Comparison of the levels of intra-specific genetic variation within Giardia muris and Giardia intestinalis.

PubMed

Andrews, R H; Monis, P T; Ey, P L; Mayrhofer, G

1998-08-01

The extent of intra-specific genetic variation between isolates of Giardia muris was assessed by allozyme electrophoresis. Additionally, the levels of allozymic variation detected within G. muris were compared with those observed between members of the two major assemblages of the morphologically distinct species Giardia intestinalis. Four isolates of G. muris were analysed. Three (Ad-120, -150, -151) were isolated from mice in Australia, while the fourth (R-T) was isolated from a golden hamster in North America. The 11 isolates of G. intestinalis (Ad-1, -12, -2, -62, representing genetic Groups I and II of Assemblage A and BAH-12, BRIS/87/HEPU/694, Ad-19, -22, -28, -45, -52, representing genetic Groups III and IV of Assemblage B) were from humans in Australia. Intra-specific genetic variation was detected between G. muris isolates at four of the 23 enzyme loci examined. Similar levels of variation were found within the genetic groups that comprise Assemblages A and B of G. intestinalis. These levels of intra-specific variation are similar to those observed within other morphologically-distinct species of protozoan parasites. We suggest that the magnitude of the genetic differences detected within G. muris provides an indication of the range of genetic variation within other species of Giardia and that this can be used as a model to delineate morphologically similar but genetically distinct (cryptic) species within this genus.

The legacy of domestication: accumulation of deleterious mutations in the dog genome.

PubMed

Cruz, Fernando; Vilà, Carles; Webster, Matthew T

2008-11-01

Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the gray wolf. We compared variation in dog and wolf genes using whole-genome single nucleotide polymorphism (SNP) data. The d(N)/d(S) ratio (omega) was around 50% greater for SNPs found in dogs than in wolves, indicating that a higher proportion of nonsynonymous alleles segregate in dogs compared with nonfunctional genetic variation. We suggest that the majority of these alleles are slightly deleterious and that two main factors may have contributed to their increase. The first is a relaxation of selective constraint due to a population bottleneck and altered breeding patterns accompanying domestication. The second is a reduction of effective population size at loci linked to those under positive selection due to Hill-Robertson interference. An increase in slightly deleterious genetic variation could contribute to the prevalence of disease in modern dog breeds.

The devil is in the details: genetic variation in introduced populations and its contributions to invasion.

PubMed

Dlugosch, Katrina M; Anderson, Samantha R; Braasch, Joseph; Cang, F Alice; Gillette, Heather D

2015-05-01

The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself. © 2015 John Wiley & Sons Ltd.

Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans

PubMed Central

Farhadifar, Reza; Ponciano, José Miguel; Andersen, Erik C.; Needleman, Daniel J.; Baer, Charles F.

2016-01-01

Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: Either mutation produces genetic variation at different rates or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in Caenorhabditis elegans and compare them to the standing genetic variances (VG) for the same suite of traits in a worldwide collection C. elegans. Two robust conclusions emerge. First, the mutational process is highly repeatable: The correlation between VM in two independent sets of mutation accumulation lines is ∼0.9. Second, VM for a trait is a good predictor of VG for that trait: The correlation between VM and VG is ∼0.9. This result is predicted for a population at mutation–selection balance; it is not predicted if balancing selection plays a primary role in maintaining genetic variation. PMID:27334268

Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids.

PubMed

Liu, Chao; Wang, Mingbo; Wang, Lingli; Guo, Qigao; Liang, Guolu

2018-04-24

We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.

Genetic differentiation among populations of Pinus ponderosa from the upper Colorado River Basin

Treesearch

Gerald Rehfeldt

1990-01-01

Genetic variation among 62 populations of ponderosa pine was studied by comparing seedlings from all populations according to (1) growth and development of 4-yr-old seedlings in three disparate common gardens and (2) patterns of shoot elongation of 2-yr-old seedlings in a greenhouse. Genetic variation was detected among populations for 19 of the variables, most of...

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

Poa secunda local collections and commercial releases: A genotypic evaluation

PubMed Central

Shaw, Alanna N.; Mummey, Daniel L.

2017-01-01

The genetics of native plants influence the success of ecological restoration, yet genetic variability of local seed collections and commercial seed releases remains unclear for most taxa. Poa secunda, a common native grass species in Intermountain West grasslands and a frequent component of restoration seed mixes, is one such species. Here, we evaluate the genetic variation of local Poa secunda collections in the context of wild populations and commercial seed releases. We evaluated AFLP markers for seven Poa secunda collections made over a 4000-hectare area and four commercial releases (High Plains, MT-1, Opportunity, and Sherman). We compare the genetic distance and distribution of genetic variation within and between local collections and commercial releases. The extent and patterns of genetic variation in our local collections indicate subtle site differences with most variation occurring within rather than between collections. Identical genetic matches were usually, but not always, found within 5 m2 collection sites. Our results suggest that the genetic variation in two Poa secunda releases (High Plains and MT-1) is similar to our local collections. Our results affirm that guidelines for Poa secunda seed collection should follow recommendations for selfing species, by collecting from many sites over large individual sites. PMID:28369130

Poa secunda local collections and commercial releases: A genotypic evaluation.

PubMed

Shaw, Alanna N; Mummey, Daniel L

2017-01-01

The genetics of native plants influence the success of ecological restoration, yet genetic variability of local seed collections and commercial seed releases remains unclear for most taxa. Poa secunda, a common native grass species in Intermountain West grasslands and a frequent component of restoration seed mixes, is one such species. Here, we evaluate the genetic variation of local Poa secunda collections in the context of wild populations and commercial seed releases. We evaluated AFLP markers for seven Poa secunda collections made over a 4000-hectare area and four commercial releases (High Plains, MT-1, Opportunity, and Sherman). We compare the genetic distance and distribution of genetic variation within and between local collections and commercial releases. The extent and patterns of genetic variation in our local collections indicate subtle site differences with most variation occurring within rather than between collections. Identical genetic matches were usually, but not always, found within 5 m2 collection sites. Our results suggest that the genetic variation in two Poa secunda releases (High Plains and MT-1) is similar to our local collections. Our results affirm that guidelines for Poa secunda seed collection should follow recommendations for selfing species, by collecting from many sites over large individual sites.

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

PubMed Central

Veltsos, P; Gregson, E; Morrissey, B; Slate, J; Hoikkala, A; Butlin, R K; Ritchie, M G

2015-01-01

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power. PMID:26198076

Quantitative Genetic Architecture at Latitudinal Range Boundaries: Reduced Variation but Higher Trait Independence.

PubMed

Paccard, Antoine; Van Buskirk, Josh; Willi, Yvonne

2016-05-01

Species distribution limits are hypothesized to be caused by small population size and limited genetic variation in ecologically relevant traits, but earlier studies have not evaluated genetic variation in multivariate phenotypes. We asked whether populations at the latitudinal edges of the distribution have altered quantitative genetic architecture of ecologically relevant traits compared with midlatitude populations. We calculated measures of evolutionary potential in nine Arabidopsis lyrata populations spanning the latitudinal range of the species in eastern and midwestern North America. Environments at the latitudinal extremes have reduced water availability, and therefore plants were assessed under wet and dry treatments. We estimated genetic variance-covariance (G-) matrices for 10 traits related to size, development, and water balance. Populations at southern and northern distribution edges had reduced levels of genetic variation across traits, but their G-matrices were more spherical; G-matrix orientation was unrelated to latitude. As a consequence, the predicted short-term response to selection was at least as strong in edge populations as in central populations. These results are consistent with genetic drift eroding variation and reducing the effectiveness of correlational selection at distribution margins. We conclude that genetic variation of isolated traits poorly predicts the capacity to evolve in response to multivariate selection and that the response to selection may frequently be greater than expected at species distribution margins because of genetic drift.

The genetic diversity and epizootiology of infectious hematopoietic necrosis virus

USGS Publications Warehouse

Oshima, Kevin H.; Arakawa, Cindy K.; Higman, Keith H.; Landolt, Marsha L.; Nichol, Stuart T.; Winton, James R.

1994-01-01

Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus which causes a serious disease in salmondd fish. The T1 ribonuclease fingerprinttin method was used to compare the RNA genomes of 26 isolates of IHNV recovered from sockeye salmon (Oncorhynchus nerka), chinook salmon (O. tshawytscha), and steelhead trout (O. mykiss) throughout the enzootic portion of western North America. Most of the isolates as a source of genetic variation. In from a single year (1987) to limit time of isolation as a source of genetic variation. In addition, isolates from different years collected at three sites were analyzed to investigate genetic drift or evolution of IHNV within specific locations. All of the isolates examined by T1 fingerprint analysis contained less than a 50% variation in spot location and were represented by a single fingerprint group. The observed variation was estimated to correspond to less than 5% variation in the nucleic acid sequence. However, sufficient variation was detected to separate the isolates into four subgroups which appeared to correlate to different geographic regions. Host species appeared not to be a significant source of variation. The evolutionary and epizootiologic significance of these findings and their relationship to other evidence of genetic variation in IHNV isolates are discussed.

Genetic variation assessed with microsatellites in mass selection lines of the Pacific oyster ( Crassostrea gigas) in China

NASA Astrophysics Data System (ADS)

Wang, Xubo; Li, Qi; Yu, Hong; Kong, Lingfeng

2016-12-01

Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding programs in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8-20.6, and a mean expected heterozygosity of 0.902-0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a relatively large number of broodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided important information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.

Phenotypic divergence despite low genetic differentiation in house sparrow populations.

PubMed

Ben Cohen, Shachar; Dor, Roi

2018-01-10

Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST ) was lower in comparison to phenotypic variation (P ST ), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.

Dynamics of genetic and morphological variability within Neandertals.

PubMed

Hawks, John

2012-01-01

Paleogenomics may suggest changes to the way anthropologists have discussed the dynamics and morphological diversity among Neandertals. Genetic comparisons show that later Neandertals had relatively low autosomal genetic variation compared to recent humans. The known mitochondrial sample from Neandertals covers a broader geographic and temporal range, and shows greater diversity. This review addresses how genetic data compare to morphological and archaeological evidence about Neandertal variation and dynamics. Traditional views emphasized the morphological differences between western and eastern Neandertal populations, and between early and later Neandertals. Genomes broadly support these groupings, without resolving the outstanding question of the affinities of specimens from southwest Asia. However, the pattern of genetic variation appears to reject a long, in situ transformation of Neandertal groups over time, suggesting instead a more rapid process of regional dispersal and partial population replacement. Archaeological indicators sample dynamics on a much finer timescale than morphological or genetic evidence, and point to dispersal and turnover among Neandertals on a regional scale. In this way, genetic evidence may provide a bridge between the timescales relevant to morphological and archaeological comparisons. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.

Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish.

PubMed

Brauer, Chris J; Unmack, Peter J; Beheregaray, Luciano B

2017-12-01

Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations. © 2017 John Wiley & Sons Ltd.

Divergent selection along climatic gradients in a rare central European endemic species, Saxifraga sponhemica

PubMed Central

Walisch, Tania J.; Colling, Guy; Bodenseh, Melanie; Matthies, Diethart

2015-01-01

Background and Aims The effects of habitat fragmentation on quantitative genetic variation in plant populations are still poorly known. Saxifraga sponhemica is a rare endemic of Central Europe with a disjunct distribution, and a stable and specialized habitat of treeless screes and cliffs. This study therefore used S. sponhemica as a model species to compare quantitative and molecular variation in order to explore (1) the relative importance of drift and selection in shaping the distribution of quantitative genetic variation along climatic gradients; (2) the relationship between plant fitness, quantitative genetic variation, molecular genetic variation and population size; and (3) the relationship between the differentiation of a trait among populations and its evolvability. Methods Genetic variation within and among 22 populations from the whole distribution area of S. sponhemica was studied using RAPD (random amplified polymorphic DNA) markers, and climatic variables were obtained for each site. Seeds were collected from each population and germinated, and seedlings were transplanted into a common garden for determination of variation in plant traits. Key Results In contrast to previous results from rare plant species, strong evidence was found for divergent selection. Most population trait means of S. sponhemica were significantly related to climate gradients, indicating adaptation. Quantitative genetic differentiation increased with geographical distance, even when neutral molecular divergence was controlled for, and QST exceeded FST for some traits. The evolvability of traits was negatively correlated with the degree of differentiation among populations (QST), i.e. traits under strong selection showed little genetic variation within populations. The evolutionary potential of a population was not related to its size, the performance of the population or its neutral genetic diversity. However, performance in the common garden was lower for plants from populations with reduced molecular genetic variation, suggesting inbreeding depression due to genetic erosion. Conclusions The findings suggest that studies of molecular and quantitative genetic variation may provide complementary insights important for the conservation of rare species. The strong differentiation of quantitative traits among populations shows that selection can be an important force for structuring variation in evolutionarily important traits even for rare endemic species restricted to very specific habitats. PMID:25862244

Association of genetic and phenotypic variability with geography and climate in three southern California oaks.

PubMed

Riordan, Erin C; Gugger, Paul F; Ortego, Joaquín; Smith, Carrie; Gaddis, Keith; Thompson, Pam; Sork, Victoria L

2016-01-01

Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-mulleri) in an environmentally heterogeneous region of southern California at three organizational levels: regional species distributions, genetic variation, and phenotypic variation. We identified climatic variables influencing regional distribution patterns using species distribution models (SDMs), and then tested whether those individual variables are important in shaping genetic (microsatellite) and phenotypic (leaf morphology) variation. We estimated the relative contributions of geography and climate using multivariate redundancy analyses (RDA) with variance partitioning. The modeled distribution of each species was influenced by climate differently. Our analysis of genetic variation using RDA identified small but significant associations between genetic variation with climate and geography in Q. engelmannii and Q. cornelius-mulleri, but not in Q. berberidifolia, and climate explained more of the variation. Our analysis of phenotypic variation in Q. engelmannii indicated that climate had more impact than geography, but not in Q. berberidifolia. Throughout our analyses, we did not find a consistent pattern in effects of individual climatic variables. Our comparative analysis illustrates that climate influences tree response at all organizational levels, but the important climate factors vary depending on the level and on the species. Because of these species-specific and level-specific responses, today's sympatric species are unlikely to have similar distributions in the future. © 2016 Botanical Society of America.

Female guppies agree to differ: phenotypic and genetic variation in mate-choice behavior and the consequences for sexual selection.

PubMed

Brooks, R; Endler, J A

2001-08-01

Variation among females in mate choice may influence evolution by sexual selection. The genetic basis of this variation is of interest because the elaboration of mating preferences requires additive genetic variation in these traits. Here we measure the repeatability and heritability of two components of female choosiness (responsiveness and discrimination) and of female preference functions for the multiple ornaments borne by male guppies (Poecilia reticulata). We show that there is significant repeatable variation in both components of choosiness and in some preference functions but not in others. There appear to be several male ornaments that females find uniformly attractive and others for which females differ in preference. One consequence is that there is no universally attractive male phenotype. Only responsiveness shows significant additive genetic variation. Variation in responsiveness appears to mask variation in discrimination and some preference functions and may be the most biologically relevant source of phenotypic and genetic variation in mate-choice behavior. To test the potential evolutionary importance of the phenotypic variation in mate choice that we report, we estimated the opportunity for and the intensity of sexual selection under models of mate choice that excluded and that incorporated individual female variation. We then compared these estimates with estimates based on measured mating success. Incorporating individual variation in mate choice generally did not predict the outcome of sexual selection any better than models that ignored such variation.

Most genetic risk for autism resides with common variation.

PubMed

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; Roeder, Kathryn; Buxbaum, Joseph D

2014-08-01

A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. Individual risk-associated genes have been identified from rare variation, especially de novo mutations. From this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial impact en masse. At issue is how much of an impact relative to rare variation this common variation has. Using a unique epidemiological sample from Sweden, new methods that distinguish total narrow-sense heritability from that due to common variation and synthesis of results from other studies, we reach several conclusions about autism's genetic architecture: its narrow-sense heritability is ∼52.4%, with most due to common variation, and rare de novo mutations contribute substantially to individual liability, yet their contribution to variance in liability, 2.6%, is modest compared to that for heritable variation.

Analysis of copy number variations among cattle breeds

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...

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

Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.

PubMed

Strachan, Norval J C; Rotariu, Ovidiu; Lopes, Bruno; MacRae, Marion; Fairley, Susan; Laing, Chad; Gannon, Victor; Allison, Lesley J; Hanson, Mary F; Dallman, Tim; Ashton, Philip; Franz, Eelco; van Hoek, Angela H A M; French, Nigel P; George, Tessy; Biggs, Patrick J; Forbes, Ken J

2015-10-07

Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei's genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei's genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.

An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

PubMed Central

Jenkins, Brittany R.; Vitousek, Maren N.; Hubbard, Joanna K.; Safran, Rebecca J.

2014-01-01

Glucocorticoid hormones (CORT) are predicted to promote adaptation to variable environments, yet little is known about the potential for CORT secretion patterns to respond to selection in free-living populations. We assessed the heritable variation underlying differences in hormonal phenotypes using a cross-foster experimental design with nestling North American barn swallows (Hirundo rustica erythrogaster). Using a bivariate animal model, we partitioned variance in baseline and stress-induced CORT concentrations into their additive genetic and rearing environment components and estimated their genetic correlation. Both baseline and stress-induced CORT were heritable with heritability of 0.152 and 0.343, respectively. We found that the variation in baseline CORT was best explained by rearing environment, whereas the variation in stress-induced CORT was contributed to by a combination of genetic and environmental factors. Further, we did not detect a genetic correlation between these two hormonal traits. Although rearing environment appears to play an important role in the secretion of both types of CORT, our results suggest that stress-induced CORT levels are underlain by greater additive genetic variance compared with baseline CORT levels. Accordingly, we infer that the glucocorticoid response to stress has a greater potential for evolutionary change in response to selection compared with baseline glucocorticoid secretion patterns. PMID:25056627

Heritability of metoprolol and torsemide pharmacokinetics.

PubMed

Matthaei, J; Brockmöller, J; Tzvetkov, M V; Sehrt, D; Sachse-Seeboth, C; Hjelmborg, J B; Möller, S; Halekoh, U; Hofmann, U; Schwab, M; Kerb, R

2015-12-01

Genetic variation in the pharmacokinetics of metoprolol and torsemide due to polymorphisms in CYP2D6, CYP2C9, and OATP1B1 has been extensively studied. However, it is still unknown how much of the variation in pharmacokinetics of these two clinically important drugs in total is due to genetic factors. Metoprolol and torsemide were intravenously administered to 44 monozygotic and 14 dizygotic twin pairs. Metoprolol area under the curve (AUC) varied 4.7-fold and torsemide AUC 3.5-fold. A very high fraction of AUC variations, 91% of metoprolol and 86% of torsemide, were found to be due to additive genetic effects. However, known genetic variants of CYP2D6, -2C9, and OATP1B1 explained only 39%, 2%, and 39% of that variation, respectively. Comparable results for genetically explained variation in pharmacokinetics and pharmacodynamics have been found for other substrates of these enzymes earlier. These findings indicate that a substantial fraction of the heritable variability in the pharmacokinetics of metoprolol and torsemide remains to be elucidated. © 2015 American Society for Clinical Pharmacology and Therapeutics.

Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits

PubMed Central

Wellington, Gerrard M.; Fox, George E.; Toonen, Robert J.

2015-01-01

Morphological variation in the geographically widespread coral Porites lobata can make it difficult to distinguish from other massive congeneric species. This morphological variation could be attributed to geographic variability, phenotypic plasticity, or a combination of such factors. We examined genetic and microscopic morphological variability in P. lobata samples from the Galápagos, Easter Island, Tahiti, Fiji, Rarotonga, and Australia. Panamanian P. evermanni specimens were used as a previously established distinct outgroup against which to test genetic and morphological methods of discrimination. We employed a molecular analysis of variance (AMOVA) based on ribosomal internal transcribed spacer region (ITS) sequence, principal component analysis (PCA) of skeletal landmarks, and Mantel tests to compare genetic and morphological variation. Both genetic and morphometric methods clearly distinguished P. lobata and P. evermanni, while significant genetic and morphological variance was attributed to differences among geographic regions for P. lobata. Mantel tests indicate a correlation between genetic and morphological variation for P. lobata across the Pacific. Here we highlight landmark morphometric measures that correlate well with genetic differences, showing promise for resolving species of Porites, one of the most ubiquitous yet challenging to identify architects of coral reefs. PMID:25674364

Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia

PubMed Central

Schrey, A.; Ragsdale, A.; Griffith, S. C.

2018-01-01

Invasive populations are often associated with low levels of genetic diversity owing to population bottlenecks at the initial stages of invasion. Despite this, the ability of invasive species to adapt rapidly in response to novel environments is well documented. Epigenetic mechanisms have recently been proposed to facilitate the success of invasive species by compensating for reduced levels of genetic variation. Here, we use methylation sensitive-amplification fragment length polymorphism and microsatellite analyses to compare levels of epigenetic and genetic diversity and differentiation across 15 sites in the introduced Australian house sparrow population. We find patterns of epigenetic and genetic differentiation that are consistent with historical descriptions of three distinct, introductions events. However unlike genetic differentiation, epigenetic differentiation was higher among sample sites than among invasion clusters, suggesting that patterns of epigenetic variation are more strongly influenced by local environmental stimuli or sequential founder events than the initial diversity in the introduction population. Interestingly, we fail to detect correlations between pairwise site comparisons of epigenetic and genetic differentiation, suggesting that some of the observed epigenetic variation has arisen independently of genetic variation. We also fail to detect the potentially compensatory relationship between epigenetic and genetic diversity that has been detected in a more recent house sparrow invasion in Africa. We discuss the potential for this relationship to be obscured by recovered genetic diversity in more established populations, and highlight the importance of incorporating introduction history into population-wide epigenetic analyses. PMID:29765671

Analysis of copy number variations reveals differences among cattle breeds

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...

Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts.

PubMed

Jelenkovic, Aline; Sund, Reijo; Hur, Yoon-Mi; Yokoyama, Yoshie; Hjelmborg, Jacob V B; Möller, Sören; Honda, Chika; Magnusson, Patrik K E; Pedersen, Nancy L; Ooki, Syuichi; Aaltonen, Sari; Stazi, Maria A; Fagnani, Corrado; D'Ippolito, Cristina; Freitas, Duarte L; Maia, José Antonio; Ji, Fuling; Ning, Feng; Pang, Zengchang; Rebato, Esther; Busjahn, Andreas; Kandler, Christian; Saudino, Kimberly J; Jang, Kerry L; Cozen, Wendy; Hwang, Amie E; Mack, Thomas M; Gao, Wenjing; Yu, Canqing; Li, Liming; Corley, Robin P; Huibregtse, Brooke M; Derom, Catherine A; Vlietinck, Robert F; Loos, Ruth J F; Heikkilä, Kauko; Wardle, Jane; Llewellyn, Clare H; Fisher, Abigail; McAdams, Tom A; Eley, Thalia C; Gregory, Alice M; He, Mingguang; Ding, Xiaohu; Bjerregaard-Andersen, Morten; Beck-Nielsen, Henning; Sodemann, Morten; Tarnoki, Adam D; Tarnoki, David L; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Burt, S Alexandra; Klump, Kelly L; Silberg, Judy L; Eaves, Lindon J; Maes, Hermine H; Krueger, Robert F; McGue, Matt; Pahlen, Shandell; Gatz, Margaret; Butler, David A; Bartels, Meike; van Beijsterveldt, Toos C E M; Craig, Jeffrey M; Saffery, Richard; Dubois, Lise; Boivin, Michel; Brendgen, Mara; Dionne, Ginette; Vitaro, Frank; Martin, Nicholas G; Medland, Sarah E; Montgomery, Grant W; Swan, Gary E; Krasnow, Ruth; Tynelius, Per; Lichtenstein, Paul; Haworth, Claire M A; Plomin, Robert; Bayasgalan, Gombojav; Narandalai, Danshiitsoodol; Harden, K Paige; Tucker-Drob, Elliot M; Spector, Timothy; Mangino, Massimo; Lachance, Genevieve; Baker, Laura A; Tuvblad, Catherine; Duncan, Glen E; Buchwald, Dedra; Willemsen, Gonneke; Skytthe, Axel; Kyvik, Kirsten O; Christensen, Kaare; Öncel, Sevgi Y; Aliev, Fazil; Rasmussen, Finn; Goldberg, Jack H; Sørensen, Thorkild I A; Boomsma, Dorret I; Kaprio, Jaakko; Silventoinen, Karri

2016-06-23

Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1-19 years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments.

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

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.

Indicator 1.07. Number and geographic distribution of forest-associated species at risk of losing genetic variation and locally adapted genotypes

Treesearch

C. H. Flather; M. S Knowles; C. H. Sieg

2011-01-01

This indicator provides information on the number and distribution of forest-associated species at risk of losing genetic variation across their geographic range. Comparing a species' current geographic distribution with its historic distribution is the basis for identifying those species whose range has contracted significantly. Human activities are accelerating...

Developmental mechanisms underlying variation in craniofacial disease and evolution.

PubMed

Fish, Jennifer L

2016-07-15

Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies. Copyright © 2015 Elsevier Inc. All rights reserved.

The Impact of Accelerating Faster than Exponential Population Growth on Genetic Variation

PubMed Central

Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

2014-01-01

Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models’ effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times. PMID:24381333

The impact of accelerating faster than exponential population growth on genetic variation.

PubMed

Reppell, Mark; Boehnke, Michael; Zöllner, Sebastian

2014-03-01

Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models' effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.

Physiological basis of genetic variation in leaf photosynthesis among rice (Oryza sativa L.) introgression lines under drought and well-watered conditions

PubMed Central

Yin, Xinyou

2012-01-01

To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background. PMID:22888131

MAINTENANCE OF ECOLOGICALLY SIGNIFICANT GENETIC VARIATION IN THE TIGER SWALLOWTAIL BUTTERFLY THROUGH DIFFERENTIAL SELECTION AND GENE FLOW.

PubMed

Bossart, J L; Scriber, J M

1995-12-01

Differential selection in a heterogeneous environment is thought to promote the maintenance of ecologically significant genetic variation. Variation is maintained when selection is counterbalanced by the homogenizing effects of gene flow and random mating. In this study, we examine the relative importance of differential selection and gene flow in maintaining genetic variation in Papilio glaucus. Differential selection on traits contributing to successful use of host plants (oviposition preference and larval performance) was assessed by comparing the responses of southern Ohio, north central Georgia, and southern Florida populations of P. glaucus to three hosts: Liriodendron tulipifera, Magnolia virginiana, and Prunus serotina. Gene flow among populations was estimated using allozyme frequencies from nine polymorphic loci. Significant genetic differentiation was observed among populations for both oviposition preference and larval performance. This differentiation was interpreted to be the result of selection acting on Florida P. glaucus for enhanced use of Magnolia, the prevalent host in Florida. In contrast, no evidence of population differentiation was revealed by allozyme frequencies. F ST -values were very small and Nm, an estimate of the relative strengths of gene flow and genetic drift, was large, indicating that genetic exchange among P. glaucus populations is relatively unrestricted. The contrasting patterns of spatial differentiation for host-use traits and lack of differentiation for electrophoretically detectable variation implies that differential selection among populations will be counterbalanced by gene flow, thereby maintaining genetic variation for host-use traits. © 1995 The Society for the Study of Evolution.

Demographic History and Reproductive Output Correlates with Intraspecific Genetic Variation in Seven Species of Indo-Pacific Mangrove Crabs

PubMed Central

Fratini, Sara; Ragionieri, Lapo; Cannicci, Stefano

2016-01-01

The spatial distribution and the amount of intraspecific genetic variation of marine organisms are strongly influenced by many biotic and abiotic factors. Comparing biological and genetic data characterizing species living in the same habitat can help to elucidate the processes driving these variation patterns. Here, we present a comparative multispecies population genetic study on seven mangrove crabs co-occurring in the West Indian Ocean characterized by planktotrophic larvae with similar pelagic larval duration. Our main aim was to investigate whether a suite of biological, behavioural and ecological traits could affect genetic diversities of the study species in combination with historical demographic parameters. As possible current explanatory factors, we used the intertidal micro-habitat colonised by adult populations, various parameters of individual and population fecundity, and the timing of larval release. As the genetic marker, we used partial sequences of cytochrome oxidase subunit I gene. Genetic and ecological data were collected by the authors and/or gathered from primary literature. Permutational multiple regression models and ANOVA tests showed that species density and their reproductive output in combination with historical demographic parameters could explain the intraspecific genetic variation indexes across the seven species. In particular, species producing consistently less eggs per spawning event showed higher values of haplotype diversity. Moreover, Tajima’s D parameters well explained the recorded values for haplotype diversity and average γst. We concluded that current intraspecific gene diversities in crabs inhabiting mangrove forests were affected by population fecundity as well as past demographic history. The results were also discussed in terms of management and conservation of fauna in the Western Indian Ocean mangroves. PMID:27379532

Demographic History and Reproductive Output Correlates with Intraspecific Genetic Variation in Seven Species of Indo-Pacific Mangrove Crabs.

PubMed

Fratini, Sara; Ragionieri, Lapo; Cannicci, Stefano

2016-01-01

The spatial distribution and the amount of intraspecific genetic variation of marine organisms are strongly influenced by many biotic and abiotic factors. Comparing biological and genetic data characterizing species living in the same habitat can help to elucidate the processes driving these variation patterns. Here, we present a comparative multispecies population genetic study on seven mangrove crabs co-occurring in the West Indian Ocean characterized by planktotrophic larvae with similar pelagic larval duration. Our main aim was to investigate whether a suite of biological, behavioural and ecological traits could affect genetic diversities of the study species in combination with historical demographic parameters. As possible current explanatory factors, we used the intertidal micro-habitat colonised by adult populations, various parameters of individual and population fecundity, and the timing of larval release. As the genetic marker, we used partial sequences of cytochrome oxidase subunit I gene. Genetic and ecological data were collected by the authors and/or gathered from primary literature. Permutational multiple regression models and ANOVA tests showed that species density and their reproductive output in combination with historical demographic parameters could explain the intraspecific genetic variation indexes across the seven species. In particular, species producing consistently less eggs per spawning event showed higher values of haplotype diversity. Moreover, Tajima's D parameters well explained the recorded values for haplotype diversity and average γst. We concluded that current intraspecific gene diversities in crabs inhabiting mangrove forests were affected by population fecundity as well as past demographic history. The results were also discussed in terms of management and conservation of fauna in the Western Indian Ocean mangroves.

Individual differences in migratory behavior shape population genetic structure and microhabitat choice in sympatric blackcaps (Sylvia atricapilla)

PubMed Central

Rolshausen, Gregor; Segelbacher, Gernot; Hermes, Claudia; Hobson, Keith A; Schaefer, H Martin

2013-01-01

In migratory birds, traits such as orientation and distance are known to have a strong genetic background, and they often exhibit considerable within-population variation. How this variation relates to evolutionary responses to ongoing selection is unknown because the underlying mechanisms that translate environmental changes into population genetic changes are unclear. We show that within-population genetic structure in southern German blackcaps (Sylvia atricapilla) is related to individual differences in migratory behavior. Our 3-year study revealed a positive correlation between individual migratory origins, denoted via isotope (δ2H) values, and genetic distances. Genetic diversity and admixture differed not only across a recently established migratory polymorphism with NW- and SW-migrating birds but also across δ2H clusters within the same migratory route. Our results suggest assortment based on individual migratory origins which would facilitate evolutionary responses. We scrutinized arrival times and microhabitat choice as potential mechanisms mediating between individual variation in migratory behavior and assortment. We found significant support that microhabitat choice, rather than timing of arrival, is associated with individual variation in migratory origins. Moreover, examining genetic diversity across the migratory divide, we found migrants following the NW route to be genetically more distinct from each other compared with migrants following the traditional SW route. Our study suggests that migratory behavior shapes population genetic structure in blackcaps not only across the migratory divide but also on an individual level independent of the divide. Thus, within-population variation in migratory behavior might play an important role in translating environmental change into genetic change. PMID:24324877

The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

PubMed

Pedersen, Casper-Emil T; Lohmueller, Kirk E; Grarup, Niels; Bjerregaard, Peter; Hansen, Torben; Siegismund, Hans R; Moltke, Ida; Albrechtsen, Anders

2017-02-01

The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe <4% increase in the number of derived deleterious alleles in the Inuit. In contrast, proxies for genetic load under a recessive model suggest that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models of dominance. Further, the Inuit population carries fewer deleterious variants than other human populations, but those that are present tend to be at higher frequency than in other populations. Overall, our results show how recent demographic history has affected patterns of deleterious variants in human populations. Copyright © 2017 by the Genetics Society of America.

Spatial difference in genetic variation for fenitrothion tolerance between local populations of Daphnia galeata in Lake Kasumigaura, Japan.

PubMed

Mano, Hiroyuki; Tanaka, Yoshinari

2017-12-01

This study examines the spatial difference in genetic variation for tolerance to a pesticide, fenitrothion, in Daphnia galeata at field sites in Lake Kasumigaura, Japan. We estimated genetic values of isofemale lines established from dormant eggs of D. galeata collected from field sampling sites with the toxicant threshold model applied using acute toxicity. We compared genetic values and variances and broad-sense heritability across different sites in the lake. Results showed that the mean tolerance values to fenitrothion did not differ spatially. The variance in genetic value and heritability of fenitrothion tolerance significantly differed between sampling sites, revealing that long-term ecological risk of fenitrothion may differ between local populations in the lake. These results have implications for aquatic toxicology research, suggesting that differences in genetic variation of tolerance to a chemical among local populations must be considered for understanding the long-term ecological risks of the chemical over a large geographic area.

Characterization of the genetic profile of five Danish dog breeds.

PubMed

Pertoldi, C; Kristensen, T N; Loeschcke, V; Berg, P; Praebel, A; Stronen, A V; Proschowsky, H F; Fredholm, M

2013-11-01

This investigation presents results from a genetic characterization of 5 Danish dog breeds genotyped on the CanineHD BeadChip microarray with 170,000 SNP. The breeds investigated were 1) Danish Spitz (DS; n=8), 2) Danish-Swedish Farm Dog (DSF; n=18), 3) Broholmer (BR; n=22), 4) Old Danish Pointing Dog (ODP; n=24), and 5) Greenland Dog (GD; n=23). The aims of the investigation were to characterize the genetic profile of the abovementioned dog breeds by quantifying the genetic differentiation among them and the degree of genetic homogeneity within breeds. The genetic profile was determined by means of principal component analysis (PCA) and through a Bayesian clustering method. Both the PCA and the Bayesian clustering method revealed a clear genetic separation of the 5 breeds. The level of genetic variation within the breeds varied. The expected heterozygosity (HE) as well as the degree of polymorphism (P%) ranked the dog breeds in the order DS>DSF>BR>ODP>GD. Interestingly, the breed with a tenfold higher census population size compared to the other breeds, the Greenland Dog, had the lowest within-breed genetic variation, emphasizing that census size is a poor predictor of genetic variation. The observed differences in variation among and within dog breeds may be related to factors such as genetic drift, founder effects, genetic admixture, and population bottlenecks. We further examined whether the observed genetic patterns in the 5 dog breeds can be used to design breeding strategies for the preservation of the genetic pool of these dog breeds.

Regeneration Methods Affect Genetic Variation and Structure in Shortleaf Pine (Pinus Echinata Mill.)

Treesearch

Rajiv G. Raja; Charles G. Tauer; Robert F. Wittwer; Yinghua Huang

1998-01-01

The effects of regene ration methods on genetic diversity and structure in shortleaf pine (Pinus echinata Mill.) were examined by quantifying the changes in genetic composition of shortleaf pine stands following harvest by monitoring changes in allele number and frequency at heterozygous loci over time. The results were also compared to the genetic...

Genetic variation and comparison of orchardgrass (Dactylis glomerata L.) cultivars and wild accessions as revealed by SSR markers.

PubMed

Xie, W G; Lu, X F; Zhang, X Q; Huang, L K; Cheng, L

2012-02-24

Orchardgrass is a highly variable, perennial forage grass that is cultivated throughout temperate and subtropical regions of the world. Despite its economic importance, the genetic relationship and distance among and within cultivars are largely unknown but would be of great interest for breeding programs. We investigated the molecular variation and structure of cultivar populations, compared the level of genetic diversity among cultivars (Baoxing, Anba, Bote, and Kaimo), subspecies (Dactylis glomerata ssp Woronowii) and advanced breeding line (YA02-116) to determine whether there is still sufficient genetic diversity within presently used cultivars for future breeding progress in China. Twenty individuals were analyzed from each of six accessions using SSR markers; 114 easily scored bands were generated from 15 SSR primer pairs, with an average of 7.6 alleles per locus. The polymorphic rate was 100% among the 120 individuals, reflecting a high degree of genetic diversity. Among the six accessions, the highest genetic diversity was observed in Kaimo (H = 0.2518; I = 0.3916; P = 87.3%) and 02-116 had a lower level of genetic diversity (H = 0.1806; I = 0.2788; P = 58.73%) compared with other cultivars tested. An of molecular variance revealed a much larger genetic variation within accessions (65%) than between them (35%). This observation suggests that these cultivars have potential for providing rich genetic resource for further breeding program. Furthermore, the study also indicated that Chinese orchardgrass breeding has involved strong selection for adaptation to forage production, which may result in restricted genetic base of orchardgrass cultivar.

Population structure and genetic variation of the endangered species Elaeagnus mollis Diels (Elaeagnaceae).

PubMed

Zhang, J M; Zhang, F

2015-06-01

Elaeagnus mollis Diels is a group of shrubs and dwarf trees endemic to China and are endangered plants. However, the reason why these plants are endangered remains controversial. The current study aimed to explore the endangered status of E. mollis from a genetic perspective and to propose conservation strategies for this species. Using 16 polymorphic allozyme loci, the population genetic structure was investigated for three populations representing the taxa and variants. The variants exhibited relatively high levels of genetic variation compared to other woody shrubs with similar geographic distributions. The overall genetic diversity (HE = 0.352) was elevated compared to long-lived woody angiosperms. The average number of alleles per locus (A), percentage polymorphic loci (P), and observed heterozygosity (HO) were 2.0, 85.2, and 0.371, respectively. Furthermore, gene flow estimates within the population groups were also elevated. The life history and habitats of E. mollis play major roles in the levels of genetic diversity. The results of this study may help to device strategies for preserving the genetic diversity of E. mollis and for promoting planting.

Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts

PubMed Central

Jelenkovic, Aline; Sund, Reijo; Hur, Yoon-Mi; Yokoyama, Yoshie; Hjelmborg, Jacob v. B.; Möller, Sören; Honda, Chika; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Ooki, Syuichi; Aaltonen, Sari; Stazi, Maria A.; Fagnani, Corrado; D’Ippolito, Cristina; Freitas, Duarte L.; Maia, José Antonio; Ji, Fuling; Ning, Feng; Pang, Zengchang; Rebato, Esther; Busjahn, Andreas; Kandler, Christian; Saudino, Kimberly J.; Jang, Kerry L.; Cozen, Wendy; Hwang, Amie E.; Mack, Thomas M.; Gao, Wenjing; Yu, Canqing; Li, Liming; Corley, Robin P.; Huibregtse, Brooke M.; Derom, Catherine A.; Vlietinck, Robert F.; Loos, Ruth J. F.; Heikkilä, Kauko; Wardle, Jane; Llewellyn, Clare H.; Fisher, Abigail; McAdams, Tom A.; Eley, Thalia C.; Gregory, Alice M.; He, Mingguang; Ding, Xiaohu; Bjerregaard-Andersen, Morten; Beck-Nielsen, Henning; Sodemann, Morten; Tarnoki, Adam D.; Tarnoki, David L.; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Burt, S. Alexandra; Klump, Kelly L.; Silberg, Judy L.; Eaves, Lindon J.; Maes, Hermine H.; Krueger, Robert F.; McGue, Matt; Pahlen, Shandell; Gatz, Margaret; Butler, David A.; Bartels, Meike; van Beijsterveldt, Toos C. E. M.; Craig, Jeffrey M.; Saffery, Richard; Dubois, Lise; Boivin, Michel; Brendgen, Mara; Dionne, Ginette; Vitaro, Frank; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Swan, Gary E.; Krasnow, Ruth; Tynelius, Per; Lichtenstein, Paul; Haworth, Claire M. A.; Plomin, Robert; Bayasgalan, Gombojav; Narandalai, Danshiitsoodol; Harden, K. Paige; Tucker-Drob, Elliot M.; Spector, Timothy; Mangino, Massimo; Lachance, Genevieve; Baker, Laura A.; Tuvblad, Catherine; Duncan, Glen E.; Buchwald, Dedra; Willemsen, Gonneke; Skytthe, Axel; Kyvik, Kirsten O.; Christensen, Kaare; Öncel, Sevgi Y.; Aliev, Fazil; Rasmussen, Finn; Goldberg, Jack H.; Sørensen, Thorkild I. A.; Boomsma, Dorret I.; Kaprio, Jaakko; Silventoinen, Karri

2016-01-01

Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1–19 years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments. PMID:27333805

Race, common genetic variation, and therapeutic response disparities in heart failure.

PubMed

Taylor, Mathew R; Sun, Albert Y; Davis, Gordon; Fiuzat, Mona; Liggett, Stephen B; Bristow, Michael R

2014-12-01

Because of its comparatively recent evolution, Homo sapiens exhibit relatively little within-species genomic diversity. However, because of genome size, a proportionately small amount of variation creates ample opportunities for both rare mutations that may cause disease as well as more common genetic variations that may be important in disease modification or pharmacogenetics. Primarily because of the East African origin of modern humans, individuals of African ancestry (AA) exhibit greater degrees of genetic diversity than more recently established populations, such as those of European ancestry (EA) or Asian ancestry. Those population effects extend to differences in frequency of common gene variants that may be important in heart failure natural history or therapy. For cell-signaling mechanisms important in heart failure, we review and present new data for genetic variation between AA and EA populations. Data indicate that: 1) neurohormonal signaling mechanisms frequently (16 of the 19 investigated polymorphisms) exhibit racial differences in the allele frequencies of variants comprising key constituents; 2) some of these differences in allele frequency may differentially affect the natural history of heart failure in AA compared with EA individuals; and 3) in many cases, these differences likely play a role in observed racial differences in drug or device response. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Proteomics insight into the biological safety of transgenic modification of rice as compared with conventional genetic breeding and spontaneous genotypic variation.

PubMed

Gong, Chun Yan; Li, Qi; Yu, Hua Tao; Wang, Zizhang; Wang, Tai

2012-05-04

The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM indica rice, herbicide-resistant Bar68-1 carrying bar and insect-resistant 2036-1a carrying cry1Ac/sck, and their respective controls D68 and MH86, as well as indica variety MH63, a parental line for breeding MH86, and japonica variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between indica and japonica cultivars, second among indica varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating japonica and indica cultivars, as well as indica varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties.

The Extended Community-Level Effects of Genetic Variation in Foliar Wax Chemistry in the Forest Tree Eucalyptus globulus.

PubMed

Gosney, Benjamin; O'Reilly-Wapstra, Julianne; Forster, Lynne; Whiteley, Carmen; Potts, Brad

2017-05-01

Genetic variation in foundation trees can influence dependent communities, but little is known about the mechanisms driving these extended genetic effects. We studied the potential chemical drivers of genetic variation in the dependent foliar community of the focal tree Eucalyptus globulus. We focus on the role of cuticular waxes and compare the effects to that of the terpenes, a well-studied group of secondary compounds known to be bioactive in eucalypts. The canopy community was quantified based on the abundance of thirty-nine distinctive arthropod and fungal symptoms on foliar samples collected from canopies of 246 progeny from 13 E. globulus sub-races grown in a common garden trial. Cuticular waxes and foliar terpenes were quantified using gas chromatography - mass spectrometry (GC-MC). A total of 4 of the 13 quantified waxes and 7 of the 16 quantified terpenes were significantly associated with the dependent foliar community. Variation in waxes explained 22.9% of the community variation among sub-races, which was equivalent to that explained by terpenes. In combination, waxes and terpenes explained 35% of the genetic variation among sub-races. Only a small proportion of wax and terpene compounds showing statistically significant differences among sub-races were implicated in community level effects. The few significant waxes have previously shown evidence of divergent selection in E. globulus, which signals that adaptive variation in phenotypic traits may have extended effects. While highlighting the role of the understudied cuticular waxes, this study demonstrates the complexity of factors likely to lead to community genetic effects in foundation trees.

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics.

PubMed

Bo, Tao; Shao, Shanshan; Wu, Dongming; Niu, Shaona; Zhao, Jiajun; Gao, Ling

2017-08-01

Recent studies performed provide mechanistic insight into effects of the microbiota on cholesterol metabolism, but less focus was given to how cholesterol impacts the gut microbiota. In this study, ApoE -/- Sprague Dawley (SD) rats and their wild-type counterparts (n = 12) were, respectively, allocated for two dietary condition groups (normal chow and high-cholesterol diet). Total 16S rDNA of fecal samples were extracted and sequenced by high-throughput sequencing to determine differences in microbiome composition. Data were collected and performed diversity analysis and phylogenetic analysis. The influence of cholesterol on gut microbiota was discussed by using cholesterol dietary treatment as exogenous cholesterol disorder factor and genetic modification as endogenous metabolic disorder factor. Relative microbial variations were compared to illustrate the causality and correlation of cholesterol and gut microbiota. It turned out comparing to genetically modified rats, exogenous cholesterol intake may play more effective role in changing gut microbiota profile, although the serum cholesterol level of genetically modified rats was even higher. Relative abundance of some representative species showed that the discrepancies due to dietary variation were more obvious, whereas some low abundance species changed because of genetic disorders. Our results partially demonstrated that gut microbiota are relatively more sensitive to dietary variation. Nevertheless, considering the important effect of bacteria in cholesterol metabolism, the influence to gut flora by "genetically caused cholesterol disorder" cannot be overlooked. Manipulation of gut microbiota might be an effective target for preventing cholesterol-related metabolic disorders. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Genome Variation Within Triticale in Comparison to its Wheat and Rye Progenitors

USDA-ARS?s Scientific Manuscript database

Genome variation in the intergeneric wheat-rye hybrid triticale (X Triticosecale Wittmack) has been a puzzle to scientists and plant breeders since the first triticale was synthesized. The existence of unexplained genetic variation in triticale as compared to the parents has been a hindrance to bre...

Environmental and genetic variation in leaf anatomy among populations of Andropogon gerardii (Poaceae) along a precipitation gradient.

PubMed

Olsen, Jacob T; Caudle, Keri L; Johnson, Loretta C; Baer, Sara G; Maricle, Brian R

2013-10-01

Phenotypes of two Andropogon gerardii subspecies, big bluestem and sand bluestem, vary throughout the prairie ecosystem of North America. This study sought to determine the role of genetics and environment in driving adaptive variation of leaf structure in big bluestem and sand bluestem. • Four populations of big bluestem and one population of sand bluestem were planted in common gardens at four sites across a precipitation gradient from western Kansas to southern Illinois. Internal leaf structure and trichome density of A. gerardii were examined by light microscopy to separate genetic and environmentally controlled traits. Leaf thickness, midrib thickness, bulliform cells, interveinal distance, vein size, and trichome density were quantified. • At all planting sites, sand bluestem and the xeric population of A. gerardii had thicker leaves and fewer bulliform cells compared with mesic populations. Environment and genetic source population were both influential for leaf anatomy. Leaves from plants grown in mesic sites (Carbondale, Illinois and Manhattan, Kansas) had thicker midribs, larger veins, fewer trichomes, and a greater proportion of bulliform cells compared to plants grown in drier sites (Colby and Hays, Kansas). • Water availability has driven adaptive variation in leaf structure in populations of A. gerardii, particularly between sand bluestem and big bluestem. Genetically based differences in leaves of A. gerardii indicate adaptive variation and evolutionary forces differentiating sand bluestem from big bluestem. Environmental responses of A. gerardii leaves suggest an ability to adjust to drought, even in populations adapted to mesic home environments.

Maintenance of genetic variation with a frequency-dependent selection model as compared to the overdominant model.

PubMed

Hedrick, P W

1972-12-01

A frequency-dependent selection model proposed by Huang, Singh and Kojima (1971) was found to be more effective at maintaining genetic variation in a finite population than the overdominant model. The fourth moment parameter of the distribution of unfixed states showed that there was a more platykurtic distribution for the frequency-dependent model. This agreed well with the expected gene frequency change found for an infinite population.

Modeling the influence of genetic and environmental variation on the expression of plant life cycles across landscapes.

PubMed

Burghardt, Liana T; Metcalf, C Jessica E; Wilczek, Amity M; Schmitt, Johanna; Donohue, Kathleen

2015-02-01

Organisms develop through multiple life stages that differ in environmental tolerances. The seasonal timing, or phenology, of life-stage transitions determines the environmental conditions to which each life stage is exposed and the length of time required to complete a generation. Both environmental and genetic factors contribute to phenological variation, yet predicting their combined effect on life cycles across a geographic range remains a challenge. We linked submodels of the plasticity of individual life stages to create an integrated model that predicts life-cycle phenology in complex environments. We parameterized the model for Arabidopsis thaliana and simulated life cycles in four locations. We compared multiple "genotypes" by varying two parameters associated with natural genetic variation in phenology: seed dormancy and floral repression. The model predicted variation in life cycles across locations that qualitatively matches observed natural phenology. Seed dormancy had larger effects on life-cycle length than floral repression, and results suggest that a genetic cline in dormancy maintains a life-cycle length of 1 year across the geographic range of this species. By integrating across life stages, this approach demonstrates how genetic variation in one transition can influence subsequent transitions and the geographic distribution of life cycles more generally.

