Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

Phylogenetic conflicts between genetic markers can help to disentangle complex histories of phylogeography and introgression among taxa. We previously proposed that the Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis himalayanus colonized Hainan Island to form the subspecies R. a. hainanus. Subsequent recolonization of the mainland formed a third taxon, R. a macrurus, and a secondary contact zone with the ancestral himalayanus. To test for historical and recurrent genetic exchange between these mainland subspecies, we sampled populations of each from two parapatric zones and undertook analyses using one mtDNA marker, three nuclear genes and 14 microsatellites. Nuclear DNA, echolocation call frequencies and morphological data all recovered two taxa; however, a mtDNA phylogeny revealed two himalayanus clades, of which one clustered with macrurus, as well as some shared or related mtDNA haplotypes in eastern populations. Isolation‐with‐migration (IM) models suggested some mtDNA gene flow from macrurus to himalayanus. However, strong population structure in himalayanus raises the possibility that macrurus captured mtDNA from a coastal population of himalayanus that has since become rare or extinct. To reconcile these two sets of results, we suggest that the IM estimates might reflect historical mtDNA gene flow among populations of himalayanus, before mtDNA was subsequently captured by macrurus. Finally, microsatellite‐based ABC analyses supported the island origin of macrurus; however, mtDNA‐based ABC analyses suggest this taxon might have evolved on the mainland. Our findings highlight the importance of understanding population history and structure for interpreting hybridization and introgression events.     

DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS)

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels (Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow.     

Evolutionary history of Scinax treefrogs on land‐bridge islands in south‐eastern Brazil

Aim We investigated how Pleistocene refugia and recent (c. 12,000 years ago) sea level incursions shaped genetic differentiation in mainland and island populations of the Scinax perpusillus treefrog group. Location Brazilian Atlantic Forest, São Paulo state, south‐eastern Brazil. Methods Using mitochondrial and microsatellite loci, we examined population structure and genetic diversity in three species from the S. perpusillus group, sampled from three land‐bridge islands and five mainland populations, in order to understand the roles of Pleistocene forest fragmentation and sea level incursions on genetic differentiation. We calculated metrics of relatedness and genetic diversity to assess whether island populations exhibit signatures of genetic drift and isolation. Two of the three island populations in this study have previously been described as new species based on a combination of distinct morphological and behavioural characters, thus we used the molecular datasets to determine whether phenotypic change is consistent with genetic differentiation. Results Our analyses recovered three distinct lineages or demes composed of northern mainland São Paulo populations, southern mainland São Paulo populations, and one divergent island population. The two remaining island populations clustered with samples from adjacent mainland populations. Estimates of allelic richness were significantly lower, and estimates of relatedness were significantly higher, in island populations relative to their mainland counterparts. Main conclusions Fine‐scale genetic structure across mainland populations indicates the possible existence of local refugia within São Paulo state, underscoring the small geographic scale at which populations diverge in this species‐rich region of the Atlantic Coastal Forest. Variation in genetic signatures across the three islands indicates that the populations experienced different demographic processes after marine incursions fragmented the distribution of the S. perpusillus group. Genetic signatures of inbreeding and drift in some island populations indicate that small population sizes, coupled with strong ecological selection, may be important evolutionary forces driving speciation on land‐bridge islands.     

Population structure of caribou in an ice‐bound archipelago

Aim

Archipelagos provide ideal natural systems for testing the effects of isolation and fragmentation of habitats on the genetic makeup of populations—an important consideration, given that many insular species are of conservation concern. Two theories predominate: Island Biogeography Theory (IBT) posits that proximity to the mainland drives the potential for migrants and gene flow. The Central Marginal Hypothesis (CMH) predicts that island populations at the periphery of a species range may experience low gene flow, small population size and high rates of genetic drift. We investigated population genetic structure, genetic diversity and key drivers of diversity for Arctic island‐dwelling caribou (Rangifer tarandus). Our aim was to inform intraspecific units for conservation and decipher how IBT and CMH could act in an archipelago where isolation is highly variable due to sea ice and open water.

Location

Canadian Arctic Archipelago, Canada (Latitude, 55–82°N; Longitude, 61–123°W).

