of this variation is not fully understood. We found substantial individual variation in resistance and tolerance to the fungal pathogen Metarhizium anisopliae Ma549 using the Drosophila melanogaster Genetic Reference Panel (DGRP). In addition, we found that host defense to Ma549 was correlated with defense to the bacterium Pseudomonas aeruginosa Pa14, and several previously published DGRP phenotypes including oxidative stress sensitivity, starvation stress resistance, hemolymph glucose levels, and sleep indices. We identified polymorphisms associated with differences between lines in both their mean survival times and microenvironmental plasticity, suggesting that lines differ in their ability to adapt to variable pathogen exposures. The majority of polymorphisms increasing resistance to Ma549 were sex biased, located in non-coding regions, had moderately large effect and were rare, suggesting that there is a general cost to defense. Nevertheless, host defense was not negatively correlated with overall longevity and fecundity. In contrast to Ma549, minor alleles were concentrated in the most Pa14-susceptible as well as the most Pa14-resistant lines. A pathway based analysis revealed a network of Pa14 and Ma549-resistance genes that are functionally connected through processes that encompass phagocytosis and engulfment, cell mobility, intermediary metabolism, protein phosphorylation, axon guidance, response to DNA damage, and drug metabolism. Functional testing with insertional mutagenesis lines indicates that 12/13 candidate genes tested influence susceptibility to Ma549. Many candidate genes have homologs identified in studies of human disease, suggesting that genes affecting variation in susceptibility are conserved across species. PMID:28257468

  18. The influence of mitonuclear genetic variation on personality in seed beetles

    PubMed Central

    Løvlie, Hanne; Immonen, Elina; Gustavsson, Emil; Kazancioğlu, Erem; Arnqvist, Göran

    2014-01-01

    There is a growing awareness of the influence of mitochondrial genetic variation on life-history phenotypes, particularly via epistatic interactions with nuclear genes. Owing to their direct effect on traits such as metabolic and growth rates, mitonuclear interactions may also affect variation in behavioural types or personalities (i.e. behavioural variation that is consistent within individuals, but differs among individuals). However, this possibility is largely unexplored. We used mitonuclear introgression lines, where three mitochondrial genomes were introgressed into three nuclear genetic backgrounds, to disentangle genetic effects on behavioural variation in a seed beetle. We found within-individual consistency in a suite of activity-related behaviours, providing evidence for variation in personality. Composite measures of overall activity of individuals in behavioural assays were influenced by both nuclear genetic variation and by the interaction between nuclear and mitochondrial genomes. More importantly, the degree of expression of behavioural and life-history phenotypes was correlated and mitonuclear genetic variation affected expression of these concerted phenotypes. These results show that mitonuclear genetic variation affects both behavioural and life-history traits, and they provide novel insights into the maintenance of genetic variation in behaviour and personality. PMID:25320161

  19. The influence of mitonuclear genetic variation on personality in seed beetles.

    PubMed

    Løvlie, Hanne; Immonen, Elina; Gustavsson, Emil; Kazancioğlu, Erem; Arnqvist, Göran

    2014-12-07

    There is a growing awareness of the influence of mitochondrial genetic variation on life-history phenotypes, particularly via epistatic interactions with nuclear genes. Owing to their direct effect on traits such as metabolic and growth rates, mitonuclear interactions may also affect variation in behavioural types or personalities (i.e. behavioural variation that is consistent within individuals, but differs among individuals). However, this possibility is largely unexplored. We used mitonuclear introgression lines, where three mitochondrial genomes were introgressed into three nuclear genetic backgrounds, to disentangle genetic effects on behavioural variation in a seed beetle. We found within-individual consistency in a suite of activity-related behaviours, providing evidence for variation in personality. Composite measures of overall activity of individuals in behavioural assays were influenced by both nuclear genetic variation and by the interaction between nuclear and mitochondrial genomes. More importantly, the degree of expression of behavioural and life-history phenotypes was correlated and mitonuclear genetic variation affected expression of these concerted phenotypes. These results show that mitonuclear genetic variation affects both behavioural and life-history traits, and they provide novel insights into the maintenance of genetic variation in behaviour and personality.

  20. Genetic variation in photosynthetic performance and tolerance to osmotic stress (desiccation, freezing, hyposalinity) in the rocky littoral foundation species Fucus vesiculosus (Fucales, Phaeophyceae).

    PubMed

    Rothäusler, Eva; Sjöroos, Joakim; Heye, Katharina; Jormalainen, Veijo

    2016-10-01

    Genetic diversity may play an analogous role to species diversity, as it can contribute to ecosystem function and stability, and provision of ecosystem services. In the Baltic Sea, perennial algal beds are often comprised of only Fucus vesiculosus and the amount of genetic variation in fitness-related traits (i.e., the ability of the alga to photosynthesize or withstand stress) will thus determine the alga's local persistence in a changing environment. To study genetic variation in the crucial traits behind persistence we grew replicate vegetative branches that came from the same genotype in common gardens. We quantified osmotic stress tolerance and recovery responses by exposing branches to desiccation, freezing, and hyposalinity regimens. Our results show that genetic variation among genotypes was apparent for some photosynthetic parameters (maximal electron transport rate, saturation irradiance for electron transport, nonphotochemical quenching) and growth. Algae tolerated freezing (1,440 min at -2.5°C) and hyposalinity (1,560 min at 2.5) well, but did not recover from desiccation (70 min at 12°C, causing ~94% water loss). Furthermore, we found very little if any evidence on genetic variation in tolerance to these stressors. Our results suggest that low salinity and cold winters in the northern marginal populations selected for hyposalinity and freezing tolerant genotypes, possibly eroding genetic variation in tolerance, but that tolerance to harsh desiccation has been lost, likely due to relaxed selection. The overall availability of genetic variation in fitness related traits might be supportive for F. vesiculosus during adaptation to gradual changes of its environment. © 2016 Phycological Society of America.

  1. Genetic Variation Among Open-Pollinated Progeny of Eastern Cottonwood

    Treesearch

    R. E. Farmer

    1970-01-01

    Improvement programs in eastern cottonwood (Populus deltoides Bartr.) are most frequently designed to produce genetically superior clones for direct commercial use. This paper describes a progeny test to assess genetic variability on which selection might be based.

  2. Folk beliefs about genetic variation predict avoidance of biracial individuals

    PubMed Central

    Kang, Sonia K.; Plaks, Jason E.; Remedios, Jessica D.

    2015-01-01

    People give widely varying estimates for the amount of genetic overlap that exists between humans. While some laypeople believe that humans are highly genetically similar to one another, others believe that humans share very little genetic overlap. These studies examine how beliefs about genetic overlap affect neural and evaluative reactions to racially-ambiguous and biracial targets. In Study 1, we found that lower genetic overlap estimates predicted a stronger neural avoidance response to biracial compared to monoracial targets. In Study 2, we found that lower genetic overlap estimates predicted longer response times to classify biracial (vs. monoracial) faces into racial categories. In Study 3, we manipulated genetic overlap beliefs and found that participants in the low overlap condition explicitly rated biracial targets more negatively than those in the high overlap condition. Taken together, these data suggest that genetic overlap beliefs influence perceivers’ processing fluency and evaluation of biracial and racially-ambiguous individuals. PMID:25904875

  3. Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs.

    PubMed

    Grossi, Daniela A; Jafarikia, Mohsen; Brito, Luiz F; Buzanskas, Marcos E; Sargolzaei, Mehdi; Schenkel, Flávio S

    2017-01-21

    Knowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers). The overall LD (r (2)) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire. An overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic

  4. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics.

    PubMed

    Wiel, Laurens; Venselaar, Hanka; Veltman, Joris A; Vriend, Gert; Gilissen, Christian

    2017-08-16

    Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains." These meta-domains consist of 30,853 homologous Pfam protein domain instances that cover 36% of all human protein coding sequences. We find that genetic tolerance is consistent across protein domain homologues, and that patterns of genetic tolerance faithfully mimic patterns of evolutionary conservation. Furthermore, for a significant fraction (68%) of the meta-domains high-frequency population variation re-occurs at the same positions across domain homologues more often than expected. In addition, we observe that the presence of pathogenic missense variants at an aligned homologous domain position is often paired with the absence of population variation and vice versa. The use of these meta-domains can improve the interpretation of genetic variation. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

  5. Genetic Variation Within and Among Collections of Falata Alfalfas

    USDA-ARS?s Scientific Manuscript database

    Yellow-flowered alfalfa (Medicago sativa subsp. falcata) persists in low precipitation rangeland and grassland environments. The origin of Medicago includes Russia, Mongolia, Scandinavia, and China (Hansen, 1909; Lesins and Lesins, 1979). The presence of legumes improves rangelands and grasslands ...

  6. Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic.

    PubMed

    Matesanz, Silvia; Rubio Teso, María Luisa; García-Fernández, Alfredo; Escudero, Adrián

    2017-01-01

    Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population's similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations' survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness, our study highlights

  7. Habitat Fragmentation Differentially Affects Genetic Variation, Phenotypic Plasticity and Survival in Populations of a Gypsum Endemic

    PubMed Central

    Matesanz, Silvia; Rubio Teso, María Luisa; García-Fernández, Alfredo; Escudero, Adrián

    2017-01-01

    Habitat fragmentation, i.e., fragment size and isolation, can differentially alter patterns of neutral and quantitative genetic variation, fitness and phenotypic plasticity of plant populations, but their effects have rarely been tested simultaneously. We assessed the combined effects of size and connectivity on these aspects of genetic and phenotypic variation in populations of Centaurea hyssopifolia, a narrow endemic gypsophile that previously showed performance differences associated with fragmentation. We grew 111 maternal families sampled from 10 populations that differed in their fragment size and connectivity in a common garden, and characterized quantitative genetic variation, phenotypic plasticity to drought for key functional traits, and plant survival, as a measure of population fitness. We also assessed neutral genetic variation within and among populations using eight microsatellite markers. Although C. hyssopifolia is a narrow endemic gypsophile, we found substantial neutral genetic variation and quantitative variation for key functional traits. The partition of genetic variance indicated that a higher proportion of variation was found within populations, which is also consistent with low population differentiation in molecular markers, functional traits and their plasticity. This, combined with the generally small effect of habitat fragmentation suggests that gene flow among populations is not restricted, despite large differences in fragment size and isolation. Importantly, population’s similarities in genetic variation and plasticity did not reflect the lower survival observed in isolated populations. Overall, our results indicate that, although the species consists of genetically variable populations able to express functional plasticity, such aspects of adaptive potential may not always reflect populations’ survival. Given the differential effects of habitat connectivity on functional traits, genetic variation and fitness, our study

  8. Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

    PubMed Central

    Ranciaro, Alessia; Campbell, Michael C.; Hirbo, Jibril B.; Ko, Wen-Ya; Froment, Alain; Anagnostou, Paolo; Kotze, Maritha J.; Ibrahim, Muntaser; Nyambo, Thomas; Omar, Sabah A.; Tishkoff, Sarah A.

    2014-01-01

    In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa. PMID:24630847

  9. Genetic variation and plasticity of Plantago coronopus under saline conditions

    NASA Astrophysics Data System (ADS)

    Smekens, Marret J.; van Tienderen, Peter H.

    2001-08-01

    Phenotypic plasticity may allow organisms to cope with variation in the environmental conditions they encounter in their natural habitats. Salt adaptation appears to be an excellent example of such a plastic response. Many plant species accumulate organic solutes in response to saline conditions. Comparative and molecular studies suggest that this is an adaptation to osmotic stress. However, evidence relating the physiological responses to fitness parameters is rare and requires assessing the potential costs and benefits of plasticity. We studied the response of thirty families derived from plants collected in three populations of Plantago coronopus in a greenhouse experiment under saline and non-saline conditions. We indeed found a positive selection gradient for the sorbitol percentage under saline conditions: plant families with a higher proportion of sorbitol produced more spikes. No effects of sorbitol on fitness parameters were found under non-saline conditions. Populations also differed genetically in leaf number, spike number, sorbitol concentration and percentages of different soluble sugars. Salt treatment led to a reduction of vegetative biomass and spike production but increased leaf dry matter percentage and leaf thickness. Both under saline and non-saline conditions there was a negative trade-off between vegetative growth and reproduction. Families with a high plasticity in leaf thickness had a lower total spike length under non-saline conditions. This would imply that natural selection under predominantly non-saline conditions would lead to a decrease in the ability to change leaf morphology in response to exposure to salt. All other tests revealed no indication for any costs of plasticity to saline conditions.