Acoustic, genetic and morphological variations within the katydid Gampsocleis sedakovii (Orthoptera, Tettigonioidea)

PubMed Central

Zhang, Xue; Wen, Ming; Li, Junjian; Zhu, Hui; Wang, Yinliang; Ren, Bingzhong

2015-01-01

Abstract In an attempt to explain the variation within this species and clarify the subspecies classification, an analysis of the genetic, calling songs, and morphological variations within the species Gampsocleis sedakovii is presented from Inner Mongolia, China. Recordings were compared of the male calling songs and analysis performed of selected acoustic variables. This analysis is combined with sequencing of mtDNA - COI and examination of morphological traits to perform cluster analyses. The trees constructed from different datasets were structurally similar, bisecting the six geographical populations studied. Based on two large branches in the analysis, the species Gampsocleis sedakovii was partitioned into two subspecies, Gampsocleis sedakovii sedakovii (Fischer von Waldheim, 1846) and Gampsocleis sedakovii obscura (Walker, 1869). Comparing all the traits, the individual of Elunchun (ELC) was the intermediate type in this species according to the acoustic, genetic, and morphological characteristics. This study provides evidence for insect acoustic signal divergence and the process of subspeciation. PMID:26692795

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.

Temporal patterns of genetic variation across a 9-year-old aerial seed bank of the shrub Banksia hookeriana (Proteaceae).

PubMed

Barrett, Luke G; He, Tianhua; Lamont, Byron B; Krauss, Siegfried L

2005-11-01

The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P(p)) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (H(j)), did not change. P(p), I, and H(j) all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H(j) or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers

PubMed Central

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption. PMID:28406956

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers.

PubMed

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.

Epigenetic changes detected in micropropagated hop plants.

PubMed

Peredo, Elena L; Arroyo-García, Rosa; Revilla, M Angeles

2009-07-01

Micropropagation is a widely used technique in hops (Humulus lupulus L.). However, to the best of our knowledge, the genetic and epigenetic stability of the microplants has never been tested before. In the present study, two hop accessions were established in vitro and micropropagated for 2 years. The genetic and epigenetic stability of the in vitro plants was analyzed with several molecular techniques: random amplified DNA polymorphism (RAPD), retrotransposon microsatellite amplified polymorphism (REMAP), and methylation-sensitive amplification polymorphism (MSAP). No genetic variation among control and treated plants was found, even after 12 cycles of micropropagation. Epigenetic variation was detected, first, when field and in vitro samples were compared. Nearly a 30% of the detected fragments presented the same pattern of alterations in all the vitroplants. Second, lower levels of epigenetic variation were detected among plants from the different subcultures. Part of this detected variation seemed to be accumulated along the 12 sequential subcultures tested.

Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

PubMed

Tabachnick, W J

1992-05-01

Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.

Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)

PubMed Central

2012-01-01

Background Small, isolated populations often experience loss of genetic variation due to random genetic drift. Unlike neutral or nearly neutral markers (such as mitochondrial genes or microsatellites), major histocompatibility complex (MHC) genes in these populations may retain high levels of polymorphism due to balancing selection. The relative roles of balancing selection and genetic drift in either small isolated or bottlenecked populations remain controversial. In this study, we examined the mechanisms maintaining polymorphisms of MHC genes in small isolated populations of the endangered golden snub-nosed monkey (Rhinopithecus roxellana) by comparing genetic variation found in MHC and microsatellite loci. There are few studies of this kind conducted on highly endangered primate species. Results Two MHC genes were sequenced and sixteen microsatellite loci were genotyped from samples representing three isolated populations. We isolated nine DQA1 alleles and sixteen DQB1 alleles and validated expression of the alleles. Lowest genetic variation for both MHC and microsatellites was found in the Shennongjia (SNJ) population. Historical balancing selection was revealed at both the DQA1 and DQB1 loci, as revealed by excess non-synonymous substitutions at antigen binding sites (ABS) and maximum-likelihood-based random-site models. Patterns of microsatellite variation revealed population structure. FST outlier analysis showed that population differentiation at the two MHC loci was similar to the microsatellite loci. Conclusions MHC genes and microsatellite loci showed the same allelic richness pattern with the lowest genetic variation occurring in SNJ, suggesting that genetic drift played a prominent role in these isolated populations. As MHC genes are subject to selective pressures, the maintenance of genetic variation is of particular interest in small, long-isolated populations. The results of this study may contribute to captive breeding and translocation programs for endangered species. PMID:23083308

Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?

PubMed Central

2010-01-01

Background Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. Results Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s < 100). Population divergence (FST) for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations. PMID:20813033

Fine-scale genetic structure of bull trout at the southern limit of their distribution

Treesearch

A. Whiteley; P. Spruell; B. Rieman; F. Allendorf

2006-01-01

We used six polymorphic microsatellite loci to analyze the population genetic structure of bull trout Salvelinus confluentus in the Boise River, Idaho, and we compared our results with previous data from similarly sized river systems in western North America. Within the Boise River, we found low genetic variation within and significant...

Understanding human DNA sequence variation.

PubMed

Kidd, K K; Pakstis, A J; Speed, W C; Kidd, J R

2004-01-01

Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.

Maintenance of Genetic Variation with a Frequency-Dependent Selection Model as Compared to the Overdominant Model

PubMed Central

Hedrick, Philip W.

1972-01-01

A frequency-dependent selection model proposed by Huang, Singh and Kojima (1971) was found to be more effective at maintaining genetic variation in a finite population than the overdominant model. The fourth moment parameter of the distribution of unfixed states showed that there was a more platykurtic distribution for the frequency-dependent model. This agreed well with the expected gene frequency change found for an infinite population. PMID:4652882

Large variations in ocular dimensions in a multiethnic population with similar genetic background.

PubMed

Niu, Zhiqiang; Li, Jun; Zhong, Hua; Yuan, Zhonghua; Zhou, Hua; Zhang, Yang; Yuan, Yuansheng; Chen, Qin; Pan, Chen-Wei

2016-03-07

We aimed to describe the ethnic variations in ocular dimensions among three ethnic groups with similar genetic ancestry from mainland of China. We included 2119 ethnic Bai, 2202 ethnic Yi and 2183 ethnic Han adults aged 50 years or older in the study. Ocular dimensions including axial length (AL), anterior chamber depth (ACD), vitreous chamber depth (VCD) and lens thickness (LT) were measured using A-scan ultrasonography. Bai Chinese had longer ALs (P < 0.001), deeper ACDs (P < 0.001) but shallower VCDs (P < 0.001) compared with the other two ethnic groups. There were no ethnic variations in LTs. Diabetes was associated with shallower ACDs and this association was stronger in Bai Chinese compared with Yi or Han Chinese (P for interaction = 0.02). Thicker lenses were associated with younger age (P = 0.04), male gender (P < 0.001), smoking history (P = 0.01), alcohol intake (P = 0.03), the presence of cataract (P < 0.001), and the presence of diabetes (P < 0.001). There were significant differences in ocular dimensions among different ethnic groups with small differences in genetics but large variations in cultures and lifestyles.

Comparative analyses of fungicide sensitivity and SSR marker variations indicate a low risk of developing azoxystrobin resistance in Phytophthora infestans

PubMed Central

Qin, Chun-Fang; He, Meng-Han; Chen, Feng-Ping; Zhu, Wen; Yang, Li-Na; Wu, E-Jiao; Guo, Zheng-Liang; Shang, Li-Ping; Zhan, Jiasui

2016-01-01

Knowledge of the evolution of fungicide resistance is important in securing sustainable disease management in agricultural systems. In this study, we analyzed and compared the spatial distribution of genetic variation in azoxystrobin sensitivity and SSR markers in 140 Phytophthora infestans isolates sampled from seven geographic locations in China. Sensitivity to azoxystrobin and its genetic variation in the pathogen populations was measured by the relative growth rate (RGR) at four fungicide concentrations and determination of the effective concentration for 50% inhibition (EC50). We found that all isolates in the current study were sensitive to azoxystrobin and their EC50 was similar to that detected from a European population about 20 years ago, suggesting the risk of developing azoxystrobin resistance in P. infestans populations is low. Further analyses indicate that reduced genetic variation and high fitness cost in resistant mutations are the likely causes for the low evolutionary likelihood of developing azoxystrobin resistance in the pathogen. We also found a negative correlation between azoxystrobin tolerance in P. infestans populations and the mean annual temperature of collection sites, suggesting that global warming may increase the efficiency of using the fungicide to control the late blight. PMID:26853908

Comparative analyses of fungicide sensitivity and SSR marker variations indicate a low risk of developing azoxystrobin resistance in Phytophthora infestans.

PubMed

Qin, Chun-Fang; He, Meng-Han; Chen, Feng-Ping; Zhu, Wen; Yang, Li-Na; Wu, E-Jiao; Guo, Zheng-Liang; Shang, Li-Ping; Zhan, Jiasui

2016-02-08

Knowledge of the evolution of fungicide resistance is important in securing sustainable disease management in agricultural systems. In this study, we analyzed and compared the spatial distribution of genetic variation in azoxystrobin sensitivity and SSR markers in 140 Phytophthora infestans isolates sampled from seven geographic locations in China. Sensitivity to azoxystrobin and its genetic variation in the pathogen populations was measured by the relative growth rate (RGR) at four fungicide concentrations and determination of the effective concentration for 50% inhibition (EC50). We found that all isolates in the current study were sensitive to azoxystrobin and their EC50 was similar to that detected from a European population about 20 years ago, suggesting the risk of developing azoxystrobin resistance in P. infestans populations is low. Further analyses indicate that reduced genetic variation and high fitness cost in resistant mutations are the likely causes for the low evolutionary likelihood of developing azoxystrobin resistance in the pathogen. We also found a negative correlation between azoxystrobin tolerance in P. infestans populations and the mean annual temperature of collection sites, suggesting that global warming may increase the efficiency of using the fungicide to control the late blight.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

PubMed

Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

USGS Publications Warehouse

Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

2012-01-01

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

Genetic approaches in comparative and evolutionary physiology

PubMed Central

Bridgham, Jamie T.; Kelly, Scott A.; Garland, Theodore

2015-01-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

Genetic approaches in comparative and evolutionary physiology.

PubMed

Storz, Jay F; Bridgham, Jamie T; Kelly, Scott A; Garland, Theodore

2015-08-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. Copyright © 2015 the American Physiological Society.

Genetic variations in the Dravidian population of South West coast of India: Implications in designing case-control studies.

PubMed

D'Cunha, Anitha; Pandit, Lekha; Malli, Chaithra

2017-06-01

Indian data have been largely missing from genome-wide databases that provide information on genetic variations in different populations. This hinders association studies for complex disorders in India. This study was aimed to determine whether the complex genetic structure and endogamy among Indians could potentially influence the design of case-control studies for autoimmune disorders in the south Indian population. A total of 12 single nucleotide variations (SNVs) related to genes associated with autoimmune disorders were genotyped in 370 healthy individuals belonging to six different caste groups in southern India. Allele frequencies were estimated; genetic divergence and phylogenetic relationship within the various caste groups and other HapMap populations were ascertained. Allele frequencies for all genotyped SNVs did not vary significantly among the different groups studied. Wright's FSTwas 0.001 per cent among study population and 0.38 per cent when compared with Gujarati in Houston (GIH) population on HapMap data. The analysis of molecular variance results showed a 97 per cent variation attributable to differences within the study population and <1 per cent variation due to differences between castes. Phylogenetic analysis showed a separation of Dravidian population from other HapMap populations and particularly from GIH population. Despite the complex genetic origins of the Indian population, our study indicated a low level of genetic differentiation among Dravidian language-speaking people of south India. Case-control studies of association among Dravidians of south India may not require stratification based on language and caste.

Genetic consequences of trumpeter swan (Cygnus buccinator) reintroductions

USGS Publications Warehouse

Ransler, F.A.; Quinn, T.W.; Oyler-McCance, S.J.

2011-01-01

Relocation programs are often initiated to restore threatened species to previously occupied portions of their range. A primary challenge of restoration efforts is to translocate individuals in a way that prevents loss of genetic diversity and decreases differentiation relative to source populations-a challenge that becomes increasingly difficult when remnant populations of the species are already genetically depauperate. Trumpeter swans were previously extirpated in the entire eastern half of their range. Physical translocations of birds over the last 70 years have restored the species to portions of its historical range. Despite the long history of management, there has been little monitoring of the genetic outcomes of these restoration attempts. We assessed the consequences of this reintroduction program by comparing patterns of genetic variation at 17 microsatellite loci across four restoration flocks (three wild-released, one captive) and their source populations. We found that a wild-released population established from a single source displayed a trend toward reduced genetic diversity relative to and significant genetic differentiation from its source population, though small founder population effects may also explain this pattern. Wild-released flocks restored from multiple populations maintained source levels of genetic variation and lacked significant differentiation from at least one of their sources. Further, the flock originating from a single source revealed significantly lower levels of genetic variation than those established from multiple sources. The distribution of genetic variation in the captive flock was similar to its source. While the case of trumpeter swans provides evidence that restorations from multiple versus single source populations may better preserve natural levels of genetic diversity, more studies are needed to understand the general applicability of this management strategy. ?? 2010 Springer Science+Business Media B.V. (outside the USA).

Sibling genes as environment: Sibling dopamine genotypes and adolescent health support frequency dependent selection.

PubMed

Rauscher, Emily; Conley, Dalton; Siegal, Mark L

2015-11-01

While research consistently suggests siblings matter for individual outcomes, it remains unclear why. At the same time, studies of genetic effects on health typically correlate variants of a gene with the average level of behavioral or health measures, ignoring more complicated genetic dynamics. Using National Longitudinal Study of Adolescent Health data, we investigate whether sibling genes moderate individual genetic expression. We compare twin variation in health-related absences and self-rated health by genetic differences at three locations related to dopamine regulation and transport to test sibship-level cross-person gene-gene interactions. Results suggest effects of variation at these genetic locations are moderated by sibling genes. Although the mechanism remains unclear, this evidence is consistent with frequency dependent selection and suggests much genetic research may violate the stable unit treatment value assumption. Copyright © 2015 Elsevier Inc. All rights reserved.

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 variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity. PMID:26420202

Distribution of human papilloma virus type 16 E6/E7 gene mutation in cervical precancer or cancer: A case control study in Guizhou Province, China.

PubMed

Yang, Yingjie; Ren, Jie; Zhang, Qizhu

2016-02-01

HPV-16 varies geographically and is correlated with cervical cancer genesis and progression. This study aimed to determine the distribution of HPV-16 E6/E7 genetic variation in patients with invasive cervical cancer or precancer in Guizhou Province, China. A case-control study was designed, and the distribution of HPV-16 E6/E7 genetic variation was compared among women with cervical cancer, precancer, and sexually active without cervical lesion. HPV infection was detected through flow-through hybridization and gene chip techniques to determine the prevalence of HPV 16 E6/E7 genetic variation. Among 90 specimens (30 cervical cancer, 30 precancer, 30 controls), 81 were subjected to HPV-16 E6/E7 gene sequencing. The rates of DNA sequence mutation and amino acid mutation were 76.5% (62/81) and 66.7% (54/81), respectively. Both E6 and E7 genes showed higher mutation rate than their prototypes. The prevalence of E6/E7 mutation significantly differed between the cervical cancer and the controls (P < 0.05) and between the cervical precancer and the controls (P < 0.05). Mutations were simultaneously detected at the E6-D32E (T96A) and E7-M28V (A82G)/L94P (T281C) sites of the amino acid sequence. The most common genetic variation was D32E/M28V/L94P, which accounted for 35.8% of the cases (29/81). D32E/M28V/L94P mutation was higher in the cervical cancer and precancer compared with the prototype. HPV-16 E6/E7 genetic variations, such as D32E/M28V/L94P, are more prevalent in cervical cancer or precancer than those in the controls. The possible correlation between genetic variation and cancerigenesis may be used to design an HPV vaccine for cervical carcinoma. © 2015 Wiley Periodicals, Inc.

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

PubMed

Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

2015-09-01

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Human red cell 2,3-diphosphoglycerate mutase and monophosphoglycerate mutase: genetic evidence for two separate loci.

PubMed Central

Chen, S H; Anderson, J E; Giblett, E R

1977-01-01

Rare genetic variants of human red cell 2,3-diphosphoglycerate mutase (DPGM) and monophosphoglycerate mutase (MPGM) were compared by starch gel electrophoresis. The isozyme patterns showed that genetic variation of the enzymes were independent from each other, thus DPGM and MPGM must be controlled by two separate loci. Images Fig. 1 PMID:195467

Will phenotypic plasticity affecting flowering phenology keep pace with climate change?

PubMed

Richardson, Bryce A; Chaney, Lindsay; Shaw, Nancy L; Still, Shannon M

2017-06-01

Rising temperatures have begun to shift flowering time, but it is unclear whether phenotypic plasticity can accommodate projected temperature change for this century. Evaluating clines in phenological traits and the extent and variation in plasticity can provide key information on assessing risk of maladaptation and developing strategies to mitigate climate change. In this study, flower phenology was examined in 52 populations of big sagebrush (Artemisia tridentata) growing in three common gardens. Flowering date (anthesis) varied 91 days from late July to late November among gardens. Mixed-effects modeling explained 79% of variation in flowering date, of which 46% could be assigned to plasticity and genetic variation in plasticity and 33% to genetics (conditional R 2  = 0.79, marginal R 2  = 0.33). Two environmental variables that explained the genetic variation were photoperiod and the onset of spring, the Julian date of accumulating degree-days >5 °C reaching 100. The genetic variation was mapped for contemporary and future climates (decades 2060 and 2090), showing flower date change varies considerably across the landscape. Plasticity was estimated to accommodate, on average, a ±13-day change in flowering date. However, the examination of genetic variation in plasticity suggests that the magnitude of plasticity could be affected by variation in the sensitivity to photoperiod and temperature. In a warmer common garden, lower-latitude populations have greater plasticity (+16 days) compared to higher-latitude populations (+10 days). Mapped climatypes of flowering date for contemporary and future climates illustrate the wide breadth of plasticity and large geographic overlap. Our research highlights the importance of integrating information on genetic variation, phenotypic plasticity and climatic niche modeling to evaluate plant responses and elucidate vulnerabilities to climate change. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

PubMed Central

Rudman, Seth M.; Rodriguez-Cabal, Mariano A.; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W.; Crutsinger, Gregory M.

2015-01-01

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

PubMed

Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

2015-08-07

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. © 2015 The Author(s).

Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease.

PubMed

Ashbrook, David G; Williams, Robert W; Lu, Lu; Stein, Jason L; Hibar, Derrek P; Nichols, Thomas E; Medland, Sarah E; Thompson, Paul M; Hager, Reinmar

2014-10-03

Variation in hippocampal volume has been linked to significant differences in memory, behavior, and cognition among individuals. To identify genetic variants underlying such differences and associated disease phenotypes, multinational consortia such as ENIGMA have used large magnetic resonance imaging (MRI) data sets in human GWAS studies. In addition, mapping studies in mouse model systems have identified genetic variants for brain structure variation with great power. A key challenge is to understand how genetically based differences in brain structure lead to the propensity to develop specific neurological disorders. We combine the largest human GWAS of brain structure with the largest mammalian model system, the BXD recombinant inbred mouse population, to identify novel genetic targets influencing brain structure variation that are linked to increased risk for neurological disorders. We first use a novel cross-species, comparative analysis using mouse and human genetic data to identify a candidate gene, MGST3, associated with adult hippocampus size in both systems. We then establish the coregulation and function of this gene in a comprehensive systems-analysis. We find that MGST3 is associated with hippocampus size and is linked to a group of neurodegenerative disorders, such as Alzheimer's.

Adaptation of human skin color in various populations.

PubMed

Deng, Lian; Xu, Shuhua

2018-01-01

Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine. Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies. Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.

Population genetic studies of the polar bear (Ursus maritimus): A summary of available data and interpretation of results

USGS Publications Warehouse

Scribner, Kim T.; Garner, G.W.; Amstrup, Steven C.; Cronin, M.A.; Dizon, Andrew E.; Chivers, Susan J.; Perrin, William F.

1997-01-01

A summary of existing population genetics literature is presented for polar bears (Ursus maritimus) and interpreted in the context of the species' life-history characteristics and regional heterogeneity in environmental regimes and movement patterns. Several nongenetic data sets including morphology, contaminant levels, geographic variation in reproductive characteristics, and the location and distribution of open-water foraging habitat suggest some degree of spatial structuring. Eleven populations are recognized by the IUCN Polar Bear Specialist Group. Few genetics studies exist for polar bears. Interpretation and generalizations of regional variation in intra- and interpopulation levels of genetic variability are confounded by the paucity of data from many regions and by the fact that no single informative genetic marker has been employed in multiple regions. Early allozyme studies revealed comparatively low levels of genetic variability and no compelling evidence of spatial structuring. Studies employing mitochondrial DNA (mtDNA) also found low levels of genetic variation, a lack of phylogenetic structure, and no significant evidence for spatial variation in haplotype frequency. In contrast, microsatellite variable number of tandem repeat (VNTR) loci have revealed significant heterogeneity in allele frequency among populations in the Canadian Arctic. These regions are characterized by archipelgic patterns of sea-ice movements. Further studies using highly polymorphic loci are needed in regions characterized by greater polar bear dependency on pelagic sea-ice movements and in regions for which no data currently exist (i.e., Laptev and Novaya Zemlya/Franz Josef).

Heritabilities of somatotype components in a population from rural Mozambique.

PubMed

Saranga, Sílvio Pedro José; Prista, António; Nhantumbo, Leonardo; Beunen, Gaston; Rocha, Jorge; Williams-Blangero, Sarah; Maia, José A

2008-01-01

There have been few genetic studies of normal variation in body size and composition conducted in Africa. In particular, the genetic determinants of somatotype remain to be established for an African population. (1) To estimate the heritabilities of aspects of somatotype and (2) to compare the quantitative genetic effects in an African population to those that have been assessed in European and American populations. The sample composed of 329 subjects (173 males and 156 females) aged 7-17 years, belonging to 132 families. The sibships in the sample ranged in size from two to seven individuals. All sampled individuals were residents of the Calanga region, an area located to the north of Maputo in Mozambique. Somatotype was assessed using the Heath-Carter technique. Herit abilities were estimated using SAGE software. Moderate heritabilities were determined for each trait. Between 30 and 40% of the variation in each somatotype measure was attributable to genetic factors. The heritability of ectomorphy was 31%. Mesomorphy was similarly moderately heritable, with approximately 30% of the variationattributable to genetic factors. The heritability of endomorph was higher in the Calanga population (h(2) = 0.40). Quantitative genetic analyses of somatotype variation among siblings indicate that genetic factors significantly influence endomorphy, mesomorhpy, and ectomorphy. However, environmental factors also have significant effects on the variation in physique present in the population of Calanga. Lack of proper nutrition, housing, medical assistance, and primary health care, together with very demanding and sex-specific daily chores may contribute to the environmental effects on these traits.

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

PubMed

Faulks, L K; Östman, Ö

2016-04-01

This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended. © 2016 The Fisheries Society of the British Isles.

An introduction to genetic quality in the context of sexual selection.

PubMed

Pitcher, Trevor E; Mays, Herman L

2008-09-01

This special issue of Genetica brings together empirical researchers and theoreticians to present the latest on the evolutionary ecology of genetic quality in the context of sexual selection. The work comes from different fields of study including behavioral ecology, quantitative genetics and molecular genetics on a diversity of organisms using different approaches from comparative studies, mathematical modeling, field studies and laboratory experiments. The papers presented in this special issue primarily focus on genetic quality in relation to (1) sources of genetic variation, (2) polyandry, (3) new theoretical developments and (4) comprehensive reviews.

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

PubMed

Shan, X H; Li, Y D; Liu, X M; Wu, Y; Zhang, M Z; Guo, W L; Liu, B; Yuan, Y P

2012-08-17

We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.

Genetic variation of Lymnaea stagnalis tolerance to copper: A test of selection hypotheses and its relevance for ecological risk assessment.

PubMed

Côte, Jessica; Bouétard, Anthony; Pronost, Yannick; Besnard, Anne-Laure; Coke, Maïra; Piquet, Fabien; Caquet, Thierry; Coutellec, Marie-Agnès

2015-10-01

The use of standardized monospecific testing to assess the ecological risk of chemicals implicitly relies on the strong assumption that intraspecific variation in sensitivity is negligible or irrelevant in this context. In this study, we investigated genetic variation in copper sensitivity of the freshwater snail Lymnaea stagnalis, using lineages stemming from eight natural populations or strains found to be genetically differentiated at neutral markers. Copper-induced mortality varied widely among populations, as did the estimated daily death rate and time to 50% mortality (LT50). Population genetic divergence in copper sensitivity was compared to neutral differentiation using the QST-FST approach. No evidence for homogenizing selection could be detected. This result demonstrates that species-level extrapolations from single population studies are highly unreliable. The study provides a simple example of how evolutionary principles could be incorporated into ecotoxicity testing in order to refine ecological risk assessment. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Effect of PCDH15 Gene Variations on the Risk of Noise-induced Hearing Loss in a Chinese Population.

PubMed

Xu, Xiang Rong; Wang, Jing Jing; Yang, Qiu Yue; Jiao, Jie; He, Li Hua; Yu, Shan Fa; Gu, Gui Zhen; Chen, Guo Shun; Zhou, Wen Hui; Wu, Hui; Li, Yan Hong; Zhang, Huan Ling; Zhang, Zeng Rui; Jin, Xian Ning

2017-02-01

Noise-induced hearing loss (NIHL) is a complex disease caused by interactions between environmental and genetic factors. This study investigated whether genetic variability in protocadherin related 15 (PCDH15) underlies an increased susceptibility to the development of NIHL in a Chinese population. The results showed that compared with the TT genotype of rs11004085, CT/CC genotypes were associated with an increased risk of NIHL [adjusted odds ratio (OR) = 2.64; 95% confidence interval (CI): 1.14-6.11, P = 0.024]. Additionally, significant interactions between the rs11004085 and rs978842 genetic variations and noise exposure were observed in the high-level exposure groups (P < 0.05). Furthermore, the risk haplotype TAGCC was observed when combined with higher levels of noise exposure (P < 0.05). Thus, our study confirms that genetic variations in PCDH15 modify the susceptibility to NIHL development in humans. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Genetic structure of Pseudococcus microcirculus (Hemiptera: Pseudococcidae) populations on epiphytic orchids in south Florida.

PubMed

Zettler, J A; Adams, K; Frederick, B; Gutting, A; Ingebretsen, N; Ragsdale, A; Schrey, A

2017-03-01

In 2012, the orchid mealy bug Pseudococcus microcirculus was first detected in situ in North America's more diverse orchid region, the Big Cypress Basin (Collier Co FL). A follow-up survey showed that the mealy bug is more widespread and found on epiphytic orchids in two locations, in both the Fakahatchee Strand State Preserve (sites B and F) and the Florida Panther National Wildlife Refuge (sites M and C). There, we collected mealy bugs (n = 54) from 35 orchid individuals and screened allelic variation at seven microsatellite loci. We estimated genetic diversity and differentiation among all sites and compared the variation among individuals collected on the same plant. Genetic differentiation between sites M and C (F ST = 0.03, P < 0.01) and,Mand B (F ST = 0.04, P < 0.01) was detected.We also detected significantly lower mean pairwise relatedness among individuals from site B compared to all the other locations, and this population had the lowest inbreeding coefficient. Genetic diversity and mean pairwise relatedness were highly variable among plants with multiple individuals; however, plants from sites F and M tend to have collections of individuals with higher mean pairwise relatedness compared to sites B and C. Our results indicate that there is genetic diversity and differentiation among mealy bugs in these locations, and that collections of individuals on the same plant are genetically diverse. As such, the mealy bugs throughout these areas are likely to be genetically diverse and exist in multiple distinct populations.

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 increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Serum chemistry reference values for the common genet (Genetta genetta): variations associated with Leishmania infantum infection.

PubMed

Millán, Javier; Chirife, Andrea D; Altet, Laura

2015-03-01

The role of wildlife in the epidemiology of leishmaniosis in under debate, and determining whether infection with Leishmania infantum causes illness in wild carnivores is important to determine its potential role as a reservoir. To provide for the first time serum biochemistry reference values for the common genet (Genetta genetta), and to determine variations associated with L. infantum infection. Twenty-five serum biochemistry parameters were determined in 22 wild-caught genets. Blood samples were analyzed for L. infantum DNA by means of real-time polymerase chain reaction (PCR). Two female genets were positive for L. infantum DNA but did not show any external clinical sign upon physical examination. Among other variations in the biochemistry values of these genets, one presented a higher concentration of gamma-globulins and cholesterol, whereas the other genet presented increased creatinine, bilirubin, and chloride levels when compared to uninfected females. Sex-related differences in some parameters were also reported. Infection with L. infantum may sometimes be accompanied by abnormal serum biochemistry in wild carnivores. Clinical disease may occur in L. infantum-infected wild carnivores. This has implications in the epidemiology of leishmaniosis. In addition, the data provided here would also be useful as reference values for researchers or rehabilitators working with the common genet.

Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

PubMed Central

Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

2010-01-01

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Significance of genetic variants in DLC1 and their association with hepatocellular carcinoma

PubMed Central

XIE, CHENG-RONG; SUN, HONG-GUANG; SUN, YU; ZHAO, WEN-XIU; ZHANG, SHENG; WANG, XIAO-MIN; YIN, ZHEN-YU

2015-01-01

DLC1 has been shown to be downregulated or absent in hepatocellular carcinoma (HCC) and is associated with tumorigenesis and development. However, only a small number of studies have focused on genetic variations of DLC1. The present study performed exon sequencing for the DLC1 gene in HCC tissue samples from 105 patients to identify functional genetic variation of DLC1 and its association with HCC susceptibility, clinicopathological features and prognosis. A novel missense mutation and four non-synonymous single nucleotide polymorphisms (SNPs; rs3816748, rs11203495, rs3816747 and rs532841) were identified. A significant correlation of rs3816747 polymorphisms with HCC susceptibility was identified. Compared to individuals with the GG genotype of rs3816747, those with the GA (odds ratio (OR)=0.486; P=0.037) or GA+AA genotype (OR=0.51; P=0.039) were associated with a significantly decreased HCC risk. Furthermore, patients with the GC+CC genotype of rs3816748, the TC+CC genotype of rs11203495 or the GA+AA genotype of rs3816747 had small-sized tumors compared with those carrying the wild-type genotype. No significant association of DLC1 SNPs with the patients' prognosis was found. These results indicated that genetic variations in the DLC1 gene may confer a risk for HCC. PMID:26095787

Condition dependence and the nature of genetic variation for male sex comb bristle number in Drosophila melanogaster.

PubMed

Ahuja, Abha; De Vito, Scott; Singh, Rama S

2011-04-01

Genetic architecture of variation underlying male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila, was examined. First, in order to test for condition dependence, diet was manipulated in a set of ten Drosophila melanogaster full-sib families. We confirmed heightened condition dependent expression of sex comb bristle number and its female homologue (distal transverse row bristles) as compared to non-sex sternopleural bristles. Significant genotype by environment effects were detected for the sex traits indicating a genetic basis for condition dependence. Next we measured sex comb bristle number and sternopleural bristle number, as well as residual mass, a commonly used condition index, in a set of thirty half-sib families. Sire effect was not significant for sex comb and sternopleural bristle number, and we detected a strong dominance and/or maternal effect or X chromosome effect for both traits. A strong sire effect was detected for condition and its heritability was the highest as compared to sex comb and sternopleural bristles. We discuss our results in light of the rapid response to divergent artificial selection for sex comb bristle number reported previously. The nature of genetic variation for male sex traits continues to be an important unresolved issue in evolutionary biology.

Genomics and museum specimens.

PubMed

Nachman, Michael W

2013-12-01

Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years. © 2013 John Wiley & Sons Ltd.

Characterization of Genome-Wide Variation in Four-Row Wax, a Waxy Maize Landrace with a Reduced Kernel Row Phenotype

PubMed Central

Liu, Hanmei; Wang, Xuewen; Wei, Bin; Wang, Yongbin; Liu, Yinghong; Zhang, Junjie; Hu, Yufeng; Yu, Guowu; Li, Jian; Xu, Zhanbin; Huang, Yubi

2016-01-01

In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1–5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement. PMID:27242868

Population and allelic variation of A-to-I RNA editing in human transcriptomes.

PubMed

Park, Eddie; Guo, Jiguang; Shen, Shihao; Demirdjian, Levon; Wu, Ying Nian; Lin, Lan; Xing, Yi

2017-07-28

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure. Our study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

PubMed Central

2011-01-01

Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. PMID:21672265

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

PubMed

Kutanan, Wibhu; Kampuansai, Jatupol; Fuselli, Silvia; Nakbunlung, Supaporn; Seielstad, Mark; Bertorelle, Giorgio; Kangwanpong, Daoroong

2011-06-15

The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. © 2011 Kutanan et al; licensee BioMed Central Ltd.

Comparative genomics of Enterococcus faecalis from healthy Norwegian infants

PubMed Central

Solheim, Margrete; Aakra, Ågot; Snipen, Lars G; Brede, Dag A; Nes, Ingolf F

2009-01-01

Background Enterococcus faecalis, traditionally considered a harmless commensal of the intestinal tract, is now ranked among the leading causes of nosocomial infections. In an attempt to gain insight into the genetic make-up of commensal E. faecalis, we have studied genomic variation in a collection of community-derived E. faecalis isolated from the feces of Norwegian infants. Results The E. faecalis isolates were first sequence typed by multilocus sequence typing (MLST) and characterized with respect to antibiotic resistance and properties associated with virulence. A subset of the isolates was compared to the vancomycin resistant strain E. faecalis V583 (V583) by whole genome microarray comparison (comparative genomic hybridization (CGH)). Several of the putative enterococcal virulence factors were found to be highly prevalent among the commensal baby isolates. The genomic variation as observed by CGH was less between isolates displaying the same MLST sequence type than between isolates belonging to different evolutionary lineages. Conclusion The variations in gene content observed among the investigated commensal E. faecalis is comparable to the genetic variation previously reported among strains of various origins thought to be representative of the major E. faecalis lineages. Previous MLST analysis of E. faecalis have identified so-called high-risk enterococcal clonal complexes (HiRECC), defined as genetically distinct subpopulations, epidemiologically associated with enterococcal infections. The observed correlation between CGH and MLST presented here, may offer a method for the identification of lineage-specific genes, and may therefore add clues on how to distinguish pathogenic from commensal E. faecalis. In this work, information on the core genome of E. faecalis is also substantially extended. PMID:19393078

Genetic characterization of brown bears of the Kodiak Archipelago

USGS Publications Warehouse

Talbot, Sandra L.; Gust, Judy R.; Sage, George K.; Fischbach, Anthony S.; Amstrup, Kristin S.; Leacock, William; Van Daele, Larry

2006-01-01

Here we examine genetic characteristics of brown bears of Kodiak and Afognak islands, using 14 variable nuclear microsatellite loci and nucleotide sequence information including the hypervariable domain I of the mtDNA control region (Wakely 1993). Because these markers, or a subset of them, have been used to characterize brown bears of the Kenai Peninsula (Jackson et al. 2005), Katmai National Park, Seward Peninsula, and nine other populations in Alaska (Talbot, unpublished data), we compared levels of genetic diversity and relationships among populations when possible. In addition, we obtained preliminary comparative information from class II DQA and DQB genes of the brown bear MHC, to examine levels of variation at this important immunology-mediating supergene. These data were used to answer the following questions: 1) are earlier findings of extremely low levels of variability at nuclear (biparentallyinherited) microsatellite loci from a small geographic area (Paetkau et al. 1998b) representative of Kodiak Archipelago populations as a whole? 2) Is the level and type of variation at the maternally-inherited mtDNA lower, or similar to, levels found in other populations in Alaska? 3) Is there concordance between low levels of genetic variation observed at neutral markers with levels of variation observed at functional genes? 4) Is there population substructuring within Kodiak and Afognak islands? 5) What is the connectivity between populations on Afognak Island and Kodiak Island? 6) What are the phylogeographic relationships between bears of the Kodiak Archipelago with brown bears on mainland Alaskan and other western Beringian populations? We also test whether these markers will provide an appropriate baseline for designing genetic tagging studies for use in future research and management activities, such as mark-recapture efforts, on the Refuge.

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

PubMed

Jasinska, Anna J; Zelaya, Ivette; Service, Susan K; Peterson, Christine B; Cantor, Rita M; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A; Fears, Scott; Furterer, Allison E; Huang, Yu S; Ramensky, Vasily; Schmitt, Christopher A; Svardal, Hannes; Jorgensen, Matthew J; Kaplan, Jay R; Villar, Diego; Aken, Bronwen L; Flicek, Paul; Nag, Rishi; Wong, Emily S; Blangero, John; Dyer, Thomas D; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K; Jentsch, J David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P; Freimer, Nelson B

2017-12-01

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

Relative contributions of neutral and non-neutral processes to clinal variation in calyx lobe length in the series Sakawanum (Asarum: Aristolochiaceae).

PubMed

Takahashi, Daiki; Teramine, Tsutomu; Sakaguchi, Shota; Setoguchi, Hiroaki

2018-01-25

Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length. A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (QCT-FST comparison). Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (FST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise QCT values were significantly higher than the neutral genetic measures of FST and G'ST. Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum. © The Author(s) 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The cancer transcriptome is shaped by genetic changes, variation in gene transcription, mRNA processing, editing and stability, and the cancer microbiome. Deciphering this variation and understanding its implications on tumorigenesis requires sophisticated computational analyses. Most RNA-Seq analyses rely on methods that first map short reads to a reference genome, and then compare them to annotated transcripts or assemble them. However, this strategy can be limited when the cancer genome is substantially different than the reference or for detecting sequences from the cancer microbiome.

Efficient modification of floral traits by heavy-ion beam irradiation on transgenic Torenia.

PubMed

Ohtsubo, Norihiro; Sasaki, Katsutomo; Aida, Ryutaro; Ryuto, Hiromichi; Ichida, Hiroyuki; Hayashi, Yoriko; Abe, Tomoko

2012-01-01

While heavy-ion beam irradiation is becoming popular technology for mutation breeding in Japan, the combination with genetic manipulation makes it more convenient to create greater variation in plant phenotypes. We have succeeded in producing over 200 varieties of transgenic torenia (Torenia fournieri Lind.) from over 2,400 regenerated plants by this procedure in only 2 years. Mutant phenotypes were observed mainly in flowers and showed wide variation in colour and shape. Higher mutation rates in the transgenics compared to those in wild type indicate the synergistic effect of genetic manipulation and heavy-ion beam irradiation, which might be advantageous to create greater variation in floral traits.

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

Genetic structure of coexisting wild and managed agave populations: implications for the evolution of plants under domestication

PubMed Central

Figueredo, Carmen Julia; Casas, Alejandro; González-Rodríguez, Antonio; Nassar, Jafet M.; Colunga-GarcíaMarín, Patricia; Rocha-Ramírez, Víctor

2015-01-01

Domestication is a continuous evolutionary process guided by humans. This process leads to divergence in characteristics such as behaviour, morphology or genetics, between wild and managed populations. Agaves have been important resources for Mesoamerican peoples since prehistory. Some species are domesticated and others vary in degree of domestication. Agave inaequidens Koch is used in central Mexico to produce mescal, and a management gradient from gathered wild and silvicultural populations, as well as cultivated plantations, has been documented. Significant morphological differences were reported among wild and managed populations, and a high phenotypic variation in cultivated populations composed of plants from different populations. We evaluated levels of genetic diversity and structure associated with management, hypothesizing that high morphological variation would be accompanied by high genetic diversity in populations with high gene flow and low genetic structure among managed and unmanaged populations. Wild, silvicultural and cultivated populations were studied, collecting tissue of 19–30 plants per population. Through 10 nuclear microsatellite loci, we compared population genetic parameters. We analysed partition of variation associated with management categories to estimate gene flow among populations. Agave inaequidens exhibits high levels of genetic diversity (He = 0.707) and moderate genetic structure (FST = 0.112). No differences were found in levels of genetic diversity among wild (He = 0.704), silviculturally managed (He = 0.733) and cultivated (He = 0.698) populations. Bayesian analysis indicated that five genetic clusters best fit the data, with genetic groups corresponding to habitats where populations grow rather than to management. Migration rates ranged from zero between two populations to markedly high among others (M = 0.73–35.25). Natural mechanisms of gene flow and the dynamic management of agave propagules among populations favour gene flow and the maintenance of high levels of variation within all populations. The slight differentiation associated with management indicates that domestication is in an incipient stage. PMID:26433707

Diversity hotspots of the laurel forest on Tenerife, Canary Islands: a phylogeographic study of Laurus and Ixanthus.

PubMed

Betzin, Anja; Thiv, Mike; Koch, Marcus A

2016-09-01

Macaronesian laurel forest is among the worldwide hotspots of threatened biodiversity. With increasing evidence that woodland composition on the Canary Islands changed dramatically during the last few thousand years, the aim of this study was to find evidence for substantial recent population dynamics of two representative species from laurel forest. Amplified fragment length polymorphism (AFLP) was used to evaluate fine-scaled genetic variation of the paradigmatic tree Laurus novocanariensis (Lauraceae) and a long-lived herbaceous gentian from core laurel forest, Ixanthus viscosus (Gentianaceae), on Tenerife. Bioclimatic variables were analysed to study the respective climate niches. A chloroplast DNA screening was performed to evaluate additional genetic variation. Genetic diversity of the laurel tree showed severe geographic partitioning. On Tenerife, fine-scaled Bayesian clustering of genetic variation revealed a western and an eastern gene pool, separated by a zone of high admixture and with a third major gene pool. Compared with genetic clusters found on the other Canary Islands, the East-West differentiation on Tenerife seems to be more recent than differentiation between islands. This is substantiated by the finding of extremly low levels of chloroplast DNA-based polymorphisms. Ixanthus showed no geographic structuring of genetic variation. Genetic data from Tenerife indicate contemporary gene flow and dispersal on a micro/local scale rather than reflecting an old and relic woodland history. In particular for Laurus, it is shown that this species occupies a broad bioclimatic niche. This is not correlated with its respective distribution of genetic variation, therefore indicating its large potential for contemporary rapid and effective colonization. Ixanthus is more specialized to humid conditions and is mostly found in the natural Monteverde húmedo vegetation types, but even for this species indications for long-term persistence in the respective bioclimatically differentiated regions was not find. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda.

PubMed

Zhu, Ying; Wan, Qiu-Hong; Yu, Bin; Ge, Yun-Fa; Fang, Sheng-Guo

2013-10-22

Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a captive breeding program be considered for the Qinling panda population.

Genetic variation for farrowing rate in pigs in response to change in photoperiod and ambient temperature.

PubMed

Sevillano, C A; Mulder, H A; Rashidi, H; Mathur, P K; Knol, E F

2016-08-01

Seasonal infertility is often observed as anestrus and a lower conception rate resulting in a reduced farrowing rate (FR) during late summer and early autumn. This is often regarded as an effect of heat stress; however, we observed a reduction in the FR of sows even after correcting for ambient temperature in our data. Therefore, we added change in photoperiod in the analysis of FR considering its effect on sow fertility. Change in photoperiod was modeled using the cosine of the day of first insemination within a year. On an average, the FR decreased by 2% during early autumn with decreasing daily photoperiod compared with early summer with almost no change in daily photoperiod. It declined 0.2% per degree Celsius of ambient temperature above 19.2°C. This result is a step forward in disentangling the 2 environmental components responsible for seasonal infertility. Our next aim was to estimate the magnitude of genetic variation in FR in response to change in photoperiod and ambient temperature to explore opportunities for selecting pigs to have a constant FR throughout the year. We used reaction norm models to estimate additive genetic variation in response to change in photoperiod and ambient temperature. The results revealed a larger genetic variation at stressful environments when daily photoperiod decreased and ambient temperatures increased above 19.2°C compared with neutral environments. Genetic correlations between stressful environments and nonstressful environments ranged from 0.90 (±0.03) to 0.46 (±0.13) depending on the severity of the stress, indicating changes in expression of FR depending on the environment. The genetic correlation between responses of pigs to changes in photoperiod and to those in ambient temperature were positive, indicating that pigs tolerant to decreasing daily photoperiod are also tolerant to high ambient temperatures. Therefore, selection for tolerance to decreasing daily photoperiod should also increase tolerance to high ambient temperatures or vice versa.

Quantifying the effects of genetic selection and genetic variation for body size, carcass composition, and meat quality in the domestic fowl (Gallus domesticus).

PubMed

Sandercock, D A; Nute, G R; Hocking, P M

2009-05-01

A multistrain experiment was conducted to quantify the extent of genetic differences in carcass and muscle yields, muscle quality, support organs, and taste panel assessments of cooked breast muscle of 296 birds from 37 lines of commercial broiler, layer, and traditional chickens. The birds were reared as broilers and 4 males from each line were slaughtered at 6 and 10 wk of age. The extent of genetic variation was measured as the intraclass correlation. The intraclass correlation for live weight; carcass yields; breast, drum, and wing portions; and associated muscle yields were high, whereas those for the thigh portion and yield were low. Broilers had more breast and thigh muscle but similar drum muscle as a proportion of carcass weight compared with layer and traditional lines. Genetic variation for muscle quality (plasma creatine kinase activity) was high; that for muscle color (L, a, and b) and hemorrhage score were moderate in size and were greater at 10 than at 6 wk of age. Broiler lines had greater creatine kinase activity indicative of greater muscle pathology; breast muscle was lighter, less red and yellow in color, and had a greater hemorrhage score than muscle from layer and traditional lines, which were similar. Intraclass correlations for taste panel scores were low and generally not significant except for texture, chicken flavor intensity, flavor liking, and overall liking at 6 wk of age. Significantly greater scores from broiler compared with layer and traditional lines for texture, chicken flavor intensity, and overall liking were observed. At 10 wk of age, chicken flavor intensity did not differ between broiler or layer birds but was significantly greater in both groups than traditional birds. Genetic variation for relative weight of abdominal fat, spleen, and heart was moderately high and greater at 10 than at 6 wk of age. Broiler carcasses had a relatively high proportion of abdominal fat and smaller spleen and heart weights.

The genetic basis of female multiple mating in a polyandrous livebearing fish

PubMed Central

Evans, Jonathan P; Gasparini, Clelia

2013-01-01

The widespread occurrence of female multiple mating (FMM) demands evolutionary explanation, particularly in the light of the costs of mating. One explanation encapsulated by “good sperm” and “sexy-sperm” (GS-SS) theoretical models is that FMM facilitates sperm competition, thus ensuring paternity by males that pass on genes for elevated sperm competitiveness to their male offspring. While support for this component of GS-SS theory is accumulating, a second but poorly tested assumption of these models is that there should be corresponding heritable genetic variation in FMM – the proposed mechanism of postcopulatory preferences underlying GS-SS models. Here, we conduct quantitative genetic analyses on paternal half-siblings to test this component of GS-SS theory in the guppy (Poecilia reticulata), a freshwater fish with some of the highest known rates of FMM in vertebrates. As with most previous quantitative genetic analyses of FMM in other species, our results reveal high levels of phenotypic variation in this trait and a correspondingly low narrow-sense heritability (h2 = 0.11). Furthermore, although our analysis of additive genetic variance in FMM was not statistically significant (probably owing to limited statistical power), the ensuing estimate of mean-standardized additive genetic variance (IA = 0.7) was nevertheless relatively low compared with estimates published for life-history traits across a broad range of taxa. Our results therefore add to a growing body of evidence that FMM is characterized by relatively low additive genetic variation, thus apparently contradicting GS-SS theory. However, we qualify this conclusion by drawing attention to potential deficiencies in most designs (including ours) that have tested for genetic variation in FMM, particularly those that fail to account for intersexual interactions that underlie FMM in many systems. PMID:23403856

Genetic variation for leaf morphology, leaf structure and leaf carbon isotope discrimination in European populations of black poplar (Populus nigra L.).

PubMed

Guet, Justine; Fabbrini, Francesco; Fichot, Régis; Sabatti, Maurizio; Bastien, Catherine; Brignolas, Franck

2015-08-01

To buffer against the high spatial and temporal heterogeneity of the riparian habitat, riparian tree species, such as black poplar (Populus nigra L.), may display a high level of genetic variation and phenotypic plasticity for functional traits. Using a multisite common garden experiment, we estimated the relative contribution of genetic and environmental effects on the phenotypic variation expressed for individual leaf area, leaf shape, leaf structure and leaf carbon isotope discrimination (Δ(13)C) in natural populations of black poplar. Twenty-four to 62 genotypes were sampled in nine metapopulations covering a latitudinal range from 48 °N to 42 °N in France and in Italy and grown in two common gardens at Orléans (ORL) and at Savigliano (SAV). In the two common gardens, substantial genetic variation was expressed for leaf traits within all metapopulations, but its expression was modulated by the environment, as attested by the genotype × environment (G × E) interaction variance being comparable to or even greater than genetic effects. For LA, G × E interactions were explained by both changes in genotype ranking between common gardens and increased variation in SAV, while these interactions were mainly attributed to changes in genotype ranking for Δ(13)C. The nine P. nigra metapopulations were highly differentiated for LA, as attested by the high coefficient of genetic differentiation (QST = 0.50 at ORL and 0.51 at SAV), and the pattern of metapopulation differentiation was highly conserved between the two common gardens. In contrast, they were moderately differentiated for Δ(13)C (QST = 0.24 at ORL and 0.25 at SAV) and the metapopulation clustering changed significantly between common gardens. Our results evidenced that the nine P. nigra metapopulations present substantial genetic variation and phenotypic plasticity for leaf traits, which both represent potentially significant determinants of populations' capacities to respond, on a short-term basis and over generations, to environmental variations. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Maintenance of genetic diversity through plant-herbivore interactions

PubMed Central

Gloss, Andrew D.; Dittrich, Anna C. Nelson; Goldman-Huertas, Benjamin; Whiteman, Noah K.

