Measures Of Genetic Differentiation Research Articles

Limited effects of population age on the genetic structure of spatially isolated forest herb populations in temperate Europe.

Due to multiple land-cover changes, forest herb populations residing in forest patches embedded in agricultural landscapes display different ages and, thus, experience differences in genetic exchange, mutation accumulation and genetic drift. The extent of divergence in present-day population genetic structure among these populations of different ages remains unclear, considering their diverse breeding systems and associated pollinators. Answering this question is essential to understand these species' persistence, maintenance of evolutionary potential and adaptability to changing environments. We applied a multi-landscape setup to compare the genetic structure of forest herb populations across forest patches of different ages (18-338 years). We studied the impact on three common slow-colonizer herb species with distinct breeding systems and associated pollinators: Polygonatum multiflorum (outcrossing, long-distance pollinators), Anemone nemorosa (outcrossing, short-distance pollinators) and Oxalis acetosella (mixed breeding). We aimed to assess if in general older populations displayed higher genetic diversity and lower differentiation than younger ones. We also anticipated that P. multiflorum would show the smallest while O. acetosella the largest difference, between old and young populations. We found that older populations had a higher observed heterozygosity (H o) but a similar level of allelic richness (A r) and expected heterozygosity (H e) as younger populations, except for A. nemorosa, which exhibited higher A r and H e in younger populations. As populations aged, their pairwise genetic differentiation measured by D PS decreased independent of species identity while the other two genetic differentiation measures showed either comparable levels between old and young populations (G" ST) or inconsistency among three species (cGD). The age difference of the two populations did not explain their genetic differentiation. Synthesis: We found restricted evidence that forest herb populations with different ages differ in their genetic structure, indicating that populations of different ages can reach a similar genetic structure within decades and thus persist in the long term after habitat disturbance. Despite their distinct breeding systems and associated pollinators, the three studied species exhibited partly similar genetic patterns, suggesting that their common characteristics, such as being slow colonizers or their ability to propagate vegetatively, are important in determining their long-term response to land-cover change.

Time-Series Sequences for Evolutionary Inferences.

The application of genomics to evolutionary biology has provided unprecedented power and resolution to investigate processes like mutation (Nachman and Crowell 2000; Rozhok and Degregori 2019), genetic drift (Whitney and Garland 2010; Funk et al. 2016), gene flow (Gallego-García et al. 2019; LaCava et al. 2021), and natural selection (Brauer et al. 2016; Martins et al. 2018). Evolutionary genomics has historically used contemporary or single-timepoint samples to study microevolutionary processes that most often depend on idealized model assumptions (e.g., Wright–Fisher model) (Butlin 2008; Hoban et al. 2016). For example, genome scanning methods aim to detect natural selection by assuming that the impact of selection can be discerned from the effects of neutral evolutionary processes on genetic differentiation (Hoban et al. 2016). However, different demographic scenarios can also produce signatures of selection, leading to false positives (Lotterhos and Whitlock 2015; Haasl and Payseur 2016). Similarly, when using measures of genetic differentiation to estimate gene flow, most models assume that population size is large enough that genetic drift is negligible—that is, not driving neutral divergence between populations (Whitlock and McCauley 1999; Ma et al. 2015).

Bray-Curtis (AFD) differentiation in molecular ecology: Forecasting, an adjustment ( A A), and comparative performance in selection detection.

Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray‐Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill “Q‐profile” measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within‐population (alpha) variation, undesirable for a between‐population (beta) measure. The first dependency is derived from similarity to GST and FST. The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data‐filtering or by a modified statistic A A or “Adjusted AFD”. The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions—which is shown in this article for A A, for equilibrium, and nonequilibrium, for the commonly used data type of single‐nucleotide‐polymorphisms (SNPs) in two locations. Thus, A A can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of A A and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that A A is in one of the best such pairwise criteria. For any application, using A A, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.

Mathematical constraints on FST: multiallelic markers in arbitrarily many populations.