  10. Performing monkeys of Bangladesh: characterizing their source and genetic variation.

    PubMed

    Hasan, M Kamrul; Feeroz, M Mostafa; Jones-Engel, Lisa; Engel, Gregory A; Akhtar, Sharmin; Kanthaswamy, Sree; Smith, David Glenn

    2016-04-01

    The acquisition and training of monkeys to perform is a centuries-old tradition in South Asia, resulting in a large number of rhesus macaques kept in captivity for this purpose. The performing monkeys are reportedly collected from free-ranging populations, and may escape from their owners or may be released into other populations. In order to determine whether this tradition involving the acquisition and movement of animals has influenced the population structure of free-ranging rhesus macaques in Bangladesh, we first characterized the source of these monkeys. Biological samples from 65 performing macaques collected between January 2010 and August 2013 were analyzed for genetic variation using 716 base pairs of mitochondrial DNA. Performing monkey sequences were compared with those of free-ranging rhesus macaque populations in Bangladesh, India and Myanmar. Forty-five haplotypes with 116 (16 %) polymorphic nucleotide sites were detected among the performing monkeys. As for the free-ranging rhesus population, most of the substitutions (89 %) were transitions, and no indels (insertion/deletion) were observed. The estimate of the mean number of pair-wise differences for the performing monkey population was 10.1264 ± 4.686, compared to 14.076 ± 6.363 for the free-ranging population. Fifteen free-ranging rhesus macaque populations were identified as the source of performing monkeys in Bangladesh; several of these populations were from areas where active provisioning has resulted in a large number of macaques. The collection of performing monkeys from India was also evident.

  11. Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

    PubMed Central

    Gooding, R H

    1996-01-01

    An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors. PMID:8809462

  12. A twin study of genetic and environmental determinants of abnormal persistence of psychotic experiences in young adulthood.

    PubMed

    Wigman, Johanna T W; van Winkel, Ruud; Jacobs, Nele; Wichers, Marieke; Derom, Catherine; Thiery, Evert; Vollebergh, Wilma A M; van Os, Jim

    2011-07-01

    Evidence suggests that subclinical psychotic experiences are more likely to cause transition to psychotic disorder if their expression becomes persistent. The study of longitudinal patterns of subclinical psychotic experiences may help to distinguish subgroups with transient and persistent psychotic symptoms, who may differ in risk of later psychosis. The current study investigated patterns of developmental course of subclinical psychotic experiences in a general population sample of 566 female twins, aged 18-45 years. The positive symptoms subscale of the Community Assessment of Psychic Experiences (CAPE), completed three times in 2 years, was analyzed with growth modeling. Using Latent Class Analysis, two developmental courses were distinguished: a Persistent and a Low (expression of subclinical psychotic experiences) group. The Persistent group reported significantly higher levels of depressive and negative symptoms and worse functioning in daily life. Childhood trauma (OR: 3.26, P < 0.0001) and stressful life events over the study period (OR: 3.15, P = 0.031) predicted membership of the Persistent group. Of the monozygotic (MZ) twins with their co-twin in the Persistent group, 49% also were in the Persistent group themselves (OR: 9.32, P < 0.0001), compared to only 14% in the dizygotic (DZ) co-twins (OR: 1.56, P = 0.42) (χ(2)(2) = 22.97; P < 0.001). The findings suggest that persistence of subclinical psychosis is influenced by both genetic and environmental factors, providing the possibility to study the (possibly modifiable) etiology underlying the longitudinal process of persistence of the early expression of psychosis liability.

  13. [Researches on relationship between genetic differentiation and chemical variation of Cinnamomum migao].

    PubMed

    Chen, Meilan; Zhou, Tao; Jiang, Weike; Jin, Yanlei; Yang, Zhannan

    2011-06-01

    To study the relationship between the genetic diversity and chemical variation of Cinnamomum migao. ISSR marker technique was used to research the genetic structure of 9 population, GC-MS was used to analyze the main ingredients of the volatile oil in C. migao. The analysis on the main ingredients of the volatile oil showed that there were significant or extremely significant differences in 9 populations. The minimum variation index of population was Yunnan Funing and the maximum variation index of population was Guangxi Yueye. ISSR marker analysis showed that the average of polymorphic loci percentage (P) was 42.41%, expected heterozygosity (H) was 0.181 0, Shannon's information index (I) was 0.293 8, the Nei's genetic diversity (H(s)) in the group was 0.188 9, genetic differentiation index (G(st)) was 2.269 1. The relationship between the genetic diversity and chemical variation showed that there was no significant correlation between the main ingredients of the volatile oil and 4 indexes of genetic structure of C. migao. The genetic diversity of C. migao was relatively high at the population levels, while it is low within the population levels, the relationship between chemical variation and genetic diversity was not obvious, that may indicate that other factors causes the chemical variation of C. migao.

  14. Phenotypic and Genetic Variations in Obligate Parthenogenetic Populations of Eriosoma lanigerum Hausmann (Hemiptera: Aphididae).

    PubMed

    Ruiz-Montoya, L; Zúñiga, G; Cisneros, R; Salinas-Moreno, Y; Peña-Martínez, R; Machkour-M'Rabet, S

    2015-12-01

    The study of phenotypic and genetic variation of obligate parthenogenetic organisms contributes to an understanding of evolution in the absence of genetic variation produced by sexual reproduction. Eriosoma lanigerum Hausmann undergoes obligate parthenogenesis in Mexico City, Mexico, due to the unavailability of the host plants required for sexual reproduction. We analysed the phenotypic and genetic variation of E. lanigerum in relation to the dry and wet season and plant phenology. Aphids were collected on two occasions per season on a secondary host plant, Pyracantha koidzumii, at five different sites in the southern area of Mexico City, Mexico. Thirteen morphological characteristics were measured from 147 to 276 individuals per site and per season. A multivariate analysis of variance was performed to test the effect of the season, site and their interaction on morphological traits. Morphological variation was summarised using a principal component analysis. Genetic variation was described using six enzymatic loci, four of which were polymorphic. Our study showed that the site and season has a significant effect on morphological trait variation. The largest aphids were recorded during cold temperatures with low relative humidity and when the plant was at the end of the fruiting period. The mean genetic diversity was low (mean H e =  .161), and populations were genetically structured by season and site. Morphological and genetic variations appear to be associated with environmental factors that directly affect aphid development and/or indirectly by host plant phenology.

  15. Aphid wing dimorphisms: linking environmental and genetic control of trait variation

    PubMed Central

    Brisson, Jennifer A.

    2010-01-01

    Both genetic and environmental factors underlie phenotypic variation. While research at the interface of evolutionary and developmental biology has made excellent advances in understanding the contribution of genes to morphology, less well understood is the manner in which environmental cues are incorporated during development to influence the phenotype. Also virtually unexplored is how evolutionary transitions between environmental and genetic control of trait variation are achieved. Here, I review investigations into molecular mechanisms underlying phenotypic plasticity in the aphid wing dimorphism system. Among aphids, some species alternate between environmentally sensitive (polyphenic) and genetic (polymorphic) control of wing morph determination in their life cycle. Therefore, a traditional molecular genetic approach into understanding the genetically controlled polymorphism may provide a unique avenue into not only understanding the molecular basis of polyphenic variation in this group, but also the opportunity to compare and contrast the mechanistic basis of environmental and genetic control of similar dimorphisms. PMID:20083636

  16. Genetic Screen Reveals the Role of Purine Metabolism in Staphylococcus aureus Persistence to Rifampicin

    PubMed Central

    Yee, Rebecca; Cui, Peng; Shi, Wanliang; Feng, Jie; Zhang, Ying

    2015-01-01

    Chronic infections with Staphylococcus aureus such as septicemia, osteomyelitis, endocarditis, and biofilm infections are difficult to treat because of persisters. Despite many efforts in understanding bacterial persistence, the mechanisms of persister formation in S. aureus remain elusive. Here, we performed a genome-wide screen of a transposon mutant library to study the molecular mechanisms involved in persistence of community-acquired S. aureus. Screening of the library for mutants defective in persistence or tolerance to rifampicin revealed many genes involved in metabolic pathways that are important for antibiotic persistence. In particular, the identified mutants belonged to metabolic pathways involved in carbohydrate, amino acid, lipid, vitamin and purine biosynthesis. Five mutants played a role in purine biosynthesis and two mutants, purB, an adenylosuccinate lyase, and purM, a phosphoribosylaminoimidazole synthetase, were selected for further confirmation. Mutants purB and purM showed defective persistence compared to the parental strain USA300 in multiple stress conditions including various antibiotics, low pH, and heat stress. The defect in persistence was restored by complementation with the wildtype purB and purM gene in the respective mutants. These findings provide new insights into the mechanisms of persistence in S. aureus and provide novel therapeutic targets for developing more effective treatment for persistent infections due to S. aureus. PMID:27025643

  17. Forward genetics by sequencing EMS variation-induced inbred lines

    USDA-ARS?s Scientific Manuscript database

    The dramatic increase in throughput of sequencing techniques enables gene cloning through pre-existing forward genetics approaches. We show that it also brings with it the potential to change the crossing designs and approach of forward genetics. To achieve this for eukaryotic organisms with complex...

  18. Genetic variation and human disease: Principles and evolutionary approaches

    SciTech Connect

    Weiss, K.M.

    1993-12-31

    The context of the book here reviewed is the evolution of human phenotypes, with an emphasis on those complex characteristics that produce the prevailing disorders of an adult population. This is achieved with a background of evolution and population genetics, with human diseases placed in the context of mutation rates, selection, genetic drift and evolutionary history.

  19. Differential genetic variation of chickens and MD vaccine protective efficacy

    USDA-ARS?s Scientific Manuscript database

    Vaccine protective efficacy is determined by multiple factors including host genetics, the type of vaccine, vaccine dosage, the virulence and dose of challenging viruses, and the interval between vaccination and viral challenge. Studies on human immune responses to vaccinations suggest host genetic...

  20. Lactase persistence/non-persistence genetic variants in irritable bowel syndrome in an endemic area for lactose malabsorption.

    PubMed

    Kumar, Sunil; Ranjan, Prabhat; Mittal, Balraj; Singh, Rajan; Ghoshal, Uday C

    2012-12-01

    Lactase non-persistence is common in India. We evaluated: (i) frequency of lactase gene (C/T-13910 and G/A-22018) polymorphisms in irritable bowel syndrome (IBS) and healthy controls (HC), (ii) association between these polymorphisms and IBS-subtypes and symptoms. A total of 150 IBS patients (Rome-III criteria) and 252 age and gender-matched HC were evaluated for C/T-13910 and G/A-22018 genotypes using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Totals of 79 (52%), 52 (35%) and 19 (13%) patients had diarrhea-predominant IBS (D-IBS), constipation predominant IBS (C-IBS) and alternating diarrhea and constipation IBS (A-IBS), respectively (Rome-III). Frequency of C/T-13910 [genotypes: CC 102 (68%), CT 43 (29%), TT 5 (3%) vs CC 155 (61%), CT 83 (33%), TT 14 (6%), P > 0.05] and G/A-22018 [GG 97 (65%), GA 41 (27%), AA 12 (8%) vs GG 154 (61%), GA 78 (31%), AA 20 (8%), P > 0.05] were similar among IBS and HC. Patients with D-IBS more often had C/T-13910 and G/A-22018 genotypes than C-IBS (CC 71 [90%], CT 6 [8%], TT 2 [2%]) versus (24 [46%], 25 [48%], 3 [6%]), A-IBS (7 [39%], 12 [63%], 0, [0%]) and HC (155 [61%], 83 [33%], 14 [6%]), P < 0.0001 and (GG 69 [87%], GA 6 [8%], AA 4 [5%]) vs (22 [42%], 24 [46%], 6 [12%]) vs (6 [32%], 11 [58%], 2 [10%]), P < 0.0001. IBS with CC and GG genotypes more often had abdominal pain (P = 0.005), distension (P = 0.031) and higher stool frequency (P = 0.003) and reported symptoms following dairy products than non-CC (P < 0.0001). Though C/T-13910 and G/A-22018 polymorphisms were comparable among IBS and HC, these were more common among D-IBS and reported some symptoms like abdominal pain, bloating and exacerbation by dairy products. © 2012 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  1. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

    PubMed Central

    Bartha, István; Brumme, Chanson; Harrigan, Richard

    2017-01-01

    We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation. PMID:28182649

  2. Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity.