2013-01-01

Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains functionally-important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously. PMID:23834766

Maintenance of genetic variation in human personality: Testing evolutionary models by estimating heritability due to common causal variants and investigating the effect of distant inbreeding

PubMed Central

Verweij, Karin J.H.; Yang, Jian; Lahti, Jari; Veijola, Juha; Hintsanen, Mirka; Pulkki-Råback, Laura; Heinonen, Kati; Pouta, Anneli; Pesonen, Anu-Katriina; Widen, Elisabeth; Taanila, Anja; Isohanni, Matti; Miettunen, Jouko; Palotie, Aarno; Penke, Lars; Service, Susan K.; Heath, Andrew C.; Montgomery, Grant W.; Raitakari, Olli; Kähönen, Mika; Viikari, Jorma; Räikkönen, Katri; Eriksson, Johan G; Keltikangas-Järvinen, Liisa; Lehtimäki, Terho; Martin, Nicholas G.; Järvelin, Marjo-Riitta; Visscher, Peter M.; Keller, Matthew C.; Zietsch, Brendan P.

2012-01-01

Personality traits are basic dimensions of behavioural variation, and twin, family, and adoption studies show that around 30% of the between-individual variation is due to genetic variation. There is rapidly-growing interest in understanding the evolutionary basis of this genetic variation. Several evolutionary mechanisms could explain how genetic variation is maintained in traits, and each of these makes predictions in terms of the relative contribution of rare and common genetic variants to personality variation, the magnitude of nonadditive genetic influences, and whether personality is affected by inbreeding. Using genome-wide SNP data from >8,000 individuals, we estimated that little variation in the Cloninger personality dimensions (7.2% on average) is due to the combined effect of common, additive genetic variants across the genome, suggesting that most heritable variation in personality is due to rare variant effects and/or a combination of dominance and epistasis. Furthermore, higher levels of inbreeding were associated with less socially-desirable personality trait levels in three of the four personality dimensions. These findings are consistent with genetic variation in personality traits having been maintained by mutation-selection balance. PMID:23025612

Variation and inheritance pattern in cone and seed characteristics of Scots pine (Pinus sylvestris L.) for evaluation of genetic diversity.

PubMed

Sevik, Hakan; Topaçoğlu, Osman

2015-09-01

Scots pine (Pinus sylvestris L.) is one of the most common and important forest tree species in Turkey due to usefulness of its wood to many commercial uses. This species is classified as one of the economically important tree species for Turkish Forestry in the "National Tree Breeding and Seed Production Program". The objective of the present study was to investigate variation and inheritance pattern in cone and seed characteristics of Scots pine and to evaluate variation in cone and seed characters within and among clones and grafts. The results showed that maximum CV among the clones was found for SWe (21.95), FS (16.99) and CWe (16.88). According to the results of SAS, variation between the clones is averaged at 19.2% and variation within the clones is averaged at 24.4 %. Variation between the clones ranged from 3.6% (SW) to 34.5% (TC) and variation within the clones ranged from 12.3% (SW) to 38.1% (WL). For CW, AL, AW, WW and TC, genetic variation among clones was higher than within clones. When the results of study like compared with results obtained from natural populations, it was seen that genetic variability in seed orchard which was subjected to study was quite low. This case may have dangerous results for the future of forests.

Low Variation in the Polymorphic Clock Gene Poly-Q Region Despite Population Genetic Structure across Barn Swallow (Hirundo rustica) Populations

PubMed Central

Dor, Roi; Lovette, Irby J.; Safran, Rebecca J.; Billerman, Shawn M.; Huber, Gernot H.; Vortman, Yoni; Lotem, Arnon; McGowan, Andrew; Evans, Matthew R.; Cooper, Caren B.; Winkler, David W.

2011-01-01

Recent studies of several species have reported a latitudinal cline in the circadian clock gene, Clock, which influences rhythms in both physiology and behavior. Latitudinal variation in this gene may hence reflect local adaptation to seasonal variation. In some bird populations, there is also an among-individual association between Clock poly-Q genotype and clutch initiation date and incubation period. We examined Clock poly-Q allele variation in the Barn Swallow (Hirundo rustica), a species with a cosmopolitan geographic distribution and considerable variation in life-history traits that may be influenced by the circadian clock. We genotyped Barn Swallows from five populations (from three subspecies) and compared variation at the Clock locus to that at microsatellite loci and mitochondrial DNA (mtDNA). We found very low variation in the Clock poly-Q region, as >96% of individuals were homozygous, and the two other alleles at this locus were globally rare. Genetic differentiation based on the Clock poly-Q locus was not correlated with genetic differentiation based on either microsatellite loci or mtDNA sequences. Our results show that high diversity in Clock poly-Q is not general across avian species. The low Clock variation in the background of heterogeneity in microsatellite and mtDNA loci in Barn Swallows may be an outcome of stabilizing selection on the Clock locus. PMID:22216124

nrDNA:mtDNA copy number ratios as a comparative metric for evolutionary and conservation genetics.

PubMed

Goodall-Copestake, William Paul

2018-05-12

Identifying genetic cues of functional relevance is key to understanding the drivers of evolution and increasingly important for the conservation of biodiversity. This study introduces nuclear ribosomal DNA (nrDNA) to mitochondrial DNA (mtDNA) copy number ratios as a metric with which to screen for this functional genetic variation prior to more extensive omics analyses. To illustrate the metric, quantitative PCR was used to estimate nrDNA (18S) to mtDNA (16S) copy number ratios in muscle tissue from samples of two zooplankton species: Salpa thompsoni caught near Elephant Island (Southern Ocean) and S. fusiformis sampled off Gough Island (South Atlantic). Average 18S:16S ratios in these samples were 9:1 and 3:1, respectively. nrDNA 45S arrays and mitochondrial genomes were then deep sequenced to uncover the sources of intra-individual genetic variation underlying these 18S:16S copy number differences. The deep sequencing profiles obtained were consistent with genetic changes resulting from adaptive processes, including an expansion of nrDNA and damage to mtDNA in S. thompsoni, potentially in response to the polar environment. Beyond this example from zooplankton, nrDNA:mtDNA copy number ratios offer a promising metric to help identify genetic variation of functional relevance in animals more broadly.

Genetic diversity of allozymes in turnip (Brassica rapa L. var. rapa) from the Nordic area.

PubMed

Persson, K; Fält, A S; von Bothmer, R

2001-01-01

Genetic diversity and relationships based on isozymes were studied in 31 accessions of turnip (Brassica rapa L. var. rapa). The material included varieties, elite stocks, landraces and older turnip of slash-and-burn type from the Nordic area. A total of 9 isozyme loci and 26 alleles were studied. The isozyme systems were ACO, DIA, GPI, GOT, PGM, PGD and SKD. The level of heterozygosity was reduced in the landraces, but it was high for the variety group 'Ostersundom'. Turnip has a higher genetic variation than other crops within B. rapa and than in other species with the same breeding system. The genetic diversity showed that 18.7% of the genetic variation was within the accessions, and the total H tau value was 0.358. Gpi-I and Pgd-I showed the lowest variation compared with the other loci. The cluster analysis revealed five clusters, with one main cluster including 25 of the 31 accessions. The dendrogram indicated that the variety group 'Ostersundom' clustered together whereas the variety group 'Bortfelder' was associated with country of origin. The landraces were spread in different clusters. The 'slash-and-burn' type of turnip belonged to two groups.

Genetic diversity of Taenia asiatica from Thailand and other geographical locations as revealed by cytochrome c oxidase subunit 1 sequences.

PubMed

Anantaphruti, Malinee Thairungroj; Thaenkham, Urusa; Watthanakulpanich, Dorn; Phuphisut, Orawan; Maipanich, Wanna; Yoonuan, Tippayarat; Nuamtanong, Supaporn; Pubampen, Somjit; Sanguankiat, Surapol

2013-02-01

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T. saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species.

Genetic Diversity of Taenia asiatica from Thailand and Other Geographical Locations as Revealed by Cytochrome c Oxidase Subunit 1 Sequences

PubMed Central

Thaenkham, Urusa; Watthanakulpanich, Dorn; Phuphisut, Orawan; Maipanich, Wanna; Yoonuan, Tippayarat; Nuamtanong, Supaporn; Pubampen, Somjit; Sanguankiat, Surapol

2013-01-01

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T. saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species. PMID:23467439

Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology.

PubMed

Tyler, Torbjörn

2002-12-01

Allozyme variation in the forest grass Milium effusum L. was studied in 21-23 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.

Genomic single-nucleotide polymorphisms confirm that Gunnison and Greater sage-grouse are genetically well differentiated and that the Bi-State population is distinct

USGS Publications Warehouse

Oyler-McCance, Sara J.; Cornman, Robert S.; Jones, Kenneth L.; Fike, Jennifer

2015-01-01

Sage-grouse are iconic, declining inhabitants of sagebrush habitats in western North America, and their management depends on an understanding of genetic variation across the landscape. Two distinct species of sage-grouse have been recognized, Greater (Centrocercus urophasianus) and Gunnison sage-grouse (C. minimus), based on morphology, behavior, and variation at neutral genetic markers. A parapatric group of Greater Sage-Grouse along the border of California and Nevada ("Bi-State") is also genetically distinct at the same neutral genetic markers, yet not different in behavior or morphology. Because delineating taxonomic boundaries and defining conservation units is often difficult in recently diverged taxa and can be further complicated by highly skewed mating systems, we took advantage of new genomic methods that improve our ability to characterize genetic variation at a much finer resolution. We identified thousands of single-nucleotide polymorphisms (SNPs) among Gunnison, Greater, and Bi-State sage-grouse and used them to comprehensively examine levels of genetic diversity and differentiation among these groups. The pairwise multilocus fixation index (FST) was high (0.49) between Gunnison and Greater sage-grouse, and both principal coordinates analysis and model-based clustering grouped samples unequivocally by species. Standing genetic variation was lower within the Gunnison Sage-Grouse. The Bi-State population was also significantly differentiated from Greater Sage-Grouse, albeit more weakly (FST = 0.09), and genetic clustering results were consistent with reduced gene flow with Greater Sage-Grouse. No comparable genetic divisions were found within the Greater Sage-Grouse sample, which spanned the southern half of the range. Thus, we provide much stronger genetic evidence supporting the recognition of Gunnison Sage-Grouse as a distinct species with low genetic diversity. Further, our work confirms that the Bi-State population is differentiated from other Greater Sage-Grouse. The level of differentiation is much less than the divergence between Greater and Gunnison sage-grouse, supporting the idea that the Bi-State represents a unique population within the Greater Sage-Grouse. New genomic methods like the restriction-site-associated DNA (RAD-tag) method used here illustrate how increasing the number of markers and coverage of the genome can better characterize patterns of genetic variation, particularly among recently diverged taxa, providing vital information for conservation and management.

A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China.

PubMed

Yuan, N; Comes, H P; Cao, Y N; Guo, R; Zhang, Y H; Qiu, Y X

2015-06-01

Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland-island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.

Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow.

PubMed

Richter-Boix, Alex; Teplitsky, Céline; Rogell, Björn; Laurila, Anssi

2010-02-01

In ectotherms, variation in life history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, as genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open-canopy or partially closed-canopy ponds. To separate local adaptation from genetic drift, we compared differentiation in quantitative genetic traits (Q(ST)) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (F(ST)). We found that R. temporaria populations differ in means and plasticities of life history traits in different temperatures at local, and in F(ST) at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature, the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure, but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among the populations, and that natural selection is strong in this system.

Evidence of low genetic variation and rare alleles in a bottlenecked endangered island endemic, the Lasan Teal (Anas laysanensis)

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Peters Jeffrey L,; Courtot, Karen; Seixas, Pedro P.

2015-01-01

Genetic diversity is assumed to reflect the evolutionary potential and adaptability of populations, and thus quantifying the genetic diversity of endangered species is useful for recovery programs. In particular, if conservation strategies include reintroductions, periodic genetic assessments are useful to evaluate whether management efforts have resulted in the maximization or loss of genetic variation within populations over generations. In this study, we collected blood, feather, and tissue samples during 1999–2009 and quantified genetic diversity for a critically endangered waterfowl species endemic to the Hawaiian archipelago, the Laysan teal or duck (Anas laysanensis; n = 239 individual birds sampled). The last extant population of this species at Laysan Island was sourced in 2004–2005 for a ‘wild to wild’ translocation of 42 individuals for an experimental reintroduction to Midway Atoll. To inform future management strategies, we compared genetic diversity sampled from the source population (n = 133 Laysan birds) including 23 of Midway’s founders and offspring of the translocated population 2–5 years post release (n = 96 Midway birds). We attempted to identify polymorphic markers by screening nuclear microsatellite (N = 83) and intronic loci (N = 19), as well as the mitochondrial control region (mtDNA) for a subset of samples. Among 83 microsatellite loci screened, six were variable. We found low nuclear variation consistent with the species’ historical population bottlenecks and sequence variation was observed at a single intron locus. We detected no variation within the mtDNA. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within islands. Two rare alleles found in the Laysan Island source population were not present in the Midway translocated group, and a rare allele was discovered in an individual on Midway in 2008. We found similar genetic diversity and low, but statistically significant, levels of differentiation (0.6%) between island populations suggesting that genetic drift (as a result of translocation-induced population bottlenecking) has had a limited effect within five years post-release. Our results have utility for informing translocation and genetic management decisions.

A functional variation in the hypocretin neuropeptide precursor gene may be associated with obstructive sleep apnea syndrome in Japan.

PubMed

Ahmed, Wael A; Tsutsumi, Makiko; Nakata, Seiichi; Mori, Terumi; Nishimura, Yoichi; Fujisawa, Toshiyuki; Kato, Ichiro; Nakashima, Mayuki; Kurahashi, Hiroki; Suzuki, Kenji

2012-04-01

To evaluate the association of hypocretin neuropeptide precursor gene (HCRT) variations with obstructive sleep apnea syndrome (OSAS) in a cohort of Japanese patients and to further evaluate whether the significant HCRT variations have potential functional consequences on HCRT expression. Case-control genetic association study. We studied the genetic variations within the HCRT gene. The study population consisted of 100 OSAS patients and 100 control subjects. The HCRT gene was amplified by polymerase chain reaction in all study subjects followed by direct sequencing and analysis of sequencing data. Two genetic variations within the HCRT intron, IVS1+16T>C (rs9902709) and IVS1-69G>C, were identified with significant differences between patients and controls (P < .05). A reporter gene assay using HeLa cells showed that the construct containing the C allele of the rs9902709 variation had significantly higher luciferase activity compared with the construct containing the T allele (P = .002). Furthermore, enzyme immunoassay revealed that subjects with T/C and C/C genotypes for rs9902709 had 1.4-fold and 1.5-fold increases in sera levels of orexin-A, respectively. Our genetic association study, followed by functional and quantitative phenotyping assays, demonstrated a functional locus within the HCRT gene, which may act to increase HCRT expression and lead to a protective effect against the development of OSAS. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

Human Genetics and Islam: Scientific and Medical Aspects

PubMed Central

Ghareeb, Bilal A.A.

2011-01-01

Objective: To relate diverse aspects of genetics and its applications to concepts in the Glorious Qur’an and the ḥadīth. Study Design: The author compared passages from the Glorious Qur’an and ḥadīth with modern concepts in genetics, such as recessive inheritance, genetic counseling, genetic variation, cytoplasmic inheritance, sex chromosomes, genetics-environment interactions, gender determination, and the hypothesis of “pairing in the universe.” Conclusions: A fresh understanding of Islamic scripture reveals references to principles of genetics that predate contemporary discoveries. This highlights the need for further exploration of possible links between science and religion. PMID:23610491

Comparative genetic structure between Sedum ussuriense and S. kamtschaticum (Crassulaceae), two stonecrops co-occurring on rocky cliffs.

PubMed

Chung, Mi Yoon; López-Pujol, Jordi; Chung, Myong Gi

2014-06-01

• Premise of the study: Geographic isolation due to discontinuities of suitable habitat may have significant effects on the genetic structure of plant populations. Even within a few kilometers, physical barriers to gene flow may lead to considerable genetic differentiation among populations.• Methods: Sedum ussuriense is a boreal species that in Korea occurs only in four valleys separated by mountain ranges in Juwangsan National Park and its vicinity (a range of ∼15 km). Its congener S. kamtschaticum, by contrast, co-occurs in the four valleys but also on the intervening mountains. Using 12 allozyme loci, we comparatively assessed genetic variability and structure in 12 population pairs of the two stonecrops.• Key results: While we found high and comparable levels of within-population genetic variation for the two species, among-population divergence was significantly higher in S. ussuriense (F ST = 0.261 vs. F ST = 0.165). Sedum ussuriense also showed a much higher percentage of among-valley variation (19%) than S. kamtschaticum (4%).• Conclusions: High levels of genetic diversity in the two Sedum species are consistent with the previous hypothesis that mountains of the Korean Peninsula served as glacial refugia for many boreal species. Given that the two congeners have similar life-history traits, the lower among-population differentiation in S. kamtschaticum is attributable to its higher abundance and more continuous distribution in the study area. This study confirms the central role of geographic isolation in the genetic structure of plant species even at very small scales. © 2014 Botanical Society of America, Inc.

Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection.

PubMed

Huang, Huateng; Rabosky, Daniel L

2015-09-16

Sexual dichromatism is the tendency for sexes to differ in color pattern and represents a striking form of within-species morphological variation. Conspicuous intersexual differences in avian plumage are generally thought to result from Darwinian sexual selection, to the extent that dichromatism is often treated as a surrogate for the intensity of sexual selection in phylogenetic comparative studies. Intense sexual selection is predicted to leave a footprint on genetic evolution by reducing the relative genetic diversity on sex chromosome to that on the autosomes. In this study, we test the association between plumage dichromatism and sex-linked genetic diversity using eight species pairs with contrasting levels of dichromatism. We estimated Z-linked and autosomal genetic diversity for these non-model avian species using restriction-site associated (RAD) loci that covered ~3 % of the genome. We find that monochromatic birds consistently have reduced sex-linked genomic variation relative to phylogenetically-paired dichromatic species and this pattern is robust to mutational biases. Our results are consistent with several interpretations. If present-day sexual selection is stronger in dichromatic birds, our results suggest that its impact on sex-linked genomic variation is offset by other processes that lead to proportionately lower Z-linked variation in monochromatic species. We discuss possible factors that may contribute to this discrepancy between phenotypes and genomic variation. Conversely, it is possible that present-day sexual selection -- as measured by the variance in male reproductive success -- is stronger in the set of monochromatic taxa we have examined, potentially reflecting the importance of song, behavior and other non-plumage associated traits as targets of sexual selection. This counterintuitive finding suggests that the relationship between genomic variation and sexual selection is complex and highlights the need for a more comprehensive survey of genomic variation in avian taxa that vary markedly in social and genetic mating systems.

The Geographic Distribution of Genetic Risk as Compared to Social Risk for Chronic Diseases in the United States.

PubMed

Rehkopf, David H; Domingue, Benjamin W; Cullen, Mark R

2016-01-01

There is an association between chronic disease and geography, and there is evidence that the environment plays a critical role in this relationship. Yet at the same time, there is known to be substantial geographic variation by ancestry across the United States. Resulting geographic genetic variation-that is, the extent to which single nucleotide polymorphisms (SNPs) related to chronic disease vary spatially-could thus drive some part of the association between geography and disease. We describe the variation in chronic disease genetic risk by state of birth by taking risk SNPs from genome-wide association study meta-analyses for coronary artery disease, diabetes, and ischemic stroke and creating polygenic risk scores. We compare the amount of variability across state of birth in these polygenic scores to the variability in parental education, own education, earnings, and wealth. Our primary finding is that the polygenic risk scores are only weakly differentially distributed across U.S. states. The magnitude of the differences in geographic distribution is very small in comparison to the distribution of social and economic factors and thus is not likely sufficient to have a meaningful effect on geographic disease differences by U.S. state.

Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA.

PubMed

Lewis, Cecil M; Long, Jeffrey C

2008-03-01

Genetic diversity in Native South Americans forms a complex pattern at both the continental and local levels. In comparing the West to the East, there is more variation within groups and smaller genetic distances between groups. From this pattern, researchers have proposed that there is more variation in the West and that a larger, more genetically diverse, founding population entered the West than the East. Here, we question this characterization of South American genetic variation and its interpretation. Our concern arises because others have inferred regional variation from the mean variation within local populations without taking into account the variation among local populations within the same region. This failure produces a biased view of the actual variation in the East. In this study, we analyze the mitochondrial DNA sequence between positions 16040 and 16322 of the Cambridge reference sequence. Our sample represents a total of 886 people from 27 indigenous populations from South (22), Central (3), and North America (2). The basic unit of our analyses is nucleotide identity by descent, which is easily modeled and proportional to nucleotide diversity. We use a forward modeling strategy to fit a series of nested models to identity by descent within and between all pairs of local populations. This method provides estimates of identity by descent at different levels of population hierarchy without assuming homogeneity within populations, regions, or continents. Our main discovery is that Eastern South America harbors more genetic variation than has been recognized. We find no evidence that there is increased identity by descent in the East relative to the total for South America. By contrast, we discovered that populations in the Western region, as a group, harbor more identity by descent than has been previously recognized, despite the fact that average identity by descent within groups is lower. In this light, there is no need to postulate separate founding populations for the East and the West because the variability in the East could serve as a source for the Western gene pools.

Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide marker-based estimation of genetic parameters and environmental effect trends.

PubMed

Atagi, Y; Onogi, A; Kinukawa, M; Ogino, A; Kurogi, K; Uchiyama, K; Yasumori, T; Adachi, K; Togashi, K; Iwata, H

2017-05-01

The semen production traits of bulls from 2 major cattle breeds in Japan, Holstein and Japanese Black, were analyzed comprehensively using genome-wide markers. Weaker genetic correlations were observed between the 2 age groups (1 to 3 yr old and 4 to 6 yr old) regarding semen volume and sperm motility compared with those observed for sperm number and motility after freeze-thawing. The preselection of collected semen for freezing had a limited effect. Given the increasing importance of bull proofs at a young age because of genomic selection and the results from preliminary studies, we used a multiple-trait model that included motility after freeze-thawing with records collected at young ages. Based on variations in contemporary group effects, accounting for both seasonal and management factors, Holstein bulls may be more sensitive than Japanese Black bulls to seasonal environmental variations; however, the seasonal variations of contemporary group effects were smaller than those of overall contemporary group effects. The improvement of motilities, recorded immediately after collection and freeze-thawing, was observed in recent years; thus, good management and better freeze-thawing protocol may alleviate seasonal phenotypic differences. The detrimental effects of inbreeding were observed in all traits of both breeds; accordingly, the selection of candidate bulls with high inbreeding coefficients should be avoided per general recommendations. Semen production traits have never been considered for bull selection. However, negative genetic trends were observed. The magnitudes of the estimated h were comparable to those of other economically important traits. A single-step genomic BLUP will provide more accurate predictions of breeding values compared with BLUP; thus, marker genotype information is useful for estimating the genetic merits of bulls for semen production traits. The selection of these traits would improve sperm viability, a component related to breeding success, and alleviate negative genetic trends.

Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni.

PubMed

Sternes, Peter R; Borneman, Anthony R

2016-04-27

Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes. Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe. By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species.

Meiotic recombination hotspots - a comparative view.

PubMed

Choi, Kyuha; Henderson, Ian R

2015-07-01

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

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.

PubMed

Kronholm, Ilkka; Picó, F Xavier; Alonso-Blanco, Carlos; Goudet, Jérôme; de Meaux, Juliette

2012-07-01

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation. © 2012 The Author(s).

Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

PubMed Central

Porto, Arthur; Sebastião, Harley; Pavan, Silvia Eliza; VandeBerg, John L.; Marroig, Gabriel; Cheverud, James M.

2015-01-01

We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation. PMID:25818173

Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

PubMed Central

Jasinska, Anna J.; Zelaya, Ivette; Service, Susan K.; Peterson, Christine B.; Cantor, Rita M.; Choi, Oi-Wa; DeYoung, Joseph; Eskin, Eleazar; Fairbanks, Lynn A.; Fears, Scott; Furterer, Allison E.; Huang, Yu S.; Ramensky, Vasily; Schmitt, Christopher A.; Svardal, Hannes; Jorgensen, Matthew J.; Kaplan, Jay R.; Villar, Diego; Aken, Bronwen L.; Flicek, Paul; Nag, Rishi; Wong, Emily S.; Blangero, John; Dyer, Thomas D.; Bogomolov, Marina; Benjamini, Yoav; Weinstock, George M.; Dewar, Ken; Sabatti, Chiara; Wilson, Richard K.; Jentsch, J. David; Warren, Wesley; Coppola, Giovanni; Woods, Roger P.; Freimer, Nelson B.

2017-01-01

By analyzing multi-tissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalogue of expression quantitative trait loci (eQTLs) in a non-human primate model. This catalogue contains more genome-wide significant eQTLs, per sample, than comparable human resources, and reveals sex and age-related expression patterns. Findings include a master regulatory locus that likely plays a role in immune function, and a locus regulating hippocampal long non-coding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders. PMID:29083405

Rates of genomic divergence in humans, chimpanzees and their lice.

PubMed

Johnson, Kevin P; Allen, Julie M; Olds, Brett P; Mugisha, Lawrence; Reed, David L; Paige, Ken N; Pittendrigh, Barry R

2014-02-22

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.

Rates of genomic divergence in humans, chimpanzees and their lice

PubMed Central

Johnson, Kevin P.; Allen, Julie M.; Olds, Brett P.; Mugisha, Lawrence; Reed, David L.; Paige, Ken N.; Pittendrigh, Barry R.

2014-01-01

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites. PMID:24403325

Variation in MHC genotypes in two populations of house sparrow (Passer domesticus) with different population histories.

PubMed

Borg, Asa Alexandra; Pedersen, Sindre Andre; Jensen, Henrik; Westerdahl, Helena

2011-10-01

Small populations are likely to have a low genetic ability for disease resistance due to loss of genetic variation through inbreeding and genetic drift. In vertebrates, the highest genetic diversity of the immune system is located at genes within the major histocompatibility complex (MHC). Interestingly, parasite-mediated selection is thought to potentially maintain variation at MHC loci even in populations that are monomorphic at other loci. Therefore, general loss of genetic variation in the genome may not necessarily be associated with low variation at MHC loci. We evaluated inter- and intrapopulation variation in MHC genotypes between an inbred (Aldra) and a relatively outbred population (Hestmannøy) of house sparrows (Passer domesticus) in a metapopulation at Helgeland, Norway. Genomic (gDNA) and transcribed (cDNA) alleles of functional MHC class I and IIB loci, along with neutral noncoding microsatellite markers, were analyzed to obtain relevant estimates of genetic variation. We found lower allelic richness in microsatellites in the inbred population, but high genetic variation in MHC class I and IIB loci in both populations. This suggests that also the inbred population could be under balancing selection to maintain genetic variation for pathogen resistance.

Variation in MHC genotypes in two populations of house sparrow (Passer domesticus) with different population histories

PubMed Central

Borg, Åsa Alexandra; Pedersen, Sindre Andre; Jensen, Henrik; Westerdahl, Helena

2011-01-01

Small populations are likely to have a low genetic ability for disease resistance due to loss of genetic variation through inbreeding and genetic drift. In vertebrates, the highest genetic diversity of the immune system is located at genes within the major histocompatibility complex (MHC). Interestingly, parasite-mediated selection is thought to potentially maintain variation at MHC loci even in populations that are monomorphic at other loci. Therefore, general loss of genetic variation in the genome may not necessarily be associated with low variation at MHC loci. We evaluated inter- and intrapopulation variation in MHC genotypes between an inbred (Aldra) and a relatively outbred population (Hestmannøy) of house sparrows (Passer domesticus) in a metapopulation at Helgeland, Norway. Genomic (gDNA) and transcribed (cDNA) alleles of functional MHC class I and IIB loci, along with neutral noncoding microsatellite markers, were analyzed to obtain relevant estimates of genetic variation. We found lower allelic richness in microsatellites in the inbred population, but high genetic variation in MHC class I and IIB loci in both populations. This suggests that also the inbred population could be under balancing selection to maintain genetic variation for pathogen resistance. PMID:22393491

An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci

NASA Astrophysics Data System (ADS)

Li, Baohua; Zhang, Yuanyuan; Mohammadi, Seyed Abolghasem; Huai, Dongxin; Zhou, Yongming; Kliebenstein, Daniel J.

2016-07-01

Studying the genetic basis of variation in plant metabolism has been greatly facilitated by genomic and metabolic profiling advances. In this study, we use metabolomics and growth measurements to map QTL in rice, a major staple crop. Previous rice metabolism studies have largely focused on identifying genes controlling major effect loci. To complement these studies, we conducted a replicated metabolomics analysis on a japonica (Lemont) by indica (Teqing) rice recombinant inbred line population and focused on the genetic variation for primary metabolism. Using independent replicated studies, we show that in contrast to other rice studies, the heritability of primary metabolism is similar to Arabidopsis. The vast majority of metabolic QTLs had small to moderate effects with significant polygenic epistasis. Two metabolomics QTL hotspots had opposing effects on carbon and nitrogen rich metabolites suggesting that they may influence carbon and nitrogen partitioning, with one locus co-localizing with SUSIBA2 (WRKY78). Comparing QTLs for metabolomic and a variety of growth related traits identified few overlaps. Interestingly, the rice population displayed fewer loci controlling stochastic variation for metabolism than was found in Arabidopsis. Thus, it is possible that domestication has differentially impacted stochastic metabolite variation more than average metabolite variation.

Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume.

PubMed

Yang, Shuyi; Grall, Aurélie; Chapman, Mark A

2018-05-01

For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop. © 2018 Botanical Society of America.

Genetic diversity of calcareous grassland plant species depends on historical landscape configuration.

PubMed

Reisch, Christoph; Schmidkonz, Sonja; Meier, Katrin; Schöpplein, Quirin; Meyer, Carina; Hums, Christian; Putz, Christina; Schmid, Christoph

2017-04-24

Habitat fragmentation is considered to be a main reason for decreasing genetic diversity of plant species. However, the results of many fragmentation studies are inconsistent. This may be due to the influence of habitat conditions, having an indirect effect on genetic variation via reproduction. Consequently we took a comparative approach to analyse the impact of habitat fragmentation and habitat conditions on the genetic diversity of calcareous grassland species in this study. We selected five typical grassland species (Primula veris, Dianthus carthusianorum, Medicago falcata, Polygala comosa and Salvia pratensis) occurring in 18 fragments of calcareous grasslands in south eastern Germany. We sampled 1286 individuals in 87 populations and analysed genetic diversity using amplified fragment length polymorphisms. Additionally, we collected data concerning habitat fragmentation (historical and present landscape structure) and habitat conditions (vegetation structure, soil conditions) of the selected study sites. The whole data set was analysed using Bayesian multiple regressions. Our investigation indicated a habitat loss of nearly 80% and increasing isolation between grasslands since 1830. Bayesian analysis revealed a significant impact of the historical landscape structure, whereas habitat conditions played no important role for the present-day genetic variation of the studied plant species. Our study indicates that the historical landscape structure may be more important for genetic diversity than present habitat conditions. Populations persisting in abandoned grassland fragments may contribute significantly to the species' variability even under deteriorating habitat conditions. Therefore, these populations should be included in approaches to preserve the genetic variation of calcareous grassland species.

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

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

Genetic Diversity of Arabica Coffee (Coffea arabica L.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

PubMed Central

Geleta, Mulatu; Herrera, Isabel; Monzón, Arnulfo; Bryngelsson, Tomas

2012-01-01

Coffea arabica L. (arabica coffee), the only tetraploid species in the genus Coffea, represents the majority of the world's coffee production and has a significant contribution to Nicaragua's economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei's gene diversity (H T) and the within-population gene diversity (H S) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (F ST = 0.13; P < 0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved through ex situ conservation of a low number of populations from each variety. PMID:22701376

Mitochondrial Variation among the Aymara and the Signatures of Population Expansion in the Central Andes

PubMed Central

BATAI, KEN; WILLIAMS, SLOAN R.

2015-01-01

Objectives The exploitation of marine resources and intensive agriculture led to a marked population increase early in central Andean prehistory. Constant historic and prehistoric population movements also characterize this region. These features undoubtedly affected regional genetic variation, but the exact nature of these effects remains uncertain. Methods Mitochondrial DNA (mtDNA) hypervariable region I sequence variation in 61 Aymara individuals from La Paz, Bolivia, was analyzed and compared to sequences from 47 other South American populations to test hypotheses of whether increased female effective population size and gene flow influenced the mtDNA variation among central Andean populations. Results The Aymara and Quechua were genetically diverse showing evidence of population expansion and large effective population size, and a demographic expansion model fits the mtDNA variation found among central Andean populations well. Estimated migration rates and the results of AMOVA and multidimensional scaling analysis suggest that female gene flow was also an important factor, influencing genetic variation among the central Andeans as well as lowland populations from western South America. mtDNA variation in south central Andes correlated better with geographic proximity than with language, and fit a population continuity model. Conclusion The mtDNA data suggests that the central Andeans experienced population expansion, most likely because of rapid demographic expansion after introduction of intensive agriculture, but roles of female gene flow need to be further explored. PMID:24449040

Patterns of Genetic Variation across Altitude in Three Plant Species of Semi-Dry Grasslands

PubMed Central

Hahn, Thomas; Kettle, Chris J.; Ghazoul, Jaboury; Frei, Esther R.; Matter, Philippe; Pluess, Andrea R.

2012-01-01

Background Environmental gradients caused by altitudinal gradients may affect genetic variation within and among plant populations and inbreeding within populations. Populations in the upper range periphery of a species may be important source populations for range shifts to higher altitude in response to climate change. In this study we investigate patterns of population genetic variation at upper peripheral and lower more central altitudes in three common plant species of semi-dry grasslands in montane landscapes. Methodology/Principal Findings In Briza media, Trifolium montanum and Ranunculus bulbosus genetic diversity, inbreeding and genetic relatedness of individuals within populations and genetic differentiation among populations was characterized using AFLP markers. Populations were sampled in the Swiss Alps at 1800 (upper periphery of the study organisms) and at 1200 m a.s.l. Genetic diversity was not affected by altitude and only in B. media inbreeding was greater at higher altitudes. Genetic differentiation was slightly greater among populations at higher altitudes in B. media and individuals within populations were more related to each other compared to individuals in lower altitude populations. A similar but less strong pattern of differentiation and relatedness was observed in T. montanum, while in R. bulbosus there was no effect of altitude. Estimations of population size and isolation of populations were similar, both at higher and lower altitudes. Conclusions/Significance Our results suggest that altitude does not affect genetic diversity in the grassland species under study. Genetic differentiation of populations increased only slightly at higher elevation, probably due to extensive (historic) gene flow among altitudes. Potentially pre-adapted genes might therefore spread easily across altitudes. Our study indicates that populations at the upper periphery are not genetically depauperate or isolated and thus may be important source populations for migration under climate change. PMID:22870236

Genomic Selection in Multi-environment Crop Trials.

PubMed

Oakey, Helena; Cullis, Brian; Thompson, Robin; Comadran, Jordi; Halpin, Claire; Waugh, Robbie

2016-05-03

Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers. Copyright © 2016 Oakey et al.

Genetic variation in the USDA Chamaecrista fasciculata collection

USDA-ARS?s Scientific Manuscript database

Germplasm collections serve as critical repositories of genetic variation. Characterizing genetic diversity in existing collections is necessary to maximize their utility and to guide future collecting efforts. We have used AFLP markers to characterize genetic variation in the USDA germplasm collect...

Genetic variation of jointed goatgrass (Aegilops cylindrica Host.) from Iran using RAPD-PCR and SDS-PAGE of seed proteins.

PubMed

Farkhari, M; Naghavi, M R; Pyghambari, S A; Sabokdast

2007-09-01

Genetic variation of 28 populations of jointed goatgrass (Aegilops cylindrica Host.), collected from different parts of Iran, were evaluated using both RAPD-PCR and SDS-PAGE of seed proteins. The diversity within and between populations for the three-band High Molecular Weight (HMW) subunits of glutenin pattern were extremely low. Out of 15 screened primers of RAPD, 14 primers generated 133 reproducible fragments which among them 92 fragments were polymorphic (69%). Genetic similarity calculated from the RAPD data ranged from 0.64 to 0.98. A dendrogram was prepared on the basis of a similarity matrix using the UPGMA algorithm and separated the 28 populations into two groups. Confusion can happen between populations with the same origin as well as between populations of very diverse geographical origins. Our results show that compare to seed storage protein, RAPD is suitable for genetic diversity assessment in Ae. cylindrica populations.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Genetic and Epigenetic Variations Induced by Wheat-Rye 2R and 5R Monosomic Addition Lines

PubMed Central

Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

2013-01-01

Background Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. Methodology/Principal Findings In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. Conclusions/Significance The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat. PMID:23342073

Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

PubMed

Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

2013-01-01

Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

Genetic drift and collective dispersal can result in chaotic genetic patchiness.

PubMed

Broquet, Thomas; Viard, Frédérique; Yearsley, Jonathan M

2013-06-01

Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free-living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex dispersal patterns to create chaotic genetic patchiness. Here we use a co-ancestry model and individual-based simulations to test this idea. We found that chaotic genetic patterns (qualified by global FST and spatio-temporal variation in FST's between pairs of samples) arise from the combined effects of (1) genetic drift created by the small local effective population sizes of the sessile phase and variance in contribution among breeding groups and (2) collective dispersal of related individuals in the larval phase. Simulations show that patchiness levels qualitatively comparable to empirical results can be produced by a combination of strong variance in reproductive success and mild collective dispersal. These results call for empirical studies of the effective number of breeders producing larval cohorts, and population genetics at the larval stage. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

Genetic variation affecting host-parasite interactions: different genes affect different aspects of sigma virus replication and transmission in Drosophila melanogaster.

PubMed

Bangham, Jenny; Kim, Kang-Wook; Webster, Claire L; Jiggins, Francis M

2008-04-01

In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.

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.

Does advertisement call variation coincide with genetic variation in the genetically diverse frog taxon currently known as Leptodactylus fuscus (Amphibia: Leptodactylidae)?

PubMed

Heyer, W Ronald; Reid, Yana R

2003-03-01

The frog Leptodactylus fuscus is found throughout much of South America in open and disturbed habitats. Previous study of genetic differentiation in L. fuscus demonstrated that there was lack of genetic exchange among population units consistent with multiple species, rather than a single species. We examine advertisement vocalizations of L. fuscus to determine whether call variation coincides with genetic differentiation. Calls were analyzed for 32 individual frogs from 25 localities throughout the distributional range of L. fuscus. Although there is variation in calls among geographic samples, call variation is not concordant with genetic variation or geographic distance and the call variation observed is less than that typically found among other closely related species of Leptodactylus. This study is an example of the rare pattern of strong genetic differentiation unaccompanied by salient differences in advertisement calls. The relative infrequency of this pattern as currently understood may only reflect the lack of detailed analyses of genetic and acoustic differentiation within population systems currently understood as single species with substantial geographic distributions.

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.

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. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Genetic variation of hepatitis B surface antigen among acute and chronic hepatitis B virus infections in The Netherlands.

PubMed

Cremer, Jeroen; Hofstraat, Sanne H I; van Heiningen, Francoise; Veldhuijzen, Irene K; van Benthem, Birgit H B; Benschop, Kimberley S M

2018-05-24

Genetic variation within hepatitis B surface antigen (HBsAg), in particular within the major hydrophobic region (MHR), is related to immune/vaccine and test failures and can have a significant impact on the vaccination and diagnosis of acute infection. This study shows, for the first time, variation among acute cases and compares the amino acid variation within the HBsAg between acute and chronic infections. We analyzed the virus isolated from 1231 acute and 585 chronic cases reported to an anonymized public health surveillance database between 2004 and 2014 in The Netherlands. HBsAg analysis revealed the circulation of 6 genotypes (Gt); GtA was the dominant genotype followed by GtD among both acute (68.2% and 17.4%, respectively) and chronic (34.9% and 34.2%, respectively) cases. Variation was the highest among chronic strains compared to that among acute strains. Both acute and chronic GtD showed the highest variation compared to that of other genotypes (P < .01). Substitutions within the MHR were found in 8.5% of the acute strains and 18.6% of the chronic strains. Specific MHR substitutions described to have an impact on vaccine/immune escape and/or HBsAg test failure were found among 4.1% of the acute strains and 7.0% of the chronic strains. In conclusion, we show a high variation of HBsAg among acute and chronic hepatitis B virus-infected cases in The Netherlands, in particular among those infected with GtD, and compare, for the first time, variation in frequencies between acute and chronic cases. Additional studies on the impact of these variations on vaccination and test failure need to be conducted, as well as whether HBsAg false-negative variants have been missed. © 2018 The Authors. Journal of Medical Virology Published by Wiley Periodicals, Inc.

Undergraduates Achieve Learning Gains in Plant Genetics through Peer Teaching of Secondary Students

PubMed Central

Chrispeels, H. E.; Klosterman, M. L.; Martin, J. B.; Lundy, S. R.; Watkins, J. M.; Gibson, C. L.

2014-01-01

This study tests the hypothesis that undergraduates who peer teach genetics will have greater understanding of genetic and molecular biology concepts as a result of their teaching experiences. Undergraduates enrolled in a non–majors biology course participated in a service-learning program in which they led middle school (MS) or high school (HS) students through a case study curriculum to discover the cause of a green tomato variant. The curriculum explored plant reproduction and genetic principles, highlighting variation in heirloom tomato fruits to reinforce the concept of the genetic basis of phenotypic variation. HS students were taught additional activities related to mole­cular biology techniques not included in the MS curriculum. We measured undergraduates’ learning outcomes using pre/postteaching content assessments and the course final exam. Undergraduates showed significant gains in understanding of topics related to the curriculum they taught, compared with other course content, on both types of assessments. Undergraduates who taught HS students scored higher on questions specific to the HS curriculum compared with undergraduates who taught MS students, despite identical lecture content, on both types of assessments. These results indicate the positive effect of service-learning peer-teaching experiences on undergraduates’ content knowledge, even for non–science major students. PMID:25452487

Environmental Noise, Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

PubMed Central

Steiner, Christopher F.

2012-01-01

The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions. PMID:23284934

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

Adaptive potential of northernmost tree populations to climate change, with emphasis on Scots pine (Pinus sylvestris L.).

PubMed

Savolainen, Outi; Kujala, Sonja T; Sokol, Catherina; Pyhäjärvi, Tanja; Avia, Komlan; Knürr, Timo; Kärkkäinen, Katri; Hicks, Sheila

2011-01-01

The adaptive potential of the northernmost Pinus sylvestris L. (and other northern tree) populations is considered by examining first the current patterns of quantitative genetic adaptive traits, which show high population differentiation and clines. We then consider the postglacial history of the populations using both paleobiological and genetic data. The current patterns of diversity at nuclear genes suggest that the traces of admixture are mostly visible in mitochondrial DNA variation patterns. There is little evidence of increased diversity due to admixture between an eastern and western colonization lineage, but no signal of reduced diversity (due to sequential bottlenecks) either. Quantitative trait variation in the north is not associated with the colonizing lineages. The current clines arose rapidly and may be based on standing genetic variation. The initial phenotypic response of Scots pine in the north is predicted to be increased survival and growth. The genetic responses are examined based on quantitative genetic predictions of sustained selection response and compared with earlier simulation results that have aimed at more ecological realism. The phenotypic responses of increased growth and survival reduce the opportunity for selection and delay the evolutionary responses. The lengthening of the thermal growing period also causes selection on the critical photoperiod in the different populations. Future studies should aim at including multiple ecological and genetic factors in evaluating potential responses.

Homozygosity mapping and sequencing identify two genes that might contribute to pointing behavior in hunting dogs.

PubMed

Akkad, Denis A; Gerding, Wanda M; Gasser, Robin B; Epplen, Jörg T

2015-01-01

The domestic dog represents an important model for studying the genetics of behavior. In spite of technological advances in genomics and phenomics, the genetic basis of most specific canine behaviors is largely unknown. Some breeds of hunting dogs exhibit a behavioral trait called "pointing" (a prolonged halt of movement to indicate the position of a game animal). Here, the genomes of pointing dogs (Large Munsterlander and Weimaraner) were compared with those of behaviorally distinct herding dogs (Berger des Pyrenées and Schapendoes). We assumed (i) that these four dog breeds initially represented inbred populations and (ii) that selective breeding for pointing behavior promotes an enrichment of the genetic trait in a homozygous state. The homozygosity mapping of 52 dogs (13 of each of the four breeds) followed by subsequent interval resequencing identified fixed genetic differences on chromosome 22 between pointers and herding dogs. In addition, we identified one non-synonomous variation in each of the coding genes SETDB2 and CYSLTR2 that might have a functional consequence. Genetic analysis of additional hunting and non-hunting dogs revealed consistent homozygosity for these two variations in six of seven pointing breeds. Based on the present findings, we propose that, together with other genetic, training and/or environmental factors, the nucleotide and associated amino acid variations identified in genes SETDB2 and CYSLTR2 contribute to pointing behavior.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.

PubMed

Alkan, Can; Kavak, Pinar; Somel, Mehmet; Gokcumen, Omer; Ugurlu, Serkan; Saygi, Ceren; Dal, Elif; Bugra, Kuyas; Güngör, Tunga; Sahinalp, S Cenk; Özören, Nesrin; Bekpen, Cemalettin

2014-11-07

Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32×-48×). We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.

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

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.

Molecular markers reveal no genetic differentiation between Myrica rivas-martinezii and M. faya (Myricaceae)

PubMed Central

González-Pérez, Miguel A.; Sosa, Pedro A.; Rivero, Elisabeth; González-González, Edna A.; Naranjo, Agustín

2009-01-01

Background and Aims Myrica rivas-martinezii is a critically endangered endemic of the laurel forest of the Canary Islands and co-occurs very close to M. faya. Some authors suggest that M. rivas-martinezii and M. faya are two morphs of the same species, so molecular markers were used to estimate the levels and structuring of genetic variation within and among natural populations in order to evaluate genetic relationships between these two congeners. Methods Six polymorphic microsatellite (simple sequence repeat, SSR) markers were used to determine the genetic diversity and the genetic relationship between both Myrica species. Key Results Most of the natural populations analysed were in Hardy–Weinberg equilibrium for both taxa. Analysis of molecular variance (AMOVA) for both species revealed that most of the genetic variability detected was contained within populations (92·48 and 85·91 % for M. faya and M. rivas-martinezii, respectively), which it is consistent with outcrossing and dioecious plants. Estimates of interpopulation genetic variation, calculated from FST and G′ST, were quite low in the two taxa, and these values did not increase substantially when M. rivas-martinezii and M. faya populations were compared. The UPGMA dendrogram based on Nei's genetic distance clustered the populations by their island origin, independently of taxon. In fact, the mixture of individuals of both taxa did not appreciably disrupt the intrapopulational genetic cohesion, and only 3·76 % variation existed between species. Conclusions All the results obtained using molecular markers indicate clearly that both taxa share the same genetic pool, and they are probably the same taxa. Considering that M. rivas-martinezii is classified as at risk of extinction, there should be a change of focus of the current management actions for the conservation of this putatively endangered Canarian endemic. PMID:19008254

Genetic consequences of cladogenetic vs. anagenetic speciation in endemic plants of oceanic islands

PubMed Central

Takayama, Koji; López-Sepúlveda, Patricio; Greimler, Josef; Crawford, Daniel J.; Peñailillo, Patricio; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F.

2015-01-01

Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1–2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs. PMID:26311732

Conceptual Variation or Incoherence? Textbook Discourse on Genes in Six Countries

ERIC Educational Resources Information Center

Gericke, Niklas M.; Hagberg, Mariana; dos Santos, Vanessa Carvalho; Joaquim, Leyla Mariane; El-Hani, Charbel N.

2014-01-01

The aim of this paper is to investigate in a systematic and comparative way previous results of independent studies on the treatment of genes and gene function in high school textbooks from six different countries. We analyze how the conceptual variation within the scientific domain of Genetics regarding gene function models and gene concepts is…

A preliminary investigation into the genetic variation and population structure of Taenia hydatigena from Sardinia, Italy.

PubMed

Boufana, Belgees; Scala, Antonio; Lahmar, Samia; Pointing, Steve; Craig, Philip S; Dessì, Giorgia; Zidda, Antonella; Pipia, Anna Paola; Varcasia, Antonio

2015-11-30

Cysticercosis caused by the metacestode stage of Taenia hydatigena is endemic in Sardinia. Information on the genetic variation of this parasite is important for epidemiological studies and implementation of control programs. Using two mitochondrial genes, the cytochrome c oxidase subunit 1 (cox1) and the NADH dehydrogenase subunit 1 (ND1) we investigated the genetic variation and population structure of Cysticercus tenuicollis from Sardinian intermediate hosts and compared it to that from other hosts from various geographical regions. The parsimony cox1 network analysis indicated the existence of a common lineage for T. hydatigena and the overall diversity and neutrality indices indicated demographic expansion. Using the cox1 sequences, low pairwise fixation index (Fst) values were recorded for Sardinian, Iranian and Palestinian sheep C. tenuicollis which suggested the absence of genetic differentiation. Using the ND1 sequences, C. tenuicollis from Sardinian sheep appeared to be differentiated from those of goat and pig origin. In addition, goat C. tenuicollis were genetically different from adult T. hydatigena as indicated by the statistically significant Fst value. Our results are consistent with biochemical and morphological studies that suggest the existence of variants of T. hydatigena. Copyright © 2015 Elsevier B.V. All rights reserved.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

PubMed Central

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Copy number variations in patients with electrical status epilepticus in sleep.