Methods

We genotyped 447 caribou at 16 microsatellite loci; these caribou represented two subspecies (R. t. groenlandicus, R. t. pearyi) and three designatable units. We used hierarchical Bayesian clustering and ordination to determine genetic groups. We evaluated the influence of ecological and geographic variables on genetic diversity using linear mixed‐effects models and compared diversity among mainland and island herds.

Results

Bayesian clustering revealed nine genetic clusters with differentiation among and within caribou subspecies. Genetic differentiation was explained predominantly by isolation‐by‐distance across all caribou, even at the scale of subspecies. Island caribou were less genetically diverse than mainland herds; individual heterozygosity was negatively correlated with distance‐to‐mainland and the extent of autumn ice‐free coastline and positively correlated with unglaciated island size.

Main conclusions

Our findings underscore the importance of hierarchical analysis when investigating genetic population structure. Genetic diversity and its key drivers lend support to both IBT and CMH and highlight the pending threat of climate change for Arctic island caribou.

     

Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo‐Oriental Region

Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus s.l. sampled from 18 populations across its pan‐Asian species range, using sequences from mitochondrial cytochrome c oxidase subunit 1 (CO1), the internal transcribed spacer 2 (ITS2) and the mannose phosphate isomerase (Mpi) gene. A hypothesis of ecological speciation for A. sundaicus involving divergent adaptation to brackish and freshwater larval habitats was also previously proposed, based on a deficiency of heterozygotes for Mpi allozyme alleles in sympatry. This hypothesis was not supported by Mpi sequence data, which exhibited no fixed differences between brackish and freshwater larval habitats. Mpi and CO1 supported the presence of up to eight genetically distinct population groupings. Counter to the hypothesis of three allopatric species, divergence was often no greater between Borneo, Sumatra/Java and the Southeast Asian mainland than it was between genetic groupings within these landmasses. An isolation‐with‐migration (IM) model indicates recurrent gene flow between the current major landmasses. Such gene flow would have been possible during glacial periods when the current landmasses merged, presenting opportunities for dispersal along expanding and contracting coastlines. Consequently, Pleistocene climatic variation has proved a homogenizing, rather than diversifying, force for A. sundaicus diversity.     

Taxonomy of cryptic species in the Cyornis rubeculoides complex in the Indian subcontinent

Taxa classified as subspecies may in fact be cryptic species. We assessed the taxonomic status of the Blue-throated Flycatcher Cyornis rubeculoides complex in India, which consists of several forms with similar plumages and song. We used mitochondrial and nuclear DNA, plumage traits, and detailed song analysis to ascertain the taxonomic status of the different forms. The molecular data identified three primary clades: (1) in the west Himalayan foothills, (2) at higher elevations in the northeast hill states of Meghalaya, Nagaland and Mizoram, and (3) at lower elevations in the northeastern hills of Meghalaya and the east Himalayas of Arunachal Pradesh. The western clade represents nominate C. rubeculoides rubeculoides. The high-elevation eastern clade was considered to be C. rubeculoides rogersi, because it included a sample from this subspecies from near the type locality in southwest Myanmar. These two sister clades had an estimated divergence time of 1.5 million years (my). The low-elevation east clade has previously been assigned to C. rubeculoides, but we showed it is closely related to the Hainan Blue Flycatcher Cyornis hainanus, formerly thought to breed only further east, with an estimated divergence time of only ~0.8 my. This clade may represent a subspecies of C. hainanus or, given reports of widespread sympatry with C. hainanus in Thailand, a distinct species, Cyornis dialilaemus. However, more research is advocated, including molecular data, from the area of overlap. Songs were remarkably similar across all taxa. In playback experiments, C. r. rubeculoides in the west responded to all taxa. This is in agreement with recent work demonstrating that song differences and responses to songs are not always a good indicator of the progress of reproductive isolation.     