    PubMed

    Taylor, John W; Branco, Sara; Gao, Cheng; Hann-Soden, Chris; Montoya, Liliam; Sylvain, Iman; Gladieux, Pierre

    2017-09-01

    The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.

  3. The Grandest Genetic Experiment Ever Performed on Man? - A Y-Chromosomal Perspective on Genetic Variation in India.

    PubMed

    Carvalho-Silva, Denise R; Tyler-Smith, Chris

    2008-05-01

    We have analysed Y-chromosomal data from Indian caste, Indian tribal and East Asian populations in order to investigate the impact of the caste system on male genetic variation. We find that variation within populations is lower in India than in East Asia, while variation between populations is overall higher. This observation can be explained by greater subdivision within the Indian population, leading to more genetic drift. However, the effect is most marked in the tribal populations, and the level of variation between caste populations is similar to the level between Chinese populations. The caste system has therefore had a detectable impact on Y-chromosomal variation, but this has been less strong than the influence of the tribal system, perhaps because of larger population sizes in the castes, more gene flow or a shorter period of time.

  4. The persistence and ecological impacts of a cyanobacterium genetically engineered to express mosquitocidal Bacillus thuringiensis toxins.

    PubMed

    Ketseoglou, Irene; Bouwer, Gustav

    2016-05-10

    The cyanobacterium Anabaena PCC 7120#11 has been genetically engineered to act as a delivery vehicle for Bacillus thuringiensis subspecies israelensis mosquitocidal toxins. To address ecological concerns about releasing this genetically engineered microorganism into the environment for mosquito larva control, the persistence and ecological impacts of PCC 7120#11 was evaluated using multi-species, standardized aquatic microcosms. The microcosms were set up as described in ASTM E1366-02 (Standard Practice for Standardized Aquatic Microcosms: Fresh Water), with a few modifications. The treatment group microcosms were inoculated with PCC 7120#11 and key water quality parameters and non-target effects were compared between the treatment and control groups over a period of 35 days. PCC 7120#11 decreased from a concentration of 4.50 × 10(6) cells/ml (at inoculation) to 1.32 × 10(3) cells/ml after 4 weeks and larvicidal activity against third instar larvae of Anopheles arabiensis was only evident for two weeks after treatment. Both treatment and the interaction of treatment and time had a significant effect on nitrate, phosphate and photosynthetic microorganism concentrations. Treatment with PCC 7120#11 caused a temporary spike in ammonia in the microcosms a week after treatment, but the concentrations were well below acute and chronic criteria values for ammonia in freshwater ecosystems. Cyprinotus vidua concentrations were not significantly different between PCC 7120#11 and control microcosms. In PCC 7120#11 microcosms, Daphnia pulex concentrations were significantly lower than control concentrations between days 18 and 25. By the end of the experiment, none of the measured variables were significantly different between the treatment groups. The standard aquatic microcosm experiments provided more data on the ecological impacts of PCC 7120#11 than single-organism assessments would have. On the basis of the relatively minor, short-term effects that PCC 7120

  5. Associations of genetic lactase non-persistence and sex with bone loss in young adulthood.

    PubMed

    Laaksonen, Marika M L; Impivaara, Olli; Sievänen, Harri; Viikari, Jorma S A; Lehtimäki, Terho J; Lamberg-Allardt, Christel J E; Kärkkäinen, Merja U M; Välimäki, Matti; Heikkinen, Jorma; Kröger, Liisa M; Kröger, Heikki P J; Jurvelin, Jukka S; Kähönen, Mika A P; Raitakari, Olli T

    2009-05-01

    Some studies have reported that after attainment of peak bone mass (PBM), slow bone loss may occur in both men and women; however, findings are inconsistent. Genetic factors play a significant role in bone loss, but the available evidence is conflicting. Genetic lactase non-persistence (lactase C/C(-13910) genotype) is suggested to increase risk for inadequate calcium intake predisposing to poorer bone health. We investigated whether this genotype is associated with PBM and bone loss in young Finnish adults. Subjects belong to the Cardiovascular Risk in Young Finns Study that is an ongoing multi-centre follow-up of atherosclerosis risk factors. From the original cohort, randomly selected subjects aged 20-29 participated in baseline bone mineral density (BMD) measurements (n=358), and in follow-up measurements 12 years later (n=157). Bone mineral content (BMC) and BMD at lumbar spine (LS) and femoral neck (FN) were measured at baseline and follow-up with dual energy X-ray absorptiometry (DXA). Lactase C/T(-13910) polymorphism was determined by PCR and allele-specific fluorogenic probes. Information on lifestyle was elicited with questionnaires. During the follow-up, bone loss at both bone sites was greater in males (LS BMD: -1.1%, FN BMD: -5.2%) than in females (LS BMD: +2.1%, FN BMD: -0.7%) (both bone sites p=0.001). Younger age predicted greater loss of FN BMC and BMD in females (p=0.013 and p=0.001, respectively). Increased calcium intake predicted FN BMD gain in both sexes (in females B=0.007 g/cm(2)/mg, p=0.002; in males B=0.006, p=0.045), and increased physical activity LS BMD gain in females (B=0.091 g/cm(2)/physical activity point, p=0.023). PBM did not differ between the lactase genotypes, but males with the CC(-13910) genotype seemed to be prone to greater bone loss during the follow-up (LS BMD: C/C vs. T/T p=0.081). In conclusion, bone loss in young adulthood was more common in males than in females and seemed to occur mainly at the femoral neck. Young

  6. Regional structuring of genetic variation in short-lived rock pool populations of Branchipodopsis wolfi (Crustacea: Anostraca).

    PubMed

    Brendonck, L; De Meester, L; Riddoch, B J

    2000-06-01

    The genetic structure of three metapopulations of the southern African anostracan Branchipodopsis wolfi was compared by analysing allozyme variation at four loci (PGM, GPI, APK, AAT). In total, 17 local populations from three sites (metapopulations) were analysed from rock pools in south-eastern Botswana ranging from 0.2 to 21 m(2) in surface area. In three populations we found significant deviations from Hardy-Weinberg (H-W) equilibrium at one or more loci due to heterozygote deficiencies. Genetic variability at one site was significantly lower than at the other sites, which may be linked to a greater incidence of extinction and recolonisation, as the basins at this site are shallower and have shorter hydrocycles. Across all local populations, a significant level of population differentiation was revealed. More than 90% of this variation was explained by differentiation among sites (metapopulations), although this differentiation did not correlate with geographic distance, or with environmental variables. Genetic differentiation among populations within metapopulations was low, but significant at all sites. At only one of the sites was a significantly positive association measured between genetic and geographic distance among local populations. Our data suggest that persistent stochastic events and limited effective long-range dispersal appear to dominate genetic differentiation among populations of B. wolfi inhabiting desert rock pools. The lack of association between geographic distance and genetic or ecological differences between rock pool sites is indicative of historical stochastic events. Low heterozygosity, the significant deviations from H-W equilibrium, and the large inter- but low intra-site differentiation are suggestive of the importance of short-range dispersal. Gene flow between metapopulations of B. wolfi appears to be seriously constrained by distances of 2 km or even less.

  7. Population genetics features for persistent, but transient, Botryllus schlosseri (Urochordata) congregations in a central Californian marina.

    PubMed

    Karahan, Arzu; Douek, Jacob; Paz, Guy; Rinkevich, Baruch

    2016-08-01

    The colonial tunicate Botryllus schlosseri is a globally distributed, invasive ascidian that has colonized the Californian coasts of the USA during the mid-late 1940s and has, since the late 1980s, spread north to Washington. This study analyzes the population genetic characteristics of transient populations residing at the Elkhorn Yacht-Club (EYC), in central California (seven sessions, 1996-2008), which suffered periodic catastrophes caused by episodic fresh-water floods and a single sampling session (in the year 2001) of five West-Coast populations using the mtDNA COI gene and five microsatellite markers. EYC microsatellite results were further compared with the closely situated but persistent population of the Santa Cruz Harbor (SCH) to understand the impact on EYC population regeneration processes after the 2005-flood catastrophe. All microsatellites were highly polymorphic, revealing a large number of unique alleles at different sampling dates. Whereas pairwise θ did not reveal significant differences between the EYC time-series samplings, the overall θ was significant, as it was between all the 2001 West Coast populations. The most likely cluster number was 3 for the EYC samples whereas two K values were obtained (2 and 5) for the 2001 samples. Tajima's D and Fu's/Fs tests did not reject the null hypothesis for COI neutral evolution, except for in the EYC-2000, 2007 and two 2001 samplings. The wide geographical range of the analyses has indicated that following the EYC 2005-flood catastrophe, newcomers could have originated from neighboring populations, from deep-water colonies that may have escaped the 2005 low salinity event, or less expectedly, from far away West-Coast populations, while revealing that the SCH population is the most probable source for the EYC population.

  8. Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast

    PubMed Central

    Brodt, Avital; Botzman, Maya; David, Eyal; Gat-Viks, Irit

    2014-01-01

    Inter-individual variation in regulatory circuits controlling gene expression is a powerful source of functional information. The study of associations among genetic variants and gene expression provides important insights about cell circuitry but cannot specify whether and when potential variants dynamically alter their genetic effect during the course of response. Here we develop a computational procedure that captures temporal changes in genetic effects, and apply it to analyze transcription during inhibition of the TOR signaling pathway in segregating yeast cells. We found a high-order coordination of gene modules: sets of genes co-associated with the same genetic variant and sharing a common temporal genetic effect pattern. The temporal genetic effects of some modules represented a single state-transitioning pattern; for example, at 10–30 minutes following stimulation, genetic effects in the phosphate utilization module attained a characteristic transition to a new steady state. In contrast, another module showed an impulse pattern of genetic effects; for example, in the poor nitrogen sources utilization module, a spike up of a genetic effect at 10–20 minutes following stimulation reflected inter-individual variation in the timing (rather than magnitude) of response. Our analysis suggests that the same mechanism typically leads to both inter-individual variation and the temporal genetic effect pattern in a module. Our methodology provides a quantitative genetic approach to studying the molecular mechanisms that shape dynamic changes in transcriptional responses. PMID:25474467

  9. Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum.

    PubMed

    Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael

    2015-08-01

    Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

  10. Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

    PubMed Central

    Matuszewski, Sebastian; Hermisson, Joachim; Kopp, Michael

    2015-01-01

    Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from preexisting standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect and (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow. PMID:26038348

  11. GENETIC VARIATION FOR COPPER RESISTANCE IN FATHEAD MINNOW TOXICITY TESTS

    EPA Science Inventory

    Unexplained variation in the results of aquatic organism toxicity tests is a consistently observed and troubling phenomenon. Possible sources of variation include differences in condition or nutritional status of the population prior to the test, as well as age, density and hand...

  12. Persistent Persister Misperceptions

    PubMed Central

    Kim, Jun-Seob; Wood, Thomas K.

