High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent,multiple refugia: evidence from mtDNA,microsatellites and nuclear genealogies

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean‐type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species’ range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear β‐fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co‐distributed taxa.     

Phylogeography and historical demography of the Lusitanian snail <Emphasis Type="Italic">Elona quimperiana</Emphasis> reveal survival in unexpected separate glacial refugia

Background  

Present day distributions of Palearctic taxa in northern latitudes mainly result from populations having survived in local patches during the Late Pleistocene and/or from recolonizing populations from southern temperate refugia. If well-studied Mediterranean and eastern European refugia are widely accepted, some recent biogeographical assumptions still remain unclear, such as the occurrence of multiple glacial refugia in Iberia and cryptic refugia in northern Europe during the last glaciations. The Lusitanian snail Elona quimperiana has a remarkably disjunct distribution, limited to northwestern France (Brittany), northwestern Spain and the Basque Country. By describing the phylogeographical structure of this species across its entire range, the present study attempts to identify refugia and subsequent recolonization routes.     

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present‐day tropical biota. Using genome‐wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post‐Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as “isolation by instability,” highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.     

Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida,Opiliones, Sclerobunus robustus) from the southwestern United States

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.     

Identifying Pleistocene refugia in North American cold deserts using phylogeographic analyses and ecological niche modelling

Aim We analysed phylogeographic patterns and ecological niche models (ENMs) of the widespread velvet ant (Hymenoptera: Mutillidae) Sphaeorpthalma difficilis to understand the history of diversification in the Nearctic deserts and to identify areas that may have been cold‐desert refugia during the Pleistocene. These areas should be targeted for conservation because of their climatic stability throughout historical climate change events. Location North American arid regions. Methods The two internal transcribed spacer regions (ITS1 and ITS2) were sequenced and analysed using Bayesian techniques to uncover phylogeographic patterns of relatedness among S. difficilis populations. History of diversification was estimated using parsimony‐based and maximum likelihood character reconstructions. Molecular dating analyses were implemented in the program r8s and were calibrated with Dominican amber fossils. ENMs were developed based on current climate data and projected onto Pleistocene climate surfaces. Results The analyses suggest that S. difficilis had a complex history of Pleistocene range expansion and contraction that led to the formation of genetically distinct populations inhabiting distinct arid regions. ENMs and phylogeographic patterns indicate that several cold‐desert refugia existed in North America, particularly in the Colorado Plateau and parts of the Great Basin Desert. Main conclusions Analyses of S. difficilis are used to identify potential Pleistocene refugia in the North American cold deserts. Because these areas represent climatically stable locations, they are critical for the long‐term persistence of biodiversity. This research provides evidence that in addition to desert‐like conditions persisting through the ice age in parts of the Nearctic warm deserts, many areas maintained desert‐like characteristics in the regional cold deserts. Further work is needed to elucidate options for preserving biodiversity in these cold‐desert refugia.     

Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius,Campanulaceae) within the Balkan refugium