Interpretations of values of the FST measure of genetic differentiation rely on an understanding of its mathematical constraints. Previously, it has been shown that FST values computed from a biallelic locus in a set of multiple populations and FST values computed from a multiallelic locus in a pair of populations are mathematically constrained as a function of the frequency of the allele that is most frequent across populations. We generalize from these cases to report here the mathematical constraint on FST given the frequency M of the most frequent allele at a multiallelic locus in a set of multiple populations. Using coalescent simulations of an island model of migration with an infinitely-many-alleles mutation model, we argue that the joint distribution of FST and M helps in disentangling the separate influences of mutation and migration on FST. Finally, we show that our results explain a puzzling pattern of microsatellite differentiation: the lower FST in an interspecific comparison between humans and chimpanzees than in the comparison of chimpanzee populations. We discuss the implications of our results for the use of FST.This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

Isolation and endemism in subterranean aquatic snails: unexpected case of Montenegrospeum bogici (Pe\u0161i\u0107 et Gl\xf6er, 2012) (Gastropoda: Truncatelloidea: Hydrobiidae)

The subterranean aquatic snails may serve as a model of endemism and isolation vs. migration in subterranean habitats. The aim of the present paper is to verify the hypothesis that subterranean aquatic snails can migrate through diverse subterranean habitats, applying four molecular markers as well as a RAPD technique and shell morphometry. They were used to estimate the differences and gene flow between populations of the hydrobiid subterranean aquatic species Montenegrospeum bogici, collected in the Dinaric karst region. Three molecularly distinct taxonomic units were distinguished. The mOTU B was found at single locality, mOTU C at two, but the mOTU A at ten localities, scattered along 236 km distance, at two of them in sympatry with either mOTU B or C. Within mOTU A, the estimated levels of the gene flow were high. The pairwise measures of genetic differentiation were statistically significantly associated with geographic distances between the populations. In general, neither the infinite-island model of interpopulation differentiation, expected for isolated populations, nor the stepping-stone one, but rather the isolation-by-distance model explained the observed pattern. Our results suggest that interstitial habitats provide ways of migration for the stygobiont M. bogici, as has been already suggested for other subterranean gastropods.

Phylogeography, Population Structure, and Historical Demography of Black Drum in North America

AbstractThe Black Drum Pogonias cromis is an abundant estuarine‐dependent fish that supports recreational and commercial fisheries. We examined the phylogeography and historical demography of the Black Drum along the Atlantic and Gulf of Mexico coasts of the United States using mitochondrial DNA sequences and nuclear DNA microsatellites. Black Drum exhibited high haplotype diversity and low nucleotide diversity across its range. We observed 249 haplotypes that resolved into two haplogroups: haplogroup 1 was most abundant along the Texas coast, and haplogroup 2 was more abundant in the Atlantic Ocean and the eastern Gulf of Mexico. Analysis of molecular variance, pairwise estimates of genetic differentiation, assessment of isolation by distance, Bayesian clustering, and multivariate ordination indicated that most population structure within Black Drum was associated with a western Gulf of Mexico versus Atlantic–eastern Gulf of Mexico split. However, analysis of molecular variance, haplotype diversity, and measures of genetic differentiation provided evidence of weak population structure on the Texas coast, perhaps due to a of combination of isolation by distance and limited emigration into and dispersal from the upper and lower Laguna Madre on the lower coast. Mismatch distributions, neutrality tests, and Bayesian skyline plots suggest that haplogroup 1 underwent rapid demographic and range expansion approximately 15,000 years ago, whereas the demographic and range expansion of haplogroup 2 was more gradual and began earlier (circa 25,000–30,000 years ago). Our results suggest that Black Drum may benefit from being managed as two stocks: (1) western Gulf of Mexico and (2) Atlantic Ocean plus eastern Gulf of Mexico. Additionally, weak but significant genetic divergence in the Laguna Madre coincides with known life history divergence in this region. Caution should be used regarding the management of Black Drum in Texas as a single demographic unit.

Reproductive barriers and genetic differentiation between continental and island populations of Epidendrum fulgens (Orchidaceae)

Studies on insular organisms provide an important framework for investigating patterns of genetic differentiation and reproductive isolation. By focusing on populations of the same species, we have the opportunity to study the mechanisms operating during the earliest stages of speciation, as reproductive barriers can be examined among divergent lineages in a geographic context. We investigated the genetic differentiation and the evolution of early stages of intrinsic postmating reproductive isolation between continental and insular populations of Epidendrum fulgens, a neotropical orchid distributed in southeastern Brazil. Genetic diversity and structure were estimated for both nuclear and plastid markers by using genetic differentiation measures and model-based assignment test. Furthermore, two components of reproductive isolation were examined by analyzing fruit set and seed viability in interpopulation crosses. Strong plastid genetic structure (FST = 0.679) was found between insular and remaining populations, indicating that E. fulgens reduced gene flow via seed dispersal, although significant nuclear genetic structure was lower (DST = 0.179), likely due to the smaller effective population size of the plastid genome. Significant differences in seed viability between self- and cross-pollinated plants were found, indicating the occurrence of inbreeding depression in all populations. Seed viability was significantly lower in crosses between insular and remaining populations, suggesting a late postzygotic reproductive barrier due to low migration associated with genetic drift (i.e., bottleneck) and its consequences. Our results confirm the importance of islands as drivers for populational differentiation and suggest a central role for outbreeding depression during the early stages of lineage diversification.

Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.

Temporal variation in regeneration events affecting population structure in different size- and life-stages contributes to overall genetic diversity of natural Zelkova serrata population

ABSTRACT To clarify the mechanisms underlying the maintenance of genetic diversity in long-lived forest tree populations, it is important to understand the influence of temporal variation in regeneration sites and its effect on population structure (i.e., nonrandom distribution of trees in spatial location and size) and the spatial genetic structure. Features of population structure in four different life stages (current-year seedlings, saplings, juveniles, and adults) were investigated in a natural population of Zelkova serrata. The genetic diversity and genetic structure of these life stages were evaluated using eight microsatellite markers, and the regeneration processes required for maintaining the genetic diversity of the adult tree population were inferred. Within a study plot, differences in spatial distribution among life stages and size classes, and significantly positive spatial autocorrelation of tree sizes (Km(r) statistic) at the adult stage were observed. Analysis of standardized measures of genetic differentiation showed a clear genetic difference among life stages (F’ST = 0.095), with the adult stage exhibiting the highest allelic richness, the highest estimated effective number of contributing parents (N eb), and the highest estimator of spatial genetic structure (Sp statistic). The adult stage may comprise many different cohorts (subpopulations), contributed by different compositions of parents, due to spatially and temporarily distinct regeneration events, and the resulting genetic heterogeneity would contribute to an increase in genetic diversity within the population.

Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird.

We tested the hypothesis that segregation in wintering areas is associated with population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and on 13 colonies in the eastern Pacific Ocean (California to Alaska), and deployed light-level geolocator tags on 12 eastern Pacific colonies to delineate wintering areas. Geolocator tags were deployed previously on one colony in Japan. There was strong genetic differentiation between populations in the eastern vs. western Pacific Ocean, likely due to two factors. First, glaciation over the North Pacific in the late Pleistocene might have forced a southward range shift that historically isolated the eastern and western populations. And second, deep-ocean habitat along the northern continental shelf appears to act as a barrier to movement; abundant on both sides of the North Pacific, the rhinoceros auklet is virtually absent as a breeder in the Aleutian Islands and Bering Sea, and no tagged birds crossed the North Pacific in the non-breeding season. While genetic differentiation was strongest between the eastern vs. western Pacific, there was also extensive differentiation within both regional groups. In pairwise comparisons among the eastern Pacific colonies, the standardized measure of genetic differentiation (FꞌST) was negatively correlated with the extent of spatial overlap in wintering areas. That result supports the hypothesis that segregation in the non-breeding season is linked to genetic structure. Philopatry and a neritic foraging habit probably also contribute to the structuring. Widely distributed, vulnerable to anthropogenic stressors, and exhibiting extensive genetic structure, the rhinoceros auklet is fully indicative of the scope of the conservation challenges posed by seabirds.

Microsatellite Genotyping Corroborated Loss of Genetic Diversity in Clarias batrachus as a Result of Lack of Regulatory Reforms in Aquaculture.

In India, over the past 50 years, aquaculture practices of species such as those used for Clarias batrachus were developed without adequate regulatory oversight. In these situations, it is important to consider the influence that genetic factors can have on such vulnerable aquaculture species. Population genetic structure can be evaluated through the use of neutral molecular markers, and this can aid in predicting the risk of the demise of populations and for framing management strategies to conserve remaining populations. The study presented here reports on the genetic status of C. batrachus populations through the analysis of data collected using 22 microsatellite markers from seven natural and one hatchery population. The mean values for observed heterozygosity across loci within populations ranged from 0.242 to 0.485. Measures of genetic differentiation were low overall, with mean values for FST of 0.270, FIS of 0.113 and FIT of 0.353. An AMOVA analysis revealed that percentages of variation among and within populations were 27.16 and 6.86, respectively, and Bayesian clustering analyses showed a population subdivision consisting of five clusters with admixture of haplotypes from other populations leading to genetic bottleneck. We also examined how hatchery management factors leading to excessive exchanges of fish between river systems through could impact the structure of the C. batrachus populations. Overall, this study shows how the systematic use of molecular markers can facilitate the development of management policies for these populations and for the development of a comprehensive set of rules for hatcheries and aquaculture practices, including avoidance of excessive homozygosity by avoiding repeated use of feral broodstock and their interrogation.

Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration.

Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g., FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.

Assessment of genetic structure of the endangered forest species Boswellia serrata population in central India

Boswellia serrata Roxb., a commercially important species for its pulp and pharmaceutical properties was sampled from three locations representing its natural distribution in central India for genetic characterization through 56 RAPD and 42 ISSR loci. The wood fiber dimensions measured for morphometric characterization confirmed 11.36% of the variation in the length and 8.75% of the variation in the width indicating its fitness for local adaptation. Bayesian and non-Bayesian approach based diversity measures resulted moderate within population gene diversity (0.26, SD-0.17), Shannon information index (0.40, SD-0.22) and panmictic heterozygosity (0.28, SD-0.01). A high estimate for genetic differentiation measures i.e. GST (0.31), GST-B (0.33,SD-0.02) and theta-II (0.45) led to the distinct clusters of the sampled genotypes representing their regional variability due to limited gene flow and total absence of natural regeneration. We report the first investigation of the species for its molecular characterization emphasizing the urgent need for the genetic improvement program for the In-situ/Ex-situ conservation and sustainable commercialization.

, Jost's D, and FST are similarly constrained by allele frequencies: A mathematical, simulation, and empirical study.

Statistics and Jost's D have been proposed for replacing FST as measures of genetic differentiation. A principal argument in favour of these statistics is the independence of their maximal values with respect to the subpopulation heterozygosity HS , a property not shared by FST . Nevertheless, it has been unclear if these alternative differentiation measures are constrained by other aspects of the allele frequencies. Here, for biallelic markers, we study the mathematical properties of the maximal values of and D, comparing them to those of FST . We show that and D exhibit the same peculiar frequency-dependence phenomena as FST , including a maximal value as a function of the frequency of the most frequent allele that lies well below one. Although the functions describing , D, and FST in terms of the frequency of the most frequent allele are different, the allele frequencies that maximize them are identical. Moreover, we show using coalescent simulations that when taking into account the specific maximal values of the three statistics, their behaviours become similar across a large range of migration rates. We use our results to explain two empirical patterns: the similar values of the three statistics among North American wolves, and the low D values compared to and FST in Atlantic salmon. The results suggest that the three statistics are often predictably similar, so that they can make quite similar contributions to data analysis. When they are not similar, the difference can be understood in relation to features of genetic diversity.

Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity

Inferring and quantifying recent barriers to connectivity is increasingly important for conservation and management in a world undergoing rapid environmental change. Traditional measures of genetic differentiation can take many generations to reflect a new barrier to connectivity. Although methods that use the linkage disequilibrium signal in mixed genetic samples are able to reflect recent levels of gene flow, they are not suitable for use in situations with low levels of genetic differentiation. Kinship-based methods, those that assess the spatio-temporal distribution of related individuals, have been used in this context, but a formal statistical framework for such approaches has been lacking. In this issue of Molecular Ecology Resources, Escoda, et al. adapt the assortativity coefficient, AC, to analyse the networks of kin relationships in the Pyrenean desman (Galemys pyrenaicus) across potential barriers to dispersal. Their modified AC quantifies the proportion of missing kin relationships across putative dispersal barriers with respect to the expected proportion if there was no barrier. This application highlights that AC can be used to test the null hypothesis that a putative barrier has no effect on gene flow, in which case AC is not significantly different from 0. The method represents a useful step forward in conservation genomics by developing and adapting tools to assess contemporary connectivity using genomic data.

Molecular analysis of clinical Burkholderia pseudomallei isolates from southwestern coastal region of India, using multi-locus sequence typing.

