Genetic Differentiation and Isolation by Distance in Mekong River Fishes With Typical Migration Patterns

Baltic and Arctic ecotypes of the marine midge Clunio emerged from a recent adaptive radiation, which is based on standing genetic variation at many loci involved in time-keeping and nervous system development.

Baltic and Arctic ecotypes of the marine midge Clunio emerged from a recent adaptive radiation, which is based on standing genetic variation at many loci involved in time-keeping and nervous system development.

FST, F ′ST, ΦST, Φ ′ ST, and Dest are the primary metrics utilized for empirically estimating and test-ing the magnitude of genetic divergence among populations. There is currently active discussion in the literature about which of these metrics are most appropriate for empirical surveys of genetic differentiation. Here we compare the performance of each metric in 80 simulated population comparisons with an a priori known level of genetic differentiation that ranges from 0 to 100%. In these simulations, we manipulate population characteristics such as the genetic distance between haplotypes and the diversity of haplotypes that are shared among populations, as well as those that are unique to specific populations, illustrating key features and differences among the metrics, with an eye toward separating biological signal from statistical noise. FST is the best choice for datasets consisting of neutral unlinked single nucleotide polymorphism (SNP) datasets involving two alleles per locus. Dest and F ′ST tend to be the best metrics for analyses with more than two alleles, at least where the genetic distance among the alleles is not important, but the use of F ′ST and, to a greater extent, Dest is currently limited to relatively simple datasets, due to a dearth of computer software. If genetic distance among alleles is an important consideration, then ΦST is the better metric, but we demonstrate that ΦST and Φ′ST can accentuate either noise or signal, depending upon the characteristics of the populations and the hypotheses being tested. In many cases, it can be informative to apply both distance-based and allele/haplotype-based metrics, or both fixation and genetic differentiation indices. All of these measures are highly sensitive to the diversity of alleles shared between populations, with common alleles dominating the behavior of all of these metrics. ΦST is shown to be relatively unaffected by the phenomenon of high allelic diversity driving down estimates of genetic differentiation that plague FST. Overall, there is no single metric that best captures population genetic differentiation, and we recommend that researchers report both a fixation index (FST or ΦST) and an index of genetic differentiation (F ′ST or Dest) for their datasets because they represent different properties of population partitioning. When indices of fixation and genetic differentiation are in agreement, one can be sure of the conclusion. When the two methods yield differing results, the pattern and direction of discord can be diagnostic of a particular phenomenon, and we provide a range of simulations across parameter space to illustrate both points.

To analyze the genetic structure and genetic diversity of Colletotrichum gloeosporioides as the dominant Colletotrichum species on Citrus, the Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genetic diversity, including 63 strains isolated and selected from 8 different sites and 5 different citrus species, was studied. A total of 19 GAPDH haplotypes were identified by genetic analysis, and the main haplotype (haplotype 5) was distributed in 28 isolates, mainly from Citrus unchiu Hort. ex Tanaka (WG) and Citrus reticulata Blanco cv. Succosa (BDZ) in Huangyan (HY), Linhai (LH), and Jiande (JD) of Zhejiang province, and Mashui tangerine (MSJ) in Mengshan of Guangxi province (GX). Using the genetic differentiation index, Fst revealed significant genetic differentiation in C. gloeosporioides populations between Jiangxi province (JXGZ) and GX, HY, LH, JD, and Chun’an (CA) of Zhejiang province, and also revealed slightly less genetic differentiation for C. gloeosporioides populations between HY, LH, JD, GX, Shaanxi province (SX), and Quzhou (QZ) of Zhejiang province. In addition, Fst revealed great genetic differentiation between the C. gloeosporioides populations obtained from MSJ and Citrus paradise Macf (PTY), and also revealed weak genetic differentiation between the C. gloeosporioides populations obtained from Citrus sinensis Osbeck (QC), WG, and BDZ. The AMOVA test showed that the levels of genetic differentiation for C. gloeosporioides were 19% and 81% among and within geographic populations, respectively. It also showed that C. gloeosporioides had levels of genetic differentiation among and within host populations of 12% and 88%, respectively. The Mantel test showed that the genetic distance was not linearly correlated with geographical distance and the haplotype phylogenetic analysis showed that C. gloeosporioides from different regions and hosts were scattered in the phylogenetic tree, implying that the genetic differentiation was independent of host variety and geographical origin. We speculated that genetic differentiation may be mainly due to gene mutation, gene recombination, or gene migration within native populations and has nothing to do with natural selection triggered by geography or host variety.

