Non-neutral Loci Research Articles

Effects of Recurrent Selection on Population Structure and Allele Frequencies in the M3S Maize Population

The effects of four cycles of recurrent selection on the allele frequencies of simple sequence repeat (SSR) markers and population structure were examined in the Maksimir 3 Synthetic (M3S) maize population (Zea mays L.). Genotyping of 32 plants from each selection cycle at 38 SSR loci revealed that the mean number of alleles per locus and the mean expected heterozygosity were preserved across selection cycles, indicating the maintenance of sufficient genetic variability in the population required for future genetic gain. The Waples test of selective neutrality revealed that genetic drift was the main force in changing allele frequencies in the population. The proportion of selectively non-neutral loci in single cycles of selection varied between 16% and 37%. Some non-neutral loci shared the same genomic locations with previously published QTLs controlling important agronomic traits. An analysis of molecular variance revealed that 5.6% of the genetic variation occurred among and 94.4% within cycle populations. Between 5% and 29% of loci were found to be in a significant Hardy–Weinberg (HW) disequilibrium, with the majority showing an excess of homozygosity. The excess of homozygosity at several loci was highly consistent across cycle populations, suggesting positive assortative mating as a possible cause of the observed HW disequilibrium. Linkage disequilibrium (LD) tests revealed that the M3S population was essentially in linkage equilibrium. The proportion of pairs of loci in significant LD varied from 0.1% to 1.8% across selection cycles, probably due to the effects of genetic drift and epistatic selection.

Assessing genetic diversity patterns at neutral and adaptive loci to inform population reinforcement of an endangered migratory vulture

One of the primary goals of conservation translocation programs should be the maintenance of both population demographic stability and genetic diversity. Here, we provide genetic management recommendations to inform a population reinforcement of the declining Egyptian Vulture population in the Balkans. Specifically, we examined whether the number of released individuals is sufficient to prevent genetic diversity loss due to random genetic drift and what the origin of the individuals should be that comprise the captive breeding pool. To this aim, we estimated and assessed genetic diversity levels and genetic structure of Egyptian Vulture populations across much of the species’ range using both neutral and non-neutral candidate loci involved in migration. We then evaluated the effects of the currently proposed population management scheme and candidate source populations on retaining allelic diversity. Our results show low differentiation values among populations and absence of genetic structure which point to past high gene flow. Furthermore, there was no predicted significant impact of different source populations on the genetic diversity of the recipient Balkan population. We also found that the declining Egyptian Vulture population in the Balkans still retains high levels of genetic diversity and therefore genetic diversity restoration is not currently needed. However, without any management, diversity is likely to decrease fast because of increased genetic drift as the population size continues to decline. Population reinforcement with nine birds per year for 20 years would provide sufficient demographic support for the population to retain > 85% of rare allelic diversity. Birds originating from the Balkans would ensure ecological and behavioral similarity and thus would be the best option for reinforcement. Nevertheless, our results demonstrate that to prevent further population contraction and loss of adaptive alleles, releasing individuals of different origin would also be appropriate.

Yearly variations of the genetic structure of Aedes aegypti (Linnaeus) (Diptera: Culicidae) in the Philippines (2017–2019)

Dengue is the fastest emerging arboviral disease in the world, imposing a substantial health and economic burden in the tropics and subtropics. The mosquito, Aedes aegypti, is the primary vector of dengue in the Philippines. We examined the genetic structure of Ae. aegypti populations collected from the Philippine major islands (Luzon, Visayas and Mindanao), each with highland (Baguio city, Cebu city mountains and Maramag, Bukidnon, respectively) and lowland sites (Quezon city; Liloan, Cebu and Cagayan de Oro [CDO] city, respectively) during the wet (2017-2018 and 2018-2019) and dry seasons (2018 and 2019). Mosquitoes (n=1800) were reared from field-collected eggs and immatures, and were analyzed using 12 microsatellite loci. Generalized linear model analyses revealed yearly variations between highlands and lowlands in the major islands as supported by Bayesian clustering analyses on: 1) stronger selection (inbreeding coefficient, FIS=0.52) in 2017-2018 than in 2018-2019 (FIS=0.32) as influenced by rainfall, 2) the number of non-neutral loci indicating selection, and 3) differences of effective population size although at p=0.05. Across sites except Baguio and CDO cities: 1) FIS varied seasonally as influenced by relative humidity (RH), and 2) the number of non-neutral loci varied as influenced by RH and rainfall indicating selection. Human-mediated activities and not isolation by distance influenced genetic differentiations of mosquito populations within (FST=0.04) the major islands and across sites (global FST=0.16). Gene flow (Nm) and potential first generation migrants among populations were observed between lowlands and highlands within and across major islands. Our results suggest that dengue control strategies in the epidemic wet season are to be changed into whole year-round approach, and water pipelines are to be installed in rural mountains to prevent the potential breeding sites of mosquitoes.

