Divergence in the face of gene flow: the case of two newts (amphibia: salamandridae)

Genomic analysis reveals complex population structure within the smooth newt, Lissotriton vulgaris, in Central Europe

Species with wide-range distributions usually display high genetic variation. This variation can be partly explained by historical lineages that were temporally isolated from each other and are back into secondary reproductive contact, and partly by local adaptations. The smooth newt (Lissotriton vulgaris) is one of the most widely distributed amphibians species across Eurasia and forms a species complex with a partially overlapping distribution and morphology. In the present study, we explored the population genomic structure of smooth newt lineages in the Carpathian Basin (CB) relying on single-nucleotide polymorphisms. Our dataset included new and previously published data to study the secondary contact zone between lineages in the CB and also tested for the barrier effect of rivers to gene flow between these lineages. We confirmed the presence of the South L. v. vulgaris Lineage distributed in Transdanubia and we provided new distribution records of L. v. ampelensis inhabiting the eastern territories of the CB. High genetic diversity of smooth newts was observed, especially in the North Hungarian Mountains and at the interfluves of the main rivers in the South with four distinct lineages of L. v. vulgaris and one lineage of L. v. ampelensis showing a low level of admixture with the spatially closest L. v. vulgaris lineage. Moreover, admixture detected at the interfluve of the main rivers (i.e. Danube and Tisza) suggested a secondary contact zone in the area. Finally, we found that the river Danube has a very weak effect on population divergence, while the river Tisza is a geographical barrier limiting gene flow between smooth newt lineages. As the range boundaries of L. v. vulgaris and L. v. ampelensis in the CB coincide with the river Tisza, our study underpins the influence of rivers in lineage diversification.

Hybrid zone analysis confirms cryptic species of banded newt and does not support competitive displacement since secondary contact

When two putatively cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia, but a formal hybrid zone analysis has never been conducted. We sample populations throughout the range, with a focus on the supposed contact zone, and genotype them for 31 nuclear DNA SNP markers and mtDNA. We determine the degree of genetic admixture, introgression, and niche overlap. We reveal an extremely narrow hybrid zone, suggesting strong selection against hybrids, in line with species status. The hybrid zone does not appear to be positioned at an ecological barrier, and there is significant niche overlap. Therefore, the hybrid zone is best classified as a tension zone, maintained by intrinsic selection against hybrids. While the two banded newt species can evidently backcross, we see negligible introgression and the pattern is symmetric, which we interpret as supporting the fact that the hybrid zone has been practically stationary since its origin (while extensive hybrid zone movement has been suggested in other newt genera in the region). Our study illustrates the use of hybrid zone analysis to test cryptic species status.

Population genetics analysis of Tolai hares (Lepus tolai) in Xinjiang, China using genome-wide SNPs from SLAF-seq and mitochondrial markers

The main topic of population genetics and evolutionary biology is the influence of the ecological environment, geographical isolation, and climatic factors on population structure and history. Here, we estimated the genetic diversity, genetic structure, and population history of two subspecies of Tolai hares (Lepus tolai Pallas, 1778), L. t. lehmanni inhabiting Northern and Northwest Xinjiang and L. t. centrasiaticus inhabiting Central and Eastern Xinjiang using SNP of specific-length amplified fragment sequencing (SLAF-seq) and four mitochondrial DNA (mtDNA). Our results showed a relatively high degree of genetic diversity for Tolai hares, and the diversity of L. t. lehmanni was slightly higher than that of L. t. centrasiaticus, likely due to the more favorable ecological environment, such as woodlands and plains. Phylogenetic analysis from SNP and mtDNA indicated a rough phylogeographical distribution pattern among Tolai hares. Strong differentiation was found between the two subspecies and the two geographical groups in L. t. centrasiaticus, possibly due to the geographical isolation of mountains, basins, and deserts. However, gene flow was also detected between the two subspecies, which might be attributed to the Tianshan Corridor and the strong migration ability of hares. Tolai hare population differentiation occurred at approximately 1.2377 MYA. Population history analysis based on SNP and mtDNA showed that the Tolai hare population has a complex history and L. t. lehmanni was less affected by the glacial event, possibly because its geographic location and terrain conditions weaken the drastic climate fluctuations. In conclusion, our results indicated that the joint effect of ecological environment, geographic events, and climatic factors might play important roles in the evolutionary process of L. t. lehmanni and L. t. centrasiaticus, thus resulting in differentiation, gene exchange, and different population history.