PubMed

Kevelam, Sietske H G; Jansen, Floor E; Binsbergen, Ellen van; Braun, Kees P J; Verbeek, Nienke E; Lindhout, Dick; Poot, Martin; Brilstra, Eva H

2012-02-01

Electrical status epilepticus in sleep syndrome is the association of the electroencephalographic pattern and deficits in language or global cognitive function and behavioral problems. The etiology is often unknown, but genetic risk factors have been implicated. Array-based comparative genomic hybridization was used to identify copy number variations in 13 children with electrical status epilepticus in sleep syndrome to identify possible underlying risk factors. Seven copy number variations were detected in 4 of the 13 patients, which consisted of 6 novel gains and 1 loss, the recurrent 15q13.3 microdeletion. Two patients carried a probable pathogenic copy number variation containing a gene involved in the cholinergic pathway. Genetic aberrations in patients with electrical status epilepticus in sleep syndrome can provide an entry in the investigation of the etiology of electrical status epilepticus in sleep. However, further studies are needed to confirm our findings.

Genotyping microarray (gene chip) for the ABCR (ABCA4) gene.

PubMed

Jaakson, K; Zernant, J; Külm, M; Hutchinson, A; Tonisson, N; Glavac, D; Ravnik-Glavac, M; Hawlina, M; Meltzer, M R; Caruso, R C; Testa, F; Maugeri, A; Hoyng, C B; Gouras, P; Simonelli, F; Lewis, R A; Lupski, J R; Cremers, F P M; Allikmets, R

2003-11-01

Genetic variation in the ABCR (ABCA4) gene has been associated with five distinct retinal phenotypes, including Stargardt disease/fundus flavimaculatus (STGD/FFM), cone-rod dystrophy (CRD), and age-related macular degeneration (AMD). Comparative genetic analyses of ABCR variation and diagnostics have been complicated by substantial allelic heterogeneity and by differences in screening methods. To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants. The ABCR genotyping microarray (the ABCR400 chip) was constructed by the arrayed primer extension (APEX) technology. Each sequence change in ABCR was included on the chip by synthesis and application of sequence-specific oligonucleotides. We validated the chip by screening 136 confirmed STGD patients and 96 healthy controls, each of whom we had analyzed previously by single strand conformation polymorphism (SSCP) technology and/or heteroduplex analysis. The microarray was >98% effective in determining the existing genetic variation and was comparable to direct sequencing in that it yielded many sequence changes undetected by SSCP. In STGD patient cohorts, the efficiency of the array to detect disease-associated alleles was between 54% and 78%, depending on the ethnic composition and degree of clinical and molecular characterization of a cohort. In addition, chip analysis suggested a high carrier frequency (up to 1:10) of ABCR variants in the general population. The ABCR genotyping microarray is a robust, cost-effective, and comprehensive screening tool for variation in one gene in which mutations are responsible for a substantial fraction of retinal disease. The ABCR chip is a prototype for the next generation of screening and diagnostic tools in ophthalmic genetics, bridging clinical and scientific research. Copyright 2003 Wiley-Liss, Inc.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations

PubMed Central

Szczecińska, Monika

2016-01-01

Background Research into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction). Methods The experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers. Results SSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers. Conclusions The results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs. PMID:27833793

Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard.

PubMed

Oliveira, Eliana Faria; Martinez, Pablo Ariel; São-Pedro, Vinícius Avelar; Gehara, Marcelo; Burbrink, Frank Thomas; Mesquita, Daniel Oliveira; Garda, Adrian Antonio; Colli, Guarino Rinaldi; Costa, Gabriel Correa

2018-03-01

Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.

Variation in populations of Yarrow's spiny lizard, Sceloporus jarrovii, in the northern Madrean Archipelago region

Treesearch

George Middendorf; Jack Frankel; Douglas Ruby

2005-01-01

Population genetic analysis of Yarrow’s spiny lizard, Sceloporus jarrovii, suggests a metapopulational distribution pattern with potential divergence of genetically based traits. Comparing male pushup displays revealed populations east and west of the San Pedro River valley to be more similar among themselves than to those on the other side....

The influence of landscape characteristics and home-range size on the quantification of landscape-genetics relationships

Treesearch

Tabitha A. Graves; Tzeidle N. Wasserman; Milton Cezar Ribeiro; Erin L. Landguth; Stephen F. Spear; Niko Balkenhol; Colleen B. Higgins; Marie-Josee Fortin; Samuel A. Cushman; Lisette P. Waits

2012-01-01

A common approach used to estimate landscape resistance involves comparing correlations of ecological and genetic distances calculated among individuals of a species. However, the location of sampled individuals may contain some degree of spatial uncertainty due to the natural variation of animals moving through their home range ormeasurement error in plant or animal...

Genetic variation at allozyme and RAPD markers in Pinus longaeva (Pinaceae) of the White Mountains, California

Treesearch

Seok-Woo Lee; F. Thomas Ledig; David R. Johnson

2002-01-01

We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees....

Molecular genetic insights on cheetah (Acinonyx jubatus) ecology and conservation in Namibia.

PubMed

Marker, Laurie L; Pearks Wilkerson, Alison J; Sarno, Ronald J; Martenson, Janice; Breitenmoser-Würsten, Christian; O'Brien, Stephen J; Johnson, Warren E

2008-01-01

The extent and geographic patterns of molecular genetic diversity of the largest remaining free-ranging cheetah population were described in a survey of 313 individuals from throughout Namibia. Levels of relatedness, including paternity/maternity (parentage), were assessed across all individuals using 19 polymorphic microsatellite loci, and unrelated cheetahs (n = 89) from 7 regions were genotyped at 38 loci to document broad geographical patterns. There was limited differentiation among regions, evidence that this is a generally panmictic population. Measures of genetic variation were similar among all regions and were comparable with Eastern African cheetah populations. Parentage analyses confirmed several observations based on field studies, including 21 of 23 previously hypothesized family groups, 40 probable parent/offspring pairs, and 8 sibling groups. These results also verified the successful integration and reproduction of several cheetahs following natural dispersal or translocation. Animals within social groups (family groups, male coalitions, or sibling groups) were generally related. Within the main study area, radio-collared female cheetahs were more closely interrelated than similarly compared males, a pattern consistent with greater male dispersal. The long-term maintenance of current patterns of genetic variation in Namibia depends on retaining habitat characteristics that promote natural dispersal and gene flow of cheetahs.

Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity.

PubMed

Copin, Richard; Wang, Xueying; Louie, Eddie; Escuyer, Vincent; Coscolla, Mireia; Gagneux, Sebastien; Palmer, Guy H; Ernst, Joel D

2016-12-01

Molecular epidemiological assessments, drug treatment optimization, and development of immunological interventions all depend on understanding pathogen adaptation and genetic variation, which differ for specific pathogens. Mycobacterium tuberculosis is an exceptionally successful human pathogen, yet beyond knowledge that this bacterium has low overall genomic variation but acquires drug resistance mutations, little is known of the factors that drive its population genomic characteristics. Here, we compared the genetic diversity of the bacteria that established infection to the bacterial populations obtained from infected tissues during murine M. tuberculosis pulmonary infection and human disseminated M. bovis BCG infection. We found that new mutations accumulate during in vitro culture, but that in vivo, purifying selection against new mutations dominates, indicating that M. tuberculosis follows a dominant lineage model of evolution. Comparing bacterial populations passaged in T cell-deficient and immunocompetent mice, we found that the presence of T cells is associated with an increase in the diversity of the M. tuberculosis genome. Together, our findings put M. tuberculosis genetic evolution in a new perspective and clarify the impact of T cells on sequence diversity of M. tuberculosis.

Antagonistic versus non-antagonistic models of balancing selection: Characterizing the relative timescales and hitchhiking effects of partial selective sweeps

PubMed Central

Connallon, Tim; Clark, Andrew G.

2012-01-01

Antagonistically selected alleles -- those with opposing fitness effects between sexes, environments, or fitness components -- represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus non-antagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, non-antagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection. PMID:23461340

Genetic variation in California oaks

Treesearch

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

1990-01-01

In forestry the importance of genetic variation for successful reproduction, survival and growth has been widely documented for commercial conifers; until recently, little genetic work has been done on the California oaks. Even before the nature of genetic variation was scientifically investigated, its importance was suspected in operational forestry. Many failures of...

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...

Spatial structure of morphological and neutral genetic variation in Brook Trout

USGS Publications Warehouse

Kazyak, David C.; Hilderbrand, Robert H.; Keller, Stephen R.; Colaw, Mark C.; Holloway, Amanda E.; Morgan, Raymond P.; King, Timothy L.

2015-01-01

Brook Trout Salvelinus fontinalis exhibit exceptional levels of life history variation, remarkable genetic variability, and fine-scale population structure. In many cases, neighboring populations may be highly differentiated from one another to an extent that is comparable with species-level distinctions in other taxa. Although genetic samples have been collected from hundreds of populations and tens of thousands of individuals, little is known about whether differentiation at neutral markers reflects phenotypic differences among Brook Trout populations. We compared differentiation in morphology and neutral molecular markers among populations from four geographically proximate locations (all within 24 km) to examine how genetic diversity covaries with morphology. We found significant differences among and/or within streams for all three morphological axes examined and identified the source stream of many individuals based on morphology (52.3% classification efficiency). Although molecular and morphological differentiation among streams ranged considerably (mean pairwise FST: 0.023–0.264; pairwise PST: 0.000–0.339), the two measures were not significantly correlated. While in some cases morphological characters appear to have diverged to a greater extent than expected by neutral genetic drift, many traits were conserved to a greater extent than were neutral genetic markers. Thus, while Brook Trout exhibit fine-scale spatial patterns in both morphology and neutral genetic diversity, these types of biological variabilities are being structured by different ecological and evolutionary processes. The relative influences of genetic drift versus selection and phenotypic plasticity in shaping morphology appear to vary among populations occupying nearby streams.

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

PubMed Central

Stavropoulos, Dimitri J; Merico, Daniele; Jobling, Rebekah; Bowdin, Sarah; Monfared, Nasim; Thiruvahindrapuram, Bhooma; Nalpathamkalam, Thomas; Pellecchia, Giovanna; Yuen, Ryan K C; Szego, Michael J; Hayeems, Robin Z; Shaul, Randi Zlotnik; Brudno, Michael; Girdea, Marta; Frey, Brendan; Alipanahi, Babak; Ahmed, Sohnee; Babul-Hirji, Riyana; Porras, Ramses Badilla; Carter, Melissa T; Chad, Lauren; Chaudhry, Ayeshah; Chitayat, David; Doust, Soghra Jougheh; Cytrynbaum, Cheryl; Dupuis, Lucie; Ejaz, Resham; Fishman, Leona; Guerin, Andrea; Hashemi, Bita; Helal, Mayada; Hewson, Stacy; Inbar-Feigenberg, Michal; Kannu, Peter; Karp, Natalya; Kim, Raymond H; Kronick, Jonathan; Liston, Eriskay; MacDonald, Heather; Mercimek-Mahmutoglu, Saadet; Mendoza-Londono, Roberto; Nasr, Enas; Nimmo, Graeme; Parkinson, Nicole; Quercia, Nada; Raiman, Julian; Roifman, Maian; Schulze, Andreas; Shugar, Andrea; Shuman, Cheryl; Sinajon, Pierre; Siriwardena, Komudi; Weksberg, Rosanna; Yoon, Grace; Carew, Chris; Erickson, Raith; Leach, Richard A; Klein, Robert; Ray, Peter N; Meyn, M Stephen; Scherer, Stephen W; Cohn, Ronald D; Marshall, Christian R

2016-01-01

The standard of care for first-tier clinical investigation of the aetiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy-number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion–deletions (indels) and single-nucleotide variant (SNV) mutations. Whole-genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilised WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a fourfold increase in diagnostic rate over CMA (8%; P value=1.42E−05) alone and more than twofold increase in CMA plus targeted gene sequencing (13%; P value=0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harbouring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counselling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis. PMID:28567303

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

PubMed

Stavropoulos, Dimitri J; Merico, Daniele; Jobling, Rebekah; Bowdin, Sarah; Monfared, Nasim; Thiruvahindrapuram, Bhooma; Nalpathamkalam, Thomas; Pellecchia, Giovanna; Yuen, Ryan K C; Szego, Michael J; Hayeems, Robin Z; Shaul, Randi Zlotnik; Brudno, Michael; Girdea, Marta; Frey, Brendan; Alipanahi, Babak; Ahmed, Sohnee; Babul-Hirji, Riyana; Porras, Ramses Badilla; Carter, Melissa T; Chad, Lauren; Chaudhry, Ayeshah; Chitayat, David; Doust, Soghra Jougheh; Cytrynbaum, Cheryl; Dupuis, Lucie; Ejaz, Resham; Fishman, Leona; Guerin, Andrea; Hashemi, Bita; Helal, Mayada; Hewson, Stacy; Inbar-Feigenberg, Michal; Kannu, Peter; Karp, Natalya; Kim, Raymond; Kronick, Jonathan; Liston, Eriskay; MacDonald, Heather; Mercimek-Mahmutoglu, Saadet; Mendoza-Londono, Roberto; Nasr, Enas; Nimmo, Graeme; Parkinson, Nicole; Quercia, Nada; Raiman, Julian; Roifman, Maian; Schulze, Andreas; Shugar, Andrea; Shuman, Cheryl; Sinajon, Pierre; Siriwardena, Komudi; Weksberg, Rosanna; Yoon, Grace; Carew, Chris; Erickson, Raith; Leach, Richard A; Klein, Robert; Ray, Peter N; Meyn, M Stephen; Scherer, Stephen W; Cohn, Ronald D; Marshall, Christian R

2016-01-13

The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

PubMed

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2014-01-01

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

Genetic and environmental influences on conduct and antisocial personality problems in childhood, adolescence, and adulthood.

PubMed

Wesseldijk, Laura W; Bartels, Meike; Vink, Jacqueline M; van Beijsterveldt, Catharina E M; Ligthart, Lannie; Boomsma, Dorret I; Middeldorp, Christel M

2017-06-21

Conduct problems in children and adolescents can predict antisocial personality disorder and related problems, such as crime and conviction. We sought an explanation for such predictions by performing a genetic longitudinal analysis. We estimated the effects of genetic, shared environmental, and unique environmental factors on variation in conduct problems measured at childhood and adolescence and antisocial personality problems measured at adulthood and on the covariation across ages. We also tested whether these estimates differed by sex. Longitudinal data were collected in the Netherlands Twin Register over a period of 27 years. Age appropriate and comparable measures of conduct and antisocial personality problems, assessed with the Achenbach System of Empirically Based Assessment, were available for 9783 9-10-year-old, 6839 13-18-year-old, and 7909 19-65-year-old twin pairs, respectively; 5114 twins have two or more assessments. At all ages, men scored higher than women. There were no sex differences in the estimates of the genetic and environmental influences. During childhood, genetic and environmental factors shared by children in families explained 43 and 44% of the variance of conduct problems, with the remaining variance due to unique environment. During adolescence and adulthood, genetic and unique environmental factors equally explained the variation. Longitudinal correlations across age varied between 0.20 and 0.38 and were mainly due to stable genetic factors. We conclude that shared environment is mainly of importance during childhood, while genetic factors contribute to variation in conduct and antisocial personality problems at all ages, and also underlie its stability over age.

Red Wine Consumption is inversely associated with 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)-DNA Adduct Levels in Prostate

PubMed Central

Rybicki, Benjamin A.; Neslund-Dudas, Christine; Bock, Cathryn H.; Nock, Nora L.; Rundle, Andrew; Jankowski, Michelle; Levin, Albert M.; Beebe-Dimmer, Jennifer; Savera, Adnan T.; Takahashi, Satoru; Shirai, Tomoyuki; Tang, Deliang

2011-01-01

In humans, genetic variation and dietary factors may alter the biologic effects of exposure to 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), one of the major heterocyclic amines generated from cooking meats at high temperatures that has carcinogenic potential through the formation of DNA adducts. Previously, we reported grilled red meat consumption associated with PhIP-DNA adduct levels in human prostate. In the present study, we expanded our investigation to estimate the associations between beverage consumption and PhIP-DNA adduct levels in prostate for 391 prostate cancer cases. Of the 15 beverages analyzed, red wine consumption had the strongest association with PhIP-DNA adduct levels showing an inverse correlation in both tumor (p=0.006) and non-tumor (p=0.002) prostate cells. Red wine consumption differed significantly between African-American and white cases, but PhIP-DNA adduct levels in prostate did not vary by race. In African Americans compared with whites, however, associations between red wine consumption and PhIP-DNA adduct levels were not as strong as associations with specific (e.g., SULT1A1 and UGT1A10 genotypes) and non-specific (e.g., African ancestry) genetic variation. In a multivariable model, the covariate for red wine consumption explained a comparable percentage (13-16%) of the variation in PhIP-DNA adduct levels in prostate across the two racial groups, but the aforementioned genetic factors explained 33% of the PhIP-DNA adduct variation in African-American cases, while only 19% of the PhIPDNA adduct variation in whites. We conclude that red wine consumption may counteract biologic effects of PhIP exposure in human prostate, but genetic factors may play an even larger role, particularly in African Americans. PMID:21846795

Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis).

PubMed

Uphyrkina, O; Miquelle, D; Quigley, H; Driscoll, C; O'Brien, S J

2002-01-01

The Far Eastern or Amur leopard (Panthera pardus orientalis) survives today as a tiny relict population of 25-40 individuals in the Russian Far East. The population descends from a 19th-century northeastern Asian subspecies whose range extended over southeastern Russia, the Korean peninsula, and northeastern China. A molecular genetic survey of nuclear microsatellite and mitochondrial DNA (mtDNA) sequence variation validates subspecies distinctiveness but also reveals a markedly reduced level of genetic variation. The amount of genetic diversity measured is the lowest among leopard subspecies and is comparable to the genetically depleted Florida panther and Asiatic lion populations. When considered in the context of nonphysiological perils that threaten small populations (e.g., chance mortality, poaching, climatic extremes, and infectious disease), the genetic and demographic data indicate a critically diminished wild population under severe threat of extinction. An established captive population of P. p. orientalis displays much higher diversity than the wild population sample, but nearly all captive individuals are derived from a history of genetic admixture with the adjacent Chinese subspecies, P. p. japonensis. The conservation management implications of potential restoration/augmentation of the wild population with immigrants from the captive population are discussed.

msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

PubMed

Pérez-Figueroa, A

2013-05-01

In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

The association of environmental, individual factors, and dopamine pathway gene variation with smoking cessation.

PubMed

Li, Suyun; Wang, Qiang; Pan, Lulu; Yang, Xiaorong; Li, Huijie; Jiang, Fan; Zhang, Nan; Han, Mingkui; Jia, Chongqi

2017-09-01

This study aimed to examine whether dopamine (DA) pathway gene variation were associated with smoking cessation, and compare the relative importance of infulence factors on smoking cessation. Participants were recruited from 17 villages of Shandong Province, China. Twenty-five single nucleotide polymorphisms in 8 DA pathway genes were genotyped. Weighted gene score of each gene was used to analyze the whole gene effect. Logistic regression was used to calculate odds ratios (OR) of the total gene score for smoking cessation. Dominance analysis was employed to compare the relative importance of individual, heaviness of smoking, psychological and genetic factors on smoking cessation. 415 successful spontaneous smoking quitters served as the cases, and 404 unsuccessful quitters served as the controls. A significant negative association of total DA pathway gene score and smoking cessation was observed (p < 0.001, OR: 0.25, 95% CI 0.16-0.38). Dominance analysis showed that the most important predictor for smoking cessation was heaviness of smoking score (42%), following by individual (40%), genetic (10%) and psychological score (8%). In conclusion, although the DA pathway gene variation was significantly associated with successful smoking cessation, heaviness of smoking and individual factors had bigger effect than genetic factors on smoking cessation.

Estimating Genetic and Maternal Effects Determining Variation in Immune Function of a Mixed-Mating Snail

PubMed Central

Seppälä, Otto; Langeloh, Laura

2016-01-01

Evolution of host defenses such as immune function requires heritable genetic variation in them. However, also non-genetic maternal effects can contribute to phenotypic variation, thus being an alternative target for natural selection. We investigated the role of individuals’ genetic background and maternal effects in determining immune defense traits (phenoloxidase and antibacterial activity of hemolymph), as well as in survival and growth, in the simultaneously hermaphroditic snail Lymnaea stagnalis. We utilized the mixed mating system of this species by producing full-sib families in which each parental snail had produced offspring as both a dam and as a sire, and tested whether genetic background (family) and non-genetic maternal effects (dam nested within family) explain trait variation. Immune defense traits and growth were affected solely by individuals’ genetic background. Survival of snails did not show family-level variation. Additionally, some snails were produced through self-fertilization. They showed reduced growth and survival suggesting recessive load or overdominance. Immune defense traits did not respond to inbreeding. Our results suggest that the variation in snail immune function and growth was due to genetic differences. Since immune traits did not respond to inbreeding, this variation is most likely due to additive or epistatic genetic variance. PMID:27551822

Genetic structure of Culex erraticus populations across the Americas.

PubMed

Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

2012-05-01

Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand

PubMed Central

2010-01-01

Background Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection. Methods This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health. Results All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation. Conclusion The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes. PMID:21176141

Genetic variation in tree structure and its relation to size in Douglas-fir: I. Biomass partitioning, foliage efficiency, stem form, and wood density.

Treesearch

J.B. St. Clair

1994-01-01

Genetic variation and covariation among traits of tree size and structure were assessed in an 18-year-old Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) genetic test in the Coast Range of Oregon. Considerable genetic variation was found in size, biomass partitioning, and wood density, and genetic gains may be...

Population genetic analysis and bioclimatic modeling in Agave striata in the Chihuahuan Desert indicate higher genetic variation and lower differentiation in drier and more variable environments.

PubMed

Trejo, Laura; Alvarado-Cárdenas, Leonardo O; Scheinvar, Enrique; Eguiarte, Luis E

2016-06-01

Is there an association between bioclimatic variables and genetic variation within species? This question can be approached by a detailed analysis of population genetics parameters along environmental gradients in recently originated species (so genetic drift does not further obscure the patterns). The genus Agave, with more than 200 recent species encompassing a diversity of morphologies and distributional patterns, is an adequate system for such analyses. We studied Agave striata, a widely distributed species from the Chihuahuan Desert, with a distinctive iteroparous reproductive ecology and two recognized subspecies with clear morphological differences. We used population genetic analyses along with bioclimatic studies to understand the effect of environment on the genetic variation and differentiation of this species. We analyzed six populations of the subspecies A. striata subsp. striata, with a southern distribution, and six populations of A. striata subsp. falcata, with a northern distribution, using 48 ISSR loci and a total of 541 individuals (averaging 45 individuals per population). We assessed correlations between population genetics parameters (the levels of genetic variation and differentiation) and the bioclimatic variables of each population. We modeled each subspecies distribution and used linear correlations and multifactorial analysis of variance. Genetic variation (measured as expected heterozygosity) increased at higher latitudes. Higher levels of genetic variation in populations were associated with a higher variation in environmental temperature and lower precipitation. Stronger population differentiation was associated with wetter and more variable precipitation in the southern distribution of the species. The two subspecies have genetic differences, which coincide with their climatic differences and potential distributions. Differences in genetic variation among populations and the genetic differentiation between A. striata subsp. striata and A. striata subsp. falcata is correlated with differences in environmental climatic variables along their distribution. We found two distinct gene pools that suggest active differentiation and perhaps incipient speciation. The detected association between genetic variation and environment variables indicates that climatic variables are playing an important role in the differentiation of A. striata. © 2016 Botanical Society of America.

Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

PubMed Central

Cruse-Sanders, Jennifer M; Parker, Kathleen C; Friar, Elizabeth A; Huang, Daisie I; Mashayekhi, Saeideh; Prince, Linda M; Otero-Arnaiz, Adriana; Casas, Alejandro

2013-01-01

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (HE = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear-cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species. PMID:23762520

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

PubMed Central

2014-01-01

Background Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. Results In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. Conclusions In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist. PMID:24447386

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity.

PubMed

Kesäniemi, Jenni E; Mustonen, Marina; Boström, Christoffer; Hansen, Benni W; Knott, K Emily

2014-01-22

Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist.

Genetic studies of African populations: an overview on disease susceptibility and response to vaccines and therapeutics.

PubMed

Sirugo, Giorgio; Hennig, Branwen J; Adeyemo, Adebowale A; Matimba, Alice; Newport, Melanie J; Ibrahim, Muntaser E; Ryckman, Kelli K; Tacconelli, Alessandra; Mariani-Costantini, Renato; Novelli, Giuseppe; Soodyall, Himla; Rotimi, Charles N; Ramesar, Raj S; Tishkoff, Sarah A; Williams, Scott M

2008-07-01

Africa is the ultimate source of modern humans and as such harbors more genetic variation than any other continent. For this reason, studies of the patterns of genetic variation in African populations are crucial to understanding how genes affect phenotypic variation, including disease predisposition. In addition, the patterns of extant genetic variation in Africa are important for understanding how genetic variation affects infectious diseases that are a major problem in Africa, such as malaria, tuberculosis, schistosomiasis, and HIV/AIDS. Therefore, elucidating the role that genetic susceptibility to infectious diseases plays is critical to improving the health of people in Africa. It is also of note that recent and ongoing social and cultural changes in sub-Saharan Africa have increased the prevalence of non-communicable diseases that will also require genetic analyses to improve disease prevention and treatment. In this review we give special attention to many of the past and ongoing studies, emphasizing those in Sub-Saharan Africans that address the role of genetic variation in human disease.

Why genes don't count (for racial differences in health).

PubMed Central

Goodman, A H

2000-01-01

There is a paradoxical relationship between "race" and genetics. Whereas genetic data were first used to prove the validity of race, since the early 1970s they have been used to illustrate the invalidity of biological races. Indeed, race does not account for human genetic variation, which is continuous, complexly structured, constantly changing, and predominantly within "races." Despite the disproof of race-as-biology, genetic variation continues to be used to explain racial differences. Such explanations require the acceptance of 2 disproved assumptions: that genetic variation explains variation in disease and that genetic variation explains racial variation in disease. While the former is a form of geneticization, the notion that genes are the primary determinants of biology and behavior, the latter represents a form of racialization, an exaggeration of the salience of race. Using race as a proxy for genetic differences limits understandings of the complex interactions among political-economic processes, lived experiences, and human biologies. By moving beyond studies of racialized genetics, we can clarify the processes by which varied and interwoven forms of racialization and racism affect individuals "under the skin." PMID:11076233

Why genes don't count (for racial differences in health).

PubMed

Goodman, A H

2000-11-01

There is a paradoxical relationship between "race" and genetics. Whereas genetic data were first used to prove the validity of race, since the early 1970s they have been used to illustrate the invalidity of biological races. Indeed, race does not account for human genetic variation, which is continuous, complexly structured, constantly changing, and predominantly within "races." Despite the disproof of race-as-biology, genetic variation continues to be used to explain racial differences. Such explanations require the acceptance of 2 disproved assumptions: that genetic variation explains variation in disease and that genetic variation explains racial variation in disease. While the former is a form of geneticization, the notion that genes are the primary determinants of biology and behavior, the latter represents a form of racialization, an exaggeration of the salience of race. Using race as a proxy for genetic differences limits understandings of the complex interactions among political-economic processes, lived experiences, and human biologies. By moving beyond studies of racialized genetics, we can clarify the processes by which varied and interwoven forms of racialization and racism affect individuals "under the skin."

Fitness consequences of avian personalities in a fluctuating environment.

PubMed Central

Dingemanse, Niels J.; Both, Christiaan; Drent, Piet J.; Tinbergen, Joost M.

2004-01-01

Individual animals differ in the way they cope with challenges in their environment, comparable with variation in human personalities. The proximate basis of variation in personality traits has received considerable attention, and one general finding is that personality traits have a substantial genetic basis. This poses the question of how variation in personality is maintained in natural populations. We show that selection on a personality trait with high heritability fluctuates across years within a natural bird population. Annual adult survival was related to this personality trait (behaviour in novel environments) but the effects were always opposite for males and females, and reversed between years. The number of offspring surviving to breeding was also related to their parents' personalities, and again selection changed between years. The observed annual changes in selection pressures coincided with changes in environmental conditions (masting of beeches) that affect the competitive regimes of the birds. We expect that the observed fluctuations in environmental factors lead to fluctuations in competition for space and food, and these, in association with variations in population density, lead to a variation in selection pressure, which maintains genetic variation in personalities. PMID:15255104

Genetics of Species Differences in the Wild Annual Sunflowers, Helianthus annuus and H. petiolaris

PubMed Central

Lexer, Christian; Rosenthal, David M.; Raymond, Olivier; Donovan, Lisa A.; Rieseberg, Loren H.

2005-01-01

Much of our knowledge of speciation genetics stems from quantitative trait locus (QTL) studies. However, interpretations of the size and distribution of QTL underlying species differences are complicated by differences in the way QTL magnitudes are estimated. Also, many studies fail to exploit information about QTL directions or to compare inter- and intraspecific QTL variation. Here, we comprehensively analyze an extensive QTL data set for an interspecific backcross between two wild annual sunflowers, Helianthus annuus and H. petiolaris, interpret different estimates of QTL magnitudes, identify trait groups that have diverged through selection, and compare inter- and intraspecific QTL magnitudes. Our results indicate that even minor QTL (in terms of backcross variance) may be surprisingly large compared to levels of standing variation in the parental species or phenotypic differences between them. Morphological traits, particularly flower morphology, were more strongly or consistently selected than life history or physiological traits. Also, intraspecific QTL were generally smaller than interspecific ones, consistent with the prediction that larger QTL are more likely to spread to fixation across a subdivided population. Our results inform the genetics of species differences in Helianthus and suggest an approach for the simultaneous mapping of inter- and intraspecific QTL. PMID:15545657

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. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Evolving Landscapes: the Effect of Genetic Variation on Salt Marsh Erosion

NASA Astrophysics Data System (ADS)

Bernik, B. M.; Blum, M. J.

2014-12-01

Ecogeomorphic studies have demonstrated that biota can exert influence over geomorphic processes, such as sediment transport, which in turn have biotic consequences and generate complex feedbacks. However, little attention has been paid to the potential for feedback to arise from evolutionary processes as population genetic composition changes in response to changing physical landscapes. In coastal ecosystems experiencing land loss, for example, shoreline erosion entails reduced plant survival and reproduction, and thereby represents a geomorphic response with inherent consequences for evolutionary fitness. To get at this topic, we examined the effect of genetic variation in the saltmarsh grass Spartina alterniflora, a renowned ecosystem engineer, on rates of shoreline erosion. Field transplantation studies and controlled greenhouse experiments were conducted to compare different genotypes from both wild and cultivated populations. Plant traits, soil properties, accretion/subsidence, and rates of land loss were measured. We found significant differences in rates of erosion between field plots occupied by different genotypes. Differences in erosion corresponded to variation in soil properties including critical shear stress and subsidence. Plant traits that differed across genotypes included belowground biomass, root tensile strength, and C:N ratios. Our results demonstrate the importance of genetic variation to salt marsh functioning, elucidating the relationship between evolutionary processes and ecogeomorphic dynamics in these systems. Because evolutionary processes can occur on ecological timescales, the direction and strength of ecogeomorphic feedbacks may be more dynamic than previously accounted for.

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

PubMed

Hall, S J G; Lenstra, J A; Deeming, D C

2012-06-01

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds. © 2011 Blackwell Verlag GmbH.

Population structure and genetic diversity of the amphiatlantic haploid peatmoss Sphagnum affine (Sphagnopsida).

PubMed

Thingsgaard, K

2001-10-01

Nineteen populations of Sphagnum affine were included in a study of genetic diversity and structure in fragmented and less fragmented landscapes, and differentiation at intercontinental and three regional levels. Isozyme electrophoresis of eight enzyme systems revealed 12 variable loci, which could be used for haplotype identification. A hierachical analysis of variance (AMOVA) revealed no significant intercontinental differentiation, and very limited differentiation among European regions. A trend of decreasing diversity with increasing latitude was apparent. Gametic phase disequilibria was high, suggesting nonrandom mating and regionally high incidences of inbreeding. The partitioning of genetic variation within and among populations in each region varied among regions, the northernmost populations having 86% of the total variation among populations, the southernmost in Scandinavia having 25% of the variation among populations, whereas the American populations displayed 89% of the variation within populations. Fifteen alleles at eight loci occurred in the U.S.A. which were not encountered in Europe, whereas only three European alleles at one locus in three populations were not encountered in U.S.A. The differences in diversity between North America and Europe may result from loss of genetic diversity caused by founder effects during postglacial recolonization of northern Europe. In Europe, the main mountain ranges extend E-W, posing severe barriers to northwards migration of lowland species, compared to the N-S trend of mountain ranges in North America. The decline in genetic diversity and increase in population differentiation and gametic phase disequilibria towards the north in Scandinavia may be caused by a series of founder effects during postglacial migration. These may have corresponded to minor climatic oscillations that influenced the migration front/leading edge in the suboceanic lowlands of Norway. According to this model random genetic drift will be an increasingly important structuring factor with latitude.

Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units

Treesearch

C. Vásquez-Carrillo; V. Friesen; L. Hall; M.Z. Peery

2013-01-01

Conserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II...

Evolutionary Determinants of Genetic Variation in Susceptibility to Infectious Diseases in Humans

PubMed Central

Baker, Christi; Antonovics, Janis

2012-01-01

Although genetic variation among humans in their susceptibility to infectious diseases has long been appreciated, little focus has been devoted to identifying patterns in levels of variation in susceptibility to different diseases. Levels of genetic variation in susceptibility associated with 40 human infectious diseases were assessed by a survey of studies on both pedigree-based quantitative variation, as well as studies on different classes of marker alleles. These estimates were correlated with pathogen traits, epidemiological characteristics, and effectiveness of the human immune response. The strongest predictors of levels of genetic variation in susceptibility were disease characteristics negatively associated with immune effectiveness. High levels of genetic variation were associated with diseases with long infectious periods and for which vaccine development attempts have been unsuccessful. These findings are consistent with predictions based on theoretical models incorporating fitness costs associated with the different types of resistance mechanisms. An appreciation of these observed patterns will be a valuable tool in directing future research given that genetic variation in disease susceptibility has large implications for vaccine development and epidemiology. PMID:22242158

Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

ERIC Educational Resources Information Center

Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

2014-01-01

Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

PubMed Central

Palmer, A. Richard

1996-01-01

Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation. PMID:8962039

Morphological outcomes of gynandromorphism in Lycaeides butterflies (Lepidoptera: Lycaenidae).

PubMed

Jahner, Joshua P; Lucas, Lauren K; Wilson, Joseph S; Forister, Matthew L

2015-01-01

The genitalia of male insects have been widely used in taxonomic identification and systematics and are potentially involved in maintaining reproductive isolation between species. Although sexual selection has been invoked to explain patterns of morphological variation in genitalia among populations and species, developmental plasticity in genitalia likely contributes to observed variation but has been rarely examined, particularly in wild populations. Bilateral gynandromorphs are individuals that are genetically male on one side of the midline and genetically female on the other, while mosaic gynandromorphs have only a portion of their body developing as the opposite sex. Gynandromorphs might offer unique insights into developmental plasticity because individuals experience abnormal cellular interactions at the genitalic midline. In this study, we compare the genitalia and wing patterns of gynandromorphic Anna and Melissa blue butterflies, Lycaeides anna (Edwards) (formerly L. idas anna) and L. melissa (Edwards) (Lepidoptera: Lycaenidae), to the morphology of normal individuals from the same populations. Gynandromorph wing markings all fell within the range of variation of normal butterflies; however, a number of genitalic measurements were outliers when compared with normal individuals. From these results, we conclude that the gynandromorphs' genitalia, but not wing patterns, can be abnormal when compared with normal individuals and that the gynandromorphic genitalia do not deviate developmentally in a consistent pattern across individuals. Finally, genetic mechanisms are considered for the development of gynandromorphism in Lycaeides butterflies. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach.

PubMed

Giardine, Belinda; Borg, Joseph; Higgs, Douglas R; Peterson, Kenneth R; Philipsen, Sjaak; Maglott, Donna; Singleton, Belinda K; Anstee, David J; Basak, A Nazli; Clark, Barnaby; Costa, Flavia C; Faustino, Paula; Fedosyuk, Halyna; Felice, Alex E; Francina, Alain; Galanello, Renzo; Gallivan, Monica V E; Georgitsi, Marianthi; Gibbons, Richard J; Giordano, Piero C; Harteveld, Cornelis L; Hoyer, James D; Jarvis, Martin; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N; Papadopoulos, Petros; Pavlovic, Sonja; Perseu, Lucia; Radmilovic, Milena; Riemer, Cathy; Satta, Stefania; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John S; Wiemann, Claudia; Zukic, Branka; Chui, David H K; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

2011-03-20

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

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. © 2015 John Wiley & Sons Ltd.

Differential influences of local subpopulations on regional diversity and differentiation for greater sage-grouse (Centrocercus urophasianus)

USGS Publications Warehouse

Row, Jeffery R.; Oyler-McCance, Sara J.; Fedy, Brad C.

2016-01-01

The distribution of spatial genetic variation across a region can shape evolutionary dynamics and impact population persistence. Local population dynamics and among-population dispersal rates are strong drivers of this spatial genetic variation, yet for many species we lack a clear understanding of how these population processes interact in space to shape within-species genetic variation. Here, we used extensive genetic and demographic data from 10 subpopulations of greater sage-grouse to parameterize a simulated approximate Bayesian computation (ABC) model and (i) test for regional differences in population density and dispersal rates for greater sage-grouse subpopulations in Wyoming, and (ii) quantify how these differences impact subpopulation regional influence on genetic variation. We found a close match between observed and simulated data under our parameterized model and strong variation in density and dispersal rates across Wyoming. Sensitivity analyses suggested that changes in dispersal (via landscape resistance) had a greater influence on regional differentiation, whereas changes in density had a greater influence on mean diversity across all subpopulations. Local subpopulations, however, varied in their regional influence on genetic variation. Decreases in the size and dispersal rates of central populations with low overall and net immigration (i.e. population sources) had the greatest negative impact on genetic variation. Overall, our results provide insight into the interactions among demography, dispersal and genetic variation and highlight the potential of ABC to disentangle the complexity of regional population dynamics and project the genetic impact of changing conditions.

Genetic diversity of resin yielder Pinus merkusii from West Java - Indonesia revealed by microsatellites marker

NASA Astrophysics Data System (ADS)

Susilowati, A.; Rachmat, H. H.; Siregar, I. Z.; Supriyanto

2018-02-01

Phenotypic observation of resin yielder Pinus merkusii showed higher value of genetic variation and narrow sense heritability values for resin production trait. This result indicated that genetic factor played as dominant aspect. However, further observation using molecular marker would still be needed to overcome the weakness of phenotypic observation. This study was carried out in order to characterize the genetic diversity and genetic differentiation of resin yielder genotype candidate P.merkusii using microsatellite markers and to characterize the genetic structure in the resin yielder populations. Seventy needle and inner bark samples were collected from resin yielder in Cijambu Seedling Seed Orchard (SSO) Sumedang, West Java and further divided into two genotype candidates (lower and high resin yielder). Seven microsatellites loci (pm01, pm04, pm05, pm07, pm08, pm09a, pm12, pde5 and SPAC 11.6) were used for detection of genetic diversity. Results showed that genetic diversity in higher resin candidates was (0.551), slightly different compared lower candidates (0.545). However, cluster analysis determined that higher resin yielder grouped with lower one. Molecular variation was found to be low among populations (21%) and high among individuals within the populations (79%). Private alleles were detected both in higher yielder and also normal population.

River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community.

PubMed

Pilger, Tyler J; Gido, Keith B; Propst, David L; Whitney, James E; Turner, Thomas F

2017-05-01

Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise F ST ) while explicitly accounting for intraspecific demographic influences on effective population size (N e ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of N e was a strong predictor of pairwise F ST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases. © 2017 John Wiley & Sons Ltd.

The Etiology of Variation in Language Skills Changes with Development: A Longitudinal Twin Study of Language from 2 to 12 Years

ERIC Educational Resources Information Center

Hayiou-Thomas, Marianna E.; Dale, Philip S.; Plomin, Robert

2012-01-01

The present study is the first long-term longitudinal examination of the etiology of individual differences in language from early childhood through to adolescence. We applied a multivariate latent factor genetic model to longitudinal data from the Twins Early Development Study in order to (a) compare the magnitude of genetic and environmental…

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries).

PubMed

Johnston, Susan E; Bérénos, Camillo; Slate, Jon; Pemberton, Josephine M

2016-05-01

Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h(2) = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3 A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals. Copyright © 2016 by the Genetics Society of America.

DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics.

PubMed

Giri, Anil K; Bharadwaj, Soham; Banerjee, Priyanka; Chakraborty, Shraddha; Parekatt, Vaisak; Rajashekar, Donaka; Tomar, Abhishek; Ravindran, Aarthi; Basu, Analabha; Tandon, Nikhil; Bharadwaj, Dwaipayan

2017-06-01

Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups. This study is based on comparative analyses of methylome from five different ethnicities with major focus on Indian subjects. The current study uses hierarchical clustering approaches, principal component analysis and locus specific differential methylation analysis on Illumina 450K methylation data to compare methylome of different ethnic subjects. Our data indicates that the variations in DNA methylation patterns of Indians are less among themselves compared to other global population. It empirically correlated with dietary, cultural and demographical divergences across different ethnic groups. Our work further suggests that Indians included in this study, despite their genetic similarity with the Caucasian population, are in close proximity with Japanese in terms of their methylation signatures.

Hemiclonal analysis of interacting phenotypes in male and female Drosophila melanogaster

PubMed Central

2014-01-01

Background Identifying the sources of variation in mating interactions between males and females is important because this variation influences the strength and/or the direction of sexual selection that populations experience. While the origins and effects of variation in male attractiveness and ornamentation have received much scrutiny, the causes and consequences of intraspecific variation in females have been relatively overlooked. We used cytogenetic cloning techniques developed for Drosophila melanogaster to create “hemiclonal” males and females with whom we directly observed sexual interaction between individuals of different known genetic backgrounds and measured subsequent reproductive outcomes. Using this approach, we were able to quantify the genetic contribution of each mate to the observed phenotypic variation in biologically important traits including mating speed, copulation duration, and subsequent offspring production, as well as measure the magnitude and direction of intersexual genetic correlation between female choosiness and male attractiveness. Results We found significant additive genetic variation contributing to mating speed that can be attributed to male genetic identity, female genetic identity, but not their interaction. Furthermore we found that phenotypic variation in copulation duration had a significant male-associated genetic component. Female genetic identity and the interaction between male and female genetic identity accounted for a substantial amount of the observed phenotypic variation in egg size. Although previous research predicts a trade-off between egg size and fecundity, this was not evident in our results. We found a strong negative genetic correlation between female choosiness and male attractiveness, a result that suggests a potentially important role for sexually antagonistic alleles in sexual selection processes in our population. Conclusion These results further our understanding of sexual selection because they identify that genetic identity plays a significant role in phenotypic variation in female behaviour and fecundity. This variation may be potentially due to ongoing sexual conflict found between the sexes for interacting phenotypes. Our unexpected observation of a negative correlation between female choosiness and male attractiveness highlights the need for more explicit theoretical models of genetic covariance to investigate the coevolution of female choosiness and male attractiveness. PMID:24884361

Heritability of seed weight in Maritime pine, a relevant trait in the transmission of environmental maternal effects

PubMed Central

Zas, R; Sampedro, L

2015-01-01

Quantitative seed provisioning is an important life-history trait with strong effects on offspring phenotype and fitness. As for any other trait, heritability estimates are vital for understanding its evolutionary dynamics. However, being a trait in between two generations, estimating additive genetic variation of seed provisioning requires complex quantitative genetic approaches for distinguishing between true genetic and environmental maternal effects. Here, using Maritime pine as a long-lived plant model, we quantified additive genetic variation of cone and seed weight (SW) mean and SW within-individual variation. We used a powerful approach combining both half-sib analysis and parent–offspring regression using several common garden tests established in contrasting environments to separate G, E and G × E effects. Both cone weight and SW mean showed significant genetic variation but were also influenced by the maternal environment. Most of the large variation in SW mean was attributable to additive genetic effects (h2=0.55–0.74). SW showed no apparent G × E interaction, particularly when accounting for cone weight covariation, suggesting that the maternal genotypes actively control the SW mean irrespective of the amount of resources allocated to cones. Within-individual variation in SW was low (12%) relative to between-individual variation (88%), and showed no genetic variation but was largely affected by the maternal environment, with greater variation in the less favourable sites for pine growth. In summary, results were very consistent between the parental and the offspring common garden tests, and clearly indicated heritable genetic variation for SW mean but not for within-individual variation in SW. PMID:25160045

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

PubMed

Griswold, Cortland K

2015-12-21

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

Application of novel polymorphic microsatellite loci identified in the Korean Pacific Abalone (Haliotis diversicolor supertexta (Haliotidae)) in the genetic characterization of wild and released populations.

PubMed

An, Hye Suck; Lee, Jang Wook; Hong, Seong Wan

2012-01-01

The small abalone, Haliotis diversicolor supertexta, of the family Haliotidae, is one of the most important species of marine shellfish in eastern Asia. Over the past few decades, this species has drastically declined in Korea. Thus, hatchery-bred seeds have been released into natural coastal areas to compensate for the reduced fishery resources. However, information on the genetic background of the small abalone is scarce. In this study, 20 polymorphic microsatellite DNA markers were identified using next-generation sequencing techniques and used to compare allelic variation between wild and released abalone populations in Korea. Using high-throughput genomic sequencing, a total of 1516 (2.26%; average length of 385 bp) reads containing simple sequence repeats were obtained from 86,011 raw reads. Among the 99 loci screened, 28 amplified successfully, and 20 were polymorphic. When comparing allelic variation between wild and released abalone populations, a total of 243 different alleles were observed, with 18.7 alleles per locus. High genetic diversity (mean heterozygosity = 0.81; mean allelic number = 15.5) was observed in both populations. A statistical analysis of the fixation index (F(ST)) and analysis of molecular variance (AMOVA) indicated limited genetic differences between the two populations (F(ST) = 0.002, p > 0.05). Although no significant reductions in the genetic diversity were found in the released population compared with the wild population (p > 0.05), the genetic diversity parameters revealed that the seeds released for stock abundance had a different genetic composition. These differences are likely a result of hatchery selection and inbreeding. Additionally, all the primer pair sets were effectively amplified in another congeneric species, H. diversicolor diversicolor, indicating that these primers are useful for both abalone species. These microsatellite loci may be valuable for future aquaculture and population genetic studies aimed at developing conservation and management plans for these two abalone species.

Host genetic variation impacts microbiome composition across human body sites.

PubMed

Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G

2015-09-15

The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale. Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes. Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.

Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada's Great Bear Lake

PubMed Central

Harris, L N; Chavarie, L; Bajno, R; Howland, K L; Wiley, S H; Tonn, W M; Taylor, E B

2015-01-01

Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change. PMID:25204304

Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada's Great Bear Lake.

PubMed

Harris, L N; Chavarie, L; Bajno, R; Howland, K L; Wiley, S H; Tonn, W M; Taylor, E B

2015-01-01

Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change.

Characterization of genetic sequence variation of 58 STR loci in four major population groups.

PubMed

Novroski, Nicole M M; King, Jonathan L; Churchill, Jennifer D; Seah, Lay Hong; Budowle, Bruce

2016-11-01

Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Maintenance of Genetic Diversity in an Introduced Island Population of Guanacos after Seven Decades and Two Severe Demographic Bottlenecks: Implications for Camelid Conservation

PubMed Central

von Borries, Rainer; Johnson, Warren E.; Franklin, William L.; Marín, Juan C.

2014-01-01

Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10–20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation. PMID:24663026

Exploration of the Genetic Organization of Morphological Modularity on the Mouse Mandible Using a Set of Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species

PubMed Central

Burgio, Gaëtan; Baylac, Michel; Heyer, Evelyne; Montagutelli, Xavier

2012-01-01

Morphological integration and modularity within semi-autonomous modules are essential mechanisms for the evolution of morphological traits. However, the genetic makeup responsible for the control of variational modularity is still relatively unknown. In our study, we tested the hypothesis that the genetic variation for mandible shape clustered into two morphogenetic components: the alveolar group and the ascending ramus. We used the mouse as a model system to investigate genetics determinants of mandible shape. To do this, we used a combination of geometric morphometric tools and a set of 18 interspecific recombinant congenic strains (IRCS) derived from the distantly related species, Mus spretus SEG/Pas and Mus musculus C57BL/6. Quantitative trait loci (QTL) analysis comparing mandible morphometry between the C57BL/6 and the IRCSs identified 42 putative SEG/Pas segments responsible for the genetic variation. The magnitude of the QTL effects was dependent on the proportion of SEG/Pas genome inherited. Using a multivariate correlation coefficient adapted for modularity assessment and a two-block partial least squares analysis to explore the morphological integration, we found that these QTL clustered into two well-integrated morphogenetic groups, corresponding to the ascending ramus and the alveolar region. Together, these results provide evidence that the mouse mandible is subjected to genetic coordination in a modular manner. PMID:23050236

Maintenance of genetic diversity in an introduced island population of guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation.

PubMed

González, Benito A; Orozco-Terwengel, Pablo; von Borries, Rainer; Johnson, Warren E; Franklin, William L; Marín, Juan C

2014-01-01

Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.

Genetic Factors in Determining Bone Mass

PubMed Central

Smith, David M.; Nance, Walter E.; Kang, Ke Won; Christian, Joe C.; Johnston, C. Conrad

1973-01-01

This investigation was undertaken to evaluate possible genetic determinants of bone mass with the premise that inheritance of bone mass could be of etiologic importance in osteoporosis. Bone mass and width measurements were made with the photon absorption technique on the right radius of 71 juvenile and 80 adult twin paris. The variance of intrapair differences of bone mass in monozygotic (MZ) juvenile twins was 0.0013 g2/cm2 compared to 0.0052 g2/cm2 in the dizygotic (DZ) twins. For the adult twins the variance of intrapair differences in bone mass was 0.0069 for MZ and 0.0137 for DZ twins. Similar results were obtained for bone width. The significantly larger variation in intrapair differences in DZ twins indicates that these traits have significant genetic determinants. These intrapair differences were found to increase with age, suggesting that genetic-environmental interaction also contributes to the observed variation in bone mass. These data provide evidence that bone mass does have significant genetic factors, which alone or in conjunction with environmental factors may predispose persons to the development of osteoporosis. PMID:4795916

Genetic variation and relationships of four species of medically important echinostomes (Trematoda: Echinostomatidae) in South-East Asia.