Assessing breed integrity of G\xf6ttingen Minipigs

BackgroundGöttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of stratification which might compromise the identity of the breed and its usability as an animal model for biomedical and human disease. We conducted whole genome re-sequencing of two DNA-pools per colony to assess genomic differentiation within and between colonies. We added publicly available samples from 13 various pig breeds and discovered overall about 32 M loci, ~ 16 M. thereof variable in GMPs. Individual samples were virtually pooled breed-wise. FST between virtual and DNA pools, a phylogenetic tree, principal component analysis (PCA) and evaluation of functional SNP classes were conducted. An F-test was performed to reveal significantly differentiated allele frequencies between colonies. Variation within a colony was quantified as expected heterozygosity.ResultsPhylogeny and PCA showed that the GMP is easily discriminable from all other breads, but that there is also differentiation between the GMP colonies. Dependent on the contrast between GMP colonies, 4 to 8% of all loci had significantly different allele frequencies. Functional annotation revealed that functionally non-neutral loci are less prone to differentiation. Annotation of highly differentiated loci revealed a couple of deleterious mutations in genes with putative effects in the GMPs .ConclusionDifferentiation and annotation results suggest that the underlying mechanisms are rather drift events than directed selection and limited to neutral genome regions. Animal exchange seems not yet necessary. The Relliehausen colony appears to be the genetically most unique GMP sub-population and could be a valuable resource if animal exchange is required to maintain uniformity of the GMP.

Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis).

Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.

Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel.

The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.

Effective population sizes and adaptive genetic variation in a captive bird population

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

Comparative tests of the species-genetic diversity correlation at neutral and nonneutral loci in four species of stream insect.

A fundamental question linking population genetics and community ecology is how adaptive processes (e.g., natural selection) and neutral processes (e.g., drift-migration equilibrium) underpin the species-genetic diversity correlation (SGDC). Here, we combine genome scans and outlier loci detection with community analysis to separately test for neutral and nonneutral SGDCs in four species of stream insect. We sampled 60 localities in Japan and examined the relationships among population AFLP band richness (Br), taxon richness of the total community (S) and of the trophic guild (Str ), and 15 habitat parameters that could potentially drive adaptation and influence richness. Neutral Br was positively correlated with S only in the dominant species of these communities, suggesting Br may be constrained when intraspecific competition is pronounced. Nonneutral Br was correlated with Str in a species restricted to high elevations where habitat heterogeneity was highest. Community distance and genetic distance (β-SGDC) was correlated in two of the four species at both neutral and nonneutral loci. Distance-based redundancy analysis found geographic isolation and elevation to drive divergence of both communities and populations. This suggests that both neutral and adaptive divergence occurred through the shared influences of geographic isolation and local adaptation at the two levels of diversity.

Biocomplexity in Populations of European Anchovy in the Adriatic Sea.

The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and environmental variability, can provide insights into the extent of adaptive variation. Here, we examined genetic variability among populations of mature European anchovies (n = 531) in the Adriatic (13 samples) and Tyrrhenian seas (2 samples) with neutral and putative non-neutral microsatellite loci. These genetic markers failed to confirm the occurrence of two anchovy species in the Adriatic Sea, as previously postulated. However, we found fine-scale population structure in the Adriatic, especially in northern areas, that was associated with four of the 13 environmental variables tested. Geographic gradients in sea temperature, salinity and dissolved oxygen appear to drive adaptive differences in spawning time and early larval development among populations. Resolving adaptive seascapes in Adriatic anchovies provides a means to understand mechanisms underpinning local adaptation and a basis for optimizing exploitation strategies for sustainable harvests.