    2016-01-01

    Persister cells survive antibiotic treatment due to their lack of metabolism, rather than through genetic change, as shown via four seminal experiments conducted by the discoverers of the phenotype (Hobby et al., 1942; Bigger, 1944). Unfortunately, over seven decades of persister cell research, the literature has been populated by misperceptions that do not withstand scrutiny. This opinion piece examines some of those misunderstandings in the literature with the hope that by shining some light on these inaccuracies, the field may be advanced and subsequent manuscripts may be reviewed more critically. PMID:28082974

  13. Analysis of Genetic Variation and Potential Applications in Genome-Scale Metabolic Modeling

    PubMed Central

    Cardoso, João G. R.; Andersen, Mikael Rørdam; Herrgård, Markus J.; Sonnenschein, Nikolaus

    2015-01-01

    Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic variation during a long term production process may lead to significant economic losses and it is important to understand how to control this type of variation. With the emergence of next-generation sequencing technologies, genetic variation in microbial strains can now be determined on an unprecedented scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular phenotypes. PMID:25763369

  14. Viral Replication, Persistence in Water and Genetic Characterization of Two Influenza A Viruses Isolated from Surface Lake Water

    PubMed Central

    Lebarbenchon, Camille; Yang, My; Keeler, Shamus P.; Ramakrishnan, Muthannan A.; Brown, Justin D.; Stallknecht, David E.; Sreevatsan, Srinand

    2011-01-01

    Water-borne transmission has been suggested as an important transmission mechanism for Influenza A (IA) viruses in wild duck populations; however, relatively few studies have attempted to detect IA viruses from aquatic habitats. Water-isolated viruses have rarely been genetically characterized and evaluation for persistence in water and infectivity in natural hosts has never been documented. In this study, we focused on two IA viruses (H3N8 and H4N6 subtypes) isolated from surface lake water in Minnesota, USA. We investigated the relative prevalence of the two virus subtypes in wild duck populations at the sampling site and their genetic relatedness to IA viruses isolated in wild waterbirds in North America. Viral persistence under different laboratory conditions (temperature and pH) and replication in experimentally infected Mallards (Anas platyrhynchos) were also characterized. Both viruses were the most prevalent subtype one year following their isolation in lake water. The viruses persisted in water for an extended time period at constant temperature (several weeks) but infectivity rapidly reduced under multiple freeze-thaw cycles. Furthermore, the two isolates efficiently replicated in Mallards. The complete genome characterization supported that these isolates originated from genetic reassortments with other IA viruses circulating in wild duck populations during the year of sampling. Based on phylogenetic analyses, we couldn't identify genetically similar viruses in duck populations in the years following their isolation from lake water. Our study supports the role for water-borne transmission for IA viruses but also highlights that additional field and experimental studies are required to support inter-annual persistence in aquatic habitats. PMID:22028909

  15. Asymmetry of genetic variation in fitness-related traits: apparent stabilizing selection on g(max).

    PubMed

    McGuigan, Katrina; Blows, Mark W

    2009-11-01

    The maintenance of genetic variation in traits closely associated with fitness remains a key unresolved issue in evolutionary genetics. One important qualification on the observation of genetic variation in fitness-related traits is that such traits respond asymmetrically to selection, evolving to a greater extent in the direction of lower fitness. Here we test the hypothesis that standing genetic variation in fitness-related traits is principally maintained for unfit phenotypes. Male Drosophila bunnanda vary in mating success (the primary determinant of male fitness) due to female mate choice. We used competitive mating success to partitioning males into two groups: successful (high fitness) and unsuccessful (low fitness). Relative to successful males, unsuccessful males harbored considerably greater levels of additive genetic variation for sexual signaling traits. This genetic asymmetry was detected for a multivariate trait that we demonstrated was not directly under stabilizing sexual selection, leading us to conclude the trait was under apparent stabilizing selection. Consequently, our results suggest genetic variance might be biased toward low fitness even for traits that are not themselves the direct targets of selection. Simple metrics of genetic variance are unlikely to be adequate descriptors of the complex nature of the genetic basis of traits under selection.

  16. The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

    USDA-ARS?s Scientific Manuscript database

    The choice of populations for quantitative genetics experiments impacts inferences about genetic architecture and prospective selection gains. Plant breeding and quantitative genetics studies are often conducted in one or a few among many possible biparental families. Trait genotypic variation withi...

  17. Genetic variation and effects on human eating behavior.

    PubMed

    de Krom, Mariken; Bauer, Florianne; Collier, David; Adan, R A H; la Fleur, Susanne E

    2009-01-01

    Feeding is a physiological process, influenced by genetic factors and the environment. In recent years, many studies have been performed to unravel the involvement of genetics in both eating behavior and its pathological forms: eating disorders and obesity. In this review, we provide a condensed introduction on the neurological aspects of eating and we describe the current status of research into the genetics of eating behavior, primarily focused on specific traits such as taste, satiation, and hunger. This is followed by an overview on the genetic studies done to unravel the heritable background of obesity and eating disorders. We examine the discussion currently taking place in the field of genetics of complex disorders and phenotypes on how to perform good and powerful studies, with the use of large-scale whole-genome association studies as one of the possible solutions. In the final part of this review, we give our view on the latest developments, including endophenotype approaches and animal studies. Studies of endophenotypes of eating behavior may help to identify core traits that are genetically influenced. Such studies would yield important knowledge on the underlying biological scaffold on which diagnostic criteria for eating disorders could be based and would provide information to influence eating behavior toward healthier living.

  18. Genetic Variation of Major Histocompatibility Complex and Microsatellite Loci: A Comparison in Bighorn Sheep

    PubMed Central

    Boyce, W. M.; Hedrick, P. W.; Muggli-Cockett, N. E.; Kalinowski, S.; Penedo, MCT.; Ramey-II, R. R.

    1997-01-01

    Examining and comparing genetic variation for major histocompatibility complex (MHC) and microsatellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean F(ST) values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC. PMID:9071595

  19. Genetic Variation in Dopamine Pathways Differentially Associated with Smoking Progression in Adolescence

    ERIC Educational Resources Information Center

    Laucht, Manfred; Becker, Katja; Frank, Josef; Schmidt, Martin H.; Esser, Gunter; Treutlein, Jens; Skowronek, Markus H.; Schumann, Gunter

    2008-01-01

    A study examines whether genetic variation in dopamine pathways differentially associate with smoking progression in adolescence. Results indicate the influence of specific dopamine genes in different stages of smoking progression in adolescents.

  20. Genetic variation of major histocompatibility complex and microsatellite loci: a comparison in bighorn sheep.

    PubMed

    Boyce, W M; Hedrick, P W; Muggli-Cockett, N E; Kalinowski, S; Penedo, M C; Ramey, R R

    1997-02-01

    Examining and comparing genetic variation for major histocompatibility complex (MHC) and micro-satellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean FST values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC.

  1. Genetic Variation in Dopamine Pathways Differentially Associated with Smoking Progression in Adolescence

    ERIC Educational Resources Information Center

    Laucht, Manfred; Becker, Katja; Frank, Josef; Schmidt, Martin H.; Esser, Gunter; Treutlein, Jens; Skowronek, Markus H.; Schumann, Gunter

    2008-01-01

    A study examines whether genetic variation in dopamine pathways differentially associate with smoking progression in adolescence. Results indicate the influence of specific dopamine genes in different stages of smoking progression in adolescents.

  2. Genetic Evaluation of Lactation Persistency for Five Breeds of Dairy Cattle

    USDA-ARS?s Scientific Manuscript database

    Cows with high persistency tend to produce less milk than expected at the beginning of lactation and more than expected at the end. Best prediction (BP) of persistency is calculated as a function of trait-specific standard lactation curves and linear regressions of test day deviations on days in mil...

  3. Lack of Variation at Phosphoglucose Isomerase (Pgi) in Bumblebees: Implications for Conservation Genetics Studies

    PubMed Central

    Ellis, Jonathan S.; Turner, Lucy M.; Knight, Mairi E.

    2013-01-01

    Assessing genetic variation underlying ecologically important traits is increasingly of interest and importance in population and conservation genetics. For some groups generally useful markers exist for examining the relative role of selection and drift in shaping genetic diversity e.g. the major histocompatibility complex in vertebrates and self-incompatibility loci in plants. For invertebrates there is no such generally useful locus. However, phosphoglucose isomerase (Pgi) has been proposed as a useful functional marker in the conservation genetics of invertebrates. Where thermal microclimate varies, balanced polymorphisms may be maintained due to trade-offs between thermally stable and kinetically advantageous allelic forms. We here report very low levels of Pgi variation in bumblebees rendering this locus to be of little use as an adaptive marker in a conservation genetics context in this group. Potential explanations for this lack of variation are considered. PMID:23750269

  4. Lack of variation at phosphoglucose isomerase (pgi) in bumblebees: implications for conservation genetics studies.

    PubMed

    Ellis, Jonathan S; Turner, Lucy M; Knight, Mairi E

    2013-01-01

    Assessing genetic variation underlying ecologically important traits is increasingly of interest and importance in population and conservation genetics. For some groups generally useful markers exist for examining the relative role of selection and drift in shaping genetic diversity e.g. the major histocompatibility complex in vertebrates and self-incompatibility loci in plants. For invertebrates there is no such generally useful locus. However, phosphoglucose isomerase (Pgi) has been proposed as a useful functional marker in the conservation genetics of invertebrates. Where thermal microclimate varies, balanced polymorphisms may be maintained due to trade-offs between thermally stable and kinetically advantageous allelic forms. We here report very low levels of Pgi variation in bumblebees rendering this locus to be of little use as an adaptive marker in a conservation genetics context in this group. Potential explanations for this lack of variation are considered.

  5. Genetic etiology in cases of recovered and persistent stuttering in an unselected, longitudinal sample of young twins

    PubMed Central

    Dworzynski, Katharina; Remington, Anna; Rijsdijk, Frühling; Howell, Peter; Plomin, Robert

    2007-01-01

    Purpose The contribution of genetic factors in persistence and early recovery from stuttering was assessed.. Method Data from the Twins Early Development Study were employed. Parental reports regarding stuttering were collected at ages 2, 3, 4 and 7 years and were used to classify speakers into recovered and persistent groups. Of 12,892 children with at least two ratings, 950 children had recovered and 135 persisted in their stutter. Results Logistic regressions showed that the rating at age 2 was not predictive of later stuttering, whereas ratings at ages 3 and 4 were. Concordance rates were consistently higher for monozygotic than for dizygotic twin pairs (with the exception of girls at age 3). At 3, 4 and 7 years, the liability to stuttering was highly heritable (h2 estimates of between .58 and .66). Heritability for the recovered and persistent groups was also high, but did not differ from each other. Conclusion Stuttering appears to be a disorder that has high heritability and little shared environment effect in early childhood and for recovered and persistent groups of children, by age 7. The clinical implications of the findings are discussed. PMID:17456895

  6. A joint history of the nature of genetic variation and the nature of schizophrenia.

    PubMed

    Kendler, K S

    2015-02-01

    This essay traces the history of concepts of genetic variation and schizophrenia from Darwin and Mendel to the present. For Darwin, the important form of genetic variation for evolution is continuous in nature and small in effect. Biometricians led by Pearson agreed and developed statistical genetic approaches utilizing trait correlations in relatives. Mendel studied discontinuous traits and subsequent Mendelians, led by Bateson, assumed that important genetic variation was large in effect producing discontinuous phenotypes. Although biometricians studied 'insanity', schizophrenia genetics under Kraepelin and Rüdin utilized Mendelian approaches congruent with their anatomical-clinical disease model of dementia praecox. Fisher showed, assuming many genes of small effect, Mendelian and Biometrical models were consilient. Echoing prior conflicts, psychiatric genetics since then has utilized both biometrical models, largely in twins, and Mendelian models, based on advancing molecular techniques. In 1968, Gottesman proposed a polygenic model for schizophrenia based on a threshold version of Fisher's theory. Since then, rigorous studies of the schizophrenia spectrum suggest that genetic risk for schizophrenia is more likely continuous than categorical. The last 5 years has seen increasingly convincing evidence from genome-wide association study (GWAS) and sequencing that genetic risk for schizophrenia is largely polygenic, and congruent with Fisher's and Gottesman's models. The gap between biometrical and molecular Mendelian models for schizophrenia has largely closed. The efforts to ground a categorical biomedical model of schizophrenia in Mendelian genetics have failed. The genetic risk for schizophrenia is widely distributed in human populations so that we all carry some degree of risk.

  7. The Effect of Genetic and Environmental Variation on Metabolic Gene Expression

    PubMed Central

    Scott, Cinda P.; Williams, Dean A.; Crawford, Douglas L.