BackgroundThe Gram-negative soil dwelling bacterium Burkholderia pseudomallei is the etiological agent of melioidosis. The disease is endemic in most parts of Southeast Asia and northern Australia. Over last few years, there has been an increase in number of melioidosis cases from India; however the disease epidemiology is less clearly understood. Multi-locus sequence typing (MLST) is a powerful genotypic method used to characterize the genetic diversity of B. Pseudomallei both within and across the geographic regions.MethodsIn this study, MLST analysis was performed on 64 B. pseudomallei clinical isolates. These isolates were obtained between 2008–2014 from southwestern coastal region of India. Broad population patterns of Indian B. pseudomallei isolates in context with isolates of Southeast Asia or global collection was determined using in silico phylogenetic tools.ResultsA total of 32 Sequence types (STs) were reported among these isolates of which 17 STs (53%) were found to be novel. ST1368 was found as group founder and the most predominant genotype (n = 11, 17%). Most of the B. pseudomallei isolates reported in this study (or other Indian isolates available in MLST database) clustered in one major group suggesting clonality in Indian isolates; however, there were a few outliers. When analyzed by measure of genetic differentiation (FST) and other phylogenetic tools (e.g. PHYLOViZ), Indian STs were found closer to Southeast Asian isolates than Australian isolates. The phylogenetic analysis further revealed that within Asian clade, Indian isolates grouped more closely with isolates from Sri Lanka, Vietnam, Bangladesh and Thailand.ConclusionsOverall, the results of this study suggest that the Indian B. pseudomallei isolates are closely related with lesser heterogeneity among them and cluster in one major group suggesting clonality of the isolates. However, it appears that there are a few outliers which are distantly related to the majority of Indian STs. Phylogenetic analysis suggest that Indian isolates are closely related to isolates from Southeast Asia, particularly from South Asia.

Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina.

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (F ST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured “master” traits (like body size) might provide good predictions of overall trait differentiation.

Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

Abstract Pairwise measures of neutral genetic differentiation are supposed to contain information about past and ongoing dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here, we tested the efficiency of two distance‐based metrics designed to capture the unique influence of spatial heterogeneity in local drift on genetic differentiation. These metrics are easily computed from estimates of effective population sizes or from environmental proxies for local carrying capacities, and allow us to introduce the hypothesis of Spatial‐Heterogeneity‐in‐Effective‐Population‐Sizes (SHNe). SHNe can be tested in a way similar to isolation‐by‐distance or isolation‐by‐resistance within the classical landscape genetics hypothesis‐testing framework. We used simulations under various models of population structure to investigate the reliability of these metrics to quantify the unique contribution of SHNe in explaining patterns of genetic differentiation. We then applied these metrics to an empirical genetic dataset obtained for a freshwater fish (Gobio occitaniae). Simulations showed that SHNe explained up to 60% of variance in genetic differentiation (measured as Fst) in the absence of gene flow, and up to 20% when migration rates were as high as 0.10. Furthermore, one of the two metrics was particularly robust to uncertainty in the estimation of effective population sizes (or proxies for carrying capacity). In the empirical dataset, the effect of SHNe on spatial patterns of Fst was five times higher than that of isolation‐by‐distance, uniquely contributing to 41% of variance in pairwise Fst. Taking the influence of SHNe into account also allowed decreasing the signal‐to‐noise ratio, and improving the upper estimate of effective dispersal distance. We conclude that the use of SHNe metrics in landscape genetics will substantially improve the understanding of evolutionary drivers of genetic variation, providing substantial information as to the actual drivers of patterns of genetic differentiation in addition to traditional measures of Euclidean distance or landscape resistance.

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa.

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in Ne . Utilizing population-level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in Ne would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population-scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (FST , PBS, dxy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.

Assessment of genetic diversity and structure of major sheep breeds from Pakistan

The present study aimed at the genetic characterization of major economically important sheep (Ovis aries) breeds from Pakistan. A total of 155 sheep from five breeds, Balkhi (PBS), Kaghani (PKS), Damani (PDS), Salt Range (PSS) and Thalli (PTS) were analyzed for measures of genetic variability, differentiation and population structure. All the five breeds exhibited moderate to high levels of genetic diversity, with an average observed heterozygosity of 0.631±0.043. The mean estimates of measures of genetic differentiation between pairs of breeds were low (FST=0.050±0.015 and DA=0.159±0.028), and the analysis of molecular variance showed that most of the total genetic variation corresponded to differences among individuals within breeds (94.41%). Despite the low level of differentiation, Bayesian clustering suggested Thalli and Damani sheep were genetically distinct from Balkhi, Kaghani and Salt Range sheep. The clustering of Pakistani sheep did not conform to their geographical locations while it was broadly consistent with their utilities (meat and coarse wool vs milk, meat and coarse wool). The results also revealed migration and admixture between Balkhi, Salt Range and Kaghani sheep. This is the first report on genetic diversity of Pakistani sheep populations of economic importance and the information generated will have implications on genetic resources management and implementation of breeding programs for these sheep breeds.