Bayesian inference of selection in a heterogeneous environment from genetic time‐series data

Evolutionary geneticists have sought to characterize the causes and molecular targets of selection in natural populations for many years. Although this research programme has been somewhat successful, most statistical methods employed were designed to detect consistent, weak to moderate selection. In contrast, phenotypic studies in nature show that selection varies in time and that individual bouts of selection can be strong. Measurements of the genomic consequences of such fluctuating selection could help test and refine hypotheses concerning the causes of ecological specialization and the maintenance of genetic variation in populations. Herein, I proposed a Bayesian nonhomogeneous hidden Markov model to estimate effective population sizes and quantify variable selection in heterogeneous environments from genetic time-series data. The model is described and then evaluated using a series of simulated data, including cases where selection occurs on a trait with a simple or polygenic molecular basis. The proposed method accurately distinguished neutral loci from non-neutral loci under strong selection, but not from those under weak selection. Selection coefficients were accurately estimated when selection was constant or when the fitness values of genotypes varied linearly with the environment, but these estimates were less accurate when fitness was polygenic or the relationship between the environment and the fitness of genotypes was nonlinear. Past studies of temporal evolutionary dynamics in laboratory populations have been remarkably successful. The proposed method makes similar analyses of genetic time-series data from natural populations more feasible and thereby could help answer fundamental questions about the causes and consequences of evolution in the wild.

Is there evidence of selection in the dopamine receptor D4 gene in Australian invasive starling populations?

Abstract Although population genetic theory is largely based on the premise that loci under study are selectively neutral, it has been acknowledged that the study of DNA sequence data under the influence of selection can be useful. In some circumstances, these loci show increased population differentiation and gene diversity. Highly polymorphic loci may be especially useful when studying populations having low levels of diversity overall, such as is often the case with threatened or newly established invasive populations. Using common starlings Sturnus vulgaris sampled from invasive Australian populations, we investigated sequence data of the dopamine receptor D4 gene (DRD4), a locus suspected to be under selection for novelty-seeking behaviour in a range of taxa including humans and passerine birds. We hypothesised that such behaviour may be advantageous when species encounter novel environments, such as during invasion. In addition to analyses to detect the presence of selection, we also estimated population differentiation and gene diversity using DRD4 data and compared these estimates to those from microsatellite and mitochondrial DNA sequence data, using the same individuals. We found little evidence for selection on DRD4 in starlings. However, we did find elevated levels of within-population gene diversity when compared to microsatellites and mitochondrial DNA sequence, as well as a greater degree of population differentiation. We suggest that sequence data from putatively nonneutral loci are a useful addition to studies of invasive populations, where low genetic variability is expected.

Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude.

A fundamental question in evolutionary biology is what promotes genetic variation at nonneutral loci, a major precursor to adaptation in changing environments. In particular, balanced polymorphism under realistic evolutionary models of temporally varying environments in finite natural populations remains to be demonstrated. Here, we propose a novel mechanism of balancing selection under temporally varying fitnesses. Using forward-in-time computer simulations and mathematical analysis, we show that cyclic selection that spatially varies in magnitude, such as along an environmental gradient, can lead to elevated levels of nonneutral genetic polymorphism in finite populations. Balanced polymorphism is more likely with an increase in gene flow, magnitude and period of fitness oscillations, and spatial heterogeneity. This polymorphism-promoting effect is robust to small systematic fitness differences between competing alleles or to random environmental perturbation. Furthermore, we demonstrate analytically that protected polymorphism arises as spatially heterogeneous cyclic fitness oscillations generate a type of storage effect that leads to negative frequency dependent selection. Our findings imply that spatially variable cyclic environments can promote elevated levels of nonneutral genetic variation in natural populations.

Adaptive genetic divergence along narrow environmental gradients in four stream insects.

A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified the environmental characteristics contributing to divergence by comparing genetic distances at non-neutral loci between sites with Euclidean distances for each of 15 environmental variables. Comparisons were made using partial Mantel tests to control for geographic distance. In all four species, we found strong evidence for non-neutral divergence along environmental gradients at between 6 and 21 loci per species. The relative contribution of these environmental variables to each species' ecological niche was quantified as the specialization index, S, based on ecological data. In each species, the variable most significantly correlated with genetic distance at non-neutral loci was the same variable along which each species was most narrowly distributed (i.e., highest S). These were gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen. This adaptive divergence occurred in the face of ongoing gene flow (F st = 0.01–0.04), indicating that selection was strong enough to overcome homogenization at the landscape scale. Our results suggest that adaptive divergence is pronounced, occurs along different environmental gradients for different species, and may consistently occur along the narrowest components of species' niche.

Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations.