    2009-01-01

    What is the relationship between genetic or environmental variation and the variation in mRNA expression? To address this, microarrays were used to examine the effect of genetic and environmental variation on cardiac mRNA expression for metabolic genes in three groups of Fundulus heteroclitus: (1) individuals sampled in the field (field), (2) field individuals acclimated for six months to laboratory conditions (acclimated) or (3) individuals bred for ten successive generations in a laboratory environment (G10). The G10 individuals have significantly less genetic variation than individuals obtained in the field and had a significantly lower variation in mRNA expression across all genes in comparison to the other two groups (p ≤ 0.001). When examining the gene specific variation, twenty-two genes had variation in expression that was significantly different among groups with lower variation in G10 individuals than in acclimated individuals. Additionally, there were fewer genes with significant differences in expression among G10 individuals versus either acclimated or field individuals: 66 genes have statistically different levels of expression versus 107 or 97 for Acclimated or Field groups. Based on the permutation of the data, these differences in the number of genes with significant differences among individuals within a group are unlikely to occur by chance (p < 0.01). Surprisingly, variation in mRNA expression in field individuals is lower than in acclimated individuals. Relative to the variation among individual within a group, few genes have significant differences in expression among groups (seven, 2.3%) and none of these are different between acclimated and field individuals. The results support the concept that genetic variation affects variation in mRNA expression and also suggests that temporal environmental variation associated with estuarine environments does not increase the variation among individuals or add to the differences among groups. PMID

  8. Genetic variation among agamid lizards of the trapelus agiliscomplex in the caspian-aral basin

    SciTech Connect

    Macey, J. Robert; Ananjeva, Natalia B.

    2004-05-19

    Allozyme variation is examined in eight populations of Trapelus from the Caspian-Aral Basin of the former USSR. Thirty-one loci (15 variable) exhibit remarkably low levels of genetic variation with only a Nei's genetic distance of 0.117 across 2500 km. An isolated population on the European side of the Caspian Sea is found to phenetically cluster inside the Asian populations examined, suggesting that it should not be considered taxonomically distinct.

  9. A joint history of the nature of genetic variation and the nature of schizophrenia

    PubMed Central

    Kendler, KS

    2014-01-01

    This essay traces the history of concepts of genetic variation and schizophrenia from Darwin and Mendel to the present. For Darwin, the important form of genetic variation for evolution is continuous in nature and small in effect. Biometricians led by Pearson agreed and developed statistical genetic approaches utilizing trait correlations in relatives. Mendel studied discontinuous traits and subsequent Mendelians, led by Bateson, assumed that important genetic variation was large in effect producing discontinuous phenotypes. Although biometricians studied ‘insanity’, schizophrenia genetics under Kraepelin and Rüdin utilized Mendelian approaches congruent with their anatomical-clinical disease model of dementia praecox. Fisher showed, assuming many genes of small effect, Mendelian and Biometrical models were consilient. Echoing prior conflicts, psychiatric genetics since then has utilized both biometrical models, largely in twins, and Mendelian models, based on advancing molecular techniques. In 1968, Gottesman proposed a polygenic model for schizophrenia based on a threshold version of Fisher’s theory. Since then, rigorous studies of the schizophrenia spectrum suggest that genetic risk for schizophrenia is more likely continuous than categorical. The last 5 years has seen increasingly convincing evidence from genome-wide association study (GWAS) and sequencing that genetic risk for schizophrenia is largely polygenic, and congruent with Fisher’s and Gottesman’s models. The gap between biometrical and molecular Mendelian models for schizophrenia has largely closed. The efforts to ground a categorical biomedical model of schizophrenia in Mendelian genetics have failed. The genetic risk for schizophrenia is widely distributed in human populations so that we all carry some degree of risk. …Variations, as Darwin and most breeders recognized, were of two types. There were sports, large discontinuous variations, relatively rare … [and] there were the less

  10. Unusually Low Levels of Genetic Variation among Giardia lamblia Isolates▿ ‡

    PubMed Central

    Teodorovic, Smilja; Braverman, John M.; Elmendorf, Heidi G.

    2007-01-01

    Giardia lamblia, an intestinal pathogen of mammals, including humans, is a significant cause of diarrheal disease around the world. Additionally, the parasite is found on a lineage which separated early from the main branch in eukaryotic evolution. The extent of genetic diversity among G. lamblia isolates is insufficiently understood, but this knowledge is a prerequisite to better understand the role of parasite variation in disease etiology and to examine the evolution of mechanisms of genetic exchange among eukaryotes. Intraisolate genetic variation in G. lamblia has never been estimated, and previous studies on interisolate genetic variation have included a limited sample of loci. Here we report a population genetics study of intra- and interisolate genetic diversity based on six coding and four noncoding regions from nine G. lamblia isolates. Our results indicate exceedingly low levels of genetic variation in two out of three G. lamblia groups that infect humans; this variation is sufficient to allow identification of isolate-specific markers. Low genetic diversity at both coding and noncoding regions, with an overall bias towards synonymous substitutions, was discovered. Surprisingly, we found a dichotomous haplotype structure in the third, more variable G. lamblia group, represented by a haplotype shared with one of the homogenous groups and an additional group-specific haplotype. We propose that the distinct patterns of genetic-variation distribution among lineages are a consequence of the presence of genetic exchange. More broadly, our findings have implications for the regulation of gene expression, as well as the mode of reproduction in the parasite. PMID:17557879

  11. Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice

    PubMed Central

    Zhao, Qiongyi; Li, Xiang; Jupp, Bianca; Chesworth, Rose; Lawrence, Andrew J.; Bredy, Timothy

    2016-01-01

    Continued vulnerability to relapse during abstinence is characteristic of cocaine addiction and suggests that drug-induced neuroadaptations persist during abstinence. However, the precise cellular and molecular attributes of these adaptations remain equivocal. One possibility is that cocaine self-administration leads to enduring changes in DNA methylation. To address this possibility, we isolated neurons from medial prefrontal cortex and performed high throughput DNA sequencing to examine changes in DNA methylation following cocaine self-administration. Twenty-nine genomic regions became persistently differentially methylated during cocaine self-administration, and an additional 28 regions became selectively differentially methylated during abstinence. Altered DNA methylation was associated with isoform-specific changes in the expression of co-localizing genes. These results provide the first neuron-specific, genome-wide profile of changes in DNA methylation induced by cocaine self-administration and protracted abstinence. Moreover, our findings suggest that altered DNA methylation facilitates long-term behavioral adaptation in a manner that extends beyond the perpetuation of altered transcriptional states. PMID:27213137

  12. Assessment of the Genetic Variation in Bone Fracture Healing

    DTIC Science & Technology

    2004-10-01

    variations in both structural and material properties of bone development will be recapitulated in the developmental mechanism(s) that controls the bone’s... structural geometry and material properties during fracture healing. Two goals were set out in the proposal to test this hypothesis. The first was to...determine how variations in basic bone structure and material properties in three in bred strains of mice is translated into the healing process of

  13. Genetic Variation and Population Structure in Native Americans

    PubMed Central

    Ramachandran, Sohini; Ray, Nicolas; Bedoya, Gabriel; Rojas, Winston; Parra, Maria V; Molina, Julio A; Gallo, Carla; Mazzotti, Guido; Poletti, Giovanni; Hill, Kim; Hurtado, Ana M; Labuda, Damian; Klitz, William; Barrantes, Ramiro; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, Maria Luiza; Tsuneto, Luiza T; Llop, Elena; Rothhammer, Francisco; Excoffier, Laurent; Feldman, Marcus W; Rosenberg, Noah A; Ruiz-Linares, Andrés

    2007-01-01

    We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas. PMID:18039031

  14. Genetic Variation in Odorant Receptors Contributes to Variation in Olfactory Behavior in a Natural Population of Drosophila melanogaster

    PubMed Central

    Richgels, P. K.

    2012-01-01

    Chemoreception is a principle modality by which organisms gain information from their environment, and extensive variation in odor-mediated behavior has been documented within and among species. To examine the mechanisms by which sensory systems mediate these responses, we ask to what extent variation in Drosophila melanogaster odorant receptor genes contributes to variation in odor-mediated behavior. Significant differences in behavioral responses to structurally similar odorants, methyl hexanoate and ethyl hexanoate, were found in a natural population. Polymorphisms in 3 genomic regions (Or22a/Or22b, Or35a, and Or47a) were identified and associated with variation in behavior to these esters. Overall similarity in association profiles for both odorants was observed, except for Or47a in which polymorphisms were associated solely with variation in responses to ethyl hexanoate. Our analyses were then extended to examine polymorphisms in 3 odorant receptors previously reported to contribute to variation in olfactory behavior for the chemically distinct odorants benzaldehyde and acetophenone. Two Or10a polymorphisms were associated with variation in response to ethyl hexanoate. Finally, differences in Or35a and Or47a expression were associated with variation in responses to ethyl hexanoate. These results demonstrate that the genetic variation at the peripheral sensory stage plays a role in mediating differences in odor-mediated behavior. PMID:22038943

  15. Regional variation in health is predominantly driven by lifestyle rather than genetics.

    PubMed

    Amador, Carmen; Xia, Charley; Nagy, Réka; Campbell, Archie; Porteous, David; Smith, Blair H; Hastie, Nick; Vitart, Veronique; Hayward, Caroline; Navarro, Pau; Haley, Chris S

    2017-10-06

    Regional differences in health-related phenotypes have been detected between and within countries. In Scotland, regions differ for a variety of health-related traits and display differences in mean lifespan of up to 7.5 years. Both genetics and lifestyle differences are potential causes of this variation. Using data on obesity-related traits of ~11,000 Scottish individuals with genome-wide genetic information and records of lifestyle and socioeconomic factors, we explored causes of regional variation by using models that incorporate genetic and environmental information jointly. We found that variation between individuals within regions showed substantial influence of both genetic variation and family environment. Regional variation for most obesity traits was associated with lifestyle and socioeconomic variables, such as smoking, diet and deprivation which are potentially modifiable. There was limited evidence that regional differences were of genetic origin. This has important implications for healthcare policies, suggesting that inequalities can be tackled with appropriate social and economic interventions.Health-related traits are known to vary geographically. Here, Amador and colleagues show that regional variation of obesity-related traits in a Scottish population is influenced more by lifestyle differences than it is by genetic differences.

  16. The majority of genetic variation in orangutan personality and subjective well-being is nonadditive.

    PubMed

    Adams, Mark James; King, James E; Weiss, Alexander

    2012-07-01

    The heritability of human personality is well-established. Recent research indicates that nonadditive genetic effects, such as dominance and epistasis, play a large role in personality variation. One possible explanation for the latter finding is that there has been recent selection on human personality. To test this possibility, we estimated additive and nonadditive genetic variance in personality and subjective well-being of zoo-housed orangutans. More than half of the genetic variance in these traits could be attributed to nonadditive genetic effects, modeled as dominance. Subjective well-being had genetic overlap with personality, though less so than has been found in humans or chimpanzees. Since a large portion of nonadditive genetic variance in personality is not unique to humans, the nonadditivity of human personality is not sufficient evidence for recent selection of personality in humans. Nonadditive genetic variance may be a general feature of the genetic structure of personality in primates and other animals.

  17. Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

    PubMed Central

    Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

  18. Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate.

    PubMed

    Brown, Rafe M; Weghorst, Jennifer A; Olson, Karen V; Duya, Mariano R M; Barley, Anthony J; Duya, Melizar V; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A; Dominy, Nathaniel J; Ong, Perry S; Moritz, Gillian L; Luczon, Adrian; Diesmos, Mae Lowe L; Diesmos, Arvin C; Siler, Cameron D

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.

  19. Framework for interpretation of genetic variations in pancreatitis patients

    PubMed Central

    Whitcomb, David C.

    2012-01-01

    Chronic pancreatitis (CP) is defined by irreversible damage to the pancreas as a result of inflammation-driven pancreatic tissue destruction and fibrosis occurring over many years. The disorder is complex, with multiple etiologies leading to the same tissue pathology, and unpredictable clinical courses with variable pain, exocrine and endocrine organ dysfunction, and cancer. Underlying genetic variants are central CP susceptibility and progression. Three genes, with Mendelian genetic biology (PRSS1, CFTR, and SPINK1) have been recognized for over a decade, and little progress has been made since then. Furthermore, application of high-throughput genetic techniques, including genome-wide association studies (GWAS) and next generation sequencing (NGS) will provide a large volume of new genetic variants that are associated with CP, but with small independent effect that are impossible to apply in the clinic. The problem of interpretation is using the old framework of the germ theory of disease to understand complex genetic disorders. To understand these variants and translate them into clinically useful information requires a new framework based on modeling and simulation of physiological processes with or without genetic, metabolic and environmental variables considered at the cellular and organ levels, with integration of the immune system, nervous system, tissue injury and repair system, and DNA repair system. The North American Pancreatitis Study 2 (NAPS2) study was designed to capture this type of date and construct a time line to understand and later predict rates of disease progression from the initial symptom to end-stage disease. This effort is needed to target the etiology of pancreatic dysfunction beginning at the first signs of disease and thereby prevent the development of irreversible damage and the complications of CP. The need for a new framework and the rational for implementing it into clinical practice are described. PMID:23230421

  20. Discovery of Genetic Variation that Enhances Improvement of Dairy Production and Health in Cattle and Buffalos

    USDA-ARS?s Scientific Manuscript database

    The hypothesis underlying this project is that genome-wide information on genetic variation will increase accuracy of predictions of genetic merit; will enhance heritability and reliability of these predictions through improved pedigree information; and will improve detection of most quantitative tr...