PubMed

Saijuntha, Weerachai; Sithithaworn, Paiboon; Duenngai, Kunyarat; Kiatsopit, Nadda; Andrews, Ross H; Petney, Trevor N

2011-03-01

Multilocus enzyme electrophoresis (MEE) and DNA sequencing of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene were used to genetically compare four species of echinostomes of human health importance. Fixed genetic differences among adults of Echinostoma revolutum, Echinostoma malayanum, Echinoparyphium recurvatum and Hypoderaeum conoideum were detected at 51-75% of the enzyme loci examined, while interspecific differences in CO1 sequence were detected at 16-32 (8-16%) of the 205 alignment positions. The results of the MEE analyses also revealed fixed genetic differences between E. revolutum from Thailand and Lao PDR at five (19%) of 27 loci, which could either represent genetic variation between geographically separated populations of a single species, or the existence of a cryptic (i.e. genetically distinct but morphologically similar) species. However, there was no support for the existence of cryptic species within E. revolutum based on the CO1 sequence between the two geographical areas sampled. Genetic variation in CO1 sequence was also detected among E. malayanum from three different species of snail intermediate host. Separate phylogenetic analyses of the MEE and DNA sequence data revealed that the two species of Echinostoma (E. revolutum and E. malayanum) did not form a monophyletic clade. These results, together with the large number of morphologically similar species with inadequate descriptions, poor specific diagnoses and extensive synonymy, suggest that the morphological characters used for species taxonomy of echinostomes in South-East Asia should be reconsidered according to the concordance of biology, morphology and molecular classification. Copyright © 2010 Elsevier B.V. All rights reserved.

Genomic Analysis of Genotype-by-Social Environment Interaction for Drosophila melanogaster Aggressive Behavior.

PubMed

Rohde, Palle Duun; Gaertner, Bryn; Ward, Kirsty; Sørensen, Peter; Mackay, Trudy F C

2017-08-01

Human psychiatric disorders such as schizophrenia, bipolar disorder, and attention-deficit/hyperactivity disorder often include adverse behaviors including increased aggressiveness. Individuals with psychiatric disorders often exhibit social withdrawal, which can further increase the probability of conducting a violent act. Here, we used the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP) to investigate the genetic basis of variation in male aggressive behavior for flies reared in a socialized and socially isolated environment. We identified genetic variation for aggressive behavior, as well as significant genotype-by-social environmental interaction (GSEI); i.e. , variation among DGRP genotypes in the degree to which social isolation affected aggression. We performed genome-wide association (GWA) analyses to identify genetic variants associated with aggression within each environment. We used genomic prediction to partition genetic variants into gene ontology (GO) terms and constituent genes, and identified GO terms and genes with high prediction accuracies in both social environments and for GSEI. The top predictive GO terms significantly increased the proportion of variance explained, compared to prediction models based on all segregating variants. We performed genomic prediction across environments, and identified genes in common between the social environments that turned out to be enriched for genome-wide associated variants. A large proportion of the associated genes have previously been associated with aggressive behavior in Drosophila and mice. Further, many of these genes have human orthologs that have been associated with neurological disorders, indicating partially shared genetic mechanisms underlying aggression in animal models and human psychiatric disorders. Copyright © 2017 by the Genetics Society of America.

Spatial and temporal drivers of phenotypic diversity in polymorphic snakes.

PubMed

Cox, Christian L; Davis Rabosky, Alison R

2013-08-01

Color polymorphism in natural populations presents an ideal opportunity to study the evolutionary drivers of phenotypic diversity. Systems with striking spatial, temporal, and qualitative variation in color can be leveraged to study the mechanisms promoting the distribution of different types of variation in nature. We used the highly polymorphic ground snake (Sonora semiannulata), a putative coral snake mimic with both cryptic and conspicuous morphs, to compare patterns of neutral genetic variation and variation over space and time in color polymorphism to investigate the mechanistic drivers of phenotypic variation across scales. We found that strong selection promotes color polymorphism across spatial and temporal scales, with morph frequencies differing markedly between juvenile and adult age classes within a single population, oscillating over time within multiple populations, and varying drastically over the landscape despite minimal population genetic structure. However, we found no evidence that conspicuousness of morphs was related to which color pattern was favored by selection or to any geographic factors, including sympatry with coral snakes. We suggest that complex patterns of phenotypic variation in polymorphic systems may be a fundamental outcome of the conspicuousness of morphs and that explicit tests of temporal and geographic variation are critical to the interpretation of conspicuousness and mimicry.

Comparison of the physiological characteristics of transgenic insect-resistant cotton and conventional lines.

PubMed

Li, Xiaogang; Ding, Changfeng; Wang, Xingxiang; Liu, Biao

2015-03-04

The introduction of transgenic insect-resistant cotton into agricultural ecosystems has raised concerns regarding its ecological effects. Many studies have been conducted to compare the differences in characteristics between transgenic cotton and conventional counterparts. However, few studies have focused on the different responses of transgenic cotton to stress conditions, especially to the challenges of pathogens. The aim of this work is to determine the extent of variation in physiological characteristics between transgenic insect-resistant cotton and the conventional counterpart infected by cotton soil-borne pathogens. The results showed that the difference in genetic backgrounds is the main factor responsible for the effects on biochemical characteristics of transgenic cotton when incubating with cotton Fusarium oxysporum. However, genetic modification had a significantly greater influence on the stomatal structure of transgenic cotton than the effects of cotton genotypes. Our results highlight that the differences in genetic background and/or genetic modifications may introduce variations in physiological characteristics and should be considered to explore the potential unexpected ecological effects of transgenic cotton.

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies

PubMed Central

Daane, Jacob M.; Rohner, Nicolas; Konstantinidis, Peter; Djuranovic, Sergej; Harris, Matthew P.

2016-01-01

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes. PMID:26452532

Biological variation in a large sample of mouse lemurs from Amboasary, Madagascar: implications for interpreting variation in primate biology and paleobiology.

PubMed

Cuozzo, Frank P; Rasoazanabary, Emilienne; Godfrey, Laurie R; Sauther, Michelle L; Youssouf, Ibrahim Antho; LaFleur, Marni M

2013-01-01

A thorough knowledge of biological variation in extant primates is imperative for interpreting variation, and for delineating species in primate biology and paleobiology. This is especially the case given the recent, rapid taxonomic expansion in many primate groups, notably among small-bodied nocturnal forms. Here we present data on dental, cranial, and pelage variation in a single-locality museum sample of mouse lemurs from Amboasary, Madagascar. To interpret these data, we include comparative information from other museum samples, and from a newly collected mouse lemur skeletal sample from the Beza Mahafaly Special Reserve (BMSR), Madagascar. We scored forty dental traits (n = 126) and three pelage variants (n = 19), and collected 21 cranial/dental measures. Most dental traits exhibit variable frequencies, with some only rarely present. Individual dental variants include misshapen and supernumerary teeth. All Amboasary pelage specimens display a "reversed V" on the cap, and a distinct dorsal median stripe on the back. All but two displayed the dominant gray-brown pelage coloration typical of Microcebus griseorufus. Cranial and dental metric variability are each quite low, and craniometric variation does not illustrate heteroscedasticity. To assess whether this sample represents a single species, we compared dental and pelage variation to a documented, single-species M. griseorufus sample from BMSR. As at Amboasary, BMSR mouse lemurs display limited odontometric variation and wide variation in non-metric dental traits. In contrast, BMSR mouse lemurs display diverse pelage, despite reported genetic homogeneity. Ranges of dental and pelage variation at BMSR and Amboasary overlap. Thus, we conclude that the Amboasary mouse lemurs represent a single species - most likely (in the absence of genetic data to the contrary) M. griseorufus, and we reject their previous allocation to Microcebus murinus. Patterns of variation in the Amboasary sample provide a comparative template for recognizing the degree of variation manifested in a single primate population, and by implication, they provide minimum values for this species' intraspecific variation. Finally, discordance between different biological systems in our mouse lemur samples illustrates the need to examine multiple systems when conducting taxonomic analyses among living or fossil primates. Copyright © 2012 Elsevier Ltd. All rights reserved.

Assessing the potential for an ongoing arms race within and between the sexes: selection and heritable variation.

PubMed

Friberg, Urban; Lew, Timothy A; Byrne, Phillip G; Rice, William R

2005-07-01

In promiscuous species, sexual selection generates two opposing male traits: offense (acquiring new mates and supplanting stored sperm) and defense (enforcing fidelity on one's mates and preventing sperm displacement when this fails). Coevolution between these traits requires both additive genetic variation and associated natural selection. Previous work with Drosophila melanogaster found autosomal genetic variation for these traits among inbred lines from a mixture of populations, but only nonheritable genetic variation was found within a single outbred population. These results do not support ongoing antagonistic coevolution between offense and defense, nor between either of these male traits and female reproductive characters. Here we use a new method (hemiclonal analysis) to study genomewide genetic variation in a large outbred laboratory population of D. melanogaster. Hemiclonal analysis estimates the additive genetic variation among random, genomewide haplotypes taken from a large, outbred, locally adapted laboratory population and determines the direction of the selection gradient on this variation. In contrast to earlier studies, we found low but biologically significant heritable variation for defensive and offensive offspring production as well as all their components (P1, fidelity, P2, and remating). Genetic correlations between these traits were substantially different from those reported for inbred lines. A positive genetic correlation was found between defense and offense, demonstrating that some shared genes influence both traits. In addition to this common variation, evidence for unique genetic variation for each trait was also found, supporting an ongoing coevolutionary arms race between defense and offense. Reproductive conflict between males can strongly influence female fitness. Correspondingly, we found genetic variation in both defense and offense that affected female fitness. No evidence was found for intersexual conflict in the context of male defense, but we found substantial intersexual conflict in the context of male offensive sperm competitive ability. These results indicate that conflict between competing males also promotes an associated arms race between the sexes.

Compatibility of breeding for increased wood production and longterm sustainability: the genetic variation of seed orchard seed and associated risks.

Treesearch

R Johnson; S. Lipow

2002-01-01

Because breeding imposes strong artificial selection for a narrow suite of economically important traits, genetic variation is reduced in seedlings derived from operational seed orchards. Both quantitative genetics theory and studies of allozyme variation show that seed orchards contain most of the genetic diversity found in natural populations, although low-frequency...

Genetic variation in tree structure and its relation to size in Douglas-fir: II. crown form, branch characters, and foliage characters.

Treesearch

J.B. St. Clair

1994-01-01

Genetic variation and covariation among traits of tree size and structure were assessed in an 18-year-old Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) genetic test in the Coast Range of Oregon. Considerable genetic variation was found for relative crown width; stem increment per crown projection area; leaf...

Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents

PubMed Central

Maghuly, Fatemeh; Jankowicz-Cieslak, Joanna; Pabinger, Stephan; Till, Bradley J; Laimer, Margit

2015-01-01

Increasing economic interest in Jatropha curcas requires a major research focus on the genetic background and geographic origin of this non-edible biofuel crop. To determine the worldwide genetic structure of this species, amplified fragment length polymorphisms, inter simple sequence repeats, and novel single nucleotide polymorphisms (SNPs) were employed for a large collection of 907 J. curcas accessions and related species (RS) from three continents, 15 countries and 53 regions. PCoA, phenogram, and cophenetic analyses separated RS from two J. curcas groups. Accessions from Mexico, Bolivia, Paraguay, Kenya, and Ethiopia with unknown origins were found in both groups. In general, there was a considerable overlap between individuals from different regions and countries. The Bayesian approach using structure demonstrated two groups with a low genetic variation. Analysis of molecular varience revealed significant variation among individuals within populations. SNPs found by in silico analyses of Δ12 fatty acid desaturase indicated possible changes in gene expression and thus in fatty acid profiles. SNP variation was higher in the curcin gene compared to genes involved in oil production. Novel SNPs allowed separating toxic, non-toxic, and Mexican accessions. The present study confirms that human activities had a major influence on the genetic diversity of J. curcas, not only because of domestication, but also because of biased selection. PMID:25511658

Genetic and environmental factors affecting birth size variation: a pooled individual-based analysis of secular trends and global geographical differences using 26 twin cohorts.

PubMed

Yokoyama, Yoshie; Jelenkovic, Aline; Hur, Yoon-Mi; Sund, Reijo; Fagnani, Corrado; Stazi, Maria A; Brescianini, Sonia; Ji, Fuling; Ning, Feng; Pang, Zengchang; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Rebato, Esther; Hopper, John L; Cutler, Tessa L; Saudino, Kimberly J; Nelson, Tracy L; Whitfield, Keith E; Corley, Robin P; Huibregtse, Brooke M; Derom, Catherine A; Vlietinck, Robert F; Loos, Ruth J F; Llewellyn, Clare H; Fisher, Abigail; Bjerregaard-Andersen, Morten; Beck-Nielsen, Henning; Sodemann, Morten; Krueger, Robert F; McGue, Matt; Pahlen, Shandell; Bartels, Meike; van Beijsterveldt, Catharina E M; Willemsen, Gonneke; Harris, Jennifer R; Brandt, Ingunn; Nilsen, Thomas S; Craig, Jeffrey M; Saffery, Richard; Dubois, Lise; Boivin, Michel; Brendgen, Mara; Dionne, Ginette; Vitaro, Frank; Haworth, Claire M A; Plomin, Robert; Bayasgalan, Gombojav; Narandalai, Danshiitsoodol; Rasmussen, Finn; Tynelius, Per; Tarnoki, Adam D; Tarnoki, David L; Ooki, Syuichi; Rose, Richard J; Pietiläinen, Kirsi H; Sørensen, Thorkild I A; Boomsma, Dorret I; Kaprio, Jaakko; Silventoinen, Karri

2018-05-19

The genetic architecture of birth size may differ geographically and over time. We examined differences in the genetic and environmental contributions to birthweight, length and ponderal index (PI) across geographical-cultural regions (Europe, North America and Australia, and East Asia) and across birth cohorts, and how gestational age modifies these effects. Data from 26 twin cohorts in 16 countries including 57 613 monozygotic and dizygotic twin pairs were pooled. Genetic and environmental variations of birth size were estimated using genetic structural equation modelling. The variance of birthweight and length was predominantly explained by shared environmental factors, whereas the variance of PI was explained both by shared and unique environmental factors. Genetic variance contributing to birth size was small. Adjusting for gestational age decreased the proportions of shared environmental variance and increased the propositions of unique environmental variance. Genetic variance was similar in the geographical-cultural regions, but shared environmental variance was smaller in East Asia than in Europe and North America and Australia. The total variance and shared environmental variance of birth length and PI were greater from the birth cohort 1990-99 onwards compared with the birth cohorts from 1970-79 to 1980-89. The contribution of genetic factors to birth size is smaller than that of shared environmental factors, which is partly explained by gestational age. Shared environmental variances of birth length and PI were greater in the latest birth cohorts and differed also across geographical-cultural regions. Shared environmental factors are important when explaining differences in the variation of birth size globally and over time.

Invasion genetics of the Bermuda buttercup (Oxalis pes-caprae): complex intercontinental patterns of genetic diversity, polyploidy and heterostyly characterize both native and introduced populations.

PubMed

Ferrero, Victoria; Barrett, Spencer C H; Castro, Sílvia; Caldeirinha, Patrícia; Navarro, Luis; Loureiro, João; Rodríguez-Echeverría, Susana

2015-05-01

Genetic diversity in populations of invasive species is influenced by a variety of factors including reproductive systems, ploidy level, stochastic forces associated with colonization and multiple introductions followed by admixture. Here, we compare genetic variation in native and introduced populations of the clonal plant Oxalis pes-caprae to investigate the influence of reproductive mode and ploidy on levels of diversity. This species is a tristylous geophyte native to South Africa. Invasive populations throughout much of the introduced range are composed of a sterile clonal pentaploid short-styled form. We examined morph ratios, ploidy level, reproductive mode and genetic diversity at nuclear microsatellite loci in 10 and 12 populations from South Africa and the Western Mediterranean region, respectively. Flow cytometry confirmed earlier reports of diploids and tetraploids in the native range, with a single population containing pentaploid individuals. Introduced populations were composed mainly of pentaploids, but sexual tetraploids were also found. There was clear genetic differentiation between ploidy levels, but sexual populations from both regions were not significantly different in levels of diversity. Invasive populations of the pentaploid exhibited dramatically reduced levels of diversity but were not genetically uniform. The occurrence of mixed ploidy levels and stylar polymorphism in the introduced range is consistent with multiple introductions to the Western Mediterranean. This inference was supported by variation patterns at microsatellite loci. Our study indicates that some invasive populations of Oxalis pes-caprae are not entirely clonal, as often assumed, and multiple introductions and recombination have the potential to increase genetic variation in the introduced range. © 2014 John Wiley & Sons Ltd.

The emergence of human-evolutionary medical genomics

PubMed Central

Crespi, Bernard J

2011-01-01

In this review, I describe how evolutionary genomics is uniquely suited to spearhead advances in understanding human disease risk, owing to the privileged position of genes as fundamental causes of phenotypic variation, and the ability of population genetic and phylogenetic methods to robustly infer processes of natural selection, drift, and mutation from genetic variation at the levels of family, population, species, and clade. I first provide an overview of models for the origins and maintenance of genetically based disease risk in humans. I then discuss how analyses of genetic disease risk can be dovetailed with studies of positive and balancing selection, to evaluate the degree to which the ‘genes that make us human’ also represent the genes that mediate risk of polygenic disease. Finally, I present four basic principles for the nascent field of human evolutionary medical genomics, each of which represents a process that is nonintuitive from a proximate perspective. Joint consideration of these principles compels novel forms of interdisciplinary analyses, most notably studies that (i) analyze tradeoffs at the level of molecular genetics, and (ii) identify genetic variants that are derived in the human lineage or in specific populations, and then compare individuals with derived versus ancestral alleles. PMID:25567974

Spatial and temporal genetic variation of Echinostoma revolutum (Trematoda: Echinostomatidae) from Thailand and the Lao PDR.

PubMed

Saijuntha, Weerachai; Tantrawatpan, Chairat; Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N

2011-05-01

A total of 314 individual Echinostoma revolutum were collected at different locations and times from domestic ducks from Khon Kaen Province, Thailand and Vientiane Province, the Lao People's Democratic Republic (PDR). Genetic variation of these parasites was analyzed using multilocus enzyme electrophoresis at three polymorphic loci namely, glucose-6-phosphate dehydrogenase (G6pd), malic enzyme (Me) and peptidase valine-leucine (PepA). High levels of genetic variability were found within and between populations. Significant heterozygote deficiencies compared with the predictions under Hardy-Weinberg equilibrium were detected in populations from Thailand and the Lao PDR for all loci except G6pd-1. Significant genetic differentiation was observed between spatially separated populations from Thailand and the Lao PDR. This as also true for some samples collected at different times in Thailand. The variability found may be consistent with a Wahlund effect, genetic drift and/or other factors such as the population structure of snail hosts. Our data provide further insight into the process of genetic divergence within and among geographically and temporally isolated populations of E. revolutum, and potentially other medically important echinostomes in Southeast Asia. Copyright © 2011 Elsevier B.V. All rights reserved.

Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus).

PubMed

Chuluunbat, B; Charruau, P; Silbermayr, K; Khorloojav, T; Burger, P A

2014-08-01

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro-ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization. © 2014 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Temperature-dependent behaviours are genetically variable in the nematode Caenorhabditis briggsae.

PubMed

Stegeman, Gregory W; de Mesquita, Matthew Bueno; Ryu, William S; Cutter, Asher D

2013-03-01

Temperature-dependent behaviours in Caenorhabditis elegans, such as thermotaxis and isothermal tracking, are complex behavioural responses that integrate sensation, foraging and learning, and have driven investigations to discover many essential genetic and neural pathways. The ease of manipulation of the Caenorhabditis model system also has encouraged its application to comparative analyses of phenotypic evolution, particularly contrasts of the classic model C. elegans with C. briggsae. And yet few studies have investigated natural genetic variation in behaviour in any nematode. Here we measure thermotaxis and isothermal tracking behaviour in genetically distinct strains of C. briggsae, further motivated by the latitudinal differentiation in C. briggsae that is associated with temperature-dependent fitness differences in this species. We demonstrate that C. briggsae performs thermotaxis and isothermal tracking largely similar to that of C. elegans, with a tendency to prefer its rearing temperature. Comparisons of these behaviours among strains reveal substantial heritable natural variation within each species that corresponds to three general patterns of behavioural response. However, intraspecific genetic differences in thermal behaviour often exceed interspecific differences. These patterns of temperature-dependent behaviour motivate further development of C. briggsae as a model system for dissecting the genetic underpinnings of complex behavioural traits.

Dissecting genetic architecture of startle response in Drosophila melanogaster using multi-omics information.

PubMed

Xue, Angli; Wang, Hongcheng; Zhu, Jun

2017-09-28

Startle behavior is important for survival, and abnormal startle responses are related to several neurological diseases. Drosophila melanogaster provides a powerful system to investigate the genetic underpinnings of variation in startle behavior. Since mechanically induced, startle responses and environmental conditions can be readily quantified and precisely controlled. The 156 wild-derived fully sequenced lines of the Drosophila Genetic Reference Panel (DGRP) were used to identify SNPs and transcripts associated with variation in startle behavior. The results validated highly significant effects of 33 quantitative trait SNPs (QTSs) and 81 quantitative trait transcripts (QTTs) directly associated with phenotypic variation of startle response. We also detected QTT variation controlled by 20 QTSs (tQTSs) and 73 transcripts (tQTTs). Association mapping based on genomic and transcriptomic data enabled us to construct a complex genetic network that underlies variation in startle behavior. Based on principles of evolutionary conservation, human orthologous genes could be superimposed on this network. This study provided both genetic and biological insights into the variation of startle response behavior of Drosophila melanogaster, and highlighted the importance of genetic network to understand the genetic architecture of complex traits.

Aggregation of population‐based genetic variation over protein domain homologues and its potential use in genetic diagnostics

PubMed Central

Wiel, Laurens; Venselaar, Hanka; Veltman, Joris A.; Vriend, Gert

2017-01-01

Abstract 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. PMID:28815929

Genetic variation affecting host-parasite interactions: major-effect quantitative trait loci affect the transmission of sigma virus in Drosophila melanogaster.

PubMed

Bangham, Jenny; Knott, Sara A; Kim, Kang-Wook; Young, Robert S; Jiggins, Francis M

2008-09-01

In natural populations, genetic variation affects resistance to disease. Whether that genetic variation comprises lots of small-effect polymorphisms or a small number of large-effect polymorphisms has implications for adaptation, selection and how genetic variation is maintained in populations. Furthermore, how much genetic variation there is, and the genes that underlie this variation, affects models of co-evolution between parasites and their hosts. We are studying the genetic variation that affects the resistance of Drosophila melanogaster to its natural pathogen--the vertically transmitted sigma virus. We have carried out three separate quantitative trait locus mapping analyses to map gene variants on the second chromosome that cause variation in the rate at which males transmit the infection to their offspring. All three crosses identified a locus in a similar chromosomal location that causes a large drop in the rate at which the virus is transmitted. We also found evidence for an additional smaller-effect quantitative trait locus elsewhere on the chromosome. Our data, together with previous experiments on the sigma virus and parasitoid wasps, indicate that the resistance of D. melanogaster to co-evolved pathogens is controlled by a limited number of major-effect polymorphisms.

QTL variations for growth-related traits in eight distinct families of common carp (Cyprinus carpio).

PubMed

Lv, Weihua; Zheng, Xianhu; Kuang, Youyi; Cao, Dingchen; Yan, Yunqin; Sun, Xiaowen

2016-05-05

Comparing QTL analyses of multiple pair-mating families can provide a better understanding of important allelic variations and distributions. However, most QTL mapping studies in common carp have been based on analyses of individual families. In order to improve our understanding of heredity and variation of QTLs in different families and identify important QTLs, we performed QTL analysis of growth-related traits in multiple segregating families. We completed a genome scan for QTLs that affect body weight (BW), total length (TL), and body thickness (BT) of 522 individuals from eight full-sib families using 250 microsatellites evenly distributed across 50 chromosomes. Sib-pair and half-sib model mapping identified 165 QTLs on 30 linkage groups. Among them, 10 (genome-wide P <0.01 or P < 0.05) and 28 (chromosome-wide P < 0.01) QTLs exhibited significant evidence of linkage, while the remaining 127 exhibited a suggestive effect on the above three traits at a chromosome-wide (P < 0.05) level. Multiple QTLs obtained from different families affect BW, TL, and BT and locate at close or identical positions. It suggests that same genetic factors may control variability in these traits. Furthermore, the results of the comparative QTL analysis of multiple families showed that one QTL was common in four of the eight families, nine QTLs were detected in three of the eight families, and 26 QTLs were found common to two of the eight families. These common QTLs are valuable candidates in marker-assisted selection. A large number of QTLs were detected in the common carp genome and associated with growth-related traits. Some of the QTLs of different growth-related traits were identified at similar chromosomal regions, suggesting a role for pleiotropy and/or tight linkage and demonstrating a common genetic basis of growth trait variations. The results have set up an example for comparing QTLs in common carp and provided insights into variations in the identified QTLs affecting body growth. Discovery of these common QTLs between families and growth-related traits represents an important step towards understanding of quantitative genetic variation in common carp.

Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds.

PubMed

Webster, Matthew T; Kamgari, Nona; Perloski, Michele; Hoeppner, Marc P; Axelsson, Erik; Hedhammar, Åke; Pielberg, Gerli; Lindblad-Toh, Kerstin

2015-06-23

The domestic dog is a rich resource for mapping the genetic components of phenotypic variation due to its unique population history involving strong artificial selection. Genome-wide association studies have revealed a number of chromosomal regions where genetic variation associates with morphological characters that typify dog breeds. A region on chromosome 10 is among those with the highest levels of genetic differentiation between dog breeds and is associated with body mass and ear morphology, a common motif of animal domestication. We characterised variation in this region to uncover haplotype structure and identify candidate functional variants. We first identified SNPs that strongly associate with body mass and ear type by comparing sequence variation in a 3 Mb region between 19 breeds with a variety of phenotypes. We next genotyped a subset of 123 candidate SNPs in 288 samples from 46 breeds to identify the variants most highly associated with phenotype and infer haplotype structure. A cluster of SNPs that associate strongly with the drop ear phenotype is located within a narrow interval downstream of the gene MSRB3, which is involved in human hearing. These SNPs are in strong genetic linkage with another set of variants that correlate with body mass within the gene HMGA2, which affects human height. In addition we find evidence that this region has been under selection during dog domestication, and identify a cluster of SNPs within MSRB3 that are highly differentiated between dogs and wolves. We characterise genetically linked variants that potentially influence ear type and body mass in dog breeds, both key traits that have been modified by selective breeding that may also be important for domestication. The finding that variants on long haplotypes have effects on more than one trait suggests that genetic linkage can be an important determinant of the phenotypic response to selection in domestic animals.

Significant genetic and phenotypic changes arising from clonal growth of a single spore of an arbuscular mycorrhizal fungus over multiple generations.

PubMed

Ehinger, Martine O; Croll, Daniel; Koch, Alexander M; Sanders, Ian R

2012-11-01

Arbuscular mycorrhizal fungi (AMF) are highly successful plant symbionts. They reproduce clonally producing multinucleate spores. It has been suggested that some AMF harbor genetically different nuclei. However, recent advances in sequencing the Glomus irregulare genome have indicated very low within-fungus polymorphism. We tested the null hypothesis that, with no genetic differences among nuclei, no significant genetic or phenotypic variation would occur among clonal single spore lines generated from one initial AMF spore. Furthermore, no additional variation would be expected in the following generations of single spore lines. Genetic diversity contained in one initial spore repeatedly gave rise to genetically different variants of the fungus with novel phenotypes. The genetic changes represented quantitative changes in allele frequencies, most probably as a result of changes in the frequency of genetic variation partitioned on different nuclei. The genetic and phenotypic variation is remarkable, given that it arose repeatedly from one clonal individual. Our results highlight the dynamic nature of AMF genetics. Even though within-fungus genetic variation is low, some is probably partitioned among nuclei and potentially causes changes in the phenotype. Our results are important for understanding AMF genetics, as well as for researchers and biotechnologists hoping to use AMF genetic diversity for the improvement of AMF inoculum. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

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.

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.

The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes

PubMed Central

2013-01-01

Background Taxa that harbor natural phenotypic variation are ideal for ecological genomic approaches aimed at understanding how the interplay between genetic and environmental factors can lead to the evolution of complex traits. Lasioglossum albipes is a polymorphic halictid bee that expresses variation in social behavior among populations, and common-garden experiments have suggested that this variation is likely to have a genetic component. Results We present the L. albipes genome assembly to characterize the genetic and ecological factors associated with the evolution of social behavior. The de novo assembly is comparable to other published social insect genomes, with an N50 scaffold length of 602 kb. Gene families unique to L. albipes are associated with integrin-mediated signaling and DNA-binding domains, and several appear to be expanded in this species, including the glutathione-s-transferases and the inositol monophosphatases. L. albipes has an intact DNA methylation system, and in silico analyses suggest that methylation occurs primarily in exons. Comparisons to other insect genomes indicate that genes associated with metabolism and nucleotide binding undergo accelerated evolution in the halictid lineage. Whole-genome resequencing data from one solitary and one social L. albipes female identify six genes that appear to be rapidly diverging between social forms, including a putative odorant receptor and a cuticular protein. Conclusions L. albipes represents a novel genetic model system for understanding the evolution of social behavior. It represents the first published genome sequence of a primitively social insect, thereby facilitating comparative genomic studies across the Hymenoptera as a whole. PMID:24359881

[Cytogenetic, molecular cytogenetic, clinical and genealogical study of mothers of children with autism: a search for family genetic markers of autistic disorders].

PubMed

Vorsanova, S G; Voinova, V Iu; Iurov, I Iu; Kurinnaia, O S; Demidova, I A; Iurov, Iu B

2009-01-01

Using modern cytogenetic and molecular cytogenetic techniques towards the study of human chromosomes, an analysis of chromosomal abnormalities/chromosomal variations as well as clinical and genealogical data in mothers of children with autism has been performed. It has been shown that mothers of autistic children exhibit an increased incidence of chromosomal abnormalities (mainly mosaic forms involving chromosome X) and an increased occurrence of chromosomal variations compared to controls. The analysis of genotype-phenotype correlations revealed the increase in the frequency of cognitive disturbances and spontaneous abortions in mothers of children with autism as well as the higher frequency of mental retardation, early death and reproductive problems in the pedigrees. The high frequency of congenital malformations in the pedigrees of mothers with chromosomal variations was observed as well. Taking into account the data obtained, we have concluded that cytogenetic and molecular cytogenetic studies of mothers of children with autism are obligatory for detection of possible genetic causes of autism and genetic counseling of families with children affected with autistic disorders.

Genetic variation in a DNA double strand break repair gene in saudi population: a comparative study with worldwide ethnic groups.

PubMed

Areeshi, Mohammed Yahya

2013-01-01

DNA repair capacity is crucial in maintaining cellular functions and homeostasis. However, it can be altered based on DNA sequence variations in DNA repair genes and this may lead to the development of many diseases including malignancies. Identification of genetic polymorphisms responsible for reduced DNA repair capacity is necessary for better prevention. Homologous recombination (HR), a major double strand break repair pathway, plays a critical role in maintaining the genome stability. The present study was performed to determine the frequency of the HR gene XRCC3 Exon 7 (C18067T, rs861539) polymorphisms in Saudi Arabian population in comparison with epidemiological studies by "MEDLINE" search to equate with global populations. The variant allelic (T) frequency of XRCC3 (C>T) was found to be 39%. Our results suggest that frequency of XRCC3 (C>T) DNA repair gene exhibits distinctive patterns compared with the Saudi Arabian population and this might be attributed to ethnic variation. The present findings may help in high-risk screening of humans exposed to environmental carcinogens and cancer predisposition in different ethnic groups.

Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep.

PubMed

Creech, Tyler G; Epps, Clinton W; Landguth, Erin L; Wehausen, John D; Crowhurst, Rachel S; Holton, Brandon; Monello, Ryan J

2017-01-01

Landscape genetic studies based on neutral genetic markers have contributed to our understanding of the influence of landscape composition and configuration on gene flow and genetic variation. However, the potential for species to adapt to changing landscapes will depend on how natural selection influences adaptive genetic variation. We demonstrate how landscape resistance models can be combined with genetic simulations incorporating natural selection to explore how the spread of adaptive variation is affected by landscape characteristics, using desert bighorn sheep (Ovis canadensis nelsoni) in three differing regions of the southwestern United States as an example. We conducted genetic sampling and least-cost path modeling to optimize landscape resistance models independently for each region, and then simulated the spread of an adaptive allele favored by selection across each region. Optimized landscape resistance models differed between regions with respect to landscape variables included and their relationships to resistance, but the slope of terrain and the presence of water barriers and major roads had the greatest impacts on gene flow. Genetic simulations showed that differences among landscapes strongly influenced spread of adaptive genetic variation, with faster spread (1) in landscapes with more continuously distributed habitat and (2) when a pre-existing allele (i.e., standing genetic variation) rather than a novel allele (i.e., mutation) served as the source of adaptive genetic variation. The combination of landscape resistance models and genetic simulations has broad conservation applications and can facilitate comparisons of adaptive potential within and between landscapes.

Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep

PubMed Central

Epps, Clinton W.; Landguth, Erin L.; Wehausen, John D.; Crowhurst, Rachel S.; Holton, Brandon; Monello, Ryan J.

2017-01-01

Landscape genetic studies based on neutral genetic markers have contributed to our understanding of the influence of landscape composition and configuration on gene flow and genetic variation. However, the potential for species to adapt to changing landscapes will depend on how natural selection influences adaptive genetic variation. We demonstrate how landscape resistance models can be combined with genetic simulations incorporating natural selection to explore how the spread of adaptive variation is affected by landscape characteristics, using desert bighorn sheep (Ovis canadensis nelsoni) in three differing regions of the southwestern United States as an example. We conducted genetic sampling and least-cost path modeling to optimize landscape resistance models independently for each region, and then simulated the spread of an adaptive allele favored by selection across each region. Optimized landscape resistance models differed between regions with respect to landscape variables included and their relationships to resistance, but the slope of terrain and the presence of water barriers and major roads had the greatest impacts on gene flow. Genetic simulations showed that differences among landscapes strongly influenced spread of adaptive genetic variation, with faster spread (1) in landscapes with more continuously distributed habitat and (2) when a pre-existing allele (i.e., standing genetic variation) rather than a novel allele (i.e., mutation) served as the source of adaptive genetic variation. The combination of landscape resistance models and genetic simulations has broad conservation applications and can facilitate comparisons of adaptive potential within and between landscapes. PMID:28464013

Genetic parameters for uniformity of harvest weight and body size traits in the GIFT strain of Nile tilapia.

PubMed

Marjanovic, Jovana; Mulder, Han A; Khaw, Hooi L; Bijma, Piter

2016-06-10

Animal breeding programs have been very successful in improving the mean levels of traits through selection. However, in recent decades, reducing the variability of trait levels between individuals has become a highly desirable objective. Reaching this objective through genetic selection requires that there is genetic variation in the variability of trait levels, a phenomenon known as genetic heterogeneity of environmental (residual) variance. The aim of our study was to investigate the potential for genetic improvement of uniformity of harvest weight and body size traits (length, depth, and width) in the genetically improved farmed tilapia (GIFT) strain. In order to quantify the genetic variation in uniformity of traits and estimate the genetic correlations between level and variance of the traits, double hierarchical generalized linear models were applied to individual trait values. Our results showed substantial genetic variation in uniformity of all analyzed traits, with genetic coefficients of variation for residual variance ranging from 39 to 58 %. Genetic correlation between trait level and variance was strongly positive for harvest weight (0.60 ± 0.09), moderate and positive for body depth (0.37 ± 0.13), but not significantly different from 0 for body length and width. Our results on the genetic variation in uniformity of harvest weight and body size traits show good prospects for the genetic improvement of uniformity in the GIFT strain. A high and positive genetic correlation was estimated between level and variance of harvest weight, which suggests that selection for heavier fish will also result in more variation in harvest weight. Simultaneous improvement of harvest weight and its uniformity will thus require index selection.

Phylogeny of Fomitopsis pinicola: A species complex

Treesearch

John Haight; Gary A. Laursen; Jessie A. Glaeser; D. Lee Taylor

2016-01-01

Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an...

Genetic variation of Taenia pisiformis collected from Sichuan, China, based on the mitochondrial cytochrome B gene.

PubMed

Yang, Deying; Ren, Yongjun; Fu, Yan; Xie, Yue; Nie, Huaming; Nong, Xiang; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

2013-08-01

Taenia pisiformis is one of the most important parasites of canines and rabbits. T. pisiformis cysticercus (the larval stage) causes severe damage to rabbit breeding, which results in huge economic losses. In this study, the genetic variation of T. pisiformis was determined in Sichuan Province, China. Fragments of the mitochondrial cytochrome b (cytb) (922 bp) gene were amplified in 53 isolates from 8 regions of T. pisiformis. Overall, 12 haplotypes were found in these 53 cytb sequences. Molecular genetic variations showed 98.4% genetic variation derived from intra-region. FST and Nm values suggested that 53 isolates were not genetically differentiated and had low levels of genetic diversity. Neutrality indices of the cytb sequences showed the evolution of T. pisiformis followed a neutral mode. Phylogenetic analysis revealed no correlation between phylogeny and geographic distribution. These findings indicate that 53 isolates of T. pisiformis keep a low genetic variation, which provide useful knowledge for monitoring changes in parasite populations for future control strategies.

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.

Investigation of Genetic Variation Underlying Central Obesity amongst South Asians

PubMed Central

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. PMID:27195708

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Population genomics reveals a candidate gene involved in bumble bee pigmentation.

PubMed

Pimsler, Meaghan L; Jackson, Jason M; Lozier, Jeffrey D

2017-05-01

Variation in bumble bee color patterns is well-documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red-banded to black-banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome-wide differentiation between red- and black-banded forms. Here, we instead focus on the closely related black-banded and intermediate forms that both belong to the subspecies B. bifarius nearcticus . We analyze an RNA sequencing (RNAseq) data set and identify a cluster of single nucleotide polymorphisms (SNPs) within one gene, Xanthine dehydrogenase/oxidase -like, that exhibit highly unusual differentiation compared to the rest of the sequenced genome. Homologs of this gene contribute to pigmentation in other insects, and results thus represent a strong candidate for investigating the genetic basis of pigment variation in B. bifarius and other bumble bee mimicry complexes.

The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

PubMed Central

Kronforst, Marcus R.; Papa, Riccardo

2015-01-01

Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

Metabolic dysregulation in first-episode schizophrenia patients with respect to genetic variation in one-carbon metabolism.

PubMed

Misiak, Błażej; Łaczmański, Łukasz; Słoka, Natalia Kinga; Szmida, Elżbieta; Piotrowski, Patryk; Loska, Olga; Ślęzak, Ryszard; Kiejna, Andrzej; Frydecka, Dorota

2016-04-30

The aim of this study was to investigate the prevalence of metabolic disturbances in patients with first-episode schizophrenia (FES) and test the hypothesis that genetic variation in one-carbon metabolism may account for metabolic dysregulation in early psychosis. We measured fasting glucose, lipid profile parameters, homocysteine, folate and vitamin B12 in 135 patients with FES and 146 healthy controls (HCs). Polymorphisms in the following genes were determined: MTHFR (C677T and A1298C), MTHFD1 (G1958A), MTRR (A66G) and BHMT (G742A). Serum levels of folate and high-density lipoproteins (HDL) were significantly lower in patients with FES compared to HCs. In turn, serum levels of homocysteine and triglycerides were significantly higher in patients with FES than in HCs. Prevalence of hyperhomocysteinemia, low folate and HDL levels together with dyslipidemia was significantly higher in patients with FES compared to HCs. Higher homocysteine levels, lower vitamin B12 levels and the presence of metabolic syndrome were associated with higher severity of negative symptoms. None of studied polymorphisms was associated with schizophrenia risk. Several associations between studied polymorphisms and cardio-metabolic parameters were found. None of them remained significant after Bonferroni correction. Our results indicate that metabolic dysregulation in patients with FES is not associated with genetic variation in one-carbon metabolism. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Estimating the actual subject-specific genetic correlations in behavior genetics.

PubMed

Molenaar, Peter C M

2012-10-01

Generalization of the standard behavior longitudinal genetic factor model for the analysis of interindividual phenotypic variation to a genetic state space model for the analysis of intraindividual variation enables the possibility to estimate subject-specific heritabilities.

Heritability, covariation and natural selection on 24 traits of common evening primrose (Oenothera biennis) from a field experiment.

PubMed

Johnson, M T J; Agrawal, A A; Maron, J L; Salminen, J-P

2009-06-01

This study explored genetic variation and co-variation in multiple functional plant traits. Our goal was to characterize selection, heritabilities and genetic correlations among different types of traits to gain insight into the evolutionary ecology of plant populations and their interactions with insect herbivores. In a field experiment, we detected significant heritable variation for each of 24 traits of Oenothera biennis and extensive genetic covariance among traits. Traits with diverse functions formed several distinct groups that exhibited positive genetic covariation with each other. Genetic variation in life-history traits and secondary chemistry together explained a large proportion of variation in herbivory (r(2) = 0.73). At the same time, selection acted on lifetime biomass, life-history traits and two secondary compounds of O. biennis, explaining over 95% of the variation in relative fitness among genotypes. The combination of genetic covariances and directional selection acting on multiple traits suggests that adaptive evolution of particular traits is constrained, and that correlated evolution of groups of traits will occur, which is expected to drive the evolution of increased herbivore susceptibility. As a whole, our study indicates that an examination of genetic variation and covariation among many different types of traits can provide greater insight into the evolutionary ecology of plant populations and plant-herbivore interactions.

GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.

PubMed

Lao, Oscar; Liu, Fan; Wollstein, Andreas; Kayser, Manfred

2014-02-01

Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations. Here we introduce a new algorithm for transforming a genetic distance matrix that reduces the within-population variation considerably. Extensive computer simulations revealed that the transformed matrix captured the genetic population differentiation better than the original one which was based on the T1 statistic. In an empirical genomic data set comprising 2,457 individuals from 23 different European subpopulations, the proportion of individuals that were determined as a genetic neighbour to another individual from the same sampling location increased from 25% with the original matrix to 52% with the transformed matrix. Similarly, the percentage of genetic variation explained between populations by means of Analysis of Molecular Variance (AMOVA) increased from 1.62% to 7.98%. Furthermore, the first two dimensions of a classical multidimensional scaling (MDS) using the transformed matrix explained 15% of the variance, compared to 0.7% obtained with the original matrix. Application of MDS with Mclust, SPA with Mclust, and GemTools algorithms to the same dataset also showed that the transformed matrix gave a better association of the genetic clusters with the sampling locations, and particularly so when it was used in the AMOVA framework with a genetic algorithm. Overall, the new matrix transformation introduced here substantially reduces the within population genetic differentiation, and can be broadly applied to methods such as AMOVA to enhance their sensitivity to reveal population substructure. We herewith provide a publically available (http://www.erasmusmc.nl/fmb/resources/GAGA) model-free method for improved genetic population substructure detection that can be applied to human as well as any other species data in future studies relevant to evolutionary biology, behavioural ecology, medicine, and forensics.

The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size.

PubMed

Elhassan, Nuha; Gebremeskel, Eyoab Iyasu; Elnour, Mohamed Ali; Isabirye, Dan; Okello, John; Hussien, Ayman; Kwiatksowski, Dominic; Hirbo, Jibril; Tishkoff, Sara; Ibrahim, Muntaser E

2014-01-01

Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.

Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association.

PubMed

Kingston, S E; Martino, P; Melendy, M; Reed, F A; Carlon, D B

2018-03-01

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here, we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a 'climate change' common garden, where we raised temperature by 3°C, decreased pH by 0.2 units and limited food supply by filtering out planktonic particles >5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170 000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of >90% when effective sample size is 900. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

The structure of cross-cultural musical diversity.

PubMed

Rzeszutek, Tom; Savage, Patrick E; Brown, Steven

2012-04-22

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.

Increased apomixis expression concurrent with genetic and epigenetic variation in a newly synthesized Eragrostis curvula polyploid

NASA Astrophysics Data System (ADS)

Zappacosta, Diego C.; Ochogavía, Ana C.; Rodrigo, Juan M.; Romero, José R.; Meier, Mauro S.; Garbus, Ingrid; Pessino, Silvina C.; Echenique, Viviana C.

2014-04-01

Eragrostis curvula includes biotypes reproducing through obligate and facultative apomixis or, rarely, full sexuality. We previously generated a ``tetraploid-dihaploid-tetraploid'' series of plants consisting of a tetraploid apomictic plant (T), a sexual dihaploid plant (D) and a tetraploid artificial colchiploid (C). Initially, plant C was nearly 100% sexual. However, its capacity to form non-reduced embryo sacs dramatically increased over a four year period (2003-2007) to reach levels of 85-90%. Here, we confirmed high rates of apomixis in plant C, and used AFLPs and MSAPs to characterize the genetic and epigenetic variation observed in this plant in 2007 as compared to 2003. Of the polymorphic sequences, some had no coding potential whereas others were homologous to retrotransposons and/or protein-coding-like sequences. Our results suggest that in this particular plant system increased apomixis expression is concurrent with genetic and epigenetic modifications, possibly involving transposable elements.

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.

PubMed

Gilman, Sarah R; Chang, Jonathan; Xu, Bin; Bawa, Tejdeep S; Gogos, Joseph A; Karayiorgou, Maria; Vitkup, Dennis

2012-12-01

Despite the successful identification of several relevant genomic loci, the underlying molecular mechanisms of schizophrenia remain largely unclear. We developed a computational approach (NETBAG+) that allows an integrated analysis of diverse disease-related genetic data using a unified statistical framework. The application of this approach to schizophrenia-associated genetic variations, obtained using unbiased whole-genome methods, allowed us to identify several cohesive gene networks related to axon guidance, neuronal cell mobility, synaptic function and chromosomal remodeling. The genes forming the networks are highly expressed in the brain, with higher brain expression during prenatal development. The identified networks are functionally related to genes previously implicated in schizophrenia, autism and intellectual disability. A comparative analysis of copy number variants associated with autism and schizophrenia suggests that although the molecular networks implicated in these distinct disorders may be related, the mutations associated with each disease are likely to lead, at least on average, to different functional consequences.

The structure of cross-cultural musical diversity

PubMed Central

Rzeszutek, Tom; Savage, Patrick E.; Brown, Steven

2012-01-01

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations. PMID:22072606

High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal

PubMed Central

Aguilar, Andres; Roemer, Gary; Debenham, Sally; Binns, Matthew; Garcelon, David; Wayne, Robert K.

2004-01-01

The San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers. Such low levels of variation imply lower resistance to pathogens, reduced fitness, and problems in distinguishing kin from non-kin. In vertebrates, the MHC contains genes that influence disease resistance and kin recognition and may be under intense balancing selection in some populations. Hence, genetic variation at the MHC might persist despite the extreme monomorphism shown by neutral markers. We examine variation of five loci within the MHC of San Nicolas Island foxes and find remarkably high levels of variation. Further, we show by simulation that genetic monomorphism at neutral loci and high MHC variation could arise only through an extreme population bottleneck of <10 individuals, ≈10–20 generations ago, accompanied by unprecedented selection coefficients of >0.5 on MHC loci. These results support the importance of balancing selection as a mechanism to maintain variation in natural populations and expose the difficulty of using neutral markers as surrogates for variation in fitness-related loci. PMID:14990802

Facing the facts: The Runx2 gene is associated with variation in facial morphology in primates.

PubMed

Ritzman, Terrence B; Banovich, Nicholas; Buss, Kaitlin P; Guida, Jennifer; Rubel, Meagan A; Pinney, Jennifer; Khang, Bao; Ravosa, Matthew J; Stone, Anne C

2017-10-01

The phylogenetic and adaptive factors that cause variation in primate facial form-including differences among the major primate clades and variation related to feeding and/or social behavior-are relatively well understood. However, comparatively little is known about the genetic mechanisms that underlie diversity in facial form in primates. Because it is essential for osteoblastic differentiation and skeletal development, the runt-related transcription factor 2 (Runx2) is one gene that may play a role in these genetic mechanisms. Specifically, polymorphisms in the QA ratio (determined by the ratio of the number of polyglutamines to polyalanines in one functional domain of Runx2) have been shown to be correlated with variation in facial length and orientation in other mammal groups. However, to date, the relationship between variation in this gene and variation in facial form in primates has not been explicitly tested. To test the hypothesis that the QA ratio is correlated with facial form in primates, the current study quantified the QA ratio, facial length, and facial angle in a sample of 33 primate species and tested for correlation using phylogenetic generalized least squares. The results indicate that the QA ratio of the Runx2 gene is positively correlated with variation in relative facial length in anthropoid primates. However, no correlation was found in strepsirrhines, and there was no correlation between facial angle and the QA ratio in any groups. These results suggest that, in primates, the QA ratio of the Runx2 gene may play a role in modulating facial size, but not facial orientation. This study therefore provides important clues about the genetic and developmental mechanisms that may underlie variation in facial form in primates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic differentiation among populations of marine algae

NASA Astrophysics Data System (ADS)

Innes, D. J.