Decision letter: Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates

The patterns of isolation by distance (IBD) entailing increased genetic differentiation among populations have aroused extensive concerns for evolutionary biologists. Although the IBD may act on spatial processes contributing to the genetic differentiation among populations in anuran species, the factors shaping the IBD of frogs among populations in natural systems are largely unknown. Here, we studied the genetic differentiation among six populations with 24 individuals of the spotted-leg treefrog along a latitudinal gradient (1860.31 km) based on 1020 single nucleotide polymorphisms from restriction site-associated DNA sequencing. The results showed that the genetic diversity differed significantly among populations and that the insular populations had higher genetic diversity than the mainland populations. Furthermore, we also found a significant genetic differentiation among populations (FST = 0.277) and no sign of inbreeding (FUNI = -0.145). The IBD was detected for all populations, and a higher degree of the IBD was indicated when controlling for the effects of the isolation between Hainan and mainland populations caused by the Qiongzhou Strait. Our findings suggest that the form of the Qiongzhou Strait plays a key role in shaping the genetic diversity and population differentiation in treefrogs.

In order to provide a theoretical basis for conservation and utilization of excellent flowering cherry germplasms, genetic diversity and genotype were analyzed based on single nucleotide polymorphism (SNP) molecular markers. A total of 47 germplasms were sequenced using restriction site-associated DNA sequencing (RAD-Seq) method, and highly consistent SNP sites have been identified for genetic diversity analysis and genotyping. The RAxML program was used for phylogenetic tree construction, based on the maximum likelihood (ML) method. The ADMIXTURE software was used to analyze genetic structure. The GCTA software was used for principal component analysis. Genetic diversity parameters, includes nucleotide diversity (π value), expected heterozygosity (exp  He ) and genetic differentiation index ( F ST ), were carried out using the PopGenome and Arlequin 3.0 software. A total of 79 667 highly consistent SNPs were obtained, after genotype integrity filtering and closely linked sites screening. According to the phylogenetic, principal components and population structure analysis results, the 47 germplasms could be divided into eight genetic clusters. The π and exp  He  value of each cluster was as follows: I: 0.128 19, 0.119 94; II: 0.139 64, 0.130 55; III: 0.21 55, 0.164 73; IV: 0.086 82, 0.061 22; V: 0.095 49, 0.069 73; VI: 0.191 22, 0.10 61; VII: 0.16 85, 0.158 78; VIII: 0.290 98, 0.183 43. The cluster IV and V presented the largest genetic differentiation, with an  F ST value of 0.4612 89, followed by IV and VI, with an  F ST  value of 0.456 958; the lowest genetic differentiation existed between the cluster VII and VIII, with an  F ST  value of 0.0976 13. Except for cluster VII and VIII, the genetic differentiation among the other clusters was at or above the medium level. The results of genotyping showed that there were 29 individuals (61.70 %) with single genetic component, and 18 individuals (38.30 %) with two or three genetic components. Based on the results of genetic components analysis, there were four potential interspecific hybridizations. There was a high genetic diversity among 47 flowering cherry germplasms, obvious genetic differentiation among the eight clusters. The genetic components of natural hybrid individuals and artificial hybrid cultivars were revealed, and their parents were inferred, based on the genotyping results.&nbsp

During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, that is, isolation by adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation by distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line-cheeked Spinetail (Cranioleuca antisiensis). At its geographic extremes, this species shows a near threefold difference in body mass (11.5 to 31.0g) with marked plumage differences. We analysed phenotypic, environmental and genetic data (5,154 SNPs) from 172 individuals and 19 populations sampled along its linear distribution in the Andes. We found that body mass was tightly correlated with environmental temperature, consistent with local adaptation as per Bergmann's rule. Using a PST -FST analysis, we found additional support for natural selection driving body mass differentiation, but these results could also be explained by environment-mediated phenotypic plasticity. When we assessed the relative support for patterns of IBA and IBD using variance partitioning, we found that IBD was the best explanation for genetic differentiation along the cline. Adaptive phenotypic or environmental divergence can reduce gene flow, a pattern interpreted as evidence of ecological speciation's role in diversification. Our results provide a counterexample to this interpretation. Despite conditions conducive to ecological speciation, our results suggest that dramatic size and environmental differentiation within C.antisiensis are not limiting gene flow.

Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana, an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (FST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.