  1. Landscape-scale genetic variation in a forest outbreak species, the mountain pine beetle (Dendroctonus ponderosae)

    Treesearch

    K. E. Mock; B. J. Bentz; E. M. O' Neill; J. P. Chong; J. Orwin; M. E. Pfrender

    2007-01-01

    The mountain pine beetle Dendroctonus ponderosae is a native species currently experiencing large-scale outbreaks in western North American pine forests. We sought to describe the pattern of genetic variation across the range of this species, to determine whether there were detectable genetic differences between D. ponderosae...

  2. Genetic variation in susceptibility to fusiform rust in seedlings from a wild population of loblolly pine

    Treesearch

    Bohun B. Kinloch Jr.; Roy W. Stonecypher

    1969-01-01

    Striking genetic variation in susceptibility to fusiform rust was observed among SS controlled-pollinated (CP) and 48 wind-pollinated (WP) families from parent trees of loblolly pine selected at random in a natural forest stand in southwest Georgia. The mating design permitted statistical tests for estimating both additive and total genetic variance. WP families were...

  3. Patterns of genetic variation and covariation in ejaculate traits reveal potential evolutionary constraints in guppies.

    PubMed

    Evans, J P

    2011-05-01

    Ejaculates comprise multiple and potentially interacting traits that determine male fertility and sperm competitiveness. Consequently, selection on these traits is likely to be intense, but the efficacy of selection will depend critically on patterns of genetic variation and covariation underlying their expression. In this study, I provide a prospective quantitative genetic analysis of ejaculate traits in the guppy Poecilia reticulata, a highly promiscuous live-bearing fish. I used a standard paternal half-sibling breeding design to characterize patterns of genetic (co)variation in components of sperm length and in vitro sperm performance. All traits exhibited high levels of phenotypic and additive genetic variation, and in several cases, patterns of genetic variation was consistent with Y-linkage. There were also highly significant negative genetic correlations between the various measures of sperm length and sperm performance. In particular, the length of the sperm's midpiece was strongly, negatively and genetically correlated with sperm's swimming velocity-an important determinant of sperm competitiveness in this and other species. Other components of sperm length, including the flagellum and head, were independently and negatively genetically correlated with the proportion of live sperm in the ejaculate (sperm viability). Whether these relationships represent evolutionary trade-offs depends on the precise relationships between these traits and competitive fertilization rates, which have yet to be fully resolved in this (and indeed most) species. Nevertheless, these prospective analyses point to potential constraints on ejaculate evolution and may explain the high level of phenotypic variability in ejaculate traits in this species.

  4. Genetic variation in bison (bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

    USDA-ARS?s Scientific Manuscript database

    Genetic variation was quantified at 29 polymorphic microsatellite DNA loci in nine herds of plains bison (Bison bison bison), three herds of wood bison (B.b. athabascae), fourteen breeds of taurine cattle (Bos Taurus Taurus), and two breeds of indicine cattle (Bos Taurus indicus). Genetic distances,...

  5. Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

    USDA-ARS?s Scientific Manuscript database

    Genetic variation was quantified at 29 polymorphic microsatellite DNA loci in nine herds of plains bison (Bison bison bison), three herds of wood bison (B. b. athabascae), fourteen breeds of taurine cattle (Bos taurus taurus), and two breeds of indicine cattle (Bos taurus indicus). Genetic distances...

  6. Genetic variation in historical and modern apple cultivars compared to wild relatives

    USDA-ARS?s Scientific Manuscript database

    Plant domestication is generally modeled as a scenario wherein strong artificial selection is applied to a small subset of the population of a wild species. The result is that the domesticated species exhibits a genome-wide reduction in genetic variation, referred to as a genetic bottleneck. This ...

  7. Incorporating latitudinal and central–marginal trends in assessing genetic variation across species ranges

    Treesearch

    Qinfeng Guo

    2012-01-01

    The genetic variation across a species’ range is an important factor in speciation and conservation, yet searching for general patterns and underlying causes remains challenging. While the majority of comparisons between central and marginal populations have revealed a general central–marginal (C-M) decline in genetic diversity, others show no clear pattern. Similarly...

  8. Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications.

    PubMed

    Maisano Delser, Pierpaolo; Fuselli, Silvia

    2013-05-01

    Understanding the role of inheritance in individual variation in drug response is the focus of pharmacogenetics (PGx). A key part of this understanding is quantifying the role of genetic ancestry in this phenotypic outcome. To provide insight into the relationship between ethnicity and drug response, this study first infers the global distribution of PGx variation and defines its structure. Second, the study evaluates if geographic population structure stems from all PGx loci in general, or if structure is caused by specific genes. Lastly, we identify the genetic variants contributing the greatest proportion of such structure. Our study describes the global genetic structure of PGx loci across the 52 populations of the Human Genome Diversity Cell-Line Panel, the most inclusive set of human populations freely available for studies on human genetic variation. By analysing genetic variation at 1,001 single nucleotide polymorphisms (SNPs) involved in biotransformation of exogenous substances, we describe the between-populations PGx variation, as well geographical groupings of diversity. In addition, with discriminant analysis of principal component (DAPC), we infer how many and which groups of populations are supported by PGx variation, and identify which SNPs actually contribute to the PGx structure between such groups. Our results show that intergenic, synonymous and non-synonymous SNPs show similar levels of genetic variation across the globe. Conversely, loci coding for Cytochrome P450s (mainly metabolizing exogenous substances) show significantly higher levels of genetic diversity between populations than the other gene categories. Overall, genetic variation at PGx loci correlates with geographic distances between populations, and the apportionment of genetic variation is similar to that observed for the rest of the genome. In other words, the pattern of PGx variation has been mainly shaped by the demographic history of our species, as in the case of most of our

  9. Regional Variation in Human Exposure to Persistent Organic Pollutants in the United States, NHANES

    PubMed Central

    Wattigney, Wendy A.; Irvin-Barnwell, Elizabeth; Pavuk, Marian; Ragin-Wilson, Angela

    2015-01-01

    We examined serum levels of persistent organic pollutants (POPs) among geographical regions of the United States as defined by the US Census Bureau. National Health and Nutrition Examination Survey (NHANES) data for adults aged 20 years and older are presented for selected survey periods between 1999 and 2010. From NHANES 1999 through 2004, dichlorodiphenyldichloroethylene (DDE) concentration levels were consistently higher among people living in the West than in the Midwest, Northeast, or South. In 2003–2010, perfluorinated compound concentrations tended to be highest in the South. The sum of 35 polychlorinated biphenyls (PCBs) congeners was significantly higher in the Northeast [GM: 189; 95% CI: 173–204 ng/g lipid] than the remaining regions. The regional differences in higher body burdens of exposure to particular POPs could be attributed to a variety of activities, including region-specific patterns of land use and industrial and agricultural chemical applications, as well as different levels of regulatory activity. PMID:26839572

  10. Finding and interpreting genetic variations that are important to ophthalmologists.

    PubMed Central

    Stone, Edwin M

    2003-01-01

    PURPOSE: To explore two approaches for making the human genome more accessible and useful to practicing ophthalmologists. METHODS: DNA samples were obtained from patients with inherited eye diseases, and these samples were screened for sequence variations in known disease genes with a combination of single-strand conformational polymorphism analysis and automated DNA sequencing. Data from this screening were then used to evaluate strategies for productively narrowing the sample space as well as for estimating the pathogenic potential of variations that were discovered in individual patients. For the latter purpose, a universal nomenclature for pathogenic potential was proposed based upon the segregation of disease alleles and the evolutionary conservation of specific residues as reflected by a substitution matrix known as blosum 62. RESULTS: Sequence variations were found to be unevenly distributed among disease-associated genes, such that screening strategies could be refined to discover more than 50% of clinically important sequence variations with only 10% of the effort. The use of the blosum 62 matrix was more statistically powerful than our previous method of estimating pathogenic probability. CONCLUSIONS: The size of the human genome requires that clinical questions be very carefully focused if they are to be meaningfully answered in a reasonable amount of time and with a reasonable amount of resources. By examining the behavior of known disease genes, one can design strategies for significantly focusing the sample space and for more effectively interpreting the variations that are found. PMID:14971589

  11. Variation, "evolution", immortality and genetic instabilities in tumour cells.

    PubMed

    Bignold, L P

    2007-08-18

    The pathological characteristics of tumour cells often include variation of their histopathological features (i.e. "degrees of de-differentiation") between cases of the same tumour type and between different foci within individual tumours. Usually, only a few cell lines from tumours are immortal. Currently, somatic mutation, replicative infidelity of DNA and aneuploidy are suggested as alternative mechanisms of genomic disturbance underlying tumours. Nevertheless, apart from Hansemann's ideas of "anaplasia" and "de-differentiation" (proposed in the 1890s), and supposed "evolutionary themes" in cancer cell biology, little has been published concerning how histopathologic variation and immortality in tumour cells might arise. This paper reviews applications of the concepts of "variation" to tumours, including concepts of "evolution" and "cellular Darwinism". It is proposed that combinations of somatic mutation, DNA replicative infidelity and aneuploidy may explain the variabilities in tumours, and provide immortality in occasional tumour cells. A possible model involves (i) an initial somatic mutation causing reduced replicative fidelity of DNA, which could be variable in intensity, and thus give rise to variations between cases; (ii) a phase of replicative infidelity of DNA causing daughter cells lines to develop various abnormalities to different degrees, and hence provide for variation between areas of the same tumour. As a last event (iii) occasional asymmetric chromosomal distributions (aneuploidy) might "refresh" the ability of a daughter cell to replicate DNA faithfully causing them to become immortal. Thus extensively mutant and variable, hyperploid, and occasionally immortal cells might arise.

  12. Genetic variation and early performance of Giant Sequoia in plantations

    Treesearch

    W. J. Libby

    1986-01-01

    Giant sequoia (Sequoiadendron giganteum [Lindl.] Buchholz) is genetically less variable than expected; furthermore, it is less variable and its populations are less structured than are several associated or related conifers. Giant sequoia seedlings from open-pollinated seeds of isolated trees or from small outlier groves do not survive and grow as...

  13. Genetic Variation in Seed and Fruit Characters in Sugar Maple

    Treesearch

    William J. Gabriel

    1978-01-01

    A study of the seeds and fruits of sugar maples from 32 provenances has shown that: (1) dry weight of seed and percentage of filled fruit varied genetically among and within provenances; (2) dry weight of seed and latitude of provenance are positively correlated; provenances from higher latitudes and colder temperatures exhibited higher weights; (3) the percentage of...

  14. Genomic exploitation of genetic variation for crop improvement

    USDA-ARS?s Scientific Manuscript database

    Crop plants produce food, fiber, and fuel that are essential to human civilization and mainstays of economic prosperity. Our society continues to cultivate and improve the crop plants for better quality and productivity with sustainable environments. The process of crop genetic improvement has bee...

  15. Ecological genetics of floret mass variation in Bromus tectorum (Poaceae)

    Treesearch

    Susan E. Meyer

    2010-01-01

    Bromus tectorum L. (cheatgrass, downy brome) is a highly invasive inbreeding annual grass that dominates millions of hectares of former shrubland in interior western North America. Factors contributing to its success include strong genetic regulation of key adaptive traits coupled with high phenotypic plasticity in response to resource availability (Meyer and Allen...

  16. Inbreeding and loss of genetic variation in a reintroduced population of Mauritius Kestrel.

    PubMed

    Ewing, Steven R; Nager, Ruedi G; Nicoll, Malcolm A C; Aumjaud, Aurelien; Jones, Carl G; Keller, Lukas F

    2008-04-01

    Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel (Falco punctatus) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N(eI)= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N(eV)= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.