Aim We investigated Quaternary range dynamics of two closely related but ecologically divergent species (cold‐tolerant Edraianthus serpyllifolius and thermophilic Edraianthus tenuifolius) with overlapping distribution ranges endemic to the western Balkan Peninsula, an important yet understudied Pleistocene refugium. Our aims were: to test predictions of the ‘refugia‐within‐refugia’ model of strong genetic subdivisions due to population isolation in separate refugia; to explore whether two ecologically divergent species reacted differently to Pleistocene climatic fluctuations; and to test predictions of the displacement refugia model of stronger differentiation among populations in the thermophilic E. tenuifolius compared with the cold‐tolerant E. serpyllifolius. Location The western Balkan Peninsula. Methods We gathered amplified fragment‐length polymorphism (AFLP) data and plastid DNA sequences from two to five individuals from 10 populations of E. serpyllifolius and 22 populations of E. tenuifolius, spanning their entire respective distribution areas. AFLP data were analysed using a Bayesian clustering approach and a distance‐based network approach. Plastid sequences were used to depict relationships among haplotypes in a statistical parsimony network, and to obtain age estimates in a Bayesian framework. Results In E. serpyllifolius, both AFLP and plastid sequence data showed clear geographic structure. Western populations showed high AFLP diversity and a high number of rare fragments. In E. tenuifolius, both markers congruently identified a major phylogeographic split along the lower Neretva valley in central Dalmatia. The most distinct and earliest diverging chloroplast DNA (cpDNA) haplotypes were found further south in the south‐easternmost populations. North‐western populations, identified as a separate cluster by Bayesian clustering, were characterized by low genetic diversity and a low number of rare AFLP markers. Main conclusions Clear evidence for multiple Pleistocene refugia is found not only in the high‐elevation E. serpyllifolius, but also in the lowland E. tenuifolius, despite the lack of obvious dispersal barriers, in line with the refugia‐within‐refugia model. Genealogical relationships and genetic diversity patterns support the hypothesis that cold‐adapted E. serpyllifolius responded to climatic oscillations mostly by elevational range shifts, whereas thermophilic E. tenuifolius did so mainly by latitudinal range shifts, with different phases (and probably extents) of range expansion. In contrast to the displacement refugia hypothesis, the two elevationally differentiated species do not differ in their genetic diversity.     

Impact of Pleistocene aridity oscillations on the population history of a widespread,vagile Australian mammal,Macropus fuliginosus

Aim Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagile southern Australian marsupial, the western grey kangaroo (Macropus fuliginosus). Location Southern Australia. Methods We examined the variation of the mitochondrial DNA (mtDNA) control region from 511 individuals of M. fuliginosus sampled throughout their transcontinental distribution. Maximum likelihood and Bayesian analyses were used to investigate the phylogeography and coalescence analyses were then used to test hypothesized biogeographical scenarios. Results The combined results of the phylogeographical and coalescence analyses revealed a complex evolutionary history. Macropus fuliginosus originated in the south‐west of the continent, with north‐western and south‐western populations subsequently diverging as a result of vicariance events during the mid‐Pleistocene. Subsequent arid phases affected these populations differently. In the north‐west, the expansion and contraction of the arid zone resulted in repeated vicariance events and multiple divergent north‐western mtDNA subclades. In contrast, the south‐western population was less impacted by climatic oscillations but gave rise to a major transcontinental eastward expansion. Main conclusions Macropus fuliginosus exhibits the genetic signature of divergence due to unidentified barriers in south‐western Western Australia, while previously identified barriers across southern Australia appear to have had little impact despite evidence of a broad‐scale range expansion prior to the Last Glacial Maximum (LGM). This pattern of localized expansion and contraction is comparable to unglaciated regions in both the Northern and Southern Hemispheres. Furthermore, this study indicates that despite the potential similarities between Northern Hemisphere glaciation and the activation of dune systems in the Australian arid zone, both of which rendered large areas inhospitable, the biotic responses and resultant phylogeographical signatures are dissimilar. Whereas a limited number of major geographically concordant refugia are observed in glaciated areas, the Southern Hemisphere arid zone appears to be associated with multiple species‐specific idiosyncratic refugia.     

Incomplete lineage sorting or secondary admixture: disentangling historical divergence from recent gene flow in the Vinous‐throated parrotbill (Paradoxornis webbianus)

Although Pleistocene glaciations had a major impact on the population genetic patterns of many species in North America and Europe, it remains unclear how these climatic fluctuations contributed to species diversification in East Asia. One reason for this is the difficulty of distinguishing genetic admixture following secondary contact from incomplete lineage sorting, both of which can generate similar patterns of genetic variation. Using a combination of multilocus analyses and coalescent simulation, we explore how these two processes occurred in the Pleistocene evolutionary history of a widespread East Asian bird, the Vinous‐throated parrotbill, Paradoxornis webbianus. Maximum likelihood (ML) tree identified two major mitochondrial lineages, which are geographically separated in most parts of its range, but are sympatric at a few sampling sites. NJ tree and Structure analysis of microsatellite data set revealed an extensive level of admixture and little population structure, suggesting recent admixture between two formerly separated groups. Networks from nuclear DNA data sets, however, did not indicate any geographically isolated groups but rather a panmictic population, thus support incomplete lineage sorting. By using coalescent simulation approaches, we show that both processes did occur, although at different temporal scales. During the Pleistocene glaciations, probably around 0.1–0.5 Ma (the Marine Isotope Stage 6, MIS6), P. webbianus contracted into two separate refugia, and subsequently accumulated genetic divergence. During the interglacial MIS5, the species expanded into previously glaciated areas allowing the once separated groups to come into contact and become admixed. Taken together, our results indicate the current genetic variation within P. webbianus is a combination pattern of widespread distribution in pre‐Pleistocene, then contraction and fragmentation into separated refugia during glacial advance, followed by recently postglacial expansion and admixture.     