Ventral and lateral spot patterns differentiation between three smooth newt species (Amphibia: Salamandridae: Lissotriton)

The location, shape and area of dark spots on the belly, throat and sides of the body of three closely related species of smooth newts (Lissotriton kosswigi, L. schmidtleri and L. vulgaris) were analysed. Differences were found between species and sexes in the location and shape of dark spots on the belly, throat and lateral surfaces of the body. Discriminant analysis of these spot characteristics allows to identificate of males of all three species with a high degree of confidence (85–91%). In females, only L. vulgaris was correctly distinguished from the other two species (accuracy 81–94%). Anatolian and Thracian populations of L. schmidtleri have very similar patterns of dark spots, which confirm their conspecificity. The differences in the location and size of dark spots make possible successful identification of the species during field research and study of museum specimens. The developed method could be useful for comparative studies of other animal species which have spotted camouflage or aposematic colouration.

Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure

Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.

Herps without borders: a new newt case and a review of transalpine alien introductions in western Europe

Biogeographic processes have led to different evolutionary taxa occurring in the northern and southern edges of the Alpine Mountains in Western Europe. The integrity of this diversity is being challenged by frequent human-mediated trans-alpine translocations, sometimes leading to biological invasions. Several alien terrestrial vertebrates of south Alpine origins (Italy, Swiss Ticino) are causing damages to native north Alpine fauna. In this paper, we used molecular tools to characterize the understudied case of the Mediterranean smooth newt (Lissotriton vulgaris meridionalis) expanding in the outskirts of Geneva since its introduction before 1975. Mitochondrial and nuclear DNA sequencing suggest that these exotic populations are a mixture between two diverged L. v. meridionalis lineages from central Italy, and traces of potential hybridization with the native L. v. vulgaris was detected. This situation echoes many other trans-alpine alien introductions. We review all comparable cases of southern to northern Alps introductions in vertebrates, including seven reptiles and four amphibians. The majority of south alpine alien lineages were presumably imported voluntarily by enthusiasts and appear to perform better in the disturbed habitats found in the anthropogenic landscapes of Western Europe compared to their native north Alpine counterparts. Most pose serious threats to related species of similar ecology, through direct competition, predation and introgressive hybridization. Difficulties to detect alien species on time lead to significant conservation costs. Better education together with more appropriate and reactive management plans will be necessary to limit the impact of future alien introductions.

The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe

The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones.

Isolation and gene flow in a speciation continuum in newts

Because reproductive isolation often evolves gradually, differentiating lineages may retain the potential for genetic exchange for prolonged periods, providing an opportunity to quantify and to understand the fundamental role of gene flow during speciation. Here we delimit evolutionary lineages, reconstruct the phylogeny and infer gene flow in newts of the Lissotriton vulgaris species complex based on 74 nuclear markers sampled from 127 localities. We demonstrate that distinct lineages along the speciation continuum in newts exchange nontrivial amounts of genes, affecting their evolutionary trajectories. By integrating a wide array of methods, we delimit nine evolutionary lineages and show that two principal factors have driven their genetic differentiation: time since the last common ancestor determining levels of shared ancestral polymorphism, and shifts in geographic distributions determining the extent of secondary contact. Post-divergence gene flow, indicative of evolutionary non-independence, has been most extensive in Central Europe, while four southern European lineages have acquired the population-genetic hallmarks of independent species (L. graecus, L. kosswigi, L. lantzi, L. schmidtleri). We obtained strong statistical support for widespread mtDNA introgression following secondary contact, previously suggested by discordance between mtDNA phylogeny and morphology. Our study reveals long-term evolutionary persistence of evolutionary lineages that may periodically exchange genes with one another: although some of these lineages may become extinct or fuse, others will acquire complete reproductive isolation and will carry signatures of this complex history in their genomes.

Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy

Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species' responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.

Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae)

Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot.

Can genomic data alone tell us whether speciation happened with gene flow?

The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.

Divergence history of the Carpathian and smooth newts modelled in space and time

Information about demographic history is essential for the understanding of the processes of divergence and speciation. Patterns of genetic variation within and between closely related species provide insights into the history of their interactions. Here, we investigated historical demography and genetic exchange between the Carpathian (Lissotriton montandoni, Lm) and smooth (L. vulgaris, Lv) newts. We combine an extensive geographical sampling and multilocus nuclear sequence data with the approximate Bayesian computation framework to test alternative scenarios of divergence and reconstruct the temporal and spatial pattern of gene flow between species. A model of recent (last glacial period) interspecific gene flow was favoured over alternative models. Thus, despite the relatively old divergence (4-6 mya) and presumably long periods of isolation, the species have retained the ability to exchange genes. Nevertheless, the low migration rates (ca. 10(-6) per gene copy per generation) are consistent with strong reproductive isolation between the species. Models allowing demographic changes were favoured, suggesting that the effective population sizes of both species at least doubled as divergence reaching the current ca. 0.2 million in Lm and 1 million in Lv. We found asymmetry in rates of interspecific gene flow between Lm and one evolutionary lineage of Lv. We suggest that intraspecific polymorphism for hybrid incompatibilities segregating within Lv could explain this pattern and propose further tests to distinguish between alternative explanations. Our study highlights the importance of incorporating intraspecific genetic structure into the models investigating the history of divergence.