Mitochondrial phylogeography,intraspecific diversity and phenotypic convergence in the four‐lined snake (Reptilia,Squamata)

The four‐lined snake, Elaphe quatuorlineata, has a fragmented distribution, restricted in continental regions and islands of the Italian and Balkan peninsulas, and includes several morphologically described subspecies. In this study, mtDNA sequences are used to investigate its evolutionary and biogeographical history, to explore the role of palaeogeography, palaeoclimate and human activities in shaping the observed phylogeographical patterns and to discuss whether current subspecific taxonomy is consistent with the intraspecific phylogeny. The phylogeography of the species is a result of both vicariant and dispersal events, some of them transmarine and even human mediated. Its diversification began approximately 3.5 Mya and continued during the Pleistocene glacial periods, when the four‐lined snake's range was restricted in the Italian and Balkan peninsulas, and subsequently expanded from subrefugia, which acted as ‘biodiversity pockets’. Our study supports the recognition of three genetic lineages that roughly correspond to the morphological subspecies, although the morphological characters used for their discrimination should be re‐evaluated. It seems that the current morphological subspecies correspond to ecomorphs associated with body size change in island snakes and the island‐dwarfism phenomenon.     

Population structure and colonization of Bactrocera dorsalis (Diptera: Tephritidae) in China,inferred from mtDNA COI sequences

The oriental fruit fly, Bactrocera dorsalis, is a serious pest of fruits and vegetables in South‐east Asia, and, because of quarantine restrictions, impedes international trade and economic development in the region. Revealing genetic variation in oriental fruit fly populations will provide a better understanding of the colonization process and facilitate the quarantine and management of this species. The genetic structure in 15 populations of oriental fruit fly from southern China, Laos and Myanmar in South‐east Asia was examined with a 640‐bp sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene. The highest levels of genetic diversity were found in Laos and Myanmar. Low to medium levels of genetic differentiation (F_ST ≤ 0.134) were observed among populations. Pooled populations from mainland China differed from those in Laos and Myanmar (F_ST = 0.024). Genetic structure across the region did not follow the isolation‐by‐distance model. The high genetic diversity observed in Laos and Myanmar supports the South‐east Asian origin of B. dorsalis. High genetic diversity and significant differentiation between some populations within mainland China indicate B. dorsalis populations have been established in the region for an extended period of time. High levels of genetic diversity observed among the five populations from Hainan Island and similarity between the Island and Chinese mainland populations indicate that B. dorsalis was introduced to Hainan from the mainland and has been on the island for many years. High genetic diversity in the recently established population in Shanghai (Pudong) suggests multiple introductions or a larger number of founders.     

拟平鳅头背部斑纹和下唇结构变异及其分类学意义

针对拟平鳅(Liniparhomaloptera disparis)的两个亚种(L.disparis disparis和L.disparis qiongzhongensis)现有形态分类特征的含糊,通过观察标本室保存的15条水系441尾标本,首次提出利用下唇结构类型作为拟平鳅亚种的补充形态鉴别依据,结合头背部斑纹特征,能有效地鉴别拟平鳅各地理种群和亚种,为拟平鳅的分类和鉴定提供参考依据。依据头背部斑纹差异归纳出4种类型,分别为小斑块型(云开山脉以东的7条水系及海南岛万泉河),虫蚀纹型(云开山脉以西的5条水系),混合斑纹型(海南岛的万泉河、南渡江、昌化江共3条水系),大斑块型(海南岛的昌化江)。依据下唇结构变化情况总结出3种下唇类型,分别是半圆型(云开山脉以西的5条水系),几字型(云开山脉以东的7条水系),马蹄型(海南岛的3条水系)。依据头背部斑纹特征结合下唇结构特征,对照模式标本的描述,重新定义了拟平鳅原有的两个亚种,将分布于云开山脉以东水系的种群鉴定为指名亚种,拟平鳅L.disparis disparis,其鉴别特征为:头背部斑纹为小斑块型并且下唇类型为几字型;将海南岛种群鉴定为琼中拟平鳅L.disparis qiongzhongensis,它们都具有独特的马蹄型下唇类结构,且头背部斑纹以混合斑纹型为主。重要的发现是,分布于云开山脉以西的种群与已命名的2个亚种在形态上有明显的差异,其头背部斑纹为独特的虫蚀纹型且下唇类型为半圆型。这可能是一个新亚种。分子生物学方法也许能证明云开山脉以西的种群在遗传上的独特性以及形成新亚种的可能性。云开山脉东、西两侧以及海南岛不同水系的拟平鳅的种群分化问题值得进一步探究。     

