Allopatric divergence,demographic history,and conservation implications of an endangered conifer <Emphasis Type="Italic">Cupressus chengiana</Emphasis> in the eastern Qinghai-Tibet Plateau

Isolation and demographic history are key factors that affect lineage divergence of tree species in topographic complex areas, such as the Qinghai-Tibet Plateau (QTP), yet few studies have evaluated these factors in a coalescent-based modeling framework. In the present study, we surveyed ten nuclear DNA sequence loci (nDNA) and six nuclear microsatellite loci (nSSR) for an endangered conifer, Cupressus chengiana, throughout its natural range in the eastern QTP. BARRIER analyses revealed a strong genetic barrier between Gansu and Sichuan populations of C. chengiana, and isolation with migration models detected limited gene flow between them, supporting the division of this species into two evolutionary significant units (ESUs). Two independent coalescent-based approaches suggest a Quaternary divergence between ESUs, their consensus age range ((0.09–) 0.59–1.53 (–2.71) Mya) largely overlaps with the time period when the largest glaciation occurred in the QTP. Both demographic inferences, IMa2 and DIYABC, suggest that both ESUs may have experienced a bottleneck or population contraction event during the late Quaternary. A documented massive recent anthropogenic habitat loss and fragmentation may have led to further decrease of the natural distribution of this conifer. We propose that the conservation and management of both natural stands and plantations of C. chengiana should be reconsidered in the light of our findings.     

Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai–Tibet Plateau (QTP). We analyzed sequences of three chloroplast, two mitochondrial DNA fragments and a further 13 nuclear loci from 216 individuals of the two species. Both species showed a low level of genetic diversity in contrast to other congeners occurring in the QTP and adjacent regions. The estimated population sizes of P. asperata and P. crassifolia are less than the ancestral population size before splitting. These results together with multiple statistical tests (Tajima's D, Fu and Li's D* and F*) suggest that these two species underwent recent bottlenecks. Based on approximate Bayesian computation (ABC), we also determined that the period of the population shrinkage was consistent with the interspecific divergence during the late Pleistocene. The reduced population sizes and the divergent selection may together have triggered the initial divergence under high gene flow between these two species. Our results therefore highlight the importance of climatic oscillations during the late Pleistocene in promoting speciation through changing demographic sizes of the ancestral species on the QTP and in adjacent regions.     

Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029), and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.     

Inter‐island divergence within Drosophila mauritiana,a species of the D. simulans complex: Past history and/or speciation in progress?

Speciation with gene flow may be more common than generally thought, which makes detailed understanding of the extent and pattern of genetic divergence between geographically isolated populations useful. Species of the Drosophila simulans complex provide a good model for speciation and evolutionary studies, and hence understanding their population genetic structure will increase our understanding of the context in which speciation has occurred. Here, we describe genetic diversity and genetic differentiation of two distant populations of D. mauritiana (Mauritius and Rodrigues Islands) at mitochondrial and nuclear loci. We surveyed the two populations for their mitochondrial haplotypes, eight nuclear genes and 18 microsatellite loci. A new mitochondrial type is fixed in the Rodrigues population of D. mauritiana. The two populations are highly differentiated, their divergence appears relatively ancient (100,000 years) compared to the origin of the species, around 0.25MYA, and they exhibit very limited gene flow. However, they have similar levels of divergence from their sibling, D. simulans. Both nuclear genes and microsatellites revealed contrasting demographic histories between the two populations, expansion for the Mauritius population and stable population size for the Rodrigues Island population. The discovery of pronounced geographic structure within D. mauritiana combined to genetic structuring and low gene flow between the two island populations illuminates the evolutionary history of the species and clearly merits further attention in the broad context of speciation.     

Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon)

We present a multilocus sequencing study to assess patterns of polymorphism and divergence in the closely related wild tomato species, Solanum peruvianum and S. chilense (Solanum section Lycopersicon, Solanaceae). The data set comprises seven mapped nuclear loci (approximately 9.3 kb of analyzed sequence across loci) and four local population samples per species that cover much of the species' range (between 80 and 88 sequenced alleles across both species). We employ the analytical framework of divergence population genetics (DPG) in evaluating the utility of the "isolation" model of speciation to explain observed patterns of polymorphism and divergence. Whereas the isolation model is not rejected by goodness-of-fit criteria established via coalescent simulations, patterns of intragenic linkage disequilibrium provide evidence for postdivergence gene flow at two of the seven loci. These results suggest that speciation occurred under residual gene flow, implying that natural selection is one of the evolutionary forces driving the divergence of these tomato species. This inference is fully consistent with their recent divergence, conservatively estimated to be 相似文献   

Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae)

The impact of gene flow and population size fluctuations in shaping genetic variation during adaptive radiation, at both the genome-wide and gene-specific levels, is very poorly understood. To examine how historical population size and gene flow patterns within and between loci have influenced lineage divergence in the Hawaiian silversword alliance, we have investigated the nucleotide sequence diversity and divergence patterns of four floral regulatory genes (ASAP1-A, ASAP1-B, ASAP3-A, ASAP3-B) and a structural gene (ASCAB9). Levels and patterns of molecular divergence across these five nuclear loci were estimated between two recently derived species (Dubautia ciliolata and Dubautia arborea) which are presumed to be sibling species. This multilocus analysis of genetic variation, haplotype divergence and historical demography indicates that population expansion and differential gene flow occurred subsequent to the divergence of these two lineages. Moreover, contrasting patterns of allele- sharing for regulatory loci vs. a structural locus between these two sibling species indicate alternative histories of genetic variation and partitioning among loci where alleles of the floral regulatory loci are shared primarily from D. arborea to D. ciliolata and alleles of the structural locus are shared in both directions. Taken together, these results suggest that adaptively radiating species can exhibit contrasting allele migration rates among loci such that allele movement at specific loci may supersede genetic divergence caused by drift and that lineage divergence during adaptive radiation can be associated with population expansion.     

Genetic evidence on the demography of speciation in allopatric dolphin species

Under a neutral model, the stochastic lineage sorting that leads to gene monophyly proceeds slowly in large populations. Therefore, in many recent species with large population size, the genome will have mixed support for monophyly unless historical bottlenecks have accelerated coalescence. We use genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters (an antitropical distribution). Despite distinct morphologies, foraging behaviors, and mitochondrial DNAs, these dolphin species are polyphyletic at all four nuclear loci. The abundance of shared polymorphisms between these sister taxa is most consistent with the maintenance of large effective population sizes (5.09 x 10(4) to 10.9 x 10(4)) during 0.74-1.05 million years of divergence. A variety of population size histories are possible, however. We used gene tree coalescent probabilities to explore the rejection region for historical bottlenecks of different intensity given best estimates of effective population size under a strict isolation model of divergence. In L. obliquidens the data are incompatible with a colonization propagule of an effective size of 10 or fewer individuals. Although the ability to reject less extreme historical bottlenecks will require data from additional loci, the intermixed genealogical patterns observed between these dolphin sister species are highly probable only under an extended history of large population size. If similar demographic histories are inferred for other marine antitropical taxa, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules. Instead, a history of large population size in L. obliquidens and L. obscurus contributes to growing biological and environmental evidence that the equatorial barrier became permeable during glacial/interglacial cycles, leading to vicariant isolation of antitropical populations.     

Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow

Multilocus studies assessing patterns of nucleotide polymorphism within and among closely related species provide access to genealogical information bearing on demographic and geographic aspects of their speciation history. However, the technical difficulties in obtaining sufficient sequence data have severely limited this approach thus far, especially in outbred plant taxa. We employ the analytical framework of divergence population genetics in testing the isolation model of speciation in three self-incompatible species of wild tomatoes (clade Lycopersicon), in particular the assumption of divergence without gene flow. Based on DNA sequence data for 13 nuclear loci, average levels of silent polymorphism vary more than three-fold among species. We estimate a large effective population size for the ancestral species, quite similar to that of the highly polymorphic L. peruvianum. The other two species, however, exhibit concordant signatures of population-size reduction. These demographic inferences are biologically plausible and consistent with results obtained from standard neutrality tests. While the isolation model cannot be rejected by goodness-of-fit criteria, patterns of intragenic linkage disequilibrium in L. peruvianum are indicative of historical introgression at least in some regions of the genome. Considered jointly with the geographic pattern of postzygotic reproductive isolation, our results suggest that speciation occurred under residual gene flow, implying natural selection as one of the evolutionary forces driving the diversification of tomato lineages.     

Nuclear gene genealogies reveal historical,demographic and selective factors associated with speciation in field crickets

Population genetics theory predicts that genetic drift should eliminate shared polymorphism, leading to monophyly or exclusivity of populations, when the elapsed time between lineage-splitting events is large relative to effective population size. We examined patterns of nucleotide variation in introns at four nuclear loci to relate processes affecting the history of genes to patterns of divergence among natural populations and species. Ancestral polymorphisms were shared among three recognized species, Gryllus firmus, G. pennsylvanicus, and G. ovisopis, and genealogical patterns suggest that successive speciation events occurred recently and rapidly relative to effective population size. High levels of shared polymorphism among these morphologically, behaviorally, and ecologically distinct species indicate that only a small fraction of the genome needs to become differentiated for speciation to occur. Among the four nuclear gene loci there was a 10-fold range in nucleotide diversity, and patterns of polymorphism and divergence suggest that natural selection has acted to maintain or eliminate variation at some loci. While nuclear gene genealogies may have limited applications in phylogeography or other approaches dependent on population monophyly, they provide important insights into the historical, demographic, and selective forces that shape speciation.     