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

From shelf to shelf: assessing historical and contemporary genetic differentiation and connectivity across the Gulf of Mexico in Gag, Mycteroperca microlepis

Describing patterns of connectivity among populations of species with widespread distributions is particularly important in understanding the ecology and evolution of marine species. In this study, we examined patterns of population differentiation, migration, and historical population dynamics using microsatellite and mitochondrial loci to test whether populations of the epinephelid fish, Gag, Mycteroperca microlepis, an important fishery species, are genetically connected across the Gulf of Mexico and if so, whether that connectivity is attributable to either contemporary or historical processes. Populations of Gag on the Campeche Bank and the West Florida Shelf show significant, but low magnitude, differentiation. Time since divergence/expansion estimates associated with historical population dynamics indicate that any population or spatial expansions indicated by population genetics would have likely occurred in the late Pleistocene. Using coalescent-based approaches, we find that the best model for explaining observed spatial patterns of contemporary genetic variation is one of asymmetric gene flow, with movement from Campeche Bank to the West Florida Shelf. Both estimated migration rates and ecological data support the hypothesis that Gag populations throughout the Gulf of Mexico are connected via present day larval dispersal. Demonstrating this greatly expanded scale of connectivity for Gag highlights the influence of “ghost” populations (sensu Beerli) on genetic patterns and presents a critical consideration for both fisheries management and conservation of this and other species with similar genetic patterns.

The distribution and taxonomy of Lissotriton newts in Turkey (Amphibia, Salamandridae)

Two and perhaps three taxa of Lissotriton newt occur in Turkey. Their species status is controversial. The distribution of these taxa and the taxonomic status of each are reviewed and discussed. A database of 128 Turkish Lissotriton localities was compiled and species distribution models were constructed. We reiterate that the presence of Lissotriton (vulgaris) lantzi in Turkey is disputed and needs confirmation. The range of Lissotriton (vulgaris) kosswigi is restricted to north-western Anatolia - given the small global range of this Turkey endemic, a closer look at its conservation status is warranted. The distribution of Lissotritonvulgarisschmidtleri covers western Asiatic and European Turkey. The findings support an allopatric distribution of the Turkish Lissotriton species. We reflect on the biological significance of previously reported morphological intermediates between Lissotriton (vulgaris) kosswigi and Lissotritonvulgarisschmidtleri in the light of the recent proposal to recognize kosswigi at the species level. The available data are in line with species status for Lissotriton (vulgaris) lantzi and Lissotriton (vulgaris) kosswigi. Although Lissotritonvulgarisschmidtleri is a genetically diverged taxon as well, the extent of gene flow with parapatric European Lissotriton taxa is as yet unknown.

Inter and intra island introgression in a wolf spider radiation from the Galápagos, and its implications for parallel evolution

Parallel radiations within island systems are often assumed to follow a simple scenario in which single colonization events are followed by in situ adaptive divergence. However, subsequent gene exchange after the initial colonization and during the divergence process might have important evolutionary impacts on species radiations. Gene exchange among ecologically similar species from different islands may lead to introgression of adaptive genetic variation and influence the parallel divergence process. In this study, we estimate levels of gene exchange within a wolf spider radiation of the genus Hogna Simon, 1885, from the Galápagos, wherein habitat specialization into 'high elevation' and 'coastal dry' species apparently evolved repeatedly on two islands. By using a multilocus approach we show that low levels of inter-island and relatively higher levels of intra island introgression shaped genetic variation in this species complex. Using these estimates, we demonstrate by means of a coalescence simulation that under these inter- and intra-island migration rates parallel evolution most likely evolves by introgression of adaptive alleles among islands, rather than through independent mutations despite the close genetic relationship of species within islands. As species phylogenies within radiations are frequently used to infer the divergence pattern, even relatively low levels of interspecific gene flow should not be neglected when interpreting parallel trait evolution.