1984-09-01

Most of the information for genetic differentiation among populations of marine algae is from studies on ecotypic variation. Physiological ecotypes have been described for individuals showing different responses to temperature and salinity conditions. Morphological ecotypes have also been found associated with areas differing in wave exposure or different intertidal positions. Little is known on how genetic variation is organized within and between populations of marine algae. The occurrence of ecotypic variation in some species is evidence for genetic differentiation among populations resulting from selection by the local environment. The rate of dispersal and subsequent gene flow will also affect the level of differentiation among populations. In species with low dispersal, differentiation can arise through chance founder events or random genetic drift. The few studies available have shown that species of algae exhibit a range of dispersal capabilities. This information can be useful for predicting the potential level of genetic differentiation among populations of these species. Crossing experiments with several species of algae have shown that populations separated by a considerable distance can be interfertile. In some cases individuals from these populations have been found to be morphologically distinct. Crosses have been used to study the genetic basis of this variation and are evidence for genetic differentiation among the populations sampled. Genetic variation of enzyme proteins detected by electrophoresis provides an additional method for measuring genetic variation within and between populations of marine algae. Electrophoretic methods have previously been used to study systematic problems in algae. However, there have been few attempts to use electrophoretic variation to study the genetic structure of populations of marine algae. This approach is outlined and includes some of the potential problems associated with interpreting electrophoretic data. Studies of electrophoretic variation in natural populations of Enteromorpha linza from Long island Sound are used as an example. This species was found to reproduce only asexually. Despite a dispersing spore stage, genetic differentiation was found on a microgeographic scale and was correlated with differences in the local environment of some of the populations. Similar studies on other species, and especially sexually reproducing species, will add to a growing understanding of the evolutionary genetics of marine algae.

[Genetic variation of geographical provenance of Pinus massoniana--review and analysis].

PubMed

Li, D; Peng, S

2000-04-01

Pinus massoniana is a significant tree species constituting the subtropical forests in China. Based on morphological, physio-ecological, chromosome, and molecular levels, the genetic variation of geographical provenance of P. massoniana and its distribution were reviewed, and the methodologies on genetic diversity and the genetic variation patterns of geographical provenance of P. massoniana were synthetically analyzed. The Key problems on molecular ecology of P. massoniana were discussed.

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

PubMed Central

Yan, Yu-Bin; Duke, Norm C.; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees. PMID:27746790

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

PubMed

Yan, Yu-Bin; Duke, Norm C; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees.

Causal Genetic Variation Underlying Metabolome Differences.

PubMed

Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye; Sudarsanam, Priya; Nayler, Darcy; Staller, Max V; Cohen, Barak A

2017-08-01

An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81 , cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype. Copyright © 2017 by the Genetics Society of America.

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. © 2012 Blackwell Publishing Ltd.

Genetic basis of aboveground productivity in two native Populus species and their hybrids.

PubMed

Lojewski, Nathan R; Fischer, Dylan G; Bailey, Joseph K; Schweitzer, Jennifer A; Whitham, Thomas G; Hart, Stephen C

2009-09-01

Demonstration of genetic control over riparian tree productivity has major implications for responses of riparian systems to shifting environmental conditions and effects of genetics on ecosystems in general. We used field studies and common gardens, applying both molecular and quantitative techniques, to compare plot-level tree aboveground net primary productivity (ANPP(tree)) and individual tree growth rate constants in relation to plant genetic identity in two naturally occurring Populus tree species and their hybrids. In field comparisons of four cross types (Populus fremontii S. Wats., Populus angustifolia James, F(1) hybrids and backcross hybrids) across 11 natural stands, productivity was greatest for P. fremontii trees, followed by hybrids and lowest in P. angustifolia. A similar pattern was observed in four common gardens across a 290 m elevation and 100 km environmental gradient. Despite a doubling in productivity across the common gardens, the relative differences among the cross types remained constant. Using clonal replicates in a common garden, we found ANPP(tree) to be a heritable plant trait (i.e., broad-sense heritability), such that plant genetic factors explained between 38% and 82% of the variation in ANPP(tree). Furthermore, analysis of the genetic composition among individual tree genotypes using restriction fragment length polymorphism molecular markers showed that genetically similar trees also exhibited similar ANPP(tree). These findings indicate strong genetic contributions to natural variation in ANPP with important ecological implications.

Landscape features impact connectivity between soil populations: a comparative study of gene flow in earthworms.

PubMed

Dupont, L; Torres-Leguizamon, M; René-Corail, P; Mathieu, J

2017-06-01

Landscape features are known to alter the spatial genetic variation of aboveground organisms. Here, we tested the hypothesis that the genetic structure of belowground organisms also responds to landscape structure. Microsatellite markers were used to carry out a landscape genetic study of two endogeic earthworm species, Allolobophora chlorotica (N = 440, eight microsatellites) and Aporrectodea icterica (N = 519, seven microsatellites), in an agricultural landscape in the North of France, where landscape features were characterized with high accuracy. We found that habitat fragmentation impacted genetic variation of earthworm populations at the local scale. A significant relationship was observed between genetic diversity (H e , A r ) and several landscape features in A. icterica populations and A. chlorotica. Moreover, a strong genetic differentiation between sites was observed in both species, with a low degree of genetic admixture and high F st values. The landscape connectivity analysis at the regional scale, including isolation by distance, least-cost path and cost-weighted distance approaches, showed that genetic distances were linked to landscape connectivity in A. chlorotica. This indicates that the fragmentation of natural habitats has shaped their dispersal patterns and local effective population sizes. Landscape connectivity analysis confirmed that a priori favourable habitats such as grasslands may constitute dispersal corridors for these species. © 2017 John Wiley & Sons Ltd.

The genetic diversity of Epstein-Barr virus in the setting of transplantation relative to non-transplant settings: A feasibility study.

PubMed

Allen, Upton D; Hu, Pingzhao; Pereira, Sergio L; Robinson, Joan L; Paton, Tara A; Beyene, Joseph; Khodai-Booran, Nasser; Dipchand, Anne; Hébert, Diane; Ng, Vicky; Nalpathamkalam, Thomas; Read, Stanley

2016-02-01

This study examines EBV strains from transplant patients and patients with IM by sequencing major EBV genes. We also used NGS to detect EBV DNA within total genomic DNA, and to evaluate its genetic variation. Sanger sequencing of major EBV genes was used to compare SNVs from samples taken from transplant patients vs. patients with IM. We sequenced EBV DNA from a healthy EBV-seropositive individual on a HiSeq 2000 instrument. Data were mapped to the EBV reference genomes (AG876 and B95-8). The number of EBNA2 SNVs was higher than for EBNA1 and the other genes sequenced within comparable reference coordinates. For EBNA2, there was a median of 15 SNV among transplant samples compared with 10 among IM samples (p = 0.036). EBNA1 showed little variation between samples. For NGS, we identified 640 and 892 variants at an unadjusted p value of 5 × 10(-8) for AG876 and B95-8 genomes, respectively. We used complementary sequence strategies to examine EBV genetic diversity and its application to transplantation. The results provide the framework for further characterization of EBV strains and related outcomes after organ transplantation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value.

PubMed

Pacheco-Villalobos, David; Hardtke, Christian S

2012-06-05

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.

Genetic variation, multiple paternity, and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata).

PubMed

González-Garza, Blanca Idalia; Stow, Adam; Sánchez-Teyer, Lorenzo Felipe; Zapata-Pérez, Omar

2015-12-01

The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within-rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

PubMed

Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Human Papillomavirus Type 6 and 11 Genetic Variants Found in 71 Oral and Anogenital Epithelial Samples from Australia

PubMed Central

Danielewski, Jennifer A.; Garland, Suzanne M.; McCloskey, Jenny; Hillman, Richard J.; Tabrizi, Sepehr N.

2013-01-01

Genetic variation of 49 human papillomavirus (HPV) 6 and 22 HPV11 isolates from recurrent respiratory papillomatosis (RRP) (n = 17), genital warts (n = 43), anal cancer (n = 6) and cervical neoplasia cells (n = 5), was determined by sequencing the long control region (LCR) and the E6 and E7 genes. Comparative analysis of genetic variability was examined to determine whether different disease states resulting from HPV6 or HPV11 infection cluster into distinct variant groups. Sequence variation analysis of HPV6 revealed that isolates cluster into variants within previously described HPV6 lineages, with the majority (65%) clustering to HPV6 sublineage B1 across the three genomic regions examined. Overall 72 HPV6 and 25 HPV11 single nucleotide variations, insertions and deletions were observed within samples examined. In addition, missense alterations were observed in the E6/E7 genes for 6 HPV6 and 5 HPV11 variants. No nucleotide variations were identified in any isolates at the four E2 binding sites for HPV6 or HPV11, nor were any isolates found to be identical to the HPV6 lineage A or HPV11 sublineage A1 reference genomes. Overall, a high degree of sequence conservation was observed between isolates across each of the regions investigated for both HPV6 and HPV11. Genetic variants identified a slight association with HPV6 and anogenital lesions (p = 0.04). This study provides important information on the genetic diversity of circulating HPV 6 and HPV11 variants within the Australian population and supports the observation that the majority of HPV6 isolates cluster to the HPV6 sublineage B1 with anogenital lesions demonstrating an association with this sublineage (p = 0.02). Comparative analysis of Australian isolates for both HPV6 and HPV11 to those from other geographical regions based on the LCR revealed a high degree of sequence similarity throughout the world, confirming previous observations that there are no geographically specific variants for these HPV types. PMID:23691108

Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses

PubMed Central

2014-01-01

Background Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia. Results Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea. Conclusions Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia. PMID:25034725

Genetic variation in transmission success of the Lyme borreliosis pathogen Borrelia afzelii.

PubMed

Tonetti, Nicolas; Voordouw, Maarten J; Durand, Jonas; Monnier, Séverine; Gern, Lise

2015-04-01

The vector-to-host and host-to-vector transmission steps are the two critical events that define the life cycle of any vector-borne pathogen. We expect negative genetic correlations between these two transmission phenotypes, if parasite genotypes specialized at invading the vector are less effective at infecting the vertebrate host and vice versa. We used the tick-borne bacterium Borrelia afzelii, a causative agent of Lyme borreliosis in Europe, to test whether genetic trade-offs exist between tick-to-host, systemic (host-to-tick), and a third mode of co-feeding (tick-to-tick) transmission. We worked with six strains of B. afzelii that were differentiated according to their ospC gene. We compared the three components of transmission among the B. afzelii strains using laboratory rodents as the vertebrate host and a laboratory colony of Ixodes ricinus as the tick vector. We used next generation matrix models to combine these transmission components into a single estimate of the reproductive number (R0) for each B. afzelii strain. We also tested whether these strain-specific estimates of R0 were correlated with the strain-specific frequencies in the field. We found significant genetic variation in the three transmission components among the B. afzelii strains. This is the first study to document genetic variation in co-feeding transmission for any tick-borne pathogen. We found no evidence of trade-offs as the three pairwise correlations of the transmission rates were all positive. The R0 values from our laboratory study explained 45% of the variation in the frequencies of the B. afzelii ospC strains in the field. Our study suggests that laboratory estimates of pathogen fitness can predict the distribution of pathogen strains in nature. Copyright © 2015 Elsevier GmbH. All rights reserved.

Natural Genetic Variation for Acclimation of Photosynthetic Light Use Efficiency to Growth Irradiance in Arabidopsis1[OPEN

PubMed Central

Harbinson, Jeremy

2015-01-01

Plants are known to be able to acclimate their photosynthesis to the level of irradiance. Here, we present the analysis of natural genetic variation for photosynthetic light use efficiency (ΦPSII) in response to five light environments among 12 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions. We measured the acclimation of ΦPSII to constant growth irradiances of four different levels (100, 200, 400, and 600 µmol m−2 s−1) by imaging chlorophyll fluorescence after 24 d of growth and compared these results with acclimation of ΦPSII to a step-wise change in irradiance where the growth irradiance was increased from 100 to 600 µmol m−2 s−1 after 24 d of growth. Genotypic variation for ΦPSII is shown by calculating heritability for the short-term ΦPSII response to different irradiance levels as well as for the relation of ΦPSII measured at light saturation (a measure of photosynthetic capacity) to growth irradiance level and for the kinetics of the response to a step-wise increase in irradiance from 100 to 600 µmol m−2 s−1. A genome-wide association study for ΦPSII measured 1 h after a step-wise increase in irradiance identified several new candidate genes controlling this trait. In conclusion, the different photosynthetic responses to a changing light environment displayed by different Arabidopsis accessions are due to genetic differences, and we have identified candidate genes for the photosynthetic response to an irradiance change. The genetic variation for photosynthetic acclimation to irradiance found in this study will allow future identification and analysis of the causal genes for the regulation of ΦPSII in plants. PMID:25670817

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née.

PubMed

Gugger, Paul F; Ikegami, Makihiko; Sork, Victoria L

2013-07-01

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28-1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11-18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion-contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions. © 2013 John Wiley & Sons Ltd.

Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.

PubMed

Abadía-Cardoso, Alicia; Freimer, Nelson B; Deiner, Kristy; Garza, John Carlos

2017-09-01

The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species. Published by Oxford University Press on behalf of The American Genetic Association 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

PubMed Central

Andersen, Erik C.; Gerke, Justin P.; Shapiro, Joshua A.; Crissman, Jonathan R.; Ghosh, Rajarshi; Bloom, Joshua S.; Félix, Marie-Anne; Kruglyak, Leonid

2011-01-01

The nematode Caenorhabditis elegans is central to research in molecular, cell, and developmental biology, but nearly all of this research has been conducted on a single strain. Comparatively little is known about the population genomic and evolutionary history of this species. We characterized C. elegans genetic variation by high-throughput selective sequencing of a worldwide collection of 200 wild strains, identifying 41,188 single nucleotide polymorphisms. Unexpectedly, C. elegans genome variation is dominated by a set of commonly shared haplotypes on four of the six chromosomes, each spanning many megabases. Population-genetic modeling shows that this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps likely occurred in the past few hundred years. These sweeps, which we hypothesize to be a result of human activity, have dramatically reshaped the global C. elegans population in the recent past. PMID:22286215

Blood type gene locus has no influence on ACE association with Alzheimer's disease.

PubMed

Braae, Anne; Medway, Christopher; Carrasquillo, Minerva; Younkin, Steven; Kehoe, Patrick G; Morgan, Kevin

2015-04-01

The ABO blood group locus was recently found to contribute independently and via interactions with angiotensin-converting enzyme (ACE) gene variation to plasma levels of ACE. Variation in ACE has previously been not only implicated as individually conferring susceptibility for Alzheimer's disease (AD) but also proposed to confer risk via interactions with other as yet unknown genes. More recently, larger studies have not supported ACE as a risk factor for AD, whereas the role of ACE pathway in AD has come under increased levels of scrutiny with respect to various aspects of AD pathology and possible therapies. We explored the potential combined involvement of ABO and ACE variations in the genetic susceptibility of 2067 AD cases compared with 1376 nondemented elderly. Including the effects of ABO haplotype did not provide any evidence for the genetic association of ACE with AD. Copyright © 2015 Elsevier Inc. All rights reserved.

Genetic variation in serotonin transporter function affects human fear expression indexed by fear-potentiated startle.

PubMed

Klumpers, Floris; Heitland, Ivo; Oosting, Ronald S; Kenemans, J Leon; Baas, Johanna M P

2012-02-01

The serotonin transporter (SERT) plays a crucial role in anxiety. Accordingly, variance in SERT functioning appears to constitute an important pathway to individual differences in anxiety. The current study tested the hypothesis that genetic variation in SERT function is associated with variability in the basic reflex physiology of defense. Healthy subjects (N=82) were presented with clearly instructed cues of shock threat and safety to induce robust anxiety reactions. Subjects carrying at least one short allele for the 5-HTTLPR polymorphism showed stronger fear-potentiated startle compared to long allele homozygotes. However, short allele carriers showed no deficit in the downregulation of fear after the offset of threat. These results suggest that natural variation in SERT function affects the magnitude of defensive reactions while not affecting the capacity for fear regulation. Copyright © 2011 Elsevier B.V. All rights reserved.

Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease.

PubMed

Moreno-Moral, Aida; Pesce, Francesco; Behmoaras, Jacques; Petretto, Enrico

2017-01-01

Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.

Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation

PubMed Central

Sandlund, Odd Terje; Karlsson, Sten; Thorstad, Eva B; Berg, Ole Kristian; Kent, Matthew P; Norum, Ine C J; Hindar, Kjetil

2014-01-01

The river-resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (FST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important. PMID:24967074

Indirect Genetic Effects and the Spread of Infectious Disease: Are We Capturing the Full Heritable Variation Underlying Disease Prevalence?

PubMed Central

Lipschutz-Powell, Debby; Woolliams, John A.; Bijma, Piter; Doeschl-Wilson, Andrea B.

2012-01-01

Reducing disease prevalence through selection for host resistance offers a desirable alternative to chemical treatment. Selection for host resistance has proven difficult, however, due to low heritability estimates. These low estimates may be caused by a failure to capture all the relevant genetic variance in disease resistance, as genetic analysis currently is not taylored to estimate genetic variation in infectivity. Host infectivity is the propensity of transmitting infection upon contact with a susceptible individual, and can be regarded as an indirect effect to disease status. It may be caused by a combination of physiological and behavioural traits. Though genetic variation in infectivity is difficult to measure directly, Indirect Genetic Effect (IGE) models, also referred to as associative effects or social interaction models, allow the estimation of this variance from more readily available binary disease data (infected/non-infected). We therefore generated binary disease data from simulated populations with known amounts of variation in susceptibility and infectivity to test the adequacy of traditional and IGE models. Our results show that a conventional model fails to capture the genetic variation in infectivity inherent in populations with simulated infectivity. An IGE model, on the other hand, does capture some of the variation in infectivity. Comparison with expected genetic variance suggests that there is scope for further methodological improvement, and that potential responses to selection may be greater than values presented here. Nonetheless, selection using an index of estimated direct and indirect breeding values was shown to have a greater genetic selection differential and reduced future disease risk than traditional selection for resistance only. These findings suggest that if genetic variation in infectivity substantially contributes to disease transmission, then breeding designs which explicitly incorporate IGEs might help reduce disease prevalence. PMID:22768088

Genetic variation in social mammals: the marmot model.

PubMed

Schwartz, O A; Armitage, K B

1980-02-08

The social substructure and the distribution of genetic variation among colonies of yellow-bellied marmots, when analyzed as an evolutionary system, suggests that this substructure enhances the intercolony variance and retards the fixation of genetic variation. This result supports a traditional theory of gradual evolution rather than recent theories suggesting accelerated evolution in social mammals.

Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent.

PubMed

Baker, Robert J; Dickins, Benjamin; Wickliffe, Jeffrey K; Khan, Faisal A A; Gaschak, Sergey; Makova, Kateryna D; Phillips, Caleb D

2017-09-01

Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole ( Myodes glareolus ) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown. Samples from contaminated localities exhibited significantly higher numbers of haplotypes and polymorphic loci, elevated genetic diversity, and a significantly higher average number of substitutions per site across mitochondrial gene regions. Observed genetic variation was dominated by synonymous mutations, which may indicate a history of purify selection against nonsynonymous or insertion/deletion mutations. These significant differences were not attributable to sample size artifacts. The observed increase in mitochondrial genomic diversity in voles from radioactive sites is consistent with the possibility that chronic, continuous irradiation resulting from the Chernobyl disaster has produced an accelerated mutation rate in this species over the last 25 years. Our results, being the first to demonstrate this phenomenon in a wild mammalian species, are important for understanding genetic consequences of exposure to low-dose radiation sources.

Forest genetic monitoring: an overview of concepts and definitions.

PubMed

Fussi, Barbara; Westergren, Marjana; Aravanopoulos, Filippos; Baier, Roland; Kavaliauskas, Darius; Finzgar, Domen; Alizoti, Paraskevi; Bozic, Gregor; Avramidou, Evangelia; Konnert, Monika; Kraigher, Hojka

2016-08-01

Safeguarding sustainability of forest ecosystems with their habitat variability and all their functions is of highest priority. Therefore, the long-term adaptability of forest ecosystems to a changing environment must be secured, e.g., through sustainable forest management. High adaptability is based on biological variation starting at the genetic level. Thus, the ultimate goal of the Convention on Biological Diversity (CBD) to halt the ongoing erosion of biological variation is of utmost importance for forest ecosystem functioning and sustainability. Monitoring of biological diversity over time is needed to detect changes that threaten these biological resources. Genetic variation, as an integral part of biological diversity, needs special attention, and its monitoring can ensure its effective conservation. We compare forest genetic monitoring to other biodiversity monitoring concepts. Forest genetic monitoring (FGM) enables early detection of potentially harmful changes of forest adaptability before these appear at higher biodiversity levels (e.g., species or ecosystem diversity) and can improve the sustainability of applied forest management practices and direct further research. Theoretical genetic monitoring concepts developed up to now need to be evaluated before being implemented on a national and international scale. This article provides an overview of FGM concepts and definitions, discusses their advantages and disadvantages, and provides a flow chart of the steps needed for the optimization and implementation of FGM. FGM is an important module of biodiversity monitoring, and we define an effective FGM scheme as consisting of an assessment of a forest population's capacity to survive, reproduce, and persist under rapid environmental changes on a long-term scale.

Differential effect of genetic variants of Na(+)-taurocholate co-transporting polypeptide (NTCP) and organic anion-transporting polypeptide 1B1 (OATP1B1) on the uptake of HMG-CoA reductase inhibitors.

PubMed

Choi, Min-Koo; Shin, Ho Jung; Choi, Young-Lim; Deng, Jian-Wei; Shin, Jae-Gook; Song, Im-Sook

2011-01-01

The purpose of this study was to investigate the effect of genetic variations in organic anion-transporting polypeptide 1B1 (OATP1B1) and Na(+)/taurocholate co-transporting polypeptide (NTCP) on the uptake of various statins having different affinities for these transporters. The functional activities and simultaneous expression of NTCP and OATP1B1 were confirmed by the uptake of taurocholate and estrone-3-sulphate as representative substrates for NTCP and OATP1B1, respectively, and by an immunofluorescence analysis. The substrate specificities of NTCP and OATP1B1 for statins and the effects of genetic variations on the uptake of rosuvastatin, pitavastatin, and atorvastatin were measured. Based on the K(m) values and intrinsic clearances of the three statins, pitavastatin was taken up more efficiently than rosuvastatin and atorvastatin by OATP1B1. Consequently, the cellular accumulation of pitavastatin was modulated according to the genetic variation of OATP1B1 (OATP1B1*15), rather than NTCP*2. In contrast, NTCP*2 displayed greater transport of atorvastatin and rosuvastatin, compared with NTCP wild type. Thus, the measurements of decreased rosuvastatin and atorvastatin transport by OATP1B1*15 were confounded by the presence of NTCP and its genetic variant, NTCP*2. In conclusion, the functional consequences of genetic variants of NTCP and OATP1B1 may be different for various statins, depending on the substrate specificity of the OATP1B1 and NTCP transporters.

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

PubMed Central

Winternitz, Jamie C; Wares, John P

2013-01-01

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

Genetic Architecture of Micro-Environmental Plasticity in Drosophila melanogaster.

PubMed

Morgante, Fabio; Sørensen, Peter; Sorensen, Daniel A; Maltecca, Christian; Mackay, Trudy F C

2015-05-06

Individuals of the same genotype do not have the same phenotype for quantitative traits when reared under common macro-environmental conditions, a phenomenon called micro-environmental plasticity. Genetic variation in micro-environmental plasticity is assumed in models of the evolution of phenotypic variance, and is important in applied breeding and personalized medicine. Here, we quantified genetic variation for micro-environmental plasticity for three quantitative traits in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel. We found substantial genetic variation for micro-environmental plasticity for all traits, with broad sense heritabilities of the same magnitude or greater than those of trait means. Micro-environmental plasticity is not correlated with residual segregating variation, is trait-specific, and has genetic correlations with trait means ranging from zero to near unity. We identified several candidate genes associated with micro-environmental plasticity of startle response, including Drosophila Hsp90, setting the stage for future genetic dissection of this phenomenon.

Neutral processes contribute to patterns of spatial variation for flower colour in the Mediterranean Iris lutescens (Iridaceae)

PubMed Central

Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric

2016-01-01

Background and Aims Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple–yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Key Results Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Conclusions Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. PMID:27084922

Neutral processes contribute to patterns of spatial variation for flower colour in the Mediterranean Iris lutescens (Iridaceae).

PubMed

Wang, Hui; Talavera, María; Min, Ya; Flaven, Elodie; Imbert, Eric

2016-05-01

Flower colour polymorphism in plants has been used as a classic model for understanding the importance of neutral processes vs. natural selection in population differentiation. However, current explanations for the maintenance of flower colour polymorphism mainly rely on balancing selection, while neutral processes have seldom been championed. Iris lutescens (Iridaceae) is a widespread species in the northern Mediterranean basin, which shows a stable and striking purple-yellow flower colour polymorphism. To evaluate the roles of neutral processes in the spatial variation for flower colour in this species, patterns of neutral genetic variation across its distribution range were quantified, and phenotypic differentiation was compared with neutral genetic differentiation. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 1120 individuals in 41 populations ranging from Spain to France, using a set of eight newly developed microsatellite markers. In addition, phenotypic differentiation for flower colour was also quantified by counting colour morph frequency in each population, and measuring the reflectance spectra of sampled individuals. Populations in Spain present a sharp colour transition from solely purple to solely yellow. The results provide evidence that genetic drift through limited gene flow is important in the evolution of monomorphic populations. In contrast, most populations in France are polymorphic with both phenotypes, and the colour frequencies vary geographically without any spatial gradients observed. A pattern of isolation by distance is detected in France, and gene flow between adjacent populations seems to be an important factor maintaining populations polymorphic. Overall, neutral processes contribute to patterns of spatial variation for flower colour in I. lutescens, but it cannot be excluded that natural selection is also operating. An interaction between neutral processes and natural selection is suggested to explain the spatial variation for flower colour in I. lutescens. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore

PubMed Central

2010-01-01

Background A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied, and can provide indirect insights into historical selection dynamics. Here we use this approach to examine the demographic and selective dynamics acting of a candidate gene involved in plant-insect interactions. Previous work documents the macroevolutionary and historical ecological importance of the nitrile-specifier protein (Nsp), which facilitated the host shift of Pieridae butterflies onto Brassicales host plants ~80 Myr ago. Results Here we assess the microevolutionary dynamics of the Nsp gene by studying the within and among-population variation at Nsp and reference genes in the butterfly Pieris rapae (Small Cabbage White). Nsp exhibits unexpectedly high amounts of amino acid polymorphism, unequally distributed across the gene. The vast majority of genetic variation exists within populations, with little to no genetic differentiation among four populations on two continents. A comparison of synonymous and nonsynonymous substitutions in 70 randomly chosen genes among P. rapae and its close relative Pieris brassicae (Large Cabbage White) finds Nsp to have a significantly relaxed functional constraint compared to housekeeping genes. We find strong evidence for a recent population expansion and no role for strong purifying or directional selection upon the Nsp gene. Conclusions The microevolutionary dynamics of the Nsp gene in P. rapae are dominated by recent population expansion and variation in functional constraint across the repeated domains of the Nsp gene. While the high amounts of amino acid diversity suggest there may be significant functional differences among allelic variants segregating within populations, indirect tests of selection could not conclusively identify a signature of historical selection. The importance of using this information for planning future studies of potential performance and fitness consequences of the observed variation is discussed. PMID:20181249

The role of genetic and chemical variation of Pinus sylvestris seedlings in influencing slug herbivory.

PubMed

O'Reilly-Wapstra, Julianne M; Iason, Glenn R; Thoss, Vera

2007-05-01

This study investigated the genetic and chemical basis of resistance of Pinus sylvestris seedlings to herbivory by a generalist mollusc, Arion ater. Using feeding trials with captive animals, we examined selective herbivory by A. ater of young P. sylvestris seedlings of different genotypes and correlated preferences with seedling monoterpene levels. We also investigated the feeding responses of A. ater to artificial diets laced with two monoterpenes, Delta(3)-carene and alpha-pinene. Logistic regression indicated that two factors were the best predictors of whether seedlings in the trial would be consumed. Individual slug variation (replicates) was the most significant factor in the model; however, alpha-pinene concentration (also representing beta-pinene, Delta(3)-carene and total monoterpenes due to multicollinearity) of needles was also a significant factor. While A. ater did not select seedlings on the basis of family, seedlings not eaten were significantly higher in levels of alpha-pinene compared to seedlings that were consumed. We also demonstrated significant genetic variation in alpha-pinene concentration of seedlings between different families of P. sylvestris. Nitrogen and three morphological seedling characteristics (stem length, needle length and stem diameter) also showed significant genetic variation between P. sylvestris families. Artificial diets laced with high (5 mg g(-1) dry matter) quantities of either Delta(3)-carene or alpha-pinene, were eaten significantly less than control diets with no added monoterpenes, supporting the results of the seedling feeding trial. This study demonstrates that A. ater selectively feed on P. sylvestris seedlings and that this selection is based, in part, on the monoterpene concentration of seedlings. These results, coupled with significant genetic variation in alpha-pinene concentration of seedlings and evidence that slug herbivory is detrimental to P. sylvestris fitness, are discussed as possible evidence for A. ater as a selective force on the evolution of defensive chemistry in P. sylvestris.

Empirical Distributions of F ST from Large-Scale Human Polymorphism Data

PubMed Central

Elhaik, Eran

2012-01-01

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s F ST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F ST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F ST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F ST distribution closely follows an exponential distribution. Third, although the overall F ST distribution is similarly shaped (inverse J), F ST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F ST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F ST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection. PMID:23185452

Empirical distributions of F(ST) from large-scale human polymorphism data.

PubMed

Elhaik, Eran

2012-01-01

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright's F(ST) that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F(ST) may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F(ST) analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F(ST) distribution closely follows an exponential distribution. Third, although the overall F(ST) distribution is similarly shaped (inverse J), F(ST) distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F(ST) of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F(ST) distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.

Oral infection of Aedes aegypti with yellow fever virus: geographic variation and genetic considerations.

PubMed

Tabachnick, W J; Wallis, G P; Aitken, T H; Miller, B R; Amato, G D; Lorenz, L; Powell, J R; Beaty, B J

1985-11-01

Twenty-eight populations representing a worldwide distribution of Aedes aegypti were tested for their ability to become orally infected with yellow fever virus (YFV). Populations had been analyzed for genetic variations at 11 isozyme loci and assigned to one of 8 genetic geographic groups of Ae. aegypti. Infection rates suggest that populations showing isozyme genetic relatedness also demonstrate similarity to oral infection rates with YFV. The findings support the hypothesis that genetic variation exists for oral susceptibility to YFV in Ae. aegypti.

Effective size of density-dependent two-sex populations: the effect of mating systems.

PubMed

Myhre, A M; Engen, S; SAEther, B-E

2017-08-01

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N e in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N e /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the N e /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

[Research progress of molecular genetic analysis in Schistosoma variation].

PubMed

Zheng, Su-Yue; Li, Fei

2014-02-01

The development of molecular biology techniques makes important contributions to the researches of heritable variation of Schistosoma. In recent years, the molecular genetic analysis in the Schistosoma variation researches mainly includes the restriction fragment length polymorphism (RFLP), random amplified polymorphism technology (RAPD), microsatellite anchored PCR (SSR-PCR), and polymerase reaction single-strand conformation polymorphism (PCR-SSCP). This article reviews the research progress of molecular genetic analysis in Schistosoma variation in recent years.

Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans.

PubMed

Green, J W M; Snoek, L B; Kammenga, J E; Harvey, S C

2013-10-01

In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly investigated. Here, we report extensive natural genetic variation in dauer larvae development within growing populations across multiple wild isolates. Moreover, bin mapping of introgression lines (ILs) derived from the genetically divergent isolates N2 and CB4856 reveals 10 quantitative trait loci (QTLs) affecting dauer formation. Comparison of individual ILs to N2 identifies an additional eight QTLs, and sequential IL analysis reveals six more QTLs. Our results also show that a behavioural, laboratory-derived, mutation controlled by the neuropeptide Y receptor homolog npr-1 can affect dauer larvae development in growing populations. These findings illustrate the complex genetic architecture of variation in dauer larvae formation in C. elegans and may help to understand how the control of variation in dauer larvae development has evolved.

Diet1, bile acid diarrhea, and FGF15/19: mouse model and human genetic variants.

PubMed

Lee, Jessica M; Ong, Jessica R; Vergnes, Laurent; de Aguiar Vallim, Thomas Q; Nolan, Jonathan; Cantor, Rita M; Walters, Julian R F; Reue, Karen

2018-03-01

Diet1 modulates intestinal production of the hormone, fibroblast growth factor (FGF)15, which signals in liver to regulate bile acid synthesis. C57BL/6ByJ mice with a spontaneous Diet1 -null mutation are resistant to hypercholesterolemia compared with wild-type C57BL/6J mice through enhanced cholesterol conversion to bile acids. To further characterize the role of Diet1 in metabolism, we generated Diet1 -/- mice on the C57BL/6J genetic background. C57BL/6J Diet1 -/- mice had elevated bile acid levels, reduced Fgf15 expression, and increased gastrointestinal motility and intestinal luminal water content, which are symptoms of bile acid diarrhea (BAD) in humans. Natural genetic variation in Diet1 mRNA expression levels across 76 inbred mouse strains correlated positively with Ffg15 mRNA and negatively with serum bile acid levels. This led us to investigate the role of DIET1 genetic variation in primary BAD patients. We identified a DIET1 coding variant ( rs12256835 ) that had skewed prevalence between BAD cases and controls. This variant causes an H1721Q amino acid substitution that increases the levels of FGF19 protein secreted from cultured cells. We propose that genetic variation in DIET1 may be a determinant of FGF19 secretion levels, and may affect bile acid metabolism in both physiological and pathological conditions. Copyright © 2018 by the American Society for Biochemistry and Molecular Biology, Inc.

Spatial genetic structure and regional demography in the southern torrent salamander: Implications for conservation and management

USGS Publications Warehouse

Miller, Mark P.; Haig, Susan M.; Wagner, R.S.

2006-01-01

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

Considerable MHC Diversity Suggests That the Functional Extinction of Baiji Is Not Related to Population Genetic Collapse

PubMed Central

Xu, Shixia; Ju, Jianfeng; Zhou, Xuming; Wang, Lian; Zhou, Kaiya; Yang, Guang

2012-01-01

To further extend our understanding of the mechanism causing the current nearly extinct status of the baiji (Lipotes vexillifer), one of the most critically endangered species in the world, genetic diversity at the major histocompatibility complex (MHC) class II DRB locus was investigated in the baiji. Nine highly divergent DRB alleles were identified in 17 samples, with an average of 28.4 (13.2%) nucleotide difference and 16.7 (23.5%) amino acid difference between alleles. The unexpectedly high levels of DRB allelic diversity in the baiji may partly be attributable to its evolutionary adaptations to the freshwater environment which is regarded to have a higher parasite diversity compared to the marine environment. In addition, balancing selection was found to be the main mechanisms in generating sequence diversity at baiji DRB gene. Considerable sequence variation at the adaptive MHC genes despite of significant loss of neutral genetic variation in baiji genome might suggest that intense selection has overpowered random genetic drift as the main evolutionary forces, which further suggested that the critically endangered or nearly extinct status of the baiji is not an outcome of genetic collapse. PMID:22272349

Haplotype diversity in 11 candidate genes across four populations.

PubMed

Beaty, T H; Fallin, M D; Hetmanski, J B; McIntosh, I; Chong, S S; Ingersoll, R; Sheng, X; Chakraborty, R; Scott, A F

2005-09-01

Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.

Hidden genetic variation in the germline genome of Tetrahymena thermophila.

PubMed

Dimond, K L; Zufall, R A

2016-06-01

Genome architecture varies greatly among eukaryotes. This diversity may profoundly affect the origin and maintenance of genetic variation within a population. Ciliates are microbial eukaryotes with unusual genome features, such as the separation of germline and somatic genomes within a single cell and amitotic division. These features have previously been proposed to increase the rate of molecular evolution in these species. Here, we assessed the fitness effects of genetic variation in the two genomes of natural isolates of the ciliate Tetrahymena thermophila. We find more extensive genetic variation in fitness in the transcriptionally silent germline genome than in the expressed somatic genome. Surprisingly, this variation is not primarily deleterious, but has both beneficial and deleterious effects. We conclude that Tetrahymena genome architecture allows for the maintenance of genetic variation that would otherwise be eliminated by selection. We consider the effect of selection on the two genomes and the impacts of reproductive strategies and the mechanism of sex determination on the structure of this variation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

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...

Genetic Brain Disorders

MedlinePlus

A genetic brain disorder is caused by a variation or a mutation in a gene. A variation is a different form ... mutation is a change in a gene. Genetic brain disorders affect the development and function of the ...

Genetic variation associated with cardiovascular risk in autoimmune diseases

PubMed Central

Perrotti, Pedro P.; Aterido, Adrià; Fernández-Nebro, Antonio; Cañete, Juan D.; Ferrándiz, Carlos; Tornero, Jesús; Gisbert, Javier P.; Domènech, Eugeni; Fernández-Gutiérrez, Benjamín; Gomollón, Fernando; García-Planella, Esther; Fernández, Emilia; Sanmartí, Raimon; Gratacós, Jordi; Martínez-Taboada, Víctor Manuel; Rodríguez-Rodríguez, Luís; Palau, Núria; Tortosa, Raül; Corbeto, Mireia L.; Lasanta, María L.; Marsal, Sara; Julià, Antonio

2017-01-01

Autoimmune diseases have a higher prevalence of cardiovascular events compared to the general population. The objective of this study was to investigate the genetic basis of cardiovascular disease (CVD) risk in autoimmunity. We analyzed genome-wide genotyping data from 6,485 patients from six autoimmune diseases that are associated with a high socio-economic impact. First, for each disease, we tested the association of established CVD risk loci. Second, we analyzed the association of autoimmune disease susceptibility loci with CVD. Finally, to identify genetic patterns associated with CVD risk, we applied the cross-phenotype meta-analysis approach (CPMA) on the genome-wide data. A total of 17 established CVD risk loci were significantly associated with CVD in the autoimmune patient cohorts. From these, four loci were found to have significantly different genetic effects across autoimmune diseases. Six autoimmune susceptibility loci were also found to be associated with CVD risk. Genome-wide CPMA analysis identified 10 genetic clusters strongly associated with CVD risk across all autoimmune diseases. Two of these clusters are highly enriched in pathways previously associated with autoimmune disease etiology (TNFα and IFNγ cytokine pathways). The results of this study support the presence of specific genetic variation associated with the increase of CVD risk observed in autoimmunity. PMID:28982122

Phylogeography and spatial genetic structure of the Southern torrent salamander: Implications for conservation and management

USGS Publications Warehouse

Miller, M.P.; Haig, S.M.; Wagner, R.S.

2006-01-01

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders. ?? The American Genetic Association. 2006. All rights reserved.

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.

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.

A New Phylogeographic Pattern of Endemic Bufo bankorensis in Taiwan Island Is Attributed to the Genetic Variation of Populations

PubMed Central

Yu, Teng-Lang; Lin, Hung-Du; Weng, Ching-Feng

2014-01-01

Aim To comprehend the phylogeographic patterns of genetic variation in anurans at Taiwan Island, this study attempted to examine (1) the existence of various geological barriers (Central Mountain Ranges, CMRs); and (2) the genetic variation of Bufo bankorensis using mtDNA sequences among populations located in different regions of Taiwan, characterized by different climates and existing under extreme conditions when compared available sequences of related species B. gargarizans of mainland China. Methodology/Principal Findings Phylogenetic analyses of the dataset with mitochondrial DNA (mtDNA) D-loop gene (348 bp) recovered a close relationship between B. bankorensis and B. gargarizans, identified three distinct lineages. Furthermore, the network of mtDNA D-loop gene (564 bp) amplified (279 individuals, 27 localities) from Taiwan Island indicated three divergent clades within B. bankorensis (Clade W, E and S), corresponding to the geography, thereby verifying the importance of the CMRs and Kaoping River drainage as major biogeographic barriers. Mismatch distribution analysis, neutrality tests and Bayesian skyline plots revealed that a significant population expansion occurred for the total population and Clade W, with horizons dated to approximately 0.08 and 0.07 Mya, respectively. These results suggest that the population expansion of Taiwan Island species B. bankorensis might have resulted from the release of available habitat in post-glacial periods, the genetic variation on mtDNA showing habitat selection, subsequent population dispersal, and co-distribution among clades. Conclusions The multiple origins (different clades) of B. bankorensis mtDNA sequences were first evident in this study. The divergent genetic clades found within B. bankorensis could be independent colonization by previously diverged lineages; inferring B. bankorensis originated from B. gargarizans of mainland China, then dispersal followed by isolation within Taiwan Island. Highly divergent clades between W and E of B. bankorensis, implies that the CMRs serve as a genetic barrier and separated the whole island into the western and eastern phylogroups. PMID:24853679

Vulnerability to cavitation, hydraulic efficiency, growth and survival in an insular pine (Pinus canariensis).

PubMed

López, Rosana; López de Heredia, Unai; Collada, Carmen; Cano, Francisco Javier; Emerson, Brent C; Cochard, Hervé; Gil, Luis

2013-06-01

It is widely accepted that hydraulic failure due to xylem embolism is a key factor contributing to drought-induced mortality in trees. In the present study, an attempt is made to disentangle phenotypic plasticity from genetic variation in hydraulic traits across the entire distribution area of a tree species to detect adaptation to local environments. A series of traits related to hydraulics (vulnerability to cavitation and hydraulic conductivity in branches), growth performance and leaf mass per area were assessed in eight Pinus canariensis populations growing in two common gardens under contrasting environments. In addition, the neutral genetic variability (FST) and the genetic differentiation of phenotypic variation (QST) were compared in order to identify the evolutionary forces acting on these traits. The variability for hydraulic traits was largely due to phenotypic plasticity. Nevertheless, the vulnerability to cavitation displayed a significant genetic variability (approx. 5 % of the explained variation), and a significant genetic × environment interaction (between 5 and 19 % of the explained variation). The strong correlation between vulnerability to cavitation and survival in the xeric common garden (r = -0·81; P < 0·05) suggests a role for the former in the adaptation to xeric environments. Populations from drier sites and higher temperature seasonality were less vulnerable to cavitation than those growing at mesic sites. No trade-off between xylem safety and efficiency was detected. QST of parameters of the vulnerability curve (0·365 for P50 and the slope of the vulnerability curve and 0·452 for P88) differed substantially from FST (0·091), indicating divergent selection. In contrast, genetic drift alone was found to be sufficient to explain patterns of differentiation for xylem efficiency and growth. The ability of P. canariensis to inhabit a wide range of ecosystems seemed to be associated with high phenotypic plasticity and some degree of local adaptations of xylem and leaf traits. Resistance to cavitation conferred adaptive potential for this species to adapt successfully to xeric conditions.

Public Willingness to Participate in and Public Opinions About Genetic Variation Research: A Review of the Literature

PubMed Central

Sterling, Rene; Henderson, Gail E.; Corbie-Smith, Giselle

2006-01-01

Scientists are turning to genetic variation research in hopes of addressing persistent racial/ethnic disparities in health. Despite ongoing controversy, the advancement of genetic variation research is likely to produce new knowledge and technologies that will substantially change the ways in which we understand and value health. They also may affect the ways in which individuals and groups organize socially, politically, and economically. Addressing concerns that may exist in different communities is vital to the scientific and ethical advancement of genetic variation research. We review empirical studies of public willingness to participate in and opinions about genetic research with particular attention to differences in consent and opinion by racial/ethnic group membership. PMID:17018829

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

PubMed

Yadav, Anupama; Dhole, Kaustubh; Sinha, Himanshu

2016-12-01

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.

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

The endocrine-genetic basis of life-history variation: the relationship between the ecdysteroid titer and morph-specific reproduction in the wing-polymorphic cricket Gryllus firmus.

PubMed

Zera, A J; Bottsford, J

2001-03-01

The hormonal basis of variation in life-history traits is a poorly studied topic in life-history evolution. An important step in identifying the endocrine-genetic causes of life-history variation is documenting statistical and functional associations between hormone titers and genotypes/phenotypes that vary in life-history traits. To this end, we compared the blood ecdysteroid titer and the mass of the ovaries during the first week of adulthood among a flight-capable morph and two flightless morphs of the wing-polymorphic cricket Gryllus firmus. Ecdysteroids are a group of structurally related hormones that regulate many important aspects of reproduction in insects. Both the ecdysteroid titer and ovarian mass were significantly higher in each of two flightless morphs compared with the flight-capable morph throughout the first week of adulthood. Genetically based differences in the ecdysteroid titer and ovarian mass between morphs from different selected lines were similar to phenotypically based differences among morphs from the same control (unselected) lines. By day 7 of adulthood, ovaries were typically 200-400% larger and the ecdysteroid titer was 60-300% higher in flightless versus the flight-capable morph. In addition, highly significant, positive, phenotypic correlations were observed between the ecdysteroid titer and ovarian mass in pooled samples of the two flightless and flight-capable crickets from control lines or from selected lines. The ecdysteroid titer was sufficiently elevated in the flightless morphs to account for their elevated ovarian growth. This is the first direct documentation that naturally occurring phenotypes/genotypes that differ in early fecundity, a key life-history trait, also differ phenotypically and genetically in the titer of a key reproductive hormone that potentially regulates that trait.

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

Host-parasite coevolution: genetic variation in a virus population and the interaction with a host gene.

PubMed

Wilfert, L; Jiggins, F M

2010-07-01

Host-parasite coevolution is considered to be an important factor in maintaining genetic variation in resistance to pathogens. Drosophila melanogaster is naturally infected by the sigma virus, a vertically transmitted and host-specific pathogen. In fly populations, there is a large amount of genetic variation in the transmission rate from parent to offspring, much of which is caused by major-effect resistance polymorphisms. We have found that there are similarly high levels of genetic variation in the rate of paternal transmission among 95 different isolates of the virus as in the host. However, when we examined a transmission-blocking gene in the host, we found that it was effective across virus isolates. Therefore, the high levels of genetic variation observed in this system do not appear to be maintained because of coevolution resulting from interactions between this host gene and parasite genes.

Genetic variation in adaptability and pleiotropy in budding yeast.

PubMed

Jerison, Elizabeth R; Kryazhimskiy, Sergey; Mitchell, James Kameron; Bloom, Joshua S; Kruglyak, Leonid; Desai, Michael M

2017-08-17

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.

An investigation of natural genetic variation in the circadian system of Drosophila melanogaster: rhythm characteristics and methods of quantification.

PubMed

Emery, P T; Morgan, E; Birley, A J

1994-04-01

Variation in four characteristics of the circadian locomotor activity rhythm was investigated in 24 true-breeding strains of Drosophila melanogaster with a view to establishing methods of phenotypic measurement sufficiently robust to allow subsequent biometric analysis. Between them, these strains formed a representative sample of the genetic variability of a natural population. Period, phase, definition (the degree to which a rhythmic signal was obscured by noise), and rhythm waveform were all found to vary continuously among the strains, although within each strain the rhythm phenotype was remarkably consistent. Each characteristic was found to be sufficiently robust to permit objective measurement using several different methods of quantification, which were then compared.

Congruence of Additive and Non-Additive Effects on Gene Expression Estimated from Pedigree and SNP Data

PubMed Central

Powell, Joseph E.; Henders, Anjali K.; McRae, Allan F.; Kim, Jinhee; Hemani, Gibran; Martin, Nicholas G.; Dermitzakis, Emmanouil T.; Gibson, Greg

2013-01-01

There is increasing evidence that heritable variation in gene expression underlies genetic variation in susceptibility to disease. Therefore, a comprehensive understanding of the similarity between relatives for transcript variation is warranted—in particular, dissection of phenotypic variation into additive and non-additive genetic factors and shared environmental effects. We conducted a gene expression study in blood samples of 862 individuals from 312 nuclear families containing MZ or DZ twin pairs using both pedigree and genotype information. From a pedigree analysis we show that the vast majority of genetic variation across 17,994 probes is additive, although non-additive genetic variation is identified for 960 transcripts. For 180 of the 960 transcripts with non-additive genetic variation, we identify expression quantitative trait loci (eQTL) with dominance effects in a sample of 339 unrelated individuals and replicate 31% of these associations in an independent sample of 139 unrelated individuals. Over-dominance was detected and replicated for a trans association between rs12313805 and ETV6, located 4MB apart on chromosome 12. Surprisingly, only 17 probes exhibit significant levels of common environmental effects, suggesting that environmental and lifestyle factors common to a family do not affect expression variation for most transcripts, at least those measured in blood. Consistent with the genetic architecture of common diseases, gene expression is predominantly additive, but a minority of transcripts display non-additive effects. PMID:23696747

Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data.

PubMed

Powell, Joseph E; Henders, Anjali K; McRae, Allan F; Kim, Jinhee; Hemani, Gibran; Martin, Nicholas G; Dermitzakis, Emmanouil T; Gibson, Greg; Montgomery, Grant W; Visscher, Peter M

2013-05-01

There is increasing evidence that heritable variation in gene expression underlies genetic variation in susceptibility to disease. Therefore, a comprehensive understanding of the similarity between relatives for transcript variation is warranted--in particular, dissection of phenotypic variation into additive and non-additive genetic factors and shared environmental effects. We conducted a gene expression study in blood samples of 862 individuals from 312 nuclear families containing MZ or DZ twin pairs using both pedigree and genotype information. From a pedigree analysis we show that the vast majority of genetic variation across 17,994 probes is additive, although non-additive genetic variation is identified for 960 transcripts. For 180 of the 960 transcripts with non-additive genetic variation, we identify expression quantitative trait loci (eQTL) with dominance effects in a sample of 339 unrelated individuals and replicate 31% of these associations in an independent sample of 139 unrelated individuals. Over-dominance was detected and replicated for a trans association between rs12313805 and ETV6, located 4MB apart on chromosome 12. Surprisingly, only 17 probes exhibit significant levels of common environmental effects, suggesting that environmental and lifestyle factors common to a family do not affect expression variation for most transcripts, at least those measured in blood. Consistent with the genetic architecture of common diseases, gene expression is predominantly additive, but a minority of transcripts display non-additive effects.