Nucleotide variation of seven genes in Drosophila kikkawai

We examined levels and patterns of nucleotide variation in 21 strains of Drosophila kikkawai from Miyako island, Japan for the partial regions of the following seven nuclear genes: Adh, Ddc, esc, ksr, Pgi, su(f), and Tpi. The nucleotide variation at total sites (pi(t)) ranged from 0.0013 in the ksr, to 0.0173 in the Adh. The nucleotide divergence at total sites (K(t)) between D. kikkawai and D. lini ranged from 0.0286 in the Tpi to 0.0687 in the su(f). The levels of nucleotide polymorphism and divergence were heterogeneous among the investigated gene regions. The HKA test, which tests imbalance between the intra and interspecific nucleotide variation, showed that the intraspecific nucleotide variation in the Pgi region was much lower than the interspecific variation, while intraspecific variation in the Tpi region was only slightly lower than interspecific variation. The MK test showed an excess of low frequency replacement polymorphic changes in the Adh region, suggesting that most replacement mutations are deleterious. Fay and Wu's test detected an excess of newly arisen variants in the Ddc region. In total, four of the seven gene regions showed significant deviation from the neutrality.     

Assessing models of speciation under different biogeographic scenarios; an empirical study using multi‐locus and RNA‐seq analyses

Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus. These lineages offer a powerful system to study speciation, because different biogeographic patterns (physical vs. ecological segregation) are observed at opposing ends of their distributions. We use 82 samples collected from 38 sites, representing the entire species' distribution and generate sequence data for mtDNA and four nuclear loci. A multilocus phylogenetic analysis in *BEAST estimates the species tree. RNA‐seq data yield 20,126 synonymous variants from 7665 contigs from two individuals of each of the three lineages. Analyses of these data using the demographic inference package ?a?i serve to test the null hypothesis of no gene flow during divergence. The best‐fit demographic model for the three taxa is concordant with the *BEAST species tree, and the ?a?i analysis does not indicate gene flow among any of the three lineages during their divergence. These analyses suggest that divergence among the lineages occurred in the absence of gene flow and in this scenario the genetic signature of ecological isolation (parapatric model) cannot be differentiated from geographic isolation (allopatric model).     

Hidden histories of gene flow in highland birds revealed with genomic markers

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species‐rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well‐studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these ‘hidden histories’ using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation‐with‐bouts‐of‐gene‐flow will turn out to be a common mode of speciation.     

Phylogeography of the genus Dasiphora (Rosaceae) in the Qinghai‐Tibetan Plateau: divergence blurred by expansion

Plateau uprisings and climatic oscillations are considered to have caused extensive allopatric divergences that account for the rich species diversity of the Qinghai‐Tibetan Plateau (QTP). However, secondary contact during range shifts in the Quaternary glacial cycles or inter‐uplift stages may have restored the gene flow between species and so counteracted these divergences, particularly in rapidly‐adapting dominant elements. We tested this hypothesis by determining the phylogeographical history of Dasiphora (Rosaceae), a genus of two species that are widely distributed on the QTP and co‐exist in numerous localities. We sequenced two chloroplast DNA fragments (rbcL, trnT‐L) for 559 individuals from 87 populations. Bayesian methods were used to identify phylogenetic relationships and to estimate divergence times. Demographic histories were inferred using neutrality tests, mismatch distribution analysis, and coalescent simulation. A total of 112 haplotypes that clustered into three major groups were identified. The formation of these groups and their subgroups was dated to between the Pliocene and the late Pleistocene. In addition, we found that some groups underwent multiple extensive expansions. Species‐specific haplotypes were identified for each species, although these haplotypes phylogenetically intermixed. These results suggest that recent plateau uplifts and climatic oscillations might have caused the deep divergences observed within this genus. However, later range expansions probably blurred these divergences and possible species boundaries. Our results shed new light on the complex evolutionary history of the QTP alpine plants. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 777–788.     

Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species‐tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation‐with‐migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene‐ and species‐based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.     