Constraint and adaptation in newt toll-like receptor genes

Acute die-offs of amphibian populations worldwide have been linked to the emergence of viral and fungal diseases. Inter and intraspecific immunogenetic differences may influence the outcome of infection. Toll-like receptors (TLRs) are an essential component of innate immunity and also prime acquired defenses. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Both ancient and recent gene duplications have occurred in urodeles, bringing the total number of TLR genes to at least 21. Purifying selection has predominated the evolution of newt TLRs in both long (∼70 Ma) and medium (∼18 Ma) timescales. However, we find evidence for both purifying and positive selection acting on TLRs in two recently diverged (2-5 Ma) allopatric evolutionary lineages (Lissotriton montandoni and L. vulgaris graecus). Overall, both forms of selection have been stronger in L. v. graecus, while constraint on most TLR genes in L. montandoni appears relaxed. The differences in selection regimes are unlikely to be biased by demographic effects because these were controlled by means of a historical demographic model derived from an independent data set of 62 loci. We infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related amphibian lineages, highlight the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggest differences between lineages in the relative roles of innate and acquired immunity.

Distinguishing between incomplete lineage sorting and genomic introgressions: complete fixation of allospecific mitochondrial DNA in a sexually reproducing fish (Cobitis; Teleostei), despite clonal reproduction of hybrids

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers--hybrids with Mendelian heredity--are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.

Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

Single nucleotide polymorphisms reveal genetic structuring of the carpathian newt and provide evidence of interspecific gene flow in the nuclear genome

Genetic variation within species is commonly structured in a hierarchical manner which may result from superimposition of processes acting at different spatial and temporal scales. In organisms of limited dispersal ability, signatures of past subdivision are detectable for a long time. Studies of contemporary genetic structure in such taxa inform about the history of isolation, range changes and local admixture resulting from geographically restricted hybridization with related species. Here we use a set of 139 transcriptome-derived, unlinked nuclear single nucleotide polymorphisms (SNP) to assess the genetic structure of the Carpathian newt (Lissotriton montandoni, Lm) and introgression from its congener, the smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of Lm populations likely originated from separate refugia, both located in the Eastern Carpathians. The colonization of the present range in north-western and south-western directions was accompanied by a modest loss of variation; admixture between the two groups has occurred in the middle of the Eastern Carpathians. Local, apparently recent introgression of Lv alleles into several Lm populations was detected, demonstrating increased power for admixture detection in comparison to a previous study based on a limited number of microsatellite markers. The level of introgression was higher in Lm populations classified as admixed than in syntopic populations. We discuss the possible causes and propose further tests to distinguish between alternatives. Several outlier loci were identified in tests of interspecific differentiation, suggesting genomic heterogeneity of gene flow between species.

Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform

Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.

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.

A phylogeographic evaluation of the Amolops mantzorum species group: cryptic species and plateau uplift

Phylogeographic analysis brings organism phylogeny, regional geological/climatic history, and population demography together, and provides insights into species history and speciation. Using DNA sequence data from a mitochondrial marker (cytochrome b) and a nuclear marker (cmyc intron 2), we examined phylogeography of the Amolops mantzorum species group. We first constructed Bayesian and maximum-likelihood gene trees and medium-joint networks for the recovered haplotypes, and estimated divergence time for each major lineage. Species boundaries were then delineated using the general mixed Yule-coalescent model (GMYC) and a Bayesian species-delimitation method (BP&P). Potential gene flow between putative species was also estimated using the isolation-with-migration model. Furthermore, species-distribution modeling was used to probe linkage between climatic changes and speciation. Lastly, extended Bayesian skyline plotting was employed to reveal historical demography for each putative species. Our analyses clearly delimit nine species in the group, including four well-recognized species and five putative species, of which three are often listed as synonyms of A. mantzorum. The nominal species A. mantzorum may in fact include two cryptic species. Divergence-time estimates align the speciation events with the recent intense uplift of the Tibetan Plateau in the last 3.6 million years. The species-distribution modeling also reveals different habitat preferences among species that are potentially linked to climatic changes associated with the uplift. Furthermore, three species sustained continuous population growth through the last glaciation, while others expanded only after the last glaciation. The eastern escarpment of Tibet is a biodiversity hotspot; its rich species diversity, unique topography, and well-established geological history provide an excellent system for evolutionary studies.