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail <Emphasis Type="Italic">Trochoidea geyeri</Emphasis> (Soós 1926) (Helicellinae,Stylommatophora)

Background  

The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of species. Trochoidea geyeri (Soós 1926) is a land snail restricted to a patchy, insular distribution in Germany and France. Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene.     

Multiple Pleistocene refugia and Holocene range expansion of an abundant southwestern American desert plant species (Melampodium leucanthum,Asteraceae)

Pleistocene climatic fluctuations had major impacts on desert biota in southwestern North America. During cooler and wetter periods, drought‐adapted species were isolated into refugia, in contrast to expansion of their ranges during the massive aridification in the Holocene. Here, we use Melampodium leucanthum (Asteraceae), a species of the North American desert and semi‐desert regions, to investigate the impact of major aridification in southwestern North America on phylogeography and evolution in a widespread and abundant drought‐adapted plant species. The evidence for three separate Pleistocene refugia at different time levels suggests that this species responded to the Quaternary climatic oscillations in a cyclic manner. In the Holocene, once differentiated lineages came into secondary contact and intermixed, but these range expansions did not follow the eastwardly progressing aridification, but instead occurred independently out of separate Pleistocene refugia. As found in other desert biota, the Continental Divide has acted as a major migration barrier for M. leucanthum since the Pleistocene. Despite being geographically restricted to the eastern part of the species’ distribution, autotetraploids in M. leucanthum originated multiple times and do not form a genetically cohesive group.     

The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus

In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent‐based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of ‘bridges’ among populations. Our study highlights the importance of species‐specific ecology in affecting responses to Pleistocene glacial–interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.     

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

Subdivided Pleistocene glacial refugia, best known as “refugia within refugia”, provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and “ghost” mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD‐sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply‐diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation‐by‐distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences.     

Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

Naturally subdivided populations such as those occupying high‐altitude habitat patches of the ‘alpine archipelago’ can provide significant insight into past biogeographical change and serve as useful models for predicting future responses to anthropogenic climate change. Among New Zealand's alpine taxa, phylogenetic studies support two major radiations: the first correlating with geological forces (Pliocene uplift) and the second with climatic processes (Pleistocene glaciations). The rock wren (Xenicus gilviventris) is a threatened alpine passerine belonging to the endemic New Zealand wren family (Acanthisittidae). Rock wren constitute a widespread, naturally fragmented population, occurring in patches of suitable habitat over c. 900 m in altitude throughout the length of the South Island, New Zealand. We investigated the relative role of historical geological versus climatic processes in shaping the genetic structure of rock wren (N = 134) throughout their range. Using microsatellites combined with nuclear and mtDNA sequence data, we identify a deep north–south divergence in rock wren (3.7 ± 0.5% at cytochrome b) consistent with the glacial refugia hypothesis whereby populations were restricted in isolated refugia during the Pleistocene c. 2 Ma. This is the first study of an alpine vertebrate to test and provide strong evidence for the glacial refugia hypothesis as an explanation for the low endemicity central zone known as the biotic ‘gap’ in the South Island of New Zealand.     