Background and aims – Sloe is a woody plant often used for plantings in the open landscape in Germany. As the use of autochthonous plant material is now required by the new German Nature Conservation Act six regions of origin have been designated according to eco-geographical parameters. As little is known about the actual genetic situation of most species affected by the new law we investigate the genetic diversity/differentiation of autochthonous sloe populations across Germany and discuss our findings with respect to conservation law and its practical implication.Methods – Fifteen autochthonous populations of sloe from all officially designated regions of origin were analysed using a highly reproducible high-annealing-temperature (HAT-) RAPD protocol. Genetic differentiation was assessed using distance based and Bayesian approaches.Key results – General heterozygosity detected within the populations was in the same range as described for other woody species (he 0.171–0.213). While the observed values of genetic differentiation between populations varied considerably (F ST 0.025–0.226) the majority was found in the moderate range. Only two moderately differentiated genetic clusters were identified for sloe in Germany.Conclusions – Moderate genetic differentiation was observed between the two main clusters of sloe populations in Germany. Here, no strong evidence was found for isolation by distance (IBD) or by adaption (IBA). The genetic constitution of sloe populations across Germany rather seems to support isolation by colonialization (IBC) as the main driver of the moderate genetic differentiation in this species. The observed genetic differentiation and the geographic location of the identified genetic clusters only partially coincide with the designated regions of origin defined by German authorities for the implementation of the Nature Conservation Act. In our opinion, those regions can only be considered a first step in the preservation of genetic diversity. Upon availability of data on genetic structure and differentiation in a given species, the regions of origin should gradually be adapted to reflect those structures for each analysed species.

Empirical population genetic studies have been dominated by a neutralist view, according to which gene flow and drift are the main forces driving population genetic structure in nature. The neutralist view in essence describes a process of isolation by dispersal limitation (IBDL) that generally leads to a pattern of isolation by distance (IBD). Recently, however, conceptual frameworks have been put forward that view local genetic adaptation as an important driver of population genetic structure. Isolation by adaptation (IBA) and monopolization (M) posit that gene flow among natural populations is reduced as a consequence of local genetic adaptation. IBA stresses that effective gene flow is reduced among habitats that show dissimilar ecological characteristics, leading to a pattern of isolation by environment. In monopolization, local genetic adaptation of initial colonizing genotypes results in a reduction in gene flow that fosters the persistence of founder effects. Here, we relate these different processes driving landscape genetic structure to patterns of IBD and isolation by environment (IBE). We propose a method to detect whether IBDL, IBA and M shape genetic differentiation in natural landscapes by studying patterns of variation at neutral and non-neutral markers as well as at ecologically relevant traits. Finally, we reinterpret a representative number of studies from the recent literature by associating patterns to processes and identify patterns associated with local genetic adaptation to be as common as IBDL in structuring regional genetic variation of populations in the wild. Our results point to the importance of quantifying environmental gradients and incorporating ecology in the analysis of population genetics.

Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry

The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

Empirical studies of landscape connectivity are limited by the difficulty of directly measuring animal movement. ‘Indirect’ approaches involving genetic analyses provide a complementary tool to ‘direct’ methods such as capture–recapture or radio-tracking. Here the effect of landscape on dispersal was investigated in a forest-dwelling species, the American marten (Martes americana) using the genetic model of isolation by distance (IBD). This model assumes isotropic dispersal in a homogeneous environment and is characterized by increasing genetic differentiation among individuals separated by increasing geographic distances. The effect of landscape features on this genetic pattern was used to test for a departure from spatially homogeneous dispersal. This study was conducted on two populations in homogeneous vs. heterogeneous habitat in a harvested boreal forest in Ontario (Canada). A pattern of IBD was evidenced in the homogeneous landscape whereas no such pattern was found in the near-by harvested forest. To test whether landscape structure may be accountable for this difference, we used effective distances that take into account the effect of landscape features on marten movement instead of Euclidean distances in the model of isolation by distance. Effective distances computed using least-cost modeling were better correlated to genetic distances in both landscapes, thereby showing that the interaction between landscape features and dispersal in Martes americana may be detected through individual-based analyses of spatial genetic structure. However, the simplifying assumptions of genetic models and the low proportions in genetic differentiation explained by these models may limit their utility in quantifying the effect of landscape structure.

Genetic structure of the common terrestrial pulmonate snail, Cryptozona siamensis (Pfeiffer, 1856), in Thailand