A new timeframe for the diversification of Japan’s mammals

Aim The main Japanese islands are land‐bridge islands divided by the biogeographic division Blakiston’s Line and represent two natural laboratories for studying land‐bridge diversification. Colonization of the current mammal fauna has been dated to the middle to late Pleistocene using fossil evidence. The purpose of this paper is to apply a molecular clock to the genetic divergences between Japanese mammalian taxa and their sister mainland taxa to test the late Pleistocene land‐bridge colonization hypothesis. Location The main Japanese islands (Kyushu, Shikoku, Honshu and Hokkaido). Methods I used mitochondrial DNA (cytochrome b) and a species tree approach to estimate the divergence times of 24 Japanese non‐volant terrestrial mammal taxa and their mainland sister taxa using the program *beast . I then tested for evidence of non‐simultaneous divergence among these taxon‐pairs by controlling for expected coalescent stochasticity using the program Ms Bayes . Results Divergence events between taxa on Japan and their mainland sister taxa were significantly older than expected under the current paradigm, which is based on fossil data. Consistent with the land‐bridge colonization hypothesis, there was evidence of multiple divergence events. Main conclusions These results implicate a colonization timeframe that is older than posited by the current paradigm based on fossil evidence. However, these results are still consistent with the land‐bridge colonization hypothesis. Multiple periods of land‐bridge connectivity may account for the current mammalian fauna in Japan. In addition, half of the divergence time estimates in the Honshu–Shikoku–Kyushu region were clumped around 2.4 Ma, which might suggest a dramatic interchange period, concordant with a period of significant global cooling, when the first land bridge may have connected Japan to the mainland.     

Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa

The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon‐primed intron‐crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate‐driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.     

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura)

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.     

Glacial Effects on Sequence Divergence of Mitochondrial COII of Polyura eudamippus (Lepidoptera: Nymphalidae) in China

Sequence divergence of mitochondrial COII was analyzed in 50 specimens belonging to five subspecies of Polyura eudamippus (Lepidoptera: Nymphalidae) collected from southern China. There were nine haplotypes in the 405 bp of partial COII sequence. Distribution of the five subspecies was primarily consistent with the spatial distribution of haplotypes. The K _st statistic showed genetic differentiation among these subspecies, except between the pair of P. e. kuangtungensis and P. e. formosana, which were separated by the Taiwan Strait. This is consistent with the 10,000-year history of the Taiwan Strait, not long enough for detectable differentiation. The present distribution pattern of COII haplotypes of P. eudamippus should be shaped by the alteration of Pleistocene glaciations, and Yunnan might be the refugium of P. eudamippus in the ice age, judging from the abundant haplotypes remaining. There were two routes for P. eudamippus in the postglacial expansion, one northward to Sichuan, Chongqing, and Hubei and another eastward to the southeastern coast of mainland China and Taiwan Island. Because the haplotype of butterflies on Hainan Island (P. e. whiteheadi) was completely different from that of mainland China, it was estimated that butterflies on Hainan Island might be from the Indo-China Peninsula rather than from mainland China.     

PHYLOGEOGRAPHIC PATTERNS INDICATE TRANSATLANTIC MIGRATION FROM EUROPE TO NORTH AMERICA IN THE RED SEAWEED CHONDRUS CRISPUS (GIGARTINALES,RHODOPHYTA)1

Inferring how the Pleistocene climate oscillations have repopulated the extant population structure of Chondrus crispus Stackh. in the North Atlantic Ocean is important both for our understanding of the glacial episode promoting diversification and for the conservation and development of marine organisms. C. crispus is an ecologically and commercially important red seaweed with broad distributions in the North Atlantic. Here, we employed both partial mtDNA Cox1 and nrDNA internal transcribed spacer region 2 (ITS2) sequences to explore the genetic structure of 17 C. crispus populations from this area. Twenty‐eight and 30 haplotypes were inferred from these two markers, respectively. Analysis of molecular variance (AMOVA) and of the population statistic Φ_ST not only revealed significant genetic structure within C. crispus populations but also detected significant levels of genetic subdivision among and within populations in the North Atlantic. On the basis of high haplotype diversity and the presence of endemic haplotypes, we postulate that C. crispus had survived in Pleistocene glacial refugia in the northeast Atlantic, such as the English Channel and the northwestern Iberian Peninsula. We also hypothesize that C. crispus from the English Channel refugium repopulated most of northeastern Europe and recolonized northeastern North America in the Late Pleistocene. The observed phylogeographic pattern of C. crispus populations is in agreement with a scenario in which severe Quaternary glaciations influenced the genetic structure of North Atlantic marine organisms with contiguous population expansion and locally restricted gene flow coupled with a transatlantic dispersal in the Late Pleistocene.     

Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo‐Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Mitochondrial gene trees support persistence of cold tolerant fairy shrimp throughout the Pleistocene glaciations in both southern and more northerly refugia

Fairy shrimp (Crustacea: Anostraca) are specialist inhabitants of temporary aquatic habitats. In many parts of the world and particularly in Western Europe, however, populations are declining while the development of adequate conservation strategies is impeded by a poor knowledge of the genetic structure and taxonomic status of remaining lineages. We reconstructed a phylogeography of the species Chirocephalus diaphanus Prévost, 1803 using partial sequences of the mitochondrial COI gene and discuss the importance of different Pleistocene refugia to explain current diversity patterns. In addition to 20 C. diaphanus populations, we also included populations of six presumably closely related chirocephalids to evaluate their taxonomic status. Based on molecular data, the Eastern European subspecies C. diaphanus romanicus deserves species status while the species status of two Italian chirocephalids, C. salinus and C. ruffoi is questionable. Results indicate European C. diaphanus lineages diverged well before the last glacial maximum and survived the Pleistocene glaciations in multiple (sub)refugia along the Iberian, Italian, and Balkan peninsula. Northern Europe was subsequently recolonized from Southern France, resulting in high levels of cryptic diversity around glacial refugia but also in more widespread haplotypes in mainland Europe.     

Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper,Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae)

Viridovipera stejnegeri is one of the most common pit vipers in Asia, with a wide distribution in southern China and Vietnam. We investigated historical demography and explored how the environment and climatic factors have shaped genetic diversity and the evolutionary history of this venomous snake. A total of 171 samples from 47 localities were sequenced and analysed for two mitochondrial gene fragments and three nuclear genes. Gene trees reveal the existence of two well‐supported clades (Southwest China and Southeast China) with seven distinct and strongly supported, geographically structured subclades within V. stejnegeri. Estimation of divergence time and ancestral area suggests that V. stejnegeri originated at ~6.0 Ma in the late Miocene on the Yunnan–Guizhou Plateau. The estimated date of origin and divergence of the island populations of Taiwan and Hainan closely matches the geological origin of the both islands. The mtDNA gene tree reveals the presence of west–east diversification in V. stejnegeri populations. Complex orogenesis and heterogeneous habitats, as well as climate‐mediated habitat differentiation including glacial cycles, all have influenced population structure and the distribution of this taxon. The validity of V. stejnegeri chenbihuii is questionable, and this subspecies most probably represents an invalid taxon.     

Genetic analysis of a contact zone between two lineages of the ocellated lizard (Lacerta lepida Daudin 1802) in south‐eastern Iberia reveal a steep and narrow hybrid zone

Measuring the diffusion of genes between diverging taxa through zones of secondary contact is an essential step to understand the extent and nature of the reproductive isolation that has been achieved. Previous studies have shown that the ocellated lizard (Lacerta lepida Daudin, 1802) has endured repeated range fragmentation associated with the climatic oscillations of the Plio‐Pleistocene that promoted diversification of many different evolutionary units within the species. However, the oldest divergence within the group is estimated to have occurred much earlier, during the Miocene, around 9 Ma and corresponds to the split between the subspecies Lacerta lepida nevadensis Buchholz (1963) and Lacerta lepida lepida Daudin (1802). Although these two evolutionary units have documented genetic and morphological differentiation, most probably accumulated during periods of allopatry, little is known about patterns of gene flow between them. In this study, we performed a population genetic analysis of a putative area of secondary contact between these two taxa, using mtDNA and microsatellite data. We assessed levels of gene flow across the contact zone to clarify to what extent gene flow may be occurring. Hybridization between the subspecies was observed by the presence of genetically introgressed individuals. However, the overall coincidence of mitochondrial and multilocus nuclear clines and generally steep clines support the idea that this contact zone is acting as a barrier to gene flow. Taken together, these results suggest that L. l. lepida and L. l. nevadensis are in independent evolutionary trajectories and should be considered as two different species.