Evolution of a genetic polymorphism with climate change in a Mediterranean landscape

PubMed Central

Thompson, John; Charpentier, Anne; Bouguet, Guillaume; Charmasson, Faustine; Roset, Stephanie; Buatois, Bruno; Vernet, Philippe; Gouyon, Pierre-Henri

2013-01-01

Many species show changes in distribution and phenotypic trait variation in response to climatic warming. Evidence of genetically based trait responses to climate change is, however, less common. Here, we detected evolutionary variation in the landscape-scale distribution of a genetically based chemical polymorphism in Mediterranean wild thyme (Thymus vulgaris) in association with modified extreme winter freezing events. By comparing current data on morph distribution with that observed in the early 1970s, we detected a significant increase in the proportion of morphs that are sensitive to winter freezing. This increase in frequency was observed in 17 of the 24 populations in which, since the 1970s, annual extreme winter freezing temperatures have risen above the thresholds that cause mortality of freezing-sensitive morphs. Our results provide an original example of rapid ongoing evolutionary change associated with relaxed selection (less extreme freezing events) on a local landscape scale. In species whose distribution and genetic variability are shaped by strong selection gradients, there may be little time lag associated with their ecological and evolutionary response to long-term environmental change. PMID:23382198

Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation.

PubMed

Gonçalves da Silva, Anders; Lalonde, Danielle R; Quse, Viviana; Shoemaker, Alan; Russello, Michael A

2010-01-01

Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (N(total) = 41; mean H(E) = 0.67 across 10 variable loci) and little evidence for relatedness among founder individuals (N(founders) = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele sharing, and we identified 2 individuals of high genetic value to the population (mk

Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus)

PubMed Central

Chuluunbat, B; Charruau, P; Silbermayr, K; Khorloojav, T; Burger, P A

2014-01-01

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro-ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization. PMID:24749721

Lack of genetic variation in tree ring delta13C suggests a uniform, stomatally-driven response to drought stress across Pinus radiata genotypes.

PubMed

Rowell, Douglas M; Ades, Peter K; Tausz, Michael; Arndt, Stefan K; Adams, Mark A

2009-02-01

We assessed the variation in delta(13)C signatures of Pinus radiata D. Don stemwood taken from three genetic trials in southern Australia. We sought to determine the potential of using delta(13)C signatures as selection criteria for drought tolerance. Increment cores were taken from P. radiata and were used to determine the basal area increment and the delta(13)C signature of extracted cellulose. Both growth increment and cellulose delta(13)C were affected by water availability. Growth increment and delta(13)C were negatively correlated suggesting that growth was water-limited. While there was significant genetic variation in growth, there was no significant genetic variation in cellulose delta(13)C of tree rings. This suggests that different genotypes of P. radiata display significant differences in growth and yet respond similarly to drought stress. The delta(13)C response to drought stress was more due to changes in stomatal conductance than to the variation in photosynthetic capacity, and this may explain the lack of genetic variation in delta(13)C. The lack of genetic variation in cellulose delta(13)C of tree rings precludes its use as a selection criterion for drought tolerance among P. radiata genotypes.

Genetic variation for agronomic and fiber quality traits in a population derived from high-quality cotton germplasm

USDA-ARS?s Scientific Manuscript database

Genetic improvement of fiber quality is necessary to meet the requirements of processors and users of cotton fiber. To foster genetic improvement of cotton fiber quality, adequate genetic variation for the quantitatively inherited physical properties of cotton is required. Additionally, knowledge of...

Impaired skeletal growth in mice with haploinsufficiency of IGF-I: genetic evidence that differences in IGF-I expression could contribute to peak bone mineral density differences

PubMed Central

Mohan, S; Baylink, D J

2010-01-01

Although it is well established that there is considerable inter-individual variation in the circulating levels of IGF-I in normal, healthy individuals and that a genetic component contributes substantially to this variation, the direct evidence that inter-individual variation in IGF-I contributes to differences in peak bone mineral density (BMD) is lacking. To examine if differences in IGF-I expression could contribute to peak BMD differences, we measured skeletal changes at days 23 (prepubertal), 31 (pubertal) and 56 (postpubertal) in mice with haploinsufficiency of IGF-I (+/−) and corresponding control mice (+/+). Mice (MF1/DBA) heterozygous for the IGF-I knockout allele were bred to generate +/+ and +/− mice (n=18–20 per group). Serum IGF-I was decreased by 23% (P<0·001) in mice with IGF-I haploinsufficiency (+/−) group at day 56 compared with the control (+/+) group. Femoral bone mineral content and BMD, as determined by dual energy X-ray absorptiometry, were reduced by 20% (P<0·001) and 12% respectively in the IGF-I (+/−) group at day 56 compared with the control group. The peripheral quantitative computed tomography measurements at the femoral mid-diaphysis revealed that periosteal circumference (7%, P<0·01) and total volumetric BMD (5%, P<0·05) were decreased significantly in the +/− group compared with the +/+ group. Furthermore, serum IGF-I showed significant positive correlations with both areal BMD (r=0·55) and periosteal circumference (r=0·66) in the pooled data from the +/+ and +/− groups. Our findings that haploinsufficiency of IGF-I caused significant reductions in serum IGF-I level, BMD and bone size, together with the previous findings, are consistent with the notion that genetic variations in IGF-I expression could, in part, contribute to inter-individual differences in peak BMD among a normal population. PMID:15930167

Variation in Airway Responsiveness of Male C57BL/6 Mice from 5 Vendors

PubMed Central

Chang, Herng-Yu Sucie; Mitzner, Wayne; Watson, Julie

2012-01-01

Mice are now the most commonly used animal model for the study of asthma. The mouse asthma model has many characteristics of the human pathology, including allergic sensitization and airway hyperresponsiveness. Inbred strains are commonly used to avoid variations due to genetic background, but variations due to rearing environment are not as well recognized. After a change in mouse vendors and a switch from C57BL/6J mice to C57BL/6N mice, we noted significant differences in airway responsiveness between the substrains. To further investigate the effect of vendor, we tested C57BL/6N mice from 3 other vendors and found significant differences between several of the substrains. To test whether this difference was due to genetic drift or rearing environment, we purchased new groups of mice from all 5 vendors, bred them in separate vendor-specific groups under uniform environmental conditions, and tested male first generation (F1) offspring at 8 to 10 wk of age. These F1 mice showed no significant differences in airway responsiveness, indicating that the rearing environment rather than genetic differences was responsible for the initial variation in pulmonary phenotype. The environmental factors that caused the phenotypic variation are unknown. However, differences between vendor in feed components, bedding type, or microbiome could have contributed. Whatever the basis, investigators using mouse models of asthma should be cautious in comparing data from mice obtained from different vendors. PMID:23043804

Geographical genetics of Pseudoplatystoma punctifer (Castelnau, 1855) (Siluriformes, Pimelodidae) in the Amazon Basin.

PubMed

Telles, M P C; Collevatti, R G; Braga, R S; Guedes, L B S; Castro, T G; Costa, M C; Silva-Júnior, N J; Barthem, R B; Diniz-Filho, J A F

2014-05-09

Geographical genetics allows the evaluation of evolutionary processes underlying genetic variation within and among local populations and forms the basis for establishing more effective strategies for biodiversity conservation at the population level. In this study, we used explicit spatial analyses to investigate molecular genetic variation (estimated using 7 microsatellite markers) of Pseudoplatystoma punctifer, by using samples obtained from 15 localities along the Madeira River and Solimões, Amazon Basin. A high genetic diversity was observed associated with a relatively low FST (0.057; P < 0.001), but pairwise FST values ranged from zero up to 0.21 when some pairs of populations were compared. These FST values have a relatively low correlation with geographic distances (r = 0.343; P = 0.074 by Mantel test), but a Mantel correlogram revealed that close populations (up to 80 km) tended to be more similar than expected by chance (r = 0.360; P = 0.015). The correlogram also showed a exponential-like decrease of genetic similarity with distance, with a patch-size of around 200 km, compatible with isolation-by-distance and analogous processes related to local constraints of dispersal and spatially structured levels of gene flow. The pattern revealed herein has important implications for establishing strategies to maintain genetic diversity in the species, especially considering the threats due to human impacts caused by building large dams in this river system.

What Use Is Population Genetics?

PubMed

Charlesworth, Brian

2015-07-01

The Genetic Society of America's Thomas Hunt Morgan Medal is awarded to an individual GSA member for lifetime achievement in the field of genetics. For over 40 years, 2015 recipient Brian Charlesworth has been a leader in both theoretical and empirical evolutionary genetics, making substantial contributions to our understanding of how evolution acts on genetic variation. Some of the areas in which Charlesworth's research has been most influential are the evolution of sex chromosomes, transposable elements, deleterious mutations, sexual reproduction, and life history. He also developed the influential theory of background selection, whereby the recurrent elimination of deleterious mutations reduces variation at linked sites, providing a general explanation for the correlation between recombination rate and genetic variation. Copyright © 2015 by the Genetics Society of America.

Comparative Agronomic Performance and Reaction to Fusarium wilt of Lens culinaris × L. orientalis and L. culinaris × L. ervoides derivatives.

PubMed

Singh, Mohar; Rana, Jai C; Singh, Badal; Kumar, Sandeep; Saxena, Deep R; Saxena, Ashok; Rizvi, Aqeel H; Sarker, Ashutosh

2017-01-01

The development of transgressive phenotype in the segregating populations has been speculated to contribute to niche divergence of hybrid lineages, which occurs most frequently at larger genetic distances. Wild Lens species are considered to be more resistant against major biotic and abiotic stresses than that of the cultivated species. In the present study, we assessed the comparative agronomic performance of lentil ( Lens culinaris subsp. culinaris ) inter-sub-specific ( L. culinaris subsp. orientalis ) and interspecific ( L. ervoides ) derivatives, also discussed its probable basis of occurrence. The F 3 , F 4 , and F 5 inter sub-specific and interspecific populations of ILL8006 × ILWL62 and ILL10829 × ILWL30, respectively revealed a substantial range of variation for majority of agro-morphological traits as reflected by the range, mean and coefficient of variation. A high level of fruitful heterosis was also observed in F 3 and F 4 progeny for important traits of interest. Phenotypic coefficient of variation (PCV) was higher in magnitude than genotypic coefficient of variation (GCV) in all generations for several quantitative characters. The results showed high heritability estimates for majority of traits in conjunction with low to high genetic advance in F 3 and F 4 generations. Further, F 5 progeny of ILL10829 × ILWL30, manifested resistant disease reaction for fifteen recombinant inbred lines (RILs) against ( Fusarium oxysporum f. sp. lentis ( Vasd. Srin .) Gord.). The multilocation agronomic evaluation of both crosses showed better results for earliness, desirable seed yield and Fusarium wilt resistance under two agro-ecological regions of north-western India. These better performing recombinants of ILL8006 × ILWL62 and ILL10829 × ILWL30 can be advanced for further genetic improvement and developing high yielding disease resistant cultivars of lentil.

Genetic Variation in the Acorn Barnacle from Allozymes to Population Genomics

PubMed Central

Flight, Patrick A.; Rand, David M.

2012-01-01

Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (FST ∼ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An FST outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. FST values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic FST for mtDNA. The majority of FST outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal. PMID:22767487

ENGINES: exploring single nucleotide variation in entire human genomes.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher

2011-04-19

Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs), population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs) uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs), as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP) repositories such as HapMap or Perlegen. ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation. Access to the data mart generating scripts and to the web interface is granted from http://spsmart.cesga.es/engines.php. © 2011 Amigo et al; licensee BioMed Central Ltd.

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

PubMed Central

2017-01-01

Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity. PMID:28796803

Genetic variation in eleven phase I drug metabolism genes in an ethnically diverse population.

PubMed

Solus, Joseph F; Arietta, Brenda J; Harris, James R; Sexton, David P; Steward, John Q; McMunn, Chara; Ihrie, Patrick; Mehall, Janelle M; Edwards, Todd L; Dawson, Elliott P

2004-10-01

The extent of genetic variation found in drug metabolism genes and its contribution to interindividual variation in response to medication remains incompletely understood. To better determine the identity and frequency of variation in 11 phase I drug metabolism genes, the exons and flanking intronic regions of the cytochrome P450 (CYP) isoenzyme genes CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4 and CYP3A5 were amplified from genomic DNA and sequenced. A total of 60 kb of bi-directional sequence was generated from each of 93 human DNAs, which included Caucasian, African-American and Asian samples. There were 388 different polymorphisms identified. These included 269 non-coding, 45 synonymous and 74 non-synonymous polymorphisms. Of these, 54% were novel and included 176 non-coding, 14 synonymous and 21 non-synonymous polymorphisms. Of the novel variants observed, 85 were represented by single occurrences of the minor allele in the sample set. Much of the variation observed was from low-frequency alleles. Comparatively, these genes are variation-rich. Calculations measuring genetic diversity revealed that while the values for the individual genes are widely variable, the overall nucleotide diversity of 7.7 x 10(-4) and polymorphism parameter of 11.5 x 10(-4) are higher than those previously reported for other gene sets. Several independent measurements indicate that these genes are under selective pressure, particularly for polymorphisms corresponding to non-synonymous amino acid changes. There is relatively little difference in measurements of diversity among the ethnic groups, but there are large differences among the genes and gene subfamilies themselves. Of the three CYP subfamilies involved in phase I drug metabolism (1, 2, and 3), subfamily 2 displays the highest levels of genetic diversity.

Genetic variation and genetic structure of the endangered species Sinowilsonia henryi Hemsi. (Hamamelidaceae) revealed by amplified fragment length polymorphism (AFLP) markers.

PubMed

Zhang, H; Ji, W L; Li, M; Zhou, L Y

2015-10-14

Comprehensive research of genetic variation is crucial in designing conservation strategies for endangered and threatened species. Sinowilsonia henryi Hemsi. is a tertiary relic with a limited geographical distribution in the central and western areas of China. It is endangered because of climate change and habitat fragmentation over the last thousands of years. In this study, amplified fragment length polymorphism markers were utilized to estimate genetic diversity and genetic structure in and among S. henryi. In this study, Nei's genetic diversity and Shannon's information index were found to be 0.192 and 0.325 respectively, indicating a moderate-to-high genetic diversity in species. According to analysis of molecular variation results, 32% of the genetic variation was shown to be partitioned among populations, demonstrating a relatively high genetic divergence; this was supported by principal coordinate analysis and unweighted pair-group method with arithmetic average analysis. Moreover, the Mantel test showed that there was no significant correlation between genetic and geographical distances. The above results can be explained by the effects of habitat fragmentation, history traits, and gene drift. Based on the results, several implications were indicated and suggestions proposed for preservation strategies for this species.

Molecular genetic contributions to socioeconomic status and intelligence

PubMed Central

Marioni, Riccardo E.; Davies, Gail; Hayward, Caroline; Liewald, Dave; Kerr, Shona M.; Campbell, Archie; Luciano, Michelle; Smith, Blair H.; Padmanabhan, Sandosh; Hocking, Lynne J.; Hastie, Nicholas D.; Wright, Alan F.; Porteous, David J.; Visscher, Peter M.; Deary, Ian J.

2014-01-01

Education, socioeconomic status, and intelligence are commonly used as predictors of health outcomes, social environment, and mortality. Education and socioeconomic status are typically viewed as environmental variables although both correlate with intelligence, which has a substantial genetic basis. Using data from 6815 unrelated subjects from the Generation Scotland study, we examined the genetic contributions to these variables and their genetic correlations. Subjects underwent genome-wide testing for common single nucleotide polymorphisms (SNPs). DNA-derived heritability estimates and genetic correlations were calculated using the ‘Genome-wide Complex Trait Analyses’ (GCTA) procedures. 21% of the variation in education, 18% of the variation in socioeconomic status, and 29% of the variation in general cognitive ability was explained by variation in common SNPs (SEs ~ 5%). The SNP-based genetic correlations of education and socioeconomic status with general intelligence were 0.95 (SE 0.13) and 0.26 (0.16), respectively. There are genetic contributions to intelligence and education with near-complete overlap between common additive SNP effects on these traits (genetic correlation ~ 1). Genetic influences on socioeconomic status are also associated with the genetic foundations of intelligence. The results are also compatible with substantial environmental contributions to socioeconomic status. PMID:24944428

Molecular genetic contributions to socioeconomic status and intelligence.

PubMed

Marioni, Riccardo E; Davies, Gail; Hayward, Caroline; Liewald, Dave; Kerr, Shona M; Campbell, Archie; Luciano, Michelle; Smith, Blair H; Padmanabhan, Sandosh; Hocking, Lynne J; Hastie, Nicholas D; Wright, Alan F; Porteous, David J; Visscher, Peter M; Deary, Ian J

2014-05-01

Education, socioeconomic status, and intelligence are commonly used as predictors of health outcomes, social environment, and mortality. Education and socioeconomic status are typically viewed as environmental variables although both correlate with intelligence, which has a substantial genetic basis. Using data from 6815 unrelated subjects from the Generation Scotland study, we examined the genetic contributions to these variables and their genetic correlations. Subjects underwent genome-wide testing for common single nucleotide polymorphisms (SNPs). DNA-derived heritability estimates and genetic correlations were calculated using the 'Genome-wide Complex Trait Analyses' (GCTA) procedures. 21% of the variation in education, 18% of the variation in socioeconomic status, and 29% of the variation in general cognitive ability was explained by variation in common SNPs (SEs ~ 5%). The SNP-based genetic correlations of education and socioeconomic status with general intelligence were 0.95 (SE 0.13) and 0.26 (0.16), respectively. There are genetic contributions to intelligence and education with near-complete overlap between common additive SNP effects on these traits (genetic correlation ~ 1). Genetic influences on socioeconomic status are also associated with the genetic foundations of intelligence. The results are also compatible with substantial environmental contributions to socioeconomic status.

Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

PubMed

Wang, Daxi; Korhonen, Pasi K; Gasser, Robin B; Young, Neil D

Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. Copyright © 2018 Elsevier Inc. All rights reserved.

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...

Tissue culture-induced genetic and epigenetic variation in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927) regenerants.

PubMed

Machczyńska, Joanna; Zimny, Janusz; Bednarek, Piotr Tomasz

2015-10-01

Plant regeneration via in vitro culture can induce genetic and epigenetic variation; however, the extent of such changes in triticale is not yet understood. In the present study, metAFLP, a variation of methylation-sensitive amplified fragment length polymorphism analysis, was used to investigate tissue culture-induced variation in triticale regenerants derived from four distinct genotypes using androgenesis and somatic embryogenesis. The metAFLP technique enabled identification of both sequence and DNA methylation pattern changes in a single experiment. Moreover, it was possible to quantify subtle effects such as sequence variation, demethylation, and de novo methylation, which affected 19, 5.5, 4.5% of sites, respectively. Comparison of variation in different genotypes and with different in vitro regeneration approaches demonstrated that both the culture technique and genetic background of donor plants affected tissue culture-induced variation. The results showed that the metAFLP approach could be used for quantification of tissue culture-induced variation and provided direct evidence that in vitro plant regeneration could cause genetic and epigenetic variation.

Local adaptation within a hybrid species

PubMed Central

Eroukhmanoff, F; Hermansen, J S; Bailey, R I; Sæther, S A; Sætre, G-P

2013-01-01

Ecological divergence among populations may be strongly influenced by their genetic background. For instance, genetic admixture through introgressive hybridization or hybrid speciation is likely to affect the genetic variation and evolvability of phenotypic traits. We studied geographic variation in two beak dimensions and three other phenotypic traits of the Italian sparrow (Passer italiae), a young hybrid species formed through interbreeding between house sparrows (P. domesticus) and Spanish sparrows (P. hispaniolensis). We found that beak morphology was strongly influenced by precipitation regimes and that it appeared to be the target of divergent selection within Italian sparrows. Interestingly, however, the degree of parental genetic contribution in the hybrid species had no effect on phenotypic beak variation. Moreover, beak height divergence may mediate genetic differentiation between populations, consistent with isolation-by-adaptation within this hybrid species. The study illustrates how hybrid species may be relatively unconstrained by their admixed genetic background, allowing them to adapt rapidly to environmental variation. PMID:23695379

Population differentiation and behavioural association of the two 'personality' genes DRD4 and SERT in dunnocks (Prunella modularis).

PubMed

Holtmann, B; Grosser, S; Lagisz, M; Johnson, S L; Santos, E S A; Lara, C E; Robertson, B C; Nakagawa, S

2016-02-01

Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two 'personality' genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced (New Zealand, NZ) population of dunnocks, Prunella modularis. The NZ population showed a significantly lower number of single nucleotide polymorphisms (SNPs) compared to the UK population. Standardized F'st estimates of the personality genes and neutral microsatellites indicate that selection (anthropogenic and natural) probably occurred during and post the introduction event. Notably, the largest genetic differentiation was found in the intronic regions of the genes. In the NZ population, we also examined the association between polymorphisms in DRD4 and SERT and two highly repeatable behavioural traits: flight-initiation distance and mating status (promiscuous females and cobreeding males). We found 38 significant associations (for different allele effect models) between the two behavioural traits and the studied genes. Further, 22 of the tested associations showed antagonistic allele effects for males and females. Our findings illustrate how introduction events and accompanying ecological changes could influence the genetic diversity of behaviour-related genes. © 2015 John Wiley & Sons Ltd.

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

USDA-ARS?s Scientific Manuscript database

Background: Crossover generated by meiotic recombination is a fundamental event which facilitates meiosis and sexual reproduction. Comparative studies have shown wide variation in recombination between species, but the characterization of recombination between bovine breeds remains elusive. Cattle p...

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Genetic Architecture of Micro-Environmental Plasticity in Drosophila melanogaster

PubMed Central

Morgante, Fabio; Sørensen, Peter; Sorensen, Daniel A.; Maltecca, Christian; Mackay, Trudy F. C.

2015-01-01

Individuals of the same genotype do not have the same phenotype for quantitative traits when reared under common macro-environmental conditions, a phenomenon called micro-environmental plasticity. Genetic variation in micro-environmental plasticity is assumed in models of the evolution of phenotypic variance, and is important in applied breeding and personalized medicine. Here, we quantified genetic variation for micro-environmental plasticity for three quantitative traits in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel. We found substantial genetic variation for micro-environmental plasticity for all traits, with broad sense heritabilities of the same magnitude or greater than those of trait means. Micro-environmental plasticity is not correlated with residual segregating variation, is trait-specific, and has genetic correlations with trait means ranging from zero to near unity. We identified several candidate genes associated with micro-environmental plasticity of startle response, including Drosophila Hsp90, setting the stage for future genetic dissection of this phenomenon. PMID:25943032

Genetic relations among procrastination, impulsivity, and goal-management ability: implications for the evolutionary origin of procrastination.

PubMed

Gustavson, Daniel E; Miyake, Akira; Hewitt, John K; Friedman, Naomi P

2014-06-01

Previous research has revealed a moderate and positive correlation between procrastination and impulsivity. However, little is known about why these two constructs are related. In the present study, we used behavior-genetics methodology to test three predictions derived from an evolutionary account that postulates that procrastination arose as a by-product of impulsivity: (a) Procrastination is heritable, (b) the two traits share considerable genetic variation, and (c) goal-management ability is an important component of this shared variation. These predictions were confirmed. First, both procrastination and impulsivity were moderately heritable (46% and 49%, respectively). Second, although the two traits were separable at the phenotypic level (r = .65), they were not separable at the genetic level (r genetic = 1.0). Finally, variation in goal-management ability accounted for much of this shared genetic variation. These results suggest that procrastination and impulsivity are linked primarily through genetic influences on the ability to use high-priority goals to effectively regulate actions. © The Author(s) 2014.

Local adaptation and evolutionary potential along a temperature gradient in the fungal pathogen Rhynchosporium commune

PubMed Central

Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

2013-01-01

To predict the response of plant pathogens to climate warming, data are needed on current thermal adaptation, the pathogen's evolutionary potential, and the link between them. We conducted a common garden experiment using isolates of the fungal pathogen Rhynchosporium commune from nine barley populations representing climatically diverse locations. Clonal replicates of 126 genetically distinct isolates were assessed for their growth rate at 12°C, 18°C, and 22°C. Populations originating from climates with higher monthly temperature variation had higher growth rate at all three temperatures compared with populations from climates with less temperature fluctuation. Population differentiation in growth rate (QST) was significantly higher at 22°C than population differentiation for neutral microsatellite loci (GST), consistent with local adaptation for growth at higher temperatures. At 18°C, we found evidence for stabilizing selection for growth rate as QST was significantly lower than GST. Heritability of growth rate under the three temperatures was substantial in all populations (0.58–0.76). Genetic variation was lower in populations with higher growth rate at the three temperatures and evolvability increased under heat stress in seven of nine populations. Our findings imply that the distribution of this pathogen is unlikely to be genetically limited under climate warming, due to its high genetic variation and plasticity for thermal tolerance. PMID:23745143

Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam

PubMed Central

Wang, Baosheng; Khalili Mahani, Marjan; Ng, Wei Lun; Kusumi, Junko; Phi, Hai Hong; Inomata, Nobuyuki; Wang, Xiao-Ru; Szmidt, Alfred E

2014-01-01

Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P. krempfii. In this study, we sampled 57 individuals from six natural populations of P. krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9 kb) and 14 mitochondrial (mt) DNA regions (approximately 10 kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P. krempfii genetic resources were discussed. PMID:25360263

Genetic variation of habitual coffee consumption and glycemic changes in response to weight-loss diet intervention: the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial.

PubMed

Han, Liyuan; Ma, Wenjie; Sun, Dianjianyi; Heianza, Yoriko; Wang, Tiange; Zheng, Yan; Huang, Tao; Duan, Donghui; Bray, J George A; Champagne, Catherine M; Sacks, Frank M; Qi, Lu

2017-11-01

Background: Coffee consumption has been associated with glucose metabolism and risk of type 2 diabetes. Objective: We examined whether the genetic variation determining habitual coffee consumption affected glycemic changes in response to weight-loss dietary intervention. Design: A genetic risk score (GRS) was calculated based on 8 habitual coffee consumption-associated single nucleotide polymorphisms. We used general linear models to test changes in glycemic traits in groups randomly assigned to high- and low-fat diets according to tertiles of the GRS. Results: We observed significant interactions between the GRS and low compared with high dietary fat intake on 6-mo changes in fasting insulin and homeostasis model assessment of insulin resistance (HOMA-IR) ( P -interaction = 0.023 and 0.022, respectively), adjusting for age, sex, race, physical activity, smoking, alcohol, seasonal variation, and baseline values of the respective outcomes. Participants with a higher GRS of habitual coffee consumption showed a greater reduction in fasting insulin and a marginally greater decrease in HOMA-IR in the low-fat diet intervention group. Conclusions: Our data suggest that participants with genetically determined high coffee consumption may benefit more by eating a low-fat diet in improving fasting insulin and HOMA-IR in a short term. This trial was registered at clinicaltrials.gov as NCT00072995 and NCT03258203. © 2017 American Society for Nutrition.

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

Genetic variation within and among populations of Rhodiola alsia (Crassulaceae) native to the Tibetan Plateau as detected by ISSR markers.

PubMed

Xia, Tao; Chen, Shilong; Chen, Shengyun; Ge, Xuejun

2005-04-01

Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai-Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai-Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.

Tolerance to deer herbivory and resistance to insect herbivores in the common evening primrose (Oenothera biennis).

PubMed

Puentes, A; Johnson, M T J

2016-01-01

The evolution of plant defence in response to herbivory will depend on the fitness effects of damage, availability of genetic variation and potential ecological and genetic constraints on defence. Here, we examine the potential for evolution of tolerance to deer herbivory in Oenothera biennis while simultaneously considering resistance to natural insect herbivores. We examined (i) the effects of deer damage on fitness, (ii) the presence of genetic variation in tolerance and resistance, (iii) selection on tolerance, (iv) genetic correlations with resistance that could constrain evolution of tolerance and (v) plant traits that might predict defence. In a field experiment, we simulated deer damage occurring early and late in the season, recorded arthropod abundances, flowering phenology and measured growth rate and lifetime reproduction. Our study showed that deer herbivory has a negative effect on fitness, with effects being more pronounced for late-season damage. Selection acted to increase tolerance to deer damage, yet there was low and nonsignificant genetic variation in this trait. In contrast, there was substantial genetic variation in resistance to insect herbivores. Resistance was genetically uncorrelated with tolerance, whereas positive genetic correlations in resistance to insect herbivores suggest there exists diffuse selection on resistance traits. In addition, growth rate and flowering time did not predict variation in tolerance, but flowering phenology was genetically correlated with resistance. Our results suggest that deer damage has the potential to exert selection because browsing reduces plant fitness, but limited standing genetic variation in tolerance is expected to constrain adaptive evolution in O. biennis. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Proceedings of the symposium on isozymes of North American forest trees and forest insects; July 27, 1979; Berkeley, California

Treesearch

M. Thompson Conkle

1981-01-01

These 10 symposium papers discuss gene resource management, basic genetics, genetic variation between and within tree species, genetic variability and growth, comparisons of tree life history characteristics, genetic variation in forest insects, breeding systems, and applied uses of isozymes in breeding programs.

Molecular Population Genetics

PubMed Central

Casillas, Sònia; Barbadilla, Antonio

2017-01-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

Molecular Population Genetics.

PubMed

Casillas, Sònia; Barbadilla, Antonio

2017-03-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

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.

Hsp90 and environmental stress transform the adaptive value of natural genetic variation.

PubMed

Jarosz, Daniel F; Lindquist, Susan

2010-12-24

How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.

Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?

PubMed

Dodd, Richard S; Hüberli, Daniel; Douhovnikoff, Vlad; Harnik, Tamar Y; Afzal-Rafii, Zara; Garbelotto, Matteo

2005-01-01

California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high.

Genetic variation in serotonin function impacts on altruistic punishment in the ultimatum game: A longitudinal approach.

PubMed

Gärtner, Anne; Strobel, Alexander; Reif, Andreas; Lesch, Klaus-Peter; Enge, Sören

2018-05-30

Growing evidence demonstrates that the serotonin system influences punishment behavior in social decision-making and that individual differences in the propensity to punish are, at least in part, due to genetic variation. However, the specific genes and their mechanisms by which they influence punishment behavior are not yet fully characterized. Here, we examined whether serotonin system-related gene variation impacts on altruistic punishment in the ultimatum game by using a longitudinal approach with three time points, covering a time frame up to four months in young adults (N = 106). Specifically, we investigated additive effects of 5-HTTLPR and TPH2 G-703T genotypes by using a composite score. This composite score was significantly associated with altruistic punishment, with individuals carrying both the S-allele and the G-allele demonstrating less punishment behavior. The results suggest that serotonin system-related gene variation contributes to individual differences in altruistic punishment. Furthermore, comparably high test-retest correlations suggest that punishment behavior in the ultimatum game represents a relatively stable, trait-like behavior. Copyright © 2018 Elsevier Inc. All rights reserved.

Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

PubMed Central

Vargas-Rodríguez, Rosa del Carmen Miluska; da Silva Bastos, Melissa; Menezes, Maria José; Orjuela-Sánchez, Pamela; Ferreira, Marcelo U.

2012-01-01

Emerging resistance to chloroquine (CQ) poses a major challenge for Plasmodium vivax malaria control, and nucleotide substitutions and copy number variation in the P. vivax multidrug resistance 1 (pvmdr-1) locus, which encodes a digestive vacuole membrane transporter, may modulate this phenotype. We describe patterns of genetic variation in pvmdr-1 alleles from Acre and Amazonas in northwestern Brazil, and compare then with those reported in other malaria-endemic regions. The pvmdr-1 mutation Y976F, which is associated with CQ resistance in Southeast Asia and Oceania, remains rare in northwestern Brazil (1.8%) and its prevalence mirrors that of CQ resistance worldwide. Gene amplification of pvmdr-1, which is associated with mefloquine resistance but increased susceptibility to CQ, remains relatively rare in northwestern Brazil (0.9%) and globally (< 4%), but became common (> 10%) in Tak Province, Thailand, possibly because of drug-mediated selection. The global database we have assembled provides a baseline for further studies of genetic variation in pvmdr-1 and drug resistance in P. vivax malaria. PMID:22949516

Single-nucleotide polymorphism and copy number variation of the multidrug resistance-1 locus of Plasmodium vivax: local and global patterns.

PubMed

Vargas-Rodríguez, Rosa del Carmen Miluska; da Silva Bastos, Melissa; Menezes, Maria José; Orjuela-Sánchez, Pamela; Ferreira, Marcelo U

2012-11-01

Emerging resistance to chloroquine (CQ) poses a major challenge for Plasmodium vivax malaria control, and nucleotide substitutions and copy number variation in the P. vivax multidrug resistance 1 (pvmdr-1) locus, which encodes a digestive vacuole membrane transporter, may modulate this phenotype. We describe patterns of genetic variation in pvmdr-1 alleles from Acre and Amazonas in northwestern Brazil, and compare then with those reported in other malaria-endemic regions. The pvmdr-1 mutation Y976F, which is associated with CQ resistance in Southeast Asia and Oceania, remains rare in northwestern Brazil (1.8%) and its prevalence mirrors that of CQ resistance worldwide. Gene amplification of pvmdr-1, which is associated with mefloquine resistance but increased susceptibility to CQ, remains relatively rare in northwestern Brazil (0.9%) and globally (< 4%), but became common (> 10%) in Tak Province, Thailand, possibly because of drug-mediated selection. The global database we have assembled provides a baseline for further studies of genetic variation in pvmdr-1 and drug resistance in P. vivax malaria.

Patterns of MHC-DRB1 polymorphism in a post-glacial island canid, the Newfoundland red fox (Vulpes vulpes deletrix), suggest balancing selection at species and population timescales.

PubMed

Marshall, H Dawn; Langille, Barbara L; Hann, Crystal A; Whitney, Hugh G

2016-05-01

As the only native insular Newfoundland canid between the extinction of the wolf in the 1930s and the recent arrival of coyotes, the red fox (Vulpes vulpes deletrix Bangs 1898) poses interesting questions about genetic distinctiveness and the post-glacial colonization history of the island's depauperate mammalian fauna. Here, we characterized genetic variability at the major histocompatibility complex (MHC) class II DR β1 domain (DRB1) locus in 28 red foxes from six sampling localities island-wide and compared it with mitochondrial control region (CR) diversity and DRB1 diversity in other canids. Our goals were to describe novel DRB1 alleles in a new canid population and to make inferences about the role of selection in maintaining their diversity. As in numerous studies of vertebrates, we found an order-of-magnitude higher nucleotide diversity at the DRB1 locus compared with the CR and significantly positive nonsynonymous-to-synonymous substitution ratios, indicative of selection in the distant past. Although the evidence is weaker, the Ewens-Watterson test of neutrality and the geographical distribution of variation compared with the CR suggest a role for selection over the evolutionary timescale of populations. We report the first genetic data from the DRB1 locus in the red fox and establish baseline information regarding immunogenetic variation in this island canid population which should inform continued investigations of population demography, adaptive genetic diversity, and wildlife disease in red foxes and related species.

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates

PubMed Central

2009-01-01

Background Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay. Results 266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators. Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour. Conclusion The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics. PMID:19922635

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

PubMed Central

Watkins, WS; Thara, R; Mowry, BJ; Zhang, Y; Witherspoon, DJ; Tolpinrud, W; Bamshad, MJ; Tirupati, S; Padmavati, R; Smith, H; Nancarrow, D; Filippich, C; Jorde, LB

2008-01-01

Background Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. Results We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data. Conclusion Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions. PMID:19077280

Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India, based on chemical profiling, horticultural traits and RAPD analysis.

PubMed

Nair, Vadakkemuriyil Divya; Raj, Rajan Pillai Dinesh; Panneerselvam, Rajaram; Gopi, Ragupathi

2014-01-01

Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions. © 2013.

Social-group identity and population substructure in admixed populations in New Mexico and Latin America.

PubMed

Healy, Meghan E; Hill, Deirdre; Berwick, Marianne; Edgar, Heather; Gross, Jessica; Hunley, Keith

2017-01-01

We examined the relationship between continental-level genetic ancestry and racial and ethnic identity in an admixed population in New Mexico with the goal of increasing our understanding of how racial and ethnic identity influence genetic substructure in admixed populations. Our sample consists of 98 New Mexicans who self-identified as Hispanic or Latino (NM-HL) and who further categorized themselves by race and ethnic subgroup membership. The genetic data consist of 270 newly-published autosomal microsatellites from the NM-HL sample and previously published data from 57 globally distributed populations, including 13 admixed samples from Central and South America. For these data, we 1) summarized the major axes of genetic variation using principal component analyses, 2) performed tests of Hardy Weinberg equilibrium, 3) compared empirical genetic ancestry distributions to those predicted under a model of admixture that lacked substructure, 4) tested the hypotheses that individuals in each sample had 100%, 0%, and the sample-mean percentage of African, European, and Native American ancestry. We found that most NM-HL identify themselves and their parents as belonging to one of two groups, conforming to a region-specific narrative that distinguishes recent immigrants from Mexico from individuals whose families have resided in New Mexico for generations and who emphasize their Spanish heritage. The "Spanish" group had significantly lower Native American ancestry and higher European ancestry than the "Mexican" group. Positive FIS values, PCA plots, and heterogeneous ancestry distributions suggest that most Central and South America admixed samples also contain substructure, and that this substructure may be related to variation in social identity. Genetic substructure appears to be common in admixed populations in the Americas and may confound attempts to identify disease-causing genes and to understand the social causes of variation in health outcomes and social inequality.

Molecular and pedigree analysis applied to conservation of animal genetic resources: the case of Brazilian Somali hair sheep.

PubMed

Paiva, Samuel R; Facó, Olivardo; Faria, Danielle A; Lacerda, Thaísa; Barretto, Gabriel B; Carneiro, Paulo L S; Lobo, Raimundo N B; McManus, Concepta

2011-10-01

The first registers of Somali sheep in Brazil are from the beginning of the 1900s. This breed, adapted to the dry climate and scarce food supply, is restricted in the northeast region of the country. Molecular marker technologies, especially those based on genotyping microsatellite and mtDNA loci, can be used in conjunction with breeding (pedigree analysis) and consequently the maintenance of genetic variation in herds. Animals from the Brazilian Somali Conservation Nuclei from Embrapa Sheep and Goats in Ceará State were used to validate genetic monitoring by traditional pedigree methods and molecular markers. Nineteen microsatellite markers and 404 base pairs from the control region of mtDNA were used. For total herd diversity, an average 5.32 alleles were found, with expected heterozygosity of 0.5896, observed heterozygosity of 0.6451, 0.4126 for molecular coancestrality, and coefficient of inbreeding (F (IS)) was -0.095. Comparing molecular coancestrality means over the years, there was a consistent increase in this parameter within the herd, increasing from 0.4157 to 0.4769 in 2 years (approx. 12% variation). Sixteen mtDNA haplotypes were identified. Inbreeding and other estimates from genealogical analyses confirm the results from molecular markers. From these results, it is possible to state that microsatellites are useful tools in genetic management of herds, especially when routine herd recording is not carried out, or there were gaps in recent generations. As well as pedigree control, genetic diversity can be optimized. Based on the results, and despite herd recording in the herd of Brazilian Somali of Embrapa Sheep and Goats, additional management measures need to be carried out in this herd to reduce inbreeding and optimize genetic variation.

Environmental Variables Explain Genetic Structure in a Beetle-Associated Nematode

PubMed Central

McGaughran, Angela; Morgan, Katy; Sommer, Ralf J.

2014-01-01

The distribution of a species is a complex expression of its ecological and evolutionary history and integrating population genetic, environmental, and ecological data can provide new insights into the effects of the environment on the population structure of species. Previous work demonstrated strong patterns of genetic differentiation in natural populations of the hermaphroditic nematode Pristionchus pacificus in its La Réunion Island habitat, but gave no clear understanding of the role of the environment in structuring this variation. Here, we present what is to our knowledge the first study to statistically evaluate the role of the environment in shaping the structure and distribution of nematode populations. We test the hypothesis that genetic structure in P. pacificus is influenced by environmental variables, by combining population genetic analyses of microsatellite data from 18 populations and 370 strains, with multivariate statistics on environmental data, and species distribution modelling. We assess and quantify the relative importance of environmental factors (geographic distance, altitude, temperature, precipitation, and beetle host) on genetic variation among populations. Despite the fact that geographic populations of P. pacificus comprise vast genetic diversity sourced from multiple ancestral lineages, we find strong evidence for local associations between environment and genetic variation. Further, we show that significantly more genetic variation in P. pacificus populations is explained by environmental variation than by geographic distances. This supports a strong role for environmental heterogeneity vs. genetic drift in the divergence of populations, which we suggest may be influenced by adaptive forces. PMID:24498073

A heuristic model on the role of plasticity in adaptive evolution: plasticity increases adaptation, population viability and genetic variation.

PubMed

Gomez-Mestre, Ivan; Jovani, Roger

2013-11-22

An ongoing new synthesis in evolutionary theory is expanding our view of the sources of heritable variation beyond point mutations of fixed phenotypic effects to include environmentally sensitive changes in gene regulation. This expansion of the paradigm is necessary given ample evidence for a heritable ability to alter gene expression in response to environmental cues. In consequence, single genotypes are often capable of adaptively expressing different phenotypes in different environments, i.e. are adaptively plastic. We present an individual-based heuristic model to compare the adaptive dynamics of populations composed of plastic or non-plastic genotypes under a wide range of scenarios where we modify environmental variation, mutation rate and costs of plasticity. The model shows that adaptive plasticity contributes to the maintenance of genetic variation within populations, reduces bottlenecks when facing rapid environmental changes and confers an overall faster rate of adaptation. In fluctuating environments, plasticity is favoured by selection and maintained in the population. However, if the environment stabilizes and costs of plasticity are high, plasticity is reduced by selection, leading to genetic assimilation, which could result in species diversification. More broadly, our model shows that adaptive plasticity is a common consequence of selection under environmental heterogeneity, and hence a potentially common phenomenon in nature. Thus, taking adaptive plasticity into account substantially extends our view of adaptive evolution.

Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario

PubMed Central

Gunz, Philipp; Bookstein, Fred L.; Mitteroecker, Philipp; Stadlmayr, Andrea; Seidler, Horst; Weber, Gerhard W.

2009-01-01

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa. PMID:19307568

Heritability and genetic covariation of sensitivity to PROP, SOA, quinine HCl, and caffeine.

PubMed

Hansen, Jonathan L; Reed, Danielle R; Wright, Margaret J; Martin, Nicholas G; Breslin, Paul A S

2006-06-01

The perceived bitterness intensity for bitter solutions of propylthiouracil (PROP), sucrose octa-acetate (SOA), quinine HCl and caffeine were examined in a genetically informative sample of 392 females and 313 males (mean age of 17.8 +/- 3.1 years), including 62 monozygotic and 131 dizygotic twin pairs and 237 sib pairs. Broad-sense heritabilities were estimated at 0.72, 0.28, 0.34, and 0.30 for PROP, SOA, quinine, and caffeine, respectively, for perceived intensity measures. Modeling showed 1) a group factor which explained a large amount of the genetic variation in SOA, quinine, and caffeine (22-28% phenotypic variation), 2) a factor responsible for all the genetic variation in PROP (72% phenotypic variation), which only accounted for 1% and 2% of the phenotypic variation in SOA and caffeine, respectively, and 3) a modest specific genetic factor for quinine (12% phenotypic variation). Unique environmental influences for all four compounds were due to a single factor responsible for 7-22% of phenotypic variation. The results suggest that the perception of PROP and the perception of SOA, quinine, and caffeine are influenced by two distinct sets of genes.

Heritability and Genetic Covariation of Sensitivity to PROP, SOA, Quinine HCl, and Caffeine

PubMed Central

Hansen, Jonathan L.; Reed, Danielle R.; Wright, Margaret J.; Martin, Nicholas G.; Breslin, Paul A. S.

2006-01-01

The perceived bitterness intensity for bitter solutions of propylthiouracil (PROP), sucrose octa-acetate (SOA), quinine HCl and caffeine were examined in a genetically informative sample of 392 females and 313 males (mean age of 17.8 ± 3.1 years), including 62 MZ and 131 DZ twin pairs and 237 sib pairs. Broad-sense heritabilities were estimated at 0.72, 0.28, 0.34, and 0.30 for PROP, SOA, quinine, and caffeine, respectively, for perceived intensity measures. Modeling showed 1) a group factor which explained a large amount of the genetic variation in SOA, quinine, and caffeine (22–28% phenotypic variation), 2) a factor responsible for all the genetic variation in PROP (72% phenotypic variation), which only accounted for 1% and 2% of the phenotypic variation in SOA and caffeine, respectively, and 3) a modest specific genetic factor for quinine (12% phenotypic variation). Unique environmental influences for all four compounds were due to a single factor responsible for 7–22% of phenotypic variation. The results suggest that the perception of PROP and the perception of SOA, quinine, and caffeine are influenced by two distinct sets of genes. PMID:16527870

Complexity of genetic mechanisms conferring nonuniformity of recombination in maize.

PubMed

Pan, Qingchun; Deng, Min; Yan, Jianbing; Li, Lin

2017-04-26

Recombinations occur nonuniformly across the maize genome. To dissect the genetic mechanisms underlying the nonuniformity of recombination, we performed quantitative trait locus (QTL) mapping using recombinant inbred line populations. Genome-wide QTL scan identified hundreds of QTLs with both cis-prone and trans- effects for recombination number variation. To provide detailed insights into cis- factors associated with recombination variation, we examined the genomic features around recombination hot regions, including density of genes, DNA transposons, retrotransposons, and some specific motifs. Compared to recombination variation in whole genome, more QTLs were mapped for variations in recombination hot regions. The majority QTLs for recombination hot regions are trans-QTLs and co-localized with genes from the recombination pathway. We also found that recombination variation was positively associated with the presence of genes and DNA transposons, but negatively related to the presence of long terminal repeat retrotransposons. Additionally, 41 recombination hot regions were fine-mapped. The high-resolution genotyping of five randomly selected regions in two F 2 populations verified that they indeed have ultra-high recombination frequency, which is even higher than that of the well-known recombination hot regions sh1-bz and a1-sh2. Taken together, our results further our understanding of recombination variation in plants.

Genetic Structure of First Nation Communities in the Pacific Northwest.

PubMed

Hughes, Cris E; Rogers, Mary P; Owings, Amanda C; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; Williams, Theresa; Goldberg, Dena; Labuda, Damian; Smith, David Glenn; Cybulski, Jerome S; Malhi, Ripan S

2016-10-01

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal, and autosomal DNA variants, we aimed to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses: genetic variation was more strongly explained by geographic proximity than by linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted trees for the three genetic systems consistently separating inland from coastal PNW populations. Furthermore, analyses of molecular variance support the trends exhibited by the unrooted trees, with geographic partitioning of PNW populations (F CT = 19.43%, p = 0.010 ± 0.009) accounting for over twice as much of the observed genetic variation as linguistic partitioning of the same populations (F CT = 9.15%, p = 0.193 ± 0.013). These findings demonstrate a consensus with previous PNW population studies examining the relationships of genome-wide variation, mitochondrial haplogroup frequencies, and skeletal morphology with geography and language.

Linking Genetic Variation in Adaptive Plant Traits to Climate in Tetraploid and Octoploid Basin Wildrye [Leymus cinereus (Scribn. & Merr.) A. Love] in the Western U.S.

PubMed

Johnson, R C; Vance-Borland, Ken

2016-01-01

Few studies have assessed how ploidy type within a species affects genetic variation among populations in relation to source climates. Basin wildrye (Leymus cinereus (Scribn. & Merr.) A. Love) is a large bunchgrass common in the intermountain Western U.S. found in both octoploid and tetraploid types. In common gardens at two sites over two years differences in both ploidy type and genetic variation within ploidy were observed in phenology, morphology, and production traits on 57 octoploid and 52 tetraploid basin wildrye from the intermountain Western U.S. (P<0.01). Octoploids had larger leaves, longer culms, and greater crown circumference than tetraploids but the numerical ranges of plant traits and their source climates overlapped between ploidy types. Still, among populations octoploids often had greater genetic variation for traits and occupied more diverse climates than tetraploids. Genetic variation for both ploidy types was linked to source climates in canonical correlation analysis, with the first two variates explaining 70% of the variation. Regression of those canonical variates with seed source climate variables produced models that explained 64% and 38% of the variation, respectively, and were used to map 15 seed zones covering 673,258 km2. Utilization of these seed zones will help ensure restoration with adaptive seed sources for both ploidy types. The link between genetic traits and seed source climates suggests climate driven natural selection and adaptive evolution in basin wildrye. The more diverse climates occupied by octoploids and higher trait variation suggests a higher capacity for ecological differentiation than tetraploids in the intermountain Western U.S.

The integration of quantitative genetics, paleontology, and neontology reveals genetic underpinnings of primate dental evolution.

PubMed

Hlusko, Leslea J; Schmitt, Christopher A; Monson, Tesla A; Brasil, Marianne F; Mahaney, Michael C

2016-08-16

Developmental genetics research on mice provides a relatively sound understanding of the genes necessary and sufficient to make mammalian teeth. However, mouse dentitions are highly derived compared with human dentitions, complicating the application of these insights to human biology. We used quantitative genetic analyses of data from living nonhuman primates and extensive osteological and paleontological collections to refine our assessment of dental phenotypes so that they better represent how the underlying genetic mechanisms actually influence anatomical variation. We identify ratios that better characterize the output of two dental genetic patterning mechanisms for primate dentitions. These two newly defined phenotypes are heritable with no measurable pleiotropic effects. When we consider how these two phenotypes vary across neontological and paleontological datasets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by a shift in these two genetic outputs. Our results build on the mouse model by combining quantitative genetics and paleontology, and thereby elucidate how genetic mechanisms likely underlie major events in primate evolution.