Evidence for microsatellite hitchhiking selection in European sardine (<i>Sardina pilchardus</i>) and implications in inferring stock structure

The genetic structure of the European sardine ( Sardina pilchardus ) was assessed throughout its geographic range using five microsatellite loci. One of the loci seemed to be under hitchhiking selection and exhibited a latitudinal cline along the eastern Atlantic, with abrupt change in allele frequencies from the Alboran Sea to the western Mediterranean and from the east Atlantic coast to the Azores and Madeira. This pattern was very similar to that previously described for the allozymic locus SOD* and these 2 loci could be linked. A Bayesian analysis of environmental factors with the genetic data indicated temperature as a potential selection factor. Selection pressure may be stronger at the southern limit of sardine distribution, because heterozygosity of the non-neutral locus was much lower there. The abrupt change in allele frequencies of the non-neutral locus in certain regions seem to be related more to strong barriers to gene flow, which were not evident for neutral loci, than to abrupt changes in selection pressure. These areas of discontinuity provide a guideline to define and delineate genetic stocks and are generally consistent with areas of phenotypic change in sardine, but they are not in concordance with the currently recognized morphological subspecies.

Effect of microsatellite outliers on the genetic structure of eight Italian goat breeds

The identification of outlier loci in multilocus datasets is a critical step for reliably inferring population demographic histories and for detecting signatures of adaptive selection, since the presence of just a few of them can lead to a biased estimation of genetic parameters. Here, we show the effect of four outliers out of 30 microsatellites on phylogeography and relationship between eight native Italian goat breeds. The presence of the outliers influenced the relationships between individuals as estimated by factorial correspondence analysis, and between breeds as estimated by Reynolds’ distances. The outliers also affected the neighbour-joining (NJ) tree topology and the computation of the putative genetic barriers separating the populations. The complete dataset supported the existence of two significant barriers: the first isolates Orobica from the surrounding northern Alpine populations and the second separates Girgentana from the southern and Sarda breeds. After removing the outliers, a single and different barrier was significant. It separated the Sarda breed from the continental populations. Our results give new insights into the genetic structure of several native goat breeds across Italy and provide a clear example of the importance of testing for the occurrence of non-neutral loci in population genetics studies. Four outlier loci demonstrated the ability to blur the effect of geography, hiding the natural genetic barrier that separates the Sarda breed from the continental populations, while highlighting the peculiar demographic and selection history of Orobica and Girgentana.

Population connectivity among migratory and stationary cod Gadus morhua in the Northeast Atlantic—A review of 80 years of study

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 435:269-283 (2011) - DOI: https://doi.org/10.3354/meps09232 REVIEW Population connectivity among migratory and stationary cod Gadus morhua in the Northeast Atlantic—A review of 80 years of study Jarle Tryti Nordeide1,*, Steinar D. Johansen1,2, Tor Erik Jørgensen1, Bård Ove Karlsen1,2, Truls Moum1 1Marine Genomics Research Group, Faculty of Biosciences and Aquaculture, University of Nordland, 8049 Bodø, Norway 2Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, Norway *Email: jarle.nordeide@uin.no ABSTRACT: The population structure of Atlantic cod Gadus morhua L. in the Barents Sea and in fjords and coastal waters in Norway and northwestern Russia has been a controversial subject since the 1930s. Eight decades of scientific inquiry have compared migratory NE Arctic (NA) and stationary Norwegian and Russian coastal cod (NC). At one extreme the existence of 2 non-interbreeding groups is advocated, whereas others find support for low genetic differentiation due to substantial gene flow, with geographical distance being the limiting factor. We review studies of a wide range of phenotypic (e.g. growth, maturation, counts of vertebrae) and polymorphic genetic markers (e.g. allozymes, mtDNA, microsatellites, single nucleotide polymorphisms). Regardless of whether or not the observed differences have a genetic basis, 70% of the 54 reviewed papers conclude that NA and NC differ with respect to the characters studied. However, few papers remain after exclusion of those relying on characteristics or markers that are generally agreed to be subject to selection and therefore less suited to assessing population connectivity. The lack of studies examining the potential influence of environments on growth of annual zones in otoliths is surprising, since otoliths are used to categorize specimens in managing the NA and NC and in scientific papers. We conclude that it is still an open question whether NA and NC effectively make up 1 large population or >1 non-interbreeding ‘groups’. As next-generation sequencing technology transforms ‘population genetics’ into ‘population genomics’, we will move towards a better understanding of differentiation among fish populations. KEY WORDS: Cod · Population genetics · Gadus morhua · NE Atlantic · Selection · Non-neutral loci Full text in pdf format PreviousNextCite this article as: Nordeide JT, Johansen SD, Jørgensen TE, Karlsen BO, Moum T (2011) Population connectivity among migratory and stationary cod Gadus morhua in the Northeast Atlantic—A review of 80 years of study. Mar Ecol Prog Ser 435:269-283. https://doi.org/10.3354/meps09232 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 435. Online publication date: August 22, 2011 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2011 Inter-Research.