  17. Variation and Genetic Structure in Platanus mexicana (Platanaceae) along Riparian Altitudinal Gradient

    PubMed Central

    Galván-Hernández, Dulce M.; Lozada-García, J. Armando; Flores-Estévez, Norma; Galindo-González, Jorge; Vázquez-Torres, S. Mario

    2015-01-01

    Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State) grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l.) using ten inter-simple sequence repeats (ISSR) markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42) and polymorphism reached the top value at the middle altitude (% p = 88.57). Analysis of molecular variance (AMOVA) and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA) dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems. PMID:25607732

  18. Variation and genetic structure in Platanus mexicana (Platanaceae) along riparian altitudinal gradient.

    PubMed

    Galván-Hernández, Dulce M; Lozada-García, J Armando; Flores-Estévez, Norma; Galindo-González, Jorge; Vázquez-Torres, S Mario

    2015-01-19

    Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State) grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l.) using ten inter-simple sequence repeats (ISSR) markers. The highest value for Shannon index and Nei's gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42) and polymorphism reached the top value at the middle altitude (% p = 88.57). Analysis of molecular variance (AMOVA) and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA) dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems.

  19. Population-genetic properties of differentiated copy number variations in cattle

    USDA-ARS?s Scientific Manuscript database

    Besides single nucleotide polymorphism (SNP), copy number variation (CNV) which comprise insertions, deletions and duplications of genomic sequence, is a new informative type of genetic variations. CNVs have been shown to be both common in mammals and important for understanding relationship between...

  20. Allozyme variation of Port-Orford-Cedar (Chamaecyparis lawsoniana): implications for genetic conservation

    Treesearch

    Constance I. Millar; Kimberly A. Marshall

    1991-01-01

    Variation at 32 allozyme loci in nine disjunct populations of Part-Orford-cedar (POC) from the California floristic region was measured to estimate the amount and pattern of genetic variability in natural stands. Variation in electrophoretically detectable loci was moderately high, with mean number of alleles per locus = 1.9, 64.9% polymorphic loci, and observed...

  1. Molecular genetic variation in cultivated peanuts germplasm of Henan and detection of their elite allelic variations

    USDA-ARS?s Scientific Manuscript database

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts i...

  2. Genetic basis of Neisseria gonorrhoeae lipooligosaccharide antigenic variation.

    PubMed Central

    Danaher, R J; Levin, J C; Arking, D; Burch, C L; Sandlin, R; Stein, D C

    1995-01-01

    Neisseria gonorrhoeae lipooligosaccharide (LOS) undergoes antigenic variation at a high rate, and this variation can be monitored by changes in a strain's ability to bind LOS-specific monoclonal antibodies. We report here the cloning and identification of a gene, lsi-2, that can mediate this variation. The DNA sequence of lsi-2 has been determined for N. gonorrhoeae 1291, a strain that expresses a high-molecular-mass LOS, and a derivative of this strain, RS132L, that produces a truncated LOS. In the parental strain, lsi-2 contains a string of 12 guanines in the middle of its coding sequence. In cells that had antigenically varied to produce a truncated LOS, the number of guanines in lsi-2 was altered. Site-specific deletions were constructed to verify that expression of a 3.6-kDa LOS is due to alterations in lsi-2. PMID:8522539

  3. Persistent Sub-Yearly Chromospheric Variations in Lower Main-Sequence Stars: Tau Booe and alpha Com

    NASA Technical Reports Server (NTRS)

    Maulik, Davesh; Donahue, Robert A.; Baliunas, Sallie L.

    1997-01-01

    The recent discoveries of extrasolar planetary systems around lower main-sequence stars such as tau Booe (HD 120136) has prompted further investigation into their stellar activity. A cursory analysis of tau Booe for cyclic chromospheric activity, based on its 30-yr record of Ca 2 H and K fluxes obtained as part of the HK Project from Mount Wilson Observatory, finds an intermediate, sub-yearly period (approximately 117 d) in chromospheric activity in addition to, and separate from, both its rotation (3.3 d) and long-term variability. As a persistent subyearly period in surface magnetic activity is unprecedented, we investigate this apparent anomaly further by examining chromospheric activity levels of other stars with similar mass, searching for variability in chromospheric activity with periods of less than one year, but longer than measured or predicted rotation. An examination of the time series of 40 mid-to-late F dwarfs yielded one other star for further analysis: alpha Com (HD 114378, P approximately 132 d). The variations for these two stars were checked for persistence and coherence. Based on these determinations, we eliminate the possibilities of rotation, long-term activity cycle, and the evolution of active regions as the cause of this variation in both stars. In particular, for tau Booe we infer that the phenomenon may be chromospheric in origin; however, beyond this, it is difficult to identify anything further regarding the cause of the activity variations, or even whether the observed modulation in the two stars have the same origin.

  4. How genetic variation is affected by geographic environments and ploidy level in Erianthus arundinaceus?

    PubMed

    Zhang, Jianbo; Yan, Jiajun; Shen, Xiaoyun; Chang, Dan; Bai, Shiqie; Zhang, Yu; Zhang, Jin

    2017-01-01

    Erianthus arundinaceus is not only a candidate plant for sugarcane breeding programs, but also a potential bioenergy grass. Genetic variation that is affected by geographic environments and ploidy level is very important for the utilization of Erianthus arundinaceus. In this study, effects of geographic environments and ploidy level on genetic variation were studied through analyzing the genetic diversity, genetic similarity and cluster analysis of 46 E. arundinaceus materials from natural habitats in China by using 7 ISSRs and 15 SSRs. Results showed that: 1) Seven ISSRs generated total 66 bands, of which 77% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.642 to 0.904 with an average value of 0.765. Fifteen SSRs generated 138 bands, of which 81% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.634 to 0.963 with an average value of 0.802. The results indicated great genetic diversity existed in the tested materials. 2)The tested materials were clustered into 3 groups and 7 subgroups, which demonstrated a strong geographic effect on variation of the local E. arundinaceus, and weak relationship was found between genetic distance and geographic distance. Five tetraploid materials were not clustered together, and were clustered together with materials from similar geographical location. 3) The genetic variation and cluster results were affected by geographic landforms and environments, the gene flow was blocked by Ocean and mountains, and promoted by river. The effect of ploidy level on genetic variation was little.

  5. Representing genetic variation as continuous surfaces: An approach for identifying spatial dependency in landscape genetic studies

    Treesearch

    Melanie A. Murphy; Jeffrey S. Evans; Samuel A. Cushman; Andrew Storfer

    2008-01-01

    Landscape genetics, an emerging field integrating landscape ecology and population genetics, has great potential to influence our understanding of habitat connectivity and distribution of organisms. Whereas typical population genetics studies summarize gene flow as pairwise measures between sampling localities, landscape characteristics that influence population...

  6. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations.

    PubMed

    Kivisild, T; Rootsi, S; Metspalu, M; Mastana, S; Kaldma, K; Parik, J; Metspalu, E; Adojaan, M; Tolk, H-V; Stepanov, V; Gölge, M; Usanga, E; Papiha, S S; Cinnioğlu, C; King, R; Cavalli-Sforza, L; Underhill, P A; Villems, R

    2003-02-01

    Two tribal groups from southern India--the Chenchus and Koyas--were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.

  7. The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations

    PubMed Central

    Kivisild, T.; Rootsi, S.; Metspalu, M.; Mastana, S.; Kaldma, K.; Parik, J.; Metspalu, E.; Adojaan, M.; Tolk, H.-V.; Stepanov, V.; Gölge, M.; Usanga, E.; Papiha, S. S.; Cinnioğlu, C.; King, R.; Cavalli-Sforza, L.; Underhill, P. A.; Villems, R.

    2003-01-01

    Two tribal groups from southern India—the Chenchus and Koyas—were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools. PMID:12536373

  8. The spread of apomixis and its effect on resident genetic variation.

    PubMed

    Adolfsson, S; Bengtsson, B O

    2007-09-01

    In a simulation model we investigated how much of the initial genetic variation that is retained in a population after a dominant mutation has brought apomixis to fixation in it. A marker allele associated with the apomixis mutation is generally retained after the fixation of apomixis, particularly if the two alleles are closely linked. The spread of asexuality, however, normally leads to almost no loss of genetic variation, neither with respect to cytotypes nor with respect to genotypes. This holds for large populations and apomixis mutants with strong pollen production. In smaller populations, and with apomicts with reduced pollen production, the outcome is more variable, ranging from no genetic variation retained to only weakly reduced variability compared with the initial state. These results help explain the high genetic variability in many apomicts. They also imply that natural selection will have many genotypes to act on even after the spread of apomixis.

  9. Variation in the management of infants hospitalized for bronchiolitis persists after the 2006 American Academy of Pediatrics bronchiolitis guidelines.

    PubMed

    Florin, Todd A; Byczkowski, Terri; Ruddy, Richard M; Zorc, Joseph J; Test, Matthew; Shah, Samir S

    2014-10-01

    To describe variation across US pediatric hospitals in the utilization of resources not recommended for routine use by the American Academy of Pediatrics guideline for infants hospitalized with bronchiolitis and to examine the association between resource utilization and disposition outcomes. We conducted a cross-sectional study of infants ≤12 months hospitalized for bronchiolitis from 2007-2012 at 42 hospitals contributing data to the Pediatric Health Information System. Patients with asthma were excluded. The primary outcome was hospital-level variation in utilization of 5 resources not recommended for routine use: albuterol, racemic epinephrine, corticosteroids, chest radiography, and antibiotics. We also examined the association of resource utilization with length of stay (LOS) and readmission. In total, 64,994 hospitalizations were analyzed. After adjustment for patient characteristics, albuterol (median, 52.4%; range, 3.5%-81%), racemic epinephrine (20.1%; 0.6%-78.8%), and chest radiography (54.9%; 24.1%-76.7%) had the greatest variation across hospitals. Utilization of albuterol, racemic epinephrine, and antibiotics did not change significantly over time compared with small decreases in corticosteroid (3.3%) and chest radiography (8.6%) use over the study period. Utilization of each resource was significantly associated with increased LOS without concomitant decreased odds of readmission. Substantial use and variation in 5 resources not recommended for routine use by the American Academy of Pediatrics bronchiolitis guideline persists with increased utilization associated with increased LOS without the benefit of decreased readmission. Future work should focus on developing processes that can be widely disseminated and easily implemented to minimize unwarranted practice variation when evidence and guidelines exist. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Genet Variation of Ectomycorrhizal Suillus granulatus Fruiting Bodies in Pinus strobus Stands

    PubMed Central

    Lee, Hwa-Yong

    2016-01-01

    The genets of Suillus granulatus in a Pinus strobus stand (13 m × 60 m) were identified using random amplified polymorphic DNA molecular markers and the DNA of mushrooms that fruited for two years, and variations in genet size and distribution were analyzed. From a total of 116 mushrooms, 73 genets were identified and were grouped into three locations. The genets of mushrooms in close proximity differed from each other. The genet sizes varied at any of the three locations. The lengths of the identified genets in the pine stand ranged from 0.09 to 2.90 m. The average number of mushrooms per genet was 1.2 to 2.3, and the percentage of genets that were represented by a single mushroom was 44% to 94%. This variation in the genets of mushrooms in close proximity suggests that the ectomycorrhizal mycelial bodies of S. granulatus propagated sexually by fusing haploid spores derived from the mushrooms gills with below-ground mycelia. Therefore, it is necessary further to investigate the formation of new genets through spores in ectomycorrhizal fungal colonies. PMID:27103849

  11. Role of novel DSP_p.Q986X genetic variation in arrhythmogenic right ventricular cardiomyopathy.

    PubMed

    Campuzano, Oscar; Alcalde, Mireia; Berne, Paola; Zorio, Esther; Iglesias, Anna; Navarro-Manchón, Josep; Brugada, Josep; Brugada, Ramon