青藏高原岷县龙胆的遗传分化与种群动态历史分析

青藏高原是全球生物多样性中心之一,是研究物种形成和适应性进化的热点地区。岷县龙胆（Gentiana algida var. purdomii）是青藏高原地区特有植物,具有很高的药用价值。本研究以岷县龙胆种群为对象,基于不同遗传方式的分子标记,通过种群遗传结构、遗传分化、种群动态历史和物种分布模型等分析,探讨其在青藏高原的分化历史。结果表明：岷县龙胆具有高的遗传多样性,叶绿体数据表明种内遗传分化程度很高（F_ST=0.452）,但核基因数据表明种内遗传分化程度很低（F_ST=0.022）,揭示岷县龙胆种内存在强烈的基因流。种群动态历史分析表明岷县龙胆种群大小经历了近期扩张,物种分布模型的结果表明岷县龙胆在末次盛冰期以来分布范围略有扩张。分子钟模型的结果表明岷县龙胆种内的遗传分化主要发生在第四纪冰期以来。以上结果一致表明,第四纪气候波动是岷县龙胆分化的主要外部因素。本研究为龙胆属及青藏高原植物类群的物种分化、适应性研究以及资源开发与保护提供了参考。     

Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection

One of the principal goals of population genetics is to understand the processes by which genetic variation within species (polymorphism) becomes converted into genetic differences between species (divergence). In this transformation, selective neutrality, near neutrality, and positive selection may each play a role, differing from one gene to the next. Synonymous nucleotide sites are often used as a uniform standard of comparison across genes on the grounds that synonymous sites are subject to relatively weak selective constraints and so may, to a first approximation, be regarded as neutral. Synonymous sites are also interdigitated with nonsynonymous sites and so are affected equally by genomic context and demographic factors. Hence a comparison of levels of polymorphism and divergence between synonymous sites and amino acid replacement sites in a gene is potentially informative about the magnitude of selective forces associated with amino acid replacements. We have analyzed 56 genes in which polymorphism data from D. simulans are compared with divergence from a reference strain of D. melanogaster. The framework of the analysis is Bayesian and assumes that the distribution of selective effects (Malthusian fitnesses) is Gaussian with a mean that differs for each gene. In such a model, the average scaled selection intensity (gamma = N(e)s) of amino acid replacements eligible to become polymorphic or fixed is -7.31, and the standard deviation of selective effects within each locus is 6.79 (assuming homoscedasticity across loci). For newly arising mutations of this type that occur in autosomal or X-linked genes, the average proportion of beneficial mutations is 19.7%. Among the amino acid polymorphisms in the sample, the expected average proportion of beneficial mutations is 47.7%, and among amino acid replacements that become fixed the average proportion of beneficial mutations is 94.3%. The average scaled selection intensity of fixed mutations is +5.1. The presence of positive selection is pervasive with the single exception of kl-5, a Y-linked fertility gene. We find no evidence that a significant fraction of fixed amino acid replacements is neutral or nearly neutral or that positive selection drives amino acid replacements at only a subset of the loci. These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed.     

Phylogeography of the Qinghai–Tibet Plateau endemic alpine herb Pomatosace filicula (Primulaceae)

In order to trace the response of alpine plants on the Qinghai–Tibet Plateau (QTP) to the Quaternary climate oscillations, the phylogeographic history of Pomatosace filicula Maxim. was investigated in the present study. Based on sequence variations of two maternally inherited plastid markers, matK and trnH-psbA, and the biparentally inherited nuclear ribosomal internal transcribed spacer (nrITS), we estimated the population genetic structure, lineage divergence timescale, and population dynamics of P. filicula. Seven plastid haplotypes and two nrITS genotypes were identified across the range-wide sampling of 200 individuals from 24 populations. Although AMOVA revealed a high level of differentiation among populations (F_ST = 0.560), no significant phylogeographic structure was detected (N_ST = 0.503, G_ST = 0.518, P > 0.05). Molecular dating suggested that the divergences between major plastid lineages and nrITS genotypes occurred during the early and middle Pleistocene, and the middle Pleistocene, respectively. This species most likely survived at multiple unglaciated sites on the QTP during the Last Glacial Maximum, with most of these sites located above 4000 m a.s.l. The species probably experienced range expansion at its distribution fringe, but demographic tests did not suggest significant population size changes. We proposed that pronounced effective gene flow (N_em = 0.393) and short generation time may have obscured the phylogeographic and demographic patterns of this species. Our findings will shed new light on the Quaternary evolutionary history of the alpine flora of the QTP.     

Pliocene intraspecific divergence and Plio‐Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai‐Tibet Plateau

A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai‐Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with intervariety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modelling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modelling of population‐genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hot spot region.     

The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations*

Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo‐genetic maps, and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflect the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.     

Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species

In geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridization occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z chromosome, suggesting an important role for genes on the Z chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyzed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.