Phylogeography of the widespread African puff adder (Bitis arietans) reveals multiple Pleistocene refugia in southern Africa

Evidence from numerous Pan‐African savannah mammals indicates that open‐habitat refugia existed in Africa during the Pleistocene, isolated by expanding tropical forests during warm and humid interglacial periods. However, comparative data from other taxonomic groups are currently lacking. We present a phylogeographic investigation of the African puff adder (Bitis arietans), a snake that occurs in open‐habitat formations throughout sub‐Saharan Africa. Multiple parapatric mitochondrial clades occur across the current distribution of B. arietans, including a widespread southern African clade that is subdivided into four separate clades. We investigated the historical processes responsible for generating these phylogeographic patterns in southern Africa using species distribution modelling and genetic approaches. Our results show that interior regions of South Africa became largely inhospitable for B. arietans during glacial maxima, whereas coastal and more northerly areas remained habitable. This corresponds well with the locations of refugia inferred from mitochondrial data using a continuous phylogeographic diffusion model. Analysis of data from five anonymous nuclear loci revealed broadly similar patterns to mtDNA. Secondary admixture was detected between previously isolated refugial populations. In some cases, this is limited to individuals occurring near mitochondrial clade contact zones, but in other cases, more extensive admixture is evident. Overall, our study reveals a complex history of refugial isolation and secondary expansion for puff adders and a mosaic of isolated refugia in southern Africa. We also identify key differences between the processes that drove isolation in B. arietans and those hypothesized for sympatric savannah mammals.     

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post‐glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice‐free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north‐west Norway. Location Alaska, Canada, Norway and Sweden. Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F‐statistics, analyses of molecular variance, and multilocus coalescent analyses. Results Significant inter‐population variation in allelic and haplotypic frequencies were observed (nuclear DNA F_ST = 0.004–0.290; mtDNA Φ_ST = 0.051–0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter‐population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene‐flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post‐glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post‐glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium. Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.     

Phylogeography of Potamon ibericum (Brachyura: Potamidae) identifies Quaternary glacial refugia within the Caucasus biodiversity hot spot

Refugia are critical for the maintenance of biodiversity during the periods of Quaternary climatic oscillations. The long‐term persistence of refugial populations in a large continuous refugium has resulted in a homogenous pattern of genetic structure among populations, while highly structured evolutionary lineages characterize the restriction of refugial populations to smaller subrefugia. These mechanisms have resulted in the identification of hot spots of biodiversity within putative glacial refugia. We studied phylogeography of Potamon ibericum (Brachyura: Potamidae) in the drainages of the western Caucasus biodiversity hot spot (i.e., Colchis and the Caucasus) to infer spatial genetic structure and potential refugia for a freshwater crab in this region. These areas have traditionally considered as a refugium due to the presence of Tertiary relict species. We integrated population genetic data and historical demographic analysis from cytochrome oxidase subunit I sequences and paleoclimatic data from species distribution modeling (SDM). The results revealed the lack of phylogeographic structure and provided evidence for demographic expansion. The SDM presented a rather homogenous and large refugium that extended from northeast Turkey to Colchis during the last glacial period. In contrast to these findings, previous phylogeographic study on P. ibericum of the eastern Caucasus biodiversity hot spot (i.e., Hyrcania) identified multiple independent refugia. By combining these results, we explain the significance of this important western Palearctic hot spot of biological diversity in shaping the geographic distribution of intraspecific genetic diversity in a freshwater taxon.     

Lasting through the ice age: The role of the proglacial refugia in the maintenance of genetic diversity,population growth,and high dispersal rate in a widespread freshwater crustacean