    2013-10-01

    Arrhythmogenic right ventricular cardiomyopathy is an inherited disease characterized by a progressive myocardium fibrofatty replacement. This abnormality disrupts electrical transmission causing ventricular arrhythmias and sudden cardiac death. This genetic disease is transmitted mainly with an autosomal dominant pattern. Our aim was to identify the genetic defect responsible for the pathology in a Spanish family, and to perform its phenotype connotations. A total of 15 individuals in a three-generation Spanish family were screened after the sudden cardiac death of one family member. All they underwent a complete physical examination, 12-lead electrocardiogram, 2-dimensional echocardiography, magnetic resonance imaging, exercise stress test, 24-h Holter and genetic testing. Autopsy revealed the presence of biventricular arrhythmogenic dysplasia in deceased member. Six family members showed clinical symptoms but only three of them fulfilled definite diagnostic criteria of the disease. Genetic analysis showed a novel nonsense genetic variation in nine family members. All family members with clinical symptoms carried the genetic variation. Genetic testing in families affected by arrhythmogenic right ventricular cardiomyopathy helps to identify the genetic cause responsible for the disease. The incomplete penetrance and variable phenotypic expression highlights the need of comprehensive genetic analysis and further phenotype implications of genetics to clarify the pathophysiology of the disease. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  12. Genetic variation of occult hepatitis B virus infection

    PubMed Central

    Zhu, Hui-Lan; Li, Xu; Li, Jun; Zhang, Zhen-Hua

    2016-01-01

    Occult hepatitis B virus infection (OBI), characterized as the persistence of hepatitis B virus (HBV) surface antigen (HBsAg) seronegativity and low viral load in blood or liver, is a special form of HBV infection. OBI may be related mainly to mutations in the HBV genome, although the underlying mechanism of it remains to be clarified. Mutations especially within the immunodominant “α” determinant of S protein are “hot spots” that could contribute to the occurrence of OBI via affecting antigenicity and immunogenicity of HBsAg or replication and secretion of virion. Clinical reports account for a large proportion of previous studies on OBI, while functional analyses, especially those based on full-length HBV genome, are rare. PMID:27053845

  13. Profiling and Spatial Variation Analysis of Persistent Organic Pollutants in South African Delphinids.

    PubMed

    Gui, Duan; Karczmarski, Leszek; Yu, Ri-Qing; Plön, Stephanie; Chen, Laiguo; Tu, Qin; Cliff, Geremy; Wu, Yuping

    2016-04-05

    The continuous disposal of persistent organic pollutants (POPs) in South Africa (SA) warrants concern about their detrimental effects on humans and wildlife. We surveyed six dolphin species (n = 90) incidentally captured in shark net installations or stranded off the SA east and south coast from 2005 to 2009 to study the POP exposure. Sousa plumbea, an inshore and estuarine species, was found to be the most contaminated by total POPs (21 100 ng g(-1) lw) of all the dolphins off SA, followed by Tursiops aduncus (19 800 ng g(-1) lw), Lagenodelphis hosei (13 600 ng g(-1) lw), and Delphinus capensis (5500 ng g(-1) lw), whereas POP levels in the offshore or pelagic delphinids were much lower. In all delphinids, dominant pollutants were dichlorodiphenyltrichloroethanes (DDTs), which represented more than 60% of the total concentration of total POPs, followed by polychlorinated biphenyls (PCBs, 30%). Concentrations of DDTs in S. plumbea and T. aduncus off SA were among the highest levels reported in delphinids globally. Approximately half of the adult T. aduncus had PCB concentrations above the effect threshold for impairment of immune functions. The concentrations of Mirex and Dieldrin in SA delphinids were higher than those found in species from other regions of the Southern Hemisphere.

  14. Effects of functionally asexual reproduction on quantitative genetic variation in the evening primroses (Oenothera, Onagraceae).

    PubMed

    Godfrey, Ryan M; Johnson, Marc T J

    2014-11-01

    It has long been predicted that a loss of sexual reproduction leads to decreased heritable variation within populations and increased differentiation between populations. Despite an abundance of theory, there are few empirical tests of how sex affects genetic variation in phenotypic traits, especially for plants. Here we test whether repeated losses of two critical components of sex (recombination and segregation) in the evening primroses (Oenothera L., Onagraceae) affect quantitative genetic variation within and between populations. We sampled multiple genetic families from 3-5 populations from each of eight Oenothera species, which represented four independent transitions between sexual reproduction and a functionally asexual genetic system called "permanent translocation heterozygosity." We used quantitative genetics methods to partition genetic variation within and between populations for eight plant traits related to growth, leaf physiology, flowering, and resistance to herbivores. Heritability was, on average, 74% higher in sexual Oenothera populations than in functionally asexual populations, with plant growth rate, specific leaf area, and the percentage of leaf water content showing the strongest differences. By contrast, genetic differentiation among populations was 2.8× higher in functionally asexual vs. sexual Oenothera species. This difference was particularly strong for specific leaf area. Sexual populations tended to exhibit higher genetic correlations among traits, but this difference was weakly supported. These results support the prediction that sexual reproduction maintains higher genetic variation within populations, which may facilitate adaptive evolution. We also found partial support for the prediction that a loss of sex leads to greater population differentiation, which may elevate speciation rates. © 2014 Botanical Society of America, Inc.

  15. Genetic Variation in the Social Environment Contributes to Health and Disease

    PubMed Central

    Ingels, Jesse F.; Bohl, Casey J.; Callebert, Jacques; Launay, Jean-Marie; Krohn, Jon; Legarra, Andres; Williams, Robert W.; Stegle, Oliver

    2017-01-01

    Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual’s genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of “missing heritability” in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects. PMID:28121987

  16. Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease

    PubMed Central

    Gomez, Felicia; Hirbo, Jibril; Tishkoff, Sarah A.

    2014-01-01

    Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent. PMID:24984772

  17. Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations

    PubMed Central

    Ciborowski, Kate; Jordan, William C; Garcia de Leaniz, Carlos; Consuegra, Sofia

    2017-01-01

    The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change. PMID:28186200

  18. Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata

    PubMed Central

    Pineda, Mari-Carmen; Lorente, Beatriz; López-Legentil, Susanna; Palacín, Creu

    2016-01-01

    Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata. PMID:27366653

  19. Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata.

    PubMed

    Pineda, Mari-Carmen; Lorente, Beatriz; López-Legentil, Susanna; Palacín, Creu; Turon, Xavier

    2016-01-01

    Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata.

  20. Altitudinal and seasonal variations of persistent organic pollutants in the Bolivian Andes Mountains.

    PubMed

    Estellano, Victor H; Pozo, Karla; Harner, Tom; Franken, Margot; Zaballa, Mauricio

    2008-04-01

    Polyurethane foam disk passive air samplers were deployed over four periods of approximately 3 months along an altitudinal gradient (1820, 2600, 4650, and 5200 masl) on the east side of the Andean mountain range in Bolivia. The purpose of the study was to assess the gas-phase concentration and the altitudinal and seasonal trends of organochlorine pesticides and polychlorinated biphenyls (PCBs). Target compounds that were regularly detected included alpha- and gamma-hexachlorocyclohexane (HCH), endosulfans, and select PCB congeners. Endosulfans and HCH concentrations increased with altitude. Enrichment factors (concentration at the highest altitude divided by concentration at the lowest altitude) ranged from 10 to 20 for HCHs and 3 to 10 for endosulfans. Air parcel back trajectory analysis indicated that, in general, the high-altitude sites were exposed to a larger airshed and hence susceptible to long-range atmospheric transport from more distant regions. Seasonal differences were also observed with SigmaHCH concentrations peaking during periods 2 and 3 (March-September 2005). Airsheds (derived from the analysis of back trajectories) for periods 2 and 3 were less oriented along the Andes range (mountain air) with greater input from coastal regions. Endosulfans peaked during periods 1 and 2 (February-June 2005) and also exhibited the highest air concentrations of the target compounds, reaching approximately 1500 pg/m3 at the two highest elevation sites. PCB air concentrations at all sites were generally typical of global background values (<12 pg/m3) and showed no increase with altitude. This is the first study to measure air concentrations of persistent organic pollutants (POPs) in Bolivia and one of only a few studies to investigate altitudinal gradients of POPs.

  1. Association between OPN genetic variations and nephrolithiasis risk

    PubMed Central

    Xiao, Xu; Dong, Zhenjia; Ye, Xianqing; Yan, Yao; Chen, Xuehua; Pan, Qin; Xie, Yongfeng; Xie, Jie; Wang, Qiangdong; Yuan, Qinbo

    2016-01-01

    Osteopontin (OPN) has an important role in urolithiasis. However, few studies have explored the association between OPN genetic variants and urolithiasis risk. In the present study, three single-nucleotide polymorphisms (SNPs) (rs28357094, rs11439060 and rs11730582) located on the promoter of OPN were genotyped in a total of 480 individuals, including 230 nephrolithiasis patients and 250 matched healthy controls, and the associations between these SNPs and nephrolithiasis risk in different genetic models was assessed. No significant differences were identified in the genotype and allele frequencies of OPN rs28357094 or rs11730582 (P=0.805 for rs28357094; P=0.577 for rs11730582, respectively). However, carriers with the OPN rs11439060 insertion (ins) types (ins/deletion and ins/ins) were overrepresented in urolithiasis patients compared with the controls [odds ratio (OR), 1.55; 95% confidence interval (CI), 1.08–2.22]. In the stratified analysis, the increased risk was more evident among younger subjects (adjusted OR, 1.68; 95% CI, 1.01–2.81), females (2.15; 1.14–4.08), overweight subjects (1.80; 1.07–3.05), normotensive subjects (2.48; 1.02–6.00), abnormal blood sugar subjects (1.58; 1.08–2.30), smokers (1.63; 1.02–2.60), and ever-drinkers (1.98; 1.10–3.60).. These findings revealed that the OPN rs11439060 polymorphism may act as genetic biomarker for the detection of high-risk nephrolithiasis patients. PMID:27602211

  2. Genetics of focal segmental glomerulosclerosis and HIV-associated collapsing glomerulopathy: the role of MYH9 genetic variation

    PubMed Central

    Winkler, Cheryl A.; Nelson, George; Oleksyk, Taras K.; Nava, M. Berenice; Kopp, Jeffrey B.

    2010-01-01

    Until recently knowledge of genetic causes of glomerular disease was limited to certain rare or uncommon inherited diseases, and to a genes, either rare or with small effect, identified in candidate gene studies. These genetic factors accounted for only a very small fraction of kidney disease. However, the striking differences in frequency of many forms of kidney disease between African Americans and European Americans, which could not be completely explained by cultural or economic factors, pointed to a large unidentified genetic influence. Since FSGS and HIV-associated collapsing glomerulopathy (HVAN) have striking racial disparities, we performed an admixture mapping study to identify contributing genetic factors. Admixture mapping identified genetic variants in the non-muscle myosin gene MYH9 as having an extreme influence on both FSGS and HIVAN, with odds ratios from 4 to 8 and attributable fractions of 70–100%. Previously identified, rare inherited MYH9 disorders point to a mechanism by which MYH9 variation disrupts the actin-myosin filaments responsible for maintaining the structure of podocytes, the cells that provide one of three filtration barriers in the glomeruli. MYH9 variation has a smaller but still highly significant effect on non-diabetic kidney disease, and a weaker but significant effect on diabetic kidney disease; it is unclear whether underlying cryptic FSGS is responsible for the MYH9 association with these diseases. The strong predicted power of MYH9 variation for disease indicates a clear role for genetic testing for these variants in personalized medicine, for assessment of genetic risk, and potentially for diagnosis. PMID:20347641

  3. Variation of linear and circular polarization persistence for changing field of view and collection area in a forward scattering environment

    NASA Astrophysics Data System (ADS)

    van der Laan, John D.; Wright, Jeremy B.; Scrymgeour, David A.; Kemme, Shanalyn A.; Dereniak, Eustace L.

    2016-05-01

    We present experimental and simulation results for a laboratory-based forward-scattering environment, where 1 μm diameter polystyrene spheres are suspended in water to model the optical scattering properties of fog. Circular polarization maintains its degree of polarization better than linear polarization as the optical thickness of the scattering environment increases. Both simulation and experiment quantify circular polarization's superior persistence, compared to that of linear polarization, and show that it is much less affected by variations in the field of view and collection area of the optical system. Our experimental environment's lateral extent was physically finite, causing a significant difference between measured and simulated degree of polarization values for incident linearly polarized light, but not for circularly polarized light. Through simulation we demonstrate that circular polarization is less susceptible to the finite environmental extent as well as the collection optic's limiti