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

PubMed

Cortázar-Chinarro, Maria; Lattenkamp, Ella Z; Meyer-Lucht, Yvonne; Luquet, Emilien; Laurila, Anssi; Höglund, Jacob

2017-08-14

Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Using outlier analyses, we identified the MHC II exon 2 (corresponding to the β-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

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

Predicting type 2 diabetes using genetic and environmental risk factors in a multi-ethnic Malaysian cohort.

PubMed

Abdullah, N; Abdul Murad, N A; Mohd Haniff, E A; Syafruddin, S E; Attia, J; Oldmeadow, C; Kamaruddin, M A; Abd Jalal, N; Ismail, N; Ishak, M; Jamal, R; Scott, R J; Holliday, E G

2017-08-01

Malaysia has a high and rising prevalence of type 2 diabetes (T2D). While environmental (non-genetic) risk factors for the disease are well established, the role of genetic variations and gene-environment interactions remain understudied in this population. This study aimed to estimate the relative contributions of environmental and genetic risk factors to T2D in Malaysia and also to assess evidence for gene-environment interactions that may explain additional risk variation. This was a case-control study including 1604 Malays, 1654 Chinese and 1728 Indians from the Malaysian Cohort Project. The proportion of T2D risk variance explained by known genetic and environmental factors was assessed by fitting multivariable logistic regression models and evaluating McFadden's pseudo R 2 and the area under the receiver-operating characteristic curve (AUC). Models with and without the genetic risk score (GRS) were compared using the log likelihood ratio Chi-squared test and AUCs. Multiplicative interaction between genetic and environmental risk factors was assessed via logistic regression within and across ancestral groups. Interactions were assessed for the GRS and its 62 constituent variants. The models including environmental risk factors only had pseudo R 2 values of 16.5-28.3% and AUC of 0.75-0.83. Incorporating a genetic score aggregating 62 T2D-associated risk variants significantly increased the model fit (likelihood ratio P-value of 2.50 × 10 -4 -4.83 × 10 -12 ) and increased the pseudo R 2 by about 1-2% and AUC by 1-3%. None of the gene-environment interactions reached significance after multiple testing adjustment, either for the GRS or individual variants. For individual variants, 33 out of 310 tested associations showed nominal statistical significance with 0.001 < P < 0.05. This study suggests that known genetic risk variants contribute a significant but small amount to overall T2D risk variation in Malaysian population groups. If gene-environment interactions involving common genetic variants exist, they are likely of small effect, requiring substantially larger samples for detection. Copyright © 2017 The Royal Society for Public Health. All rights reserved.

Whole genome comparison of donor and cloned dogs

PubMed Central

Kim, Hak-Min; Cho, Yun Sung; Kim, Hyunmin; Jho, Sungwoong; Son, Bongjun; Choi, Joung Yoon; Kim, Sangsoo; Lee, Byeong Chun; Bhak, Jong; Jang, Goo

2013-01-01

Cloning is a process that produces genetically identical organisms. However, the genomic degree of genetic resemblance in clones needs to be determined. In this report, the genomes of a cloned dog and its donor were compared. Compared with a human monozygotic twin, the genome of the cloned dog showed little difference from the genome of the nuclear donor dog in terms of single nucleotide variations, chromosomal instability, and telomere lengths. These findings suggest that cloning by somatic cell nuclear transfer produced an almost identical genome. The whole genome sequence data of donor and cloned dogs can provide a resource for further investigations on epigenetic contributions in phenotypic differences. PMID:24141358

Association of serotonin transporter promoter regulatory region polymorphism and cerebral activity to visual presentation of food.

PubMed

Kaurijoki, Salla; Kuikka, Jyrki T; Niskanen, Eini; Carlson, Synnöve; Pietiläinen, Kirsi H; Pesonen, Ullamari; Kaprio, Jaakko M; Rissanen, Aila; Tiihonen, Jari; Karhunen, Leila

2008-07-01

Recent functional magnetic resonance imaging (fMRI) studies have revealed links between genetic polymorphisms and cognitive and behavioural processes. Serotonin is a classical neurotransmitter of central nervous system, and it is connected to the control of appetite and satiety. In this study, the relationship between the functional variation in the serotonin transporter gene and the activity in the left posterior cingulate cortex (PCC), a brain area activated by visual food stimuli was explored. Thirty subjects underwent serial fMRI studies and provided DNA for genetic analyses. Subjects homozygous for the long allele exhibited greater left PCC activity in the comparison food > non-food compared with individuals heterozygous or homozygous for the short allele. The association between genotype and activation was linear, the subjects with two copies of the long allele variant having the strongest activation. These results demonstrate the possible genetically driven variation in the response of the left PCC to visual presentation of food in humans.

Museum genomics: low-cost and high-accuracy genetic data from historical specimens.

PubMed

Rowe, Kevin C; Singhal, Sonal; Macmanes, Matthew D; Ayroles, Julien F; Morelli, Toni Lyn; Rubidge, Emily M; Bi, Ke; Moritz, Craig C

2011-11-01

Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome. © 2011 Blackwell Publishing Ltd.

Comparative analysis of genetic diversity among Indian populations of Scirpophaga incertulas by ISSR-PCR and RAPD-PCR.

PubMed

Kumar, L S; Sawant, A S; Gupta, V S; Ranjekar, P K

2001-10-01

Genetic variation between 28 Indian populations of the rice pest, Scirpophaga incertulas was evaluated using inter-simple sequence repeats (ISSR)-PCR assay. Nine SSR primers gave rise to 79 amplification products of which 67 were polymorphic. A dendrogram constructed from this data indicates that there is no geographical bias to the clustering and that gene flow between populations appears to be relatively unrestricted, substantiating our earlier conclusion based on the RAPD (random amplified polymorphic DNA) data. The dendrograms obtained using each of these marker systems were poorly correlated with each other as determined by Mantel's test for matrix correlation. Estimates of expected heterozygosity and marker index for each of these marker systems suggests that both these marker systems are equally efficient in determining polymorphisms. Matrix correlation analyses suggest that reliable estimates of genetic variation among the S. incertulas pest populations can be obtained by using RAPDs alone or in combination with ISSRs, but ISSRs alone cannot be used for this purpose.

Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

PubMed Central

Zhang, Chunyan; Plastow, Graham

2011-01-01

We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (FIS), population differentiation (FST), and Nei’s genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher FIS, and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies. PMID:21966252

Undergraduates achieve learning gains in plant genetics through peer teaching of secondary students.

PubMed

Chrispeels, H E; Klosterman, M L; Martin, J B; Lundy, S R; Watkins, J M; Gibson, C L; Muday, G K

2014-01-01

This study tests the hypothesis that undergraduates who peer teach genetics will have greater understanding of genetic and molecular biology concepts as a result of their teaching experiences. Undergraduates enrolled in a non-majors biology course participated in a service-learning program in which they led middle school (MS) or high school (HS) students through a case study curriculum to discover the cause of a green tomato variant. The curriculum explored plant reproduction and genetic principles, highlighting variation in heirloom tomato fruits to reinforce the concept of the genetic basis of phenotypic variation. HS students were taught additional activities related to mole-cular biology techniques not included in the MS curriculum. We measured undergraduates' learning outcomes using pre/postteaching content assessments and the course final exam. Undergraduates showed significant gains in understanding of topics related to the curriculum they taught, compared with other course content, on both types of assessments. Undergraduates who taught HS students scored higher on questions specific to the HS curriculum compared with undergraduates who taught MS students, despite identical lecture content, on both types of assessments. These results indicate the positive effect of service-learning peer-teaching experiences on undergraduates' content knowledge, even for non-science major students. © 2014 H. E. Chrispeels et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut

PubMed Central

Small, Clayton M.; Milligan-Myhre, Kathryn; Bassham, Susan; Guillemin, Karen

2017-01-01

Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes. PMID:28391321

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...

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

PubMed Central

Fournier-Level, Alexandre; Perry, Emily O.; Wang, Jonathan A.; Braun, Peter T.; Migneault, Andrew; Cooper, Martha D.; Metcalf, C. Jessica E.; Schmitt, Johanna

2016-01-01

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation. PMID:27140640

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana.

PubMed

Fournier-Level, Alexandre; Perry, Emily O; Wang, Jonathan A; Braun, Peter T; Migneault, Andrew; Cooper, Martha D; Metcalf, C Jessica E; Schmitt, Johanna

2016-05-17

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.

Isoprenoid emission variation of Norway spruce across a European latitudinal transect

NASA Astrophysics Data System (ADS)

van Meeningen, Ylva; Wang, Min; Karlsson, Tomas; Seifert, Ana; Schurgers, Guy; Rinnan, Riikka; Holst, Thomas

2017-12-01

Norway spruce (Picea abies) is one of the dominant tree species in the European boreal zone with the capacity to grow over large areas within Europe. It is an important emitter of biogenic volatile organic compounds (BVOCs), which can act as precursors of photochemical smog and ozone and contribute to the formation and growth of secondary organic aerosols (SOA) in the atmosphere. Isoprenoid emissions were measured from Norway spruce trees at seven different sites, distributed from Ljubljana in Slovenia to Piikkiö in Finland. Four of the sites were part of a network of genetically identical spruce trees and contained two separate provenances. The remaining three sites were part of other networks which have been used to conduct studies in the European boreal zone. There were minimal differences in the standardized emission rates between sites and across latitudes. The emission profile differed between provenances and sites, but there were not any distinct patterns which could be connected to a change in latitude. By using genetically identical trees and comparing the emission rates between sites and with genetically different trees, it was observed that the emission patterns were mostly influenced by genetics. But in order to confirm this possible stability of the relative emission profile based on genetics, more studies need to be performed. The effects of branch height, season and variation between years on observed emission pattern variations were also investigated. There were indications of potential influences of all three factors. However, due to different experimental setups between measurement campaigns, it is difficult to draw any robust conclusions.

Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

2015-01-01

Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster.

PubMed

Magwire, Michael M; Fabian, Daniel K; Schweyen, Hannah; Cao, Chuan; Longdon, Ben; Bayer, Florian; Jiggins, Francis M

2012-01-01

Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations. We have used genome-wide association studies (GWAS) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection. We found that there is substantially more genetic variation in susceptibility to two viruses that naturally infect D. melanogaster (DCV and DMelSV) than to two viruses isolated from other insects (FHV and DAffSV). Furthermore, this increased variation is caused by a small number of common polymorphisms that have a major effect on resistance and can individually explain up to 47% of the heritability in disease susceptibility. For two of these polymorphisms, it has previously been shown that they have been driven to a high frequency by natural selection. An advantage of GWAS in Drosophila is that the results can be confirmed experimentally. We verified that a gene called pastrel--which was previously not known to have an antiviral function--is associated with DCV-resistance by knocking down its expression by RNAi. Our data suggest that selection for resistance to infectious disease can increase genetic variation by increasing the frequency of major-effect alleles, and this has resulted in a simple genetic basis to variation in virus resistance.

Forensic genetics and ethical, legal and social implications beyond the clinic

PubMed Central

Cho, Mildred K; Sankar, Pamela

2008-01-01

Data on human genetic variation help scientists to understand human origins, susceptibility to illness and genetic causes of disease. Destructive episodes in the history of genetic research make it crucial to consider the ethical and social implications of research in genomics, especially human genetic variation. The analysis of ethical, legal and social implications should be integrated into genetic research, with the participation of scientists who can anticipate and monitor the full range of possible applications of the research from the earliest stages. The design and implementation of research directs the ways in which its results can be used, and data and technology, rather than ethical considerations or social needs, drive the use of science in unintended ways. Here we examine forensic genetics and argue that all geneticists should anticipate the ethical and social issues associated with nonmedical applications of genetic variation research. PMID:15510102

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...

Unleashing the power of human genetic variation knowledge: New Zealand stakeholder perspectives.

PubMed

Gu, Yulong; Warren, James Roy; Day, Karen Jean

2011-01-01

This study aimed to characterize the challenges in using genetic information in health care and to identify opportunities for improvement. Taking a grounded theory approach, semistructured interviews were conducted with 48 participants to collect multiple stakeholder perspectives on genetic services in New Zealand. Three themes emerged from the data: (1) four service delivery models were identified in operation, including both those expected models involving genetic counselors and variations that do not route through the formal genetic service program; (2) multiple barriers to sharing and using genetic information were perceived, including technological, organizational, institutional, legal, ethical, and social issues; and (3) impediments to wider use of genetic testing technology, including variable understanding of genetic test utilities among clinicians and the limited capacity of clinical genetic services. Targeting these problems, information technologies and knowledge management tools have the potential to support key tasks in genetic services delivery, improve knowledge processes, and enhance knowledge networks. Because of the effect of issues in genetic information and knowledge management, the potential of human genetic variation knowledge to enhance health care delivery has been put on a "leash."

Biophysical Aspects of Spindle Evolution

NASA Astrophysics Data System (ADS)

Farhadifar, Reza; Baer, Charlie; Needleman, Daniel

2011-03-01

The continual propagation of genetic material from one generation to the next is one of the most basic characteristics of all organisms. In eukaryotes, DNA is segregated into the two daughter cells by a highly dynamic, self-organizing structure called the mitotic spindle. Mitotic spindles can show remarkable variability between tissues and organisms, but there is currently little understanding of the biophysical and evolutionary basis of this diversity. We are studying how spontaneous mutations modify cell division during nematode development. By comparing the mutational variation - the raw material of evolution - with the variation present in nature, we are investigating how the mitotic spindle is shaped over the course of evolution. This combination of quantitative genetics and cellular biophysics gives insight into how the structure and dynamics of the spindle is formed through selection, drift, and biophysical constraints.

Changes in composition of cuticular biochemicals of the facultatively polygynous ant Petalomyrmex phylax during range expansion in Cameroon with respect to social, spatial and genetic variation.

PubMed

Dalecky, Ambroise; Renucci, Marielle; Tirard, Alain; Debout, Gabriel; Roux, Maurice; Kjellberg, Finn; Provost, Erick

2007-09-01

In social insects, biochemicals found at the surface of the cuticle are involved in the recognition process and in protection against desiccation and pathogens. However, the relative contribution of evolutionary forces in shaping diversity of these biochemicals remains largely unresolved in ants. We determined the composition of epicuticular biochemicals for workers sampled in 12 populations of the ant Petalomyrmex phylax from Cameroon. Genetic variation at 12 microsatellite markers was used to infer population history and to provide null expectations under the neutrality hypothesis. Genetic data suggest a recent southward range expansion of this ant species. Furthermore, there is a decline southward in the numbers of queens present in mature colonies. Here, we contrast the pattern of biochemical variation against genetic, social and spatial parameters. We thus provide the first estimates of the relative contribution of neutral and selective processes on variation of ant cuticular profile. Populations in migration-drift disequilibrium showed reduction of within-population variation for genetic markers as well as for cuticular profiles. In these populations, the cuticular profile became biased towards a limited number of high molecular weight molecules. Within- and among-population biochemical variation was explained by both genetic and social variation and by the spatial distribution of populations. We therefore propose that during range expansion of P. phylax, the composition of epicuticular compounds has been affected by a combination of neutral processes - genetic drift and spatially limited dispersal - and spatially varying selection, social organization and environmental effects.

Conserved Genetic Architecture Underlying Individual Recombination Rate Variation in a Wild Population of Soay Sheep (Ovis aries)

PubMed Central

Johnston, Susan E.; Bérénos, Camillo; Slate, Jon; Pemberton, Josephine M.

2016-01-01

Meiotic recombination breaks down linkage disequilibrium (LD) and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and in understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rates. Individual rates were high relative to other mammal systems and were higher in males than in females (autosomal map lengths of 3748 and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 and 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a subtelomeric region on chromosome 6; a genome-wide association study showed the strongest associations at locus RNF212, with further associations observed at a nearby ∼374-kb region of complete LD containing three additional candidate loci, CPLX1, GAK, and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle, and humans, suggesting a common genetic architecture of recombination rate variation in mammals. PMID:27029733

Genetic Variation within a Lotic Population of Janthinobacterium lividum

PubMed Central

Saeger, Jennifer L.; Hale, Alan B.

1993-01-01

An understanding of the genetic variation within and between populations should allow scientists to address many problems, including those associated with endangered species and the release of genetically modified organisms into the environment. With respect to microorganisms, the release of genetically engineered microorganisms is likely to increase dramatically given the current growth in the bioremediation industry. In this study, genetic variation within a lotic, bacterial population of Janthinobacterium lividum was measured with restriction fragment length polymorphism analysis. Chromosomal DNA from 10 Kettle Creek (Hawk Mountain Sanctuary, Kempton, Pa.) J. lividum isolates was digested with six restriction endonucleases and probed with a 7.5-kb pKK3535 fragment containing the E. coli rrnB rRNA operon. Genetic variation, as measured in terms of nucleotide diversity, was high within the population. The 0.0781 value for genetic variation was especially high given the conservative nature of the genetic probe. The average percent similarity among isolates within the population was 67.25%. Pairwise comparisons of nucleotide diversity values (π) and similarity coefficients (F) yielded values ranging from 0.0032 to 0.1816 and 0.3363 to 0.9808, respectively. Putative clonemates were not present within the group of isolates; however, all isolates shared 14 fragments across a spectrum of six restriction enzymes. The presence of these common fragments indicates that restriction fragment length polymorphism analysis may provide population- or species-specific diagnostic markers for J. lividum. Data that suggest a plume effect with respect to the downstream movement of J. lividum are also presented. An increase in genetic variation within groups of isolates along the longitudinal gradient of Kettle Creek is also suggested. PMID:16348995

Genetic Variation within a Lotic Population of Janthinobacterium lividum.

PubMed

Saeger, J L; Hale, A B

1993-07-01

An understanding of the genetic variation within and between populations should allow scientists to address many problems, including those associated with endangered species and the release of genetically modified organisms into the environment. With respect to microorganisms, the release of genetically engineered microorganisms is likely to increase dramatically given the current growth in the bioremediation industry. In this study, genetic variation within a lotic, bacterial population of Janthinobacterium lividum was measured with restriction fragment length polymorphism analysis. Chromosomal DNA from 10 Kettle Creek (Hawk Mountain Sanctuary, Kempton, Pa.) J. lividum isolates was digested with six restriction endonucleases and probed with a 7.5-kb pKK3535 fragment containing the E. coli rrnB rRNA operon. Genetic variation, as measured in terms of nucleotide diversity, was high within the population. The 0.0781 value for genetic variation was especially high given the conservative nature of the genetic probe. The average percent similarity among isolates within the population was 67.25%. Pairwise comparisons of nucleotide diversity values (pi) and similarity coefficients (F) yielded values ranging from 0.0032 to 0.1816 and 0.3363 to 0.9808, respectively. Putative clonemates were not present within the group of isolates; however, all isolates shared 14 fragments across a spectrum of six restriction enzymes. The presence of these common fragments indicates that restriction fragment length polymorphism analysis may provide population- or species-specific diagnostic markers for J. lividum. Data that suggest a plume effect with respect to the downstream movement of J. lividum are also presented. An increase in genetic variation within groups of isolates along the longitudinal gradient of Kettle Creek is also suggested.

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.

Antigenic variation: Molecular and genetic mechanisms of relapsing disease

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

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.

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

PubMed

Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

2013-08-01

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure. © 2013 John Wiley & Sons Ltd.

A test of the influence of continental axes of orientation on patterns of human gene flow

PubMed Central

Ramachandran, Sohini; Rosenberg, Noah A.

2012-01-01

The geographic distribution of genetic variation reflects trends in past population migrations, and can be used to make inferences about these migrations. It has been proposed that the east-west orientation of the Eurasian landmass facilitated the rapid spread of ancient technological innovations across Eurasia, while the north-south orientation of the Americas led to a slower diffusion of technology there. If the diffusion of technology was accompanied by gene flow, then this hypothesis predicts that genetic differentiation in the Americas along lines of longitude will be greater than that in Eurasia along lines of latitude. We use 678 microsatellite loci from 68 indigenous populations in Eurasia and the Americas to investigate the spatial axes that underlie population-genetic variation. We find that genetic differentiation increases more rapidly along lines of longitude in the Americas than along lines of latitude in Eurasia. Distance along lines of latitude explains a sizeable portion of genetic distance in Eurasia, whereas distance along lines of longitude does not explain a large proportion of Eurasian genetic variation. Genetic differentiation in the Americas occurs along both latitudinal and longitudinal axes and has a greater magnitude than corresponding differentiation in Eurasia, even when adjusting for the lower level of genetic variation in the American populations. These results support the view that continental orientation has influenced migration patterns and has played an important role in determining both the structure of human genetic variation and the distribution and spread of cultural traits. (240 words) PMID:21913175

Single nucleotide polymorphism (SNP) variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves, dogs, and coyotes in North America.

PubMed

Cronin, Matthew A; Cánovas, Angela; Bannasch, Danika L; Oberbauer, Anita M; Medrano, Juan F

2015-01-01

There is considerable interest in the genetics of wolves (Canis lupus) because of their close relationship to domestic dogs (C. familiaris) and the need for informed conservation and management. This includes wolf populations in Southeast Alaska for which we determined genotypes of 305 wolves at 173662 single nucleotide polymorphism (SNP) loci. After removal of invariant and linked SNP, 123801 SNP were used to quantify genetic differentiation of wolves in Southeast Alaska and wolves, coyotes (C. latrans), and dogs from other areas in North America. There is differentiation of SNP allele frequencies between the species (wolves, coyotes, and dogs), although differentiation is relatively low between some wolf and coyote populations. There are varying levels of differentiation among populations of wolves, including low differentiation of wolves in interior Alaska, British Columbia, and the northern US Rocky Mountains. There is considerable differentiation of SNP allele frequencies of wolves in Southeast Alaska from wolves in other areas. However, wolves in Southeast Alaska are not a genetically homogeneous group and there are comparable levels of genetic differentiation among areas within Southeast Alaska and between Southeast Alaska and other geographic areas. SNP variation and other genetic data are discussed regarding taxonomy and management. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic component of sensitivity to heat stress for nonreturn rate of Brazilian Holstein cattle.

PubMed

Santana, M L; Bignardi, A B; Stefani, G; El Faro, L

2017-08-01

The objectives of the present study were: 1) to investigate variation in the genetic component of heat stress for nonreturn rate at 56 days after first artificial insemination (NR56); 2) to identify and characterize the genotype by environment interaction (G × E) due to heat stress for NR56 of Brazilian Holstein cattle. A linear random regression model (reaction norm model) was applied to 51,748 NR56 records of 28,595 heifers and multiparous cows. The decline in NR56 due to heat stress was more pronounced in milking cows compared to heifers. The age of females at first artificial insemination and temperature-humidity index (THI) exerted an important influence on the genetic parameters of NR56. Several evidence of G × E on NR56 were found as the high slope/intercept ratio and frequent intersection of reaction norms. Additionally, the genetic correlation between NR56 at opposite extremes of the THI scale reached estimates below zero, indicating that few of the same genes are responsible for NR56 under conditions of thermoneutrality and heat stress. The genetic evaluation and selection for NR56 in Holstein cattle reared under (sub)tropical conditions should therefore take into consideration the genetic variation on age at insemination and G × E due to heat stress. Copyright © 2017 Elsevier Inc. All rights reserved.

DYZ1 arrays show sequence variation between the monozygotic males

PubMed Central

2014-01-01

Background Monozygotic twins (MZT) are an important resource for genetical studies in the context of normal and diseased genomes. In the present study we used DYZ1, a satellite fraction present in the form of tandem arrays on the long arm of the human Y chromosome, as a tool to uncover sequence variations between the monozygotic males. Results We detected copy number variation, frequent insertions and deletions within the sequences of DYZ1 arrays amongst all the three sets of twins used in the present study. MZT1b showed loss of 35 bp compared to that in 1a, whereas 2a showed loss of 31 bp compared to that in 2b. Similarly, 3b showed 10 bp insertion compared to that in 3a. MZT1a germline DNA showed loss of 5 bp and 1b blood DNA showed loss of 26 bp compared to that of 1a blood and 1b germline DNA, respectively. Of the 69 restriction sites detected in DYZ1 arrays, MboII, BsrI, TspEI and TaqI enzymes showed frequent loss and or gain amongst all the 3 pairs studied. MZT1 pair showed loss/gain of VspI, BsrDI, AgsI, PleI, TspDTI, TspEI, TfiI and TaqI restriction sites in both blood and germline DNA. All the three sets of MZT showed differences in the number of DYZ1 copies. FISH signals reflected somatic mosaicism of the DYZ1 copies across the cells. Conclusions DYZ1 showed both sequence and copy number variation between the MZT males. Sequence variation was also noticed between germline and blood DNA samples of the same individual as we observed at least in one set of sample. The result suggests that DYZ1 faithfully records all the genetical changes occurring after the twining which may be ascribed to the environmental factors. PMID:24495361

Geologic events coupled with Pleistocene climatic oscillations drove genetic variation of Omei treefrog (Rhacophorus omeimontis) in southern China.

PubMed

Li, Jun; Zhao, Mian; Wei, Shichao; Luo, Zhenhua; Wu, Hua

2015-12-21

Pleistocene climatic oscillations and historical geological events may both influence current patterns of genetic variation, and the species in southern China that faced unique climatic and topographical events have complex evolutionary histories. However, the relative contributions of climatic oscillations and geographical events to the genetic variation of these species remain undetermined. To investigate patterns of genetic variation and to test the hypotheses about the factors that shaped the distribution of this genetic variation in species of southern China, mitochondrial genes (cytochrome b and NADH dehydrogenase subunit 2) and nine microsatellite loci of the Omei tree frog (Rhacophorus omeimontis) were amplified in this study. The genetic diversity in the populations of R. omeimontis was high. The phylogenetic trees reconstructed from the mitochondrial DNA (mtDNA) haplotypes and the Bayesian genetic clustering analysis based on microsatellite data both revealed that all populations were divided into three lineages (SC, HG and YN). The two most recent splitting events among the lineages coincided with recent geological events (including the intense uplift of the Qinghai-Tibet Plateau, QTP and the subsequent movements of the Yun-Gui Plateau, YGP) and the Pleistocene glaciations. Significant expansion signals were not detected in mismatch analyses or neutrality tests. And the effective population size of each lineage was stable during the Pleistocene. Based on the results of this study, complex geological events (the recent dramatic uplift of the QTP and the subsequent movements of the YGP) and the Pleistocene glaciations were apparent drivers of the rapid divergence of the R. omeimontis lineages. Each diverged lineages survived in situ with limited gene exchanges, and the stable demographics of lineages indicate that the Pleistocene climatic oscillations were inconsequential for this species. The analysis of genetic variation in populations of R. omeimontis contributes to the understanding of the effects of changes in climate and of geographical events on the dynamic development of contemporary patterns of genetic variation in the species of southern China.

Short communication: Genetic variation of saturated fatty acids in Holsteins in the Walloon region of Belgium.

PubMed

Arnould, V M-R; Hammami, H; Soyeurt, H; Gengler, N

2010-09-01

Random regression test-day models using Legendre polynomials are commonly used for the estimation of genetic parameters and genetic evaluation for test-day milk production traits. However, some researchers have reported that these models present some undesirable properties such as the overestimation of variances at the edges of lactation. Describing genetic variation of saturated fatty acids expressed in milk fat might require the testing of different models. Therefore, 3 different functions were used and compared to take into account the lactation curve: (1) Legendre polynomials with the same order as currently applied for genetic model for production traits; 2) linear splines with 10 knots; and 3) linear splines with the same 10 knots reduced to 3 parameters. The criteria used were Akaike's information and Bayesian information criteria, percentage square biases, and log-likelihood function. These criteria indentified Legendre polynomials and linear splines with 10 knots reduced to 3 parameters models as the most useful. Reducing more complex models using eigenvalues seemed appealing because the resulting models are less time demanding and can reduce convergence difficulties, because convergence properties also seemed to be improved. Finally, the results showed that the reduced spline model was very similar to the Legendre polynomials model. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The genetic architecture of body mass index from infancy to adulthood modified by parental education.

PubMed

Silventoinen, Karri; Huppertz, Charlotte; van Beijsterveldt, Catharina E M; Bartels, Meike; Willemsen, Gonneke; Boomsma, Dorret I

2016-09-01

A higher prevalence of obesity in lower socioeconomic classes is common in Western societies. This study examined the role of gene-environment interactions in the association between parental education and body mass index (BMI) from infancy to the onset of adulthood. Parentally reported BMI from 1 to 13 and self-reported BMI from 14 to 20 years of age were collected in 16,646 complete Dutch twin pairs and analyzed by genetic twin modeling. At 7 to 8 years of age, children whose parents had middle or low educational levels had more excess weight than the children of more highly educated parents, and the difference increased until 18 to 20 years of age. The major part of the BMI variation was explained by additive genetic factors (a(2)  = 0.55-0.85), but environmental factors common for co-twins also played a significant role, especially from 3 to 7-8 years of age (c(2)  = 0.15-0.29). The genetic variation in BMI was higher in children whose parents had middle or low educational levels compared with children whose parents had a high educational level. The interaction between genetic factors and the childhood social environment may contribute to the formation of socioeconomic differences in obesity. © 2016 The Obesity Society.

Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size.

PubMed

Joganic, Jessica L; Willmore, Katherine E; Richtsmeier, Joan T; Weiss, Kenneth M; Mahaney, Michael C; Rogers, Jeffrey; Cheverud, James M

2018-02-01

Determining the genetic architecture of quantitative traits and genetic correlations among them is important for understanding morphological evolution patterns. We address two questions regarding papionin evolution: (1) what effect do body and cranial size, age, and sex have on phenotypic (V P ) and additive genetic (V A ) variation in baboon crania, and (2) how might additive genetic correlations between craniofacial traits and body mass affect morphological evolution? We use a large captive pedigreed baboon sample to estimate quantitative genetic parameters for craniofacial dimensions (EIDs). Our models include nested combinations of the covariates listed above. We also simulate the correlated response of a given EID due to selection on body mass alone. Covariates account for 1.2-91% of craniofacial V P . EID V A decreases across models as more covariates are included. The median genetic correlation estimate between each EID and body mass is 0.33. Analysis of the multivariate response to selection reveals that observed patterns of craniofacial variation in extant baboons cannot be attributed solely to correlated response to selection on body mass, particularly in males. Because a relatively large proportion of EID V A is shared with body mass variation, different methods of correcting for allometry by statistically controlling for size can alter residual V P patterns. This may conflate direct selection effects on craniofacial variation with those resulting from a correlated response to body mass selection. This shared genetic variation may partially explain how selection for increased body mass in two different papionin lineages produced remarkably similar craniofacial phenotypes. © 2017 Wiley Periodicals, Inc.

Fire Increases Genetic Diversity of Populations of Six-Lined Racerunner.

PubMed

Ragsdale, Alexandria K; Frederick, Bridget M; Dukes, David W; Liebl, Andrea L; Ashton, Kyle G; McCoy, Earl D; Mushinsky, Henry R; Schrey, Aaron W

2016-01-01

Wildfires are highly variable and can disturb habitats, leading to direct and indirect effects on the genetic characteristics of local populations. Florida scrub is a fire-dependent, highly fragmented, and severely threatened habitat. Understanding the effect of fire on genetic characteristics of the species that use this habitat is critically important. We investigated one such lizard, the Six-lined Racerunner (Aspidoscelis sexlineata), which has a strong preference for open areas. We collected Six-lined Racerunners (n = 154) from 11 sites in Highlands County, FL, and defined 2 time-since-last-fire (TSF) categories: recently burned and long unburned. We screened genetic variation at 6 microsatellites to estimate genetic differentiation and compare genetic diversity among sites to determine the relationship with TSF. A clear pattern exists between genetic diversity and TSF in the absence of strong genetic differentiation. Genetic diversity was greater and inbreeding was lower in sites with more recent TSF, and genetic characteristics had significantly larger variance in long unburned sites compared with more recently burned sites. Our results suggest that fire suppression increases variance in genetic characteristics of the Six-lined Racerunner. More generally, fire may benefit genetic characteristics of some species that use fire-dependent habitats and management efforts for such severely fragmented habitat will be challenged by the presence of multiple species with incompatible fire preferences. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Hemiclonal analysis reveals significant genetic, environmental and genotype x environment effects on sperm size in Drosophila melanogaster.

PubMed

Morrow, E H; Leijon, A; Meerupati, A

2008-11-01

Spermatozoa are the most diverse of all animal cells. Variation in size alone is enormous and yet there are still no clear evolutionary explanations that can account for such diversity. The basic genetics of sperm form is also poorly understood, although sperm size is known to have a strong genetic component. Here, using hemiclonal analysis of Drosophila melanogaster, we demonstrate that there is not only a significant additive genetic component contributing to phenotypic variation in sperm length but also a significant environmental effect. Furthermore, the plasticity of sperm size has a significant genetic component to it (a genotype x environment interaction). A genotype x environment interaction could contribute to the maintenance of the substantial genetic variation in this trait and thereby explain the persistent inter-male differences in sperm size seen in numerous taxa. We suggest that the low conditional dependence and high heritability but low evolvability (the coefficient of additive genetic variation) of sperm length is more consistent with a history of stabilizing selection rather than either sexual selection or strong directional selection.

The role of invertases in plant compensatory responses to simulated herbivory

USDA-ARS?s Scientific Manuscript database

The ability of a plant to recover from mammalian herbivory by exhibiting enhanced growth and reproduction compared to unharmed plants, is called compensation. Although it is clear that genetic variation for compensation exists, little is known about the specific genes underpinnings leading this fitn...

Molecular Darwinism: The Contingency of Spontaneous Genetic Variation

PubMed Central

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. PMID:21979160

Low genetic variance in the duration of the incubation period in a collared flycatcher (Ficedula albicollis) population.

PubMed

Husby, Arild; Gustafsson, Lars; Qvarnström, Anna

2012-01-01

The avian incubation period is associated with high energetic costs and mortality risks suggesting that there should be strong selection to reduce the duration to the minimum required for normal offspring development. Although there is much variation in the duration of the incubation period across species, there is also variation within species. It is necessary to estimate to what extent this variation is genetically determined if we want to predict the evolutionary potential of this trait. Here we use a long-term study of collared flycatchers to examine the genetic basis of variation in incubation duration. We demonstrate limited genetic variance as reflected in the low and nonsignificant additive genetic variance, with a corresponding heritability of 0.04 and coefficient of additive genetic variance of 2.16. Any selection acting on incubation duration will therefore be inefficient. To our knowledge, this is the first time heritability of incubation duration has been estimated in a natural bird population. © 2011 by The University of Chicago.

Genetic Relations Among Procrastination, Impulsivity, and Goal-Management Ability: Implications for the Evolutionary Origin of Procrastination

PubMed Central

Gustavson, Daniel E.; Miyake, Akira; Hewitt, John K.; Friedman, Naomi P.

2014-01-01

Previous research has revealed a moderate positive correlation between procrastination and impulsivity. However, little is known about why these two constructs are related. This study used behavioral genetic methodology to test three predictions derived from an evolutionary account that postulates that procrastination arose as a by-product of impulsivity (Steel, 2010): (a) Procrastination is heritable; (b) the two traits share considerable genetic variation; and (c) goal-management ability is an important component of this shared variation. These predictions were confirmed. First, both procrastination and impulsivity were moderately heritable (46% and 49%, respectively). Second, although the two traits were separable at the phenotypic level (r=.65), they were not separable at the genetic level (rg=1.0). Finally, variation in goal-management ability accounted for much of this shared genetic variation. These results suggest that procrastination and impulsivity are linked primarily through genetic influences on the ability to use their high-priority goals effectively to regulate their action. PMID:24705635

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.

Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute.

PubMed

Hiss, Manuel; Meyberg, Rabea; Westermann, Jens; Haas, Fabian B; Schneider, Lucas; Schallenberg-Rüdinger, Mareike; Ullrich, Kristian K; Rensing, Stefan A

2017-05-01

Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-genetics studies that involve progression through the life cycle and multiple generations. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

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

Treesearch

Helen Neville; Daniel Isaak; Russell Thurow; Jason Dunham; Bruce Rieman

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...

Yellowstone bison genetics: let us move forward

USGS Publications Warehouse

Halbert, Natalie D.; Gogan, Peter J.P.; Hedrick, Philip W.; Wahl, Jacquelyn M.; Derr, James N.

2012-01-01

White and Wallen (2012) disagree with the conclusions and suggestions made in our recent assessment of population structure among Yellowstone National Park (YNP) bison based on 46 autosomal microsatellite loci in 661 animals (Halbert et al. 2012). First, they suggest that "the existing genetic substructure (that we observed) was artificially created." Specifically, they suggest that the substructure observed between the northern and central populations is the result of human activities, both historical and recent. In fact, the genetic composition of all known existing bison herds was created by, or has been influenced by, anthropogenic activities, although this obviously does not reduce the value of these herds for genetic conservation (Dratch and Gogan 2010). As perspective, many, if not most, species of conservation concern have been influenced by human actions and as a result currently exist as isolated populations. However, it is quite difficult to distinguish between genetic differences caused by human actions and important ancestral variation contained in separate populations without data from early time periods. Therefore, to not lose genetic variation that may be significant or indicative of important genetic variation, the generally acceptable management approach is to attempt to retain this variation based on the observed population genetic subdivision (Hedrick et al. 1986).

Genetic constraints on wing pattern variation in Lycaeides butterflies: A case study on mapping complex, multifaceted traits in structured populations.

PubMed

Lucas, Lauren K; Nice, Chris C; Gompert, Zachariah

2018-03-13

Patterns of phenotypic variation within and among species can be shaped and constrained by trait genetic architecture. This is particularly true for complex traits, such as butterfly wing patterns, that consist of multiple elements. Understanding the genetics of complex trait variation across species boundaries is difficult, as it necessitates mapping in structured populations and can involve many loci with small or variable phenotypic effects. Here, we investigate the genetic architecture of complex wing pattern variation in Lycaeides butterflies as a case study of mapping multivariate traits in wild populations that include multiple nominal species or groups. We identify conserved modules of integrated wing pattern elements within populations and species. We show that trait covariances within modules have a genetic basis and thus represent genetic constraints that can channel evolution. Consistent with this, we find evidence that evolutionary changes in wing patterns among populations and species occur in the directions of genetic covariances within these groups. Thus, we show that genetic constraints affect patterns of biological diversity (wing pattern) in Lycaeides, and we provide an analytical template for similar work in other systems. © 2018 John Wiley & Sons Ltd.

Genetic diversity and sex ratio of naked mole rat, Heterocephalus glaber, zoo populations.

PubMed

Chau, Linh M; Groh, Amy M; Anderson, Emily C; Alcala, Micaela O; Mendelson, Joseph R; Slade, Stephanie B; Kerns, Kenton; Sarro, Steve; Lusardi, Clinton; Goodisman, Michael A D

2018-05-01

The naked mole rat, Heterocephalus glaber, is a highly unusual mammal that displays a complex social system similar to that found in eusocial insects. Colonies of H. glaber are commonly maintained in zoo collections because they represent fascinating educational exhibits for the public. However, little is known about the genetic structure or sex ratio of captive populations of H. glaber. In this study, we developed a set of microsatellite markers to examine genetic variation in three captive zoo populations of H. glaber. We also studied sex ratio of these captive populations. Our goal was to determine levels of genetic variation within, and genetic differences between, captive populations of H. glaber. Overall, we found modest levels of genetic variation in zoo populations. We also uncovered little evidence for inbreeding within the captive populations. However, zoo populations did differ genetically, which may reflect the isolation of captive naked mole rat colonies. Finally, we found no evidence of biased sex ratios within colonies. Overall, our study documents levels of genetic variation and sex ratios in a captive eusocial mammalian population. Our results may provide insight into how to manage captive populations of H. glaber. © 2018 Wiley Periodicals, Inc.

Farmers prevailing perception profiles regarding GM crops: A classification proposal.

PubMed

Almeida, Carla; Massarani, Luisa

2018-04-01

Genetically modified organisms have been at the centre of a major public controversy, involving different interests and actors. While much attention has been devoted to consumer views on genetically modified food, there have been few attempts to understand the perceptions of genetically modified technology among farmers. By investigating perceptions of genetically modified organisms among Brazilian farmers, we intend to contribute towards filling this gap and thereby add the views of this stakeholder group to the genetically modified debate. A comparative analysis of our data and data from other studies indicate there is a complex variety of views on genetically modified organisms among farmers. Despite this diversity, we found variations in such views occur within limited parameters, concerned principally with expectations or concrete experiences regarding the advantages of genetically modified crops, perceptions of risks associated with them, and ethical questions they raise. We then propose a classification of prevailing profiles to represent the spectrum of perceptions of genetically modified organisms among farmers.

The Genetic Basis for Variation in Sensitivity to Lead Toxicity in Drosophila melanogaster.

PubMed

Zhou, Shanshan; Morozova, Tatiana V; Hussain, Yasmeen N; Luoma, Sarah E; McCoy, Lenovia; Yamamoto, Akihiko; Mackay, Trudy F C; Anholt, Robert R H

2016-07-01

Lead toxicity presents a worldwide health problem, especially due to its adverse effects on cognitive development in children. However, identifying genes that give rise to individual variation in susceptibility to lead toxicity is challenging in human populations. Our goal was to use Drosophila melanogaster to identify evolutionarily conserved candidate genes associated with individual variation in susceptibility to lead exposure. To identify candidate genes associated with variation in susceptibility to lead toxicity, we measured effects of lead exposure on development time, viability and adult activity in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association analyses to identify candidate genes. We used mutants to assess functional causality of candidate genes and constructed a genetic network associated with variation in sensitivity to lead exposure, on which we could superimpose human orthologs. We found substantial heritabilities for all three traits and identified candidate genes associated with variation in susceptibility to lead exposure for each phenotype. The genetic architectures that determine variation in sensitivity to lead exposure are highly polygenic. Gene ontology and network analyses showed enrichment of genes associated with early development and function of the nervous system. Drosophila melanogaster presents an advantageous model to study the genetic underpinnings of variation in susceptibility to lead toxicity. Evolutionary conservation of cellular pathways that respond to toxic exposure allows predictions regarding orthologous genes and pathways across phyla. Thus, studies in the D. melanogaster model system can identify candidate susceptibility genes to guide subsequent studies in human populations. Zhou S, Morozova TV, Hussain YN, Luoma SE, McCoy L, Yamamoto A, Mackay TF, Anholt RR. 2016. The genetic basis for variation in sensitivity to lead toxicity in Drosophila melanogaster. Environ Health Perspect 124:1062-1070; http://dx.doi.org/10.1289/ehp.1510513.

Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

PubMed Central

Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

2016-01-01

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact epistatically with mutant alleles. PMID:27459710

Genetic characterization of fig tree mutants with molecular markers.

PubMed

Rodrigues, M G F; Martins, A B G; Desidério, J A; Bertoni, B W; Alves, M C

2012-08-06

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes.

Phylogeographic analyses and genetic structure illustrate the complex evolutionary history of Phragmites australis in Mexico.

PubMed

Colin, Ricardo; Eguiarte, Luis E

2016-05-01

Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico. We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages. We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya. Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico. © 2016 Botanical Society of America.

Fire alters patterns of genetic diversity among 3 lizard species in Florida Scrub habitat.

PubMed

Schrey, Aaron W; Ashton, Kyle G; Heath, Stacy; McCoy, Earl D; Mushinsky, Henry R

2011-01-01

The Florida Sand Skink (Plestiodon reynoldsi), the Florida Scrub Lizard (Sceloporus woodi), and the Six-lined Racerunner (Aspidoscelis sexlineata) occur in the threatened and fire-maintained Florida scrub habitat. Fire may have different consequences to local genetic diversity of these species because they each have different microhabitat preference. We collected tissue samples of each species from 3 sites with different time-since-fire: Florida Sand Skink n = 73, Florida Scrub Lizard n = 70, and Six-lined Racerunner n = 66. We compared the effect of fire on genetic diversity at microsatellite loci for each species. We screened 8 loci for the Florida Sand Skink, 6 loci for the Florida Scrub Lizard, and 6 loci for the Six-lined Racerunner. We also tested 2 potential driving mechanisms for the observed change in genetic diversity, a metapopulation source/sink model and a local demographic model. Genetic diversity varied with fire history, and significant genetic differentiation occurred among sites. The Florida Scrub Lizard had highest genetic variation at more recently burned sites, whereas the Florida Sand Skink and the Six-lined Racerunner had highest genetic variation at less recently burned sites. Habitat preferences of the Florida Sand Skink and the Florida Scrub Lizard may explain their discordant results, and the Six-lined Racerunner may have a more complicated genetic response to fire or is acted on at a different geographic scale than we have investigated. Our results indicate that these species may respond to fire in a more complicated manner than predicted by our metapopulation model or local demographic model. Our results show that the population-level responses in genetic diversity to fire are species-specific mandating conservation management of habitat diversity through a mosaic of burn frequencies.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

PubMed

Hunter, Chad M; Huang, Wen; Mackay, Trudy F C; Singh, Nadia D

2016-04-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster

PubMed Central

Hunter, Chad M.; Huang, Wen; Mackay, Trudy F. C.; Singh, Nadia D.

2016-01-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. PMID:27035832

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

PubMed

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.

SRD5A1 Genetic Variation and Prostate Cancer Epidemiology

DTIC Science & Technology

2006-05-01

DAMD17-03-1-0136 TITLE: SRD5A1 Genetic Variation and Prostate Cancer Epidemiology PRINCIPAL INVESTIGATOR: Troy Phipps...DATES COVERED (From - To) 1 May 2003 – 30 Apr 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER SRD5A1 Genetic Variation and Prostate Cancer...Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The human steroid 5-alpha reductase type I ( SRD5A1 ) gene was sequenced in 101

Cordova: web-based management of genetic variation data.

PubMed

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

2014-12-01

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. Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Published by Oxford University Press. This work is written by US Government employees and is in the public domain in the US.

The Genetics of Urinary Tract Infections and the Innate Defense of the Kidney and Urinary tract

PubMed Central

Ambite, Ines; Rydstrom, Gustav; Schwaderer, Andrew L.; Hains, David S.

2015-01-01

The urinary tract is a sterile organ system. Urinary tract infections (UTIs) are common and often serious infections. Research has focused on uropathogen, environment, and host factors leading to UTI pathogenesis. A growing body of evidence exists implicating genetic factors that can contribute to UTI risks. In this review, we highlight genetic variations in aspects of the innate immune system critical to the host response to uropathogens. This overview includes genetic variations in pattern recognition receptor molecules, chemokines/cytokines, and neutrophil activation. We also comprehensively cover murine knockout models of UTI, genetic variations involved in renal scarring as a result of ascending UTIs, and asymptomatic bacteriuria. PMID:27617139

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. © 2016 John Wiley & Sons Ltd/CNRS.

AFLP analysis of Cynodon dactylon (L.) Pers. var. dactylon genetic variation.

PubMed

Wu, Y Q; Taliaferro, C M; Bai, G H; Anderson, M P

2004-08-01

Cynodon dactylon (L.) Pers. var. dactylon (common bermudagrass) is geographically widely distributed between about lat 45 degrees N and lat 45 degrees S, penetrating to about lat 53 degrees N in Europe. The extensive variation of morphological and adaptive characteristics of the taxon is substantially documented, but information is lacking on DNA molecular variation in geographically disparate forms. Accordingly, this study was conducted to assess molecular genetic variation and genetic relatedness among 28 C. dactylon var. dactylon accessions originating from 11 countries on 4 continents (Africa, Asia, Australia, and Europe). A fluorescence-labeled amplified fragment length polymorphism (AFLP) DNA profiling method was used to detect the genetic diversity and relatedness. On the basis of 443 polymorphic AFLP fragments from 8 primer combinations, the accessions were grouped into clusters and subclusters associating with their geographic origins. Genetic similarity coefficients (SC) for the 28 accessions ranged from 0.53 to 0.98. Accessions originating from Africa, Australia, Asia, and Europe formed major groupings as indicated by cluster and principal coordinate analysis. Accessions from Australia and Asia, though separately clustered, were relatively closely related and most distantly related to accessions of European origin. African accessions formed two distant clusters and had the greatest variation in genetic relatedness relative to accessions from other geographic regions. Sampling the full extent of genetic variation in C. dactylon var. dactylon would require extensive germplasm collection in the major geographic regions of its distributional range.

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

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones

PubMed Central

Fuller, Trevon L.; Thomassen, Henri A.; Peralvo, Manuel; Buermann, Wolfgang; Milá, Borja; Kieswetter, Charles M.; Jarrín-V, Pablo; Devitt, Susan E. Cameron; Mason, Eliza; Schweizer, Rena M.; Schlunegger, Jasmin; Chan, Janice; Wang, Ophelia; Schneider, Christopher J.; Pollinger, John P.; Saatchi, Sassan; Graham, Catherine H.; Wayne, Robert K.; Smith, Thomas B.

2013-01-01

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible. PMID:23595273

Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies.

PubMed

Huber, B; Whibley, A; Poul, Y L; Navarro, N; Martin, A; Baxter, S; Shah, A; Gilles, B; Wirth, T; McMillan, W O; Joron, M

2015-05-01

Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pattern variants, we used genome-wide restriction site-associated DNA (RAD) genotyping, traditional linkage mapping and multivariate image analysis to study the evolution of the architecture of adaptive variation in two closely related species: Heliconius hecale and H. ismenius. We implemented a new morphometric procedure for the analysis of whole-wing pattern variation, which allows visualising spatial heatmaps of genotype-to-phenotype association for each quantitative trait locus separately. We used the H. melpomene reference genome to fine-map variation for each major wing-patterning region uncovered, evaluated the role of candidate genes and compared genetic architectures across the genus. Our results show that, although the loci responding to mimicry selection are highly conserved between species, their effect size and phenotypic action vary throughout the clade. Multilocus architecture is ancestral and maintained across species under directional selection, whereas the single-locus (supergene) inheritance controlling polymorphism in H. numata appears to have evolved only once. Nevertheless, the conservatism in the wing-patterning toolkit found throughout the genus does not appear to constrain phenotypic evolution towards local adaptive optima.