1. The severe climatic changes during the Pleistocene ice ages have shaped the genetic structure and distribution of biota in Europe. We aimed to reveal in detail the genetic diversity, geographical population structure, historical and present demography, migration patterns, and the presence of possible glacial refugia within the nominative subspecies Asellus aquaticus aquaticus.
2. We analysed DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene and nuclear noncoding internal transcribed spacer II region, from populations inhabiting post-glacial Europe (from the British Isles and Scandinavia to the northern Mediterranean and Black Sea coasts).
3. The origin of the taxon, including establishment in the Dinaric Western Balkans, dates to the Middle/Late Pliocene, but most of its genetic diversity emerged during the Middle/Late Pleistocene before the Last Glacial Maximum.
4. Despite the general absence of spatial genetic structure with population growth, we discovered two different phylogeographic stories across 11 clusters revealed by a coalescent approach. Firstly, the periglacial cluster group—spatially restricted mainly to the northern Balkans, Pannonian Basin, and Pontic Region—is older and more divergent. It apparently retained a relatively stable population size during the glacial-interglacial cycles. Conversely, the proglacial cluster group—widely distributed in areas close to the glacier margins (north of the Alps, Sudetes, Carpathians) and in the Pannonian Basin—is younger and composed of closely related individuals. It originated in Pleistocene and lasted continuously through the Last Glacial Maximum in numerous high latitude refugia. This was probably due to the vast network of proglacial lakes and rivers, which played a crucial role in the maintenance of genetic diversity, population growth, and high dispersal rate.
5. The evolutionary history of A. a. aquaticus reveals unexpected patterns and is an important lesson when making predictions for other aquatic taxa. Our results suggest that we should stop perceiving the proglacial habitats as lifeless ice desert.

     

Intervarietal and intravarietal genetic structure in Douglas‐fir: nuclear SSRs bring novel insights into past population demographic processes,phylogeography, and intervarietal hybridization

Douglas‐fir (Pseudotsuga menziesii) is one of numerous wide‐range forest tree species represented by subspecies/varieties, which hybridize in contact zones. This study examined the genetic structure of this North American conifer and its two hybridizing varieties, coastal and Rocky Mountain, at intervarietal and intravarietal level. The genetic structure was subsequently associated with the Pleistocene refugial history, postglacial migration and intervarietal hybridization/introgression. Thirty‐eight populations from the USA and Canada were genotyped for 13 nuclear SSRs and analyzed with simulations and traditional population genetic structuring methods. Eight genetic clusters were identified. The coastal clusters embodied five refugial populations originating from five distinct refugia. Four coastal refugial populations, three from California and one from western Canada, diverged during the Pleistocene (56.9–40.1 ka). The three Rocky Mountain clusters reflected distinct refugial populations of three glacial refugia. For Canada, ice covered during the Last Glacial Maximum, we present the following three findings. (1) One refugial population of each variety was revealed in the north of the distribution range. Additional research including paleodata is required to support and determine whether both northern populations originated from cryptic refugia situated south or north of the ice‐covered area. (2) An interplay between intravarietal gene flow of different refugial populations and intervarietal gene flow by hybridization and introgression was identified. (3) The Canadian hybrid zone displayed predominantly introgressants of the Rocky Mountain into the coastal variety. This study provides new insights into the complex Quaternary dynamics of this conifer essential for understanding its evolution (outside and inside the native range), adaptation to future climates and for forest management.     

Identifying glacial refugia in a geographic parthenogen using palaeoclimate modelling and phylogeography: the New Zealand stick insect Argosarchus horridus (White)

We have used phylogeographic analysis of mitochondrial DNA (COI and COII genes) and ecological niche modelling (ENM) to reconstruct the population history of Argosarchus horridus (White), a widespread species of New Zealand stick insect. These data were used to address outstanding questions on the role of glacial refugia in determining the distribution and genetic structure of New Zealand species. Phylogeographic analysis shows a general pattern of high diversity in upper North Island and reduced diversity in lower North Island and South Island. The ENM indicates that during the last glacial maximum, A. horridus was largely restricted to refugia around coastal areas of North Island. The ENM also suggests refugia on the northeast coast of South Island and southeast coast of North Island and this prediction is verified by phylogeographic analysis, which shows a clade restricted to this region. Argosarchus horridus is also most likely a geographic parthenogen where males are much rarer at higher latitudes. The higher levels of genetic variation in northern, bisexual populations suggest southern and largely unisexual populations originated from southwardly expanding parthenogenetic lineages. Bayesian skyline analysis also provides support for a recent population size increase consistent with a large increase in geographic distribution in the late Pleistocene. These results exemplify the utility of integrating ENM and phylogeographic analysis in testing hypotheses on the origin of geographic parthenogenesis and effects of Pleistocene environmental change on biodiversity.