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

Development, validation and high-throughput analysis of sequence markers in nonmodel species

DNA sequences derived from multiple regions of the nuclear genome are essential for historical inferences in the fields of phylogeography and phylogenetics. The appropriate markers should be single-copy, variable, easy to amplify from multiple samples and easy to sequence using high-throughput technologies. This may be difficult to achieve for species lacking sequenced genomes and particularly challenging for species possessing large genomes, which consist mostly of repetitive sequences. Here, we present a cost-effective, broadly applicable framework for designing, validating and high-throughput sequencing of multiple markers in nonmodel species without sequenced genomes. We demonstrate its utility in two closely related species of newts, representatives of urodeles, a vertebrate group characterized by large genomes. We show that over 80 markers, c. 600 bp each, developed mainly from 3' untranslated transcript regions (3'UTR) may be effectively multiplexed and sequenced. Data are further processed using standard, freely available bioinformatic tools, producing phase-resolved sequences. The approach does not require barcoded PCR primers, and the cost of library preparation is independent of the number of markers investigated. We hope that this approach will be of broad interest for researchers working at the interface of population genetics and phylogenetics, exploring deep intraspecific genetic structure, species boundaries and phylogeographies of closely related species.

How complex is the Bufo bufo species group?

Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and García-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that García-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level.

Pleistocene climate change and the origin of two desert plant species, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China

Pleistocene climate change has had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium (Brassicaceae), Pugionium cornutum and Pugionium dolabratum, which occupy different desert habitats in northwest China. We surveyed sequence variation for internal transcribed spacer (ITS), three chloroplast (cp) DNA fragments, and eight low-copy nuclear genes among individuals sampled from 11 populations of each species across their geographic ranges. One ITS mutation distinguished the two species, whereas mutations in cpDNA and the eight low-copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China. Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium as a result of divergence in different habitats that formed in association with the expansion of deserts in China.

Identifying loci under selection against gene flow in isolation-with-migration models

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).

A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species

The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.

Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

Gene flow and effective population size in two life-history types of broad whitefish Coregonus nasus from the Canadian Arctic

In this study, the magnitude and direction of gene flow and estimates of effective population sizes (N(e) ) were quantified among two life-history types (lacustrine and anadromous) of broad whitefish Coregonus nasus in the lower Mackenzie River system. The data suggest that dispersal and subsequent gene flow occurs between these groups, with the former appearing to be asymmetrical. Gene flow may potentially be directionally biased as well, a result attributed to source-sink population dynamics and the ongoing process of post-glacial colonization and contemporary range expansion. Additionally, average N(e) estimates were consistently lower for lacustrine populations of C. nasus although confidence intervals for both contemporary and historical estimates broadly overlapped. The lower average estimates of N(e) for lacustrine populations was suggested to be the result of more recent founding events following post-glacial dispersal. This study provides one of the first assessments of gene flow and N(e) in an Arctic coregonine, results that may be relevant to other freshwater and anadromous Arctic species persisting in systems near the periphery of their range.

Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands

Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and interpopulation gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multilocus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, Euphaea formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the southeast Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.

Fish migrate underground: the example of Delminichthys adspersus (Cyprinidae)

Complex aquatic systems of karst harbour a rich but little-investigated biodiversity. In Croatia and Bosnia-Herzegovina karst, temporal springs are inhabited by a group of minnow-like fishes that retreat to the associated ground water during dry seasons and spend several months underground. The most abundant species in this group is Delminichthys adspersus (Heckel 1843), which also has the most fragmented distribution range. To determine the population composition and dispersal patterns, and to detect potential underground migration, a large genetic data set comprising 544 specimens of D. adspersus covering most of its distribution area was analysed. Analysis of mitochondrial cytochrome b sequences (∼1000 bp) and eight microsatellite loci showed that D. adspersus comprises at least three subpopulations with gene flow occurring among them. Coalescent-based analysis revealed a complex migration pattern, with several unidirectional dispersal paths, including between temporal springs that share no surface connection. The results of this study suggest the existence of recurrent underground migration of fish in a karst environment and demonstrate the complexity of its hydrological network. The findings are relevant to conservation strategies for endemic karst organisms and karst ecosystems as a whole.

Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai-Tibetan Plateau

Speciation remains a fundamental issue in biology. Herein, we report an investigation into speciation in the Rana chensinensis species complex using DNA sequence data from one mitochondrial and five nuclear genes. A phylogenetic analysis of the data revealed four major clades in the complex, and each of them was found to likely represent a species, including one cryptic species. Ecological niche models were generated from 19 climatic variables for three of the four major clades, which were represented by widespread sampling, including R. chensinensis, Rana kukunoris and the potential cryptic species. Each clade is associated with a unique ecological unit, and this indicates that ecological divergence probably drove speciation. Ecological divergence is likely related to the late Cenozoic orogenesis of the Qinghai-Tibetan Plateau. In addition, gene flow between species was detected but only in peripheral portions of the ranges of the four major clades, thus likely had little influence on the speciation processes. Discordances between mitochondrial and nuclear genes were also found; the nominal species, R. chensinensis, contains multiple maternal clades, suggesting potential mitochondrial introgression between R. chensinensis and R. kukunoris.