Isolation by Elevation: Genetic Structure at Neutral and Putatively Non-Neutral Loci in a Dominant Tree of Subtropical Forests, Castanopsis eyrei

BackgroundThe distribution of genetic diversity among plant populations growing along elevational gradients can be affected by neutral as well as selective processes. Molecular markers used to study these patterns usually target neutral processes only, but may also be affected by selection. In this study, the effects of elevation and successional stage on genetic diversity of a dominant tree species were investigated controlling for neutrality of the microsatellite loci used.Methodology/Principal FindingsDiversity and differentiation among 24 populations of Castanopsis eyrei from different elevations (251–920 m) and successional stages were analysed by eight microsatellite loci. We found that one of the loci (Ccu97H18) strongly deviated from a neutral model of differentiation among populations due to either divergent selection or hitchhiking with an unknown selected locus. The analysis showed that C. eyrei populations had a high level of genetic diversity within populations (AR = 7.6, HE = 0.82). Genetic variation increased with elevation for both the putatively selected locus Ccu97H18 and the neutral loci. At locus Ccu97H18 one allele was dominant at low elevations, which was replaced at higher elevations by an increasing number of other alleles. The level of genetic differentiation at neutral loci was similar to that of other Fagaceae species (FST = 0.032, = 0.15). Population differentiation followed a model of isolation by distance but additionally, strongly significant isolation by elevation was found, both for neutral loci and the putatively selected locus.Conclusions/SignificanceThe results indicate higher gene flow among similar elevational levels than across different elevational levels and suggest a selective influence of elevation on the distribution of genetic diversity in C. eyrei. The study underlines the importance to check the selective neutrality of marker loci in analyses of population structure.

Single‐Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed‐Stock Analyses of Sockeye Salmon from the Copper River, Alaska

AbstractGenetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single‐nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single‐nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south‐central Alaska. We evaluated the information content of the four nonneutral loci for use in genetic stock identification and assessed their ability to improve the accuracy and precision of composition estimates. The average measure of informativeness for assignment (In) for neutral loci was 0.019, and the average In for nonneutral loci was 0.064. A simulation‐based approach indicated that the addition of the nonneutral SNP loci to a neutral marker panel provided significantly higher resolution in the assignment of individuals to their populations of origin than would have been accomplished by adding an equal number of neutral loci. Nonneutral SNP loci improved the ability to identify the origin of individual fish and to estimate the composition of Pacific salmon populations in mixed fisheries.

Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation

Habitat fragmentation may influence the genetic make-up and adaptability of endangered populations. To facilitate genetic monitoring of the endangered European ground squirrel (EGS), we analyzed 382 individuals from 16 populations in Central Europe, covering almost half of its natural range. We tested how fragmentation affects the genetic architecture of presumably selectively neutral (12 microsatellites) and non-neutral (the major histocompatibility class II DRB gene) loci. Spatial genetic analyses defined two groups of populations, “western” and “eastern”, with a significantly higher level of habitat fragmentation in the former group. The highly fragmented western populations had significantly lower genetic diversity in both types of markers. Only one allele of the DRB gene predominated in populations of the western group, while four alleles were evenly distributed across the eastern populations. Coefficient of inbreeding values (FIS) calculated from microsatellites were significantly higher in the western (0.27–0.79) than in eastern populations (−0.060–0.119). Inter-population differentiation was very high, but similar in both groups (western FST = 0.23, eastern FST = 0.25). The test of isolation by distance was significant for the whole dataset, as well as for the two groups analyzed separately. Comparison of genetic variability and structure on microsatellites and the DRB gene does not provide any evidence for contemporary selection on MHC genes. We suggest that genetic drift in small bottlenecked and fragmented populations may overact the role of balancing selection. Based on the resulting risk of inbreeding depression in the western populations, we support population management by crossbreeding between the western and eastern populations.