Multiple Refugia Research Articles

Two sides of the same coin? Transient hybridization in refugia and rapid postglacial ecological divergence ensure the evolutionary persistence of sister Nothofagus.

Glacial periods have been considered as inhospitable environments that consist of treeless vegetation at higher latitudes. The fossil record suggests many species survived the Last Glacial Maximum within refugia, usually at lower latitudes. However, phylogeographic studies have given support to the existence of previously unknown high-latitude refugia that were not detected in the fossil record. Here, we test the hypothesis that cold-tolerant trees of Patagonia survived cold periods in microclimatically favourable locales where hybridization occurred between sister taxa. To study local presence through glacial periods in multiple refugia, we used pollen records and genetic information (isozymes, microsatellites, and combined nuclear and chloroplast DNA sequences) of population pairs of Nothofagus antarctica and N. pumilio that belong to the ancient subgenus Nothofagus which can potentially hybridize in nature, along their entire latitudinal range in Patagonia. Studied species share the N. dombeyi type pollen, which was abundant at >20% in the northernmost latitudinal bands (35-43°S), even during the Last Glacial Maximum. Mid- and southern latitudinal records (44-55°S) yielded lower abundances of ~10% that increased after c. 15.0 cal. ka BP. Therefore, fossil pollen evidence suggests a long-lasting local presence of Nothofagus throughout glacial-interglacial cycles but mostly as small populations between 44°S and 51°S. We found species-specific and shared genetic variants, the latter of which attained relatively high frequencies, thus providing evidence of ancestral polymorphisms. Populations of each species were similarly diverse, suggesting survival throughout the latitudinal range. Estimates of coalescent divergence times were broadly synchronous across latitudes, suggesting that regional climates similarly affected populations and species that hybridized through climate cycles, fostering local persistence.

Climate cycling did not affect haplotype distribution in an abundant Southern African avian habitat generalist species, the familiar chat (Oenanthe familiaris).

Avian species diversity in Southern Africa is remarkably high, yet the mechanisms responsible for that diversity are poorly understood. While this is particularly true with respect to species endemic to the subregion, it is unclear as to how more broadly distributed African species may have colonized southern Africa. One process that may in part account for the high bird species diversity in southern Africa is a "species pump" model, wherein the region was repeatedly colonized by lineages from areas further north: a pattern related to climate cycling and the eastern African arid corridor. Once occupying southern Africa, with its many varied biomes, it is possible that climate cycling further affected lineages by generating genetic diversity in multiple refugia, a pattern recently shown for several southern African bird species. Here, we used mtDNA to address these questions in a widespread, sedentary habitat generalist bird species, the familiar chat (Oenanthe familiaris). The phylogenetic structure suggests a north-to-south colonization pattern, supporting the "species pump" model. Haplotype diversity was partitioned into two distinct clusters: southern Africa and Malawi (East Africa). Southern African haplotypes were not geographically partitioned, and we hypothesize that this pattern has arisen because this species is a habitat generalist, and as such resilient to habitat-altering climate perturbations. Based on our phylogenetic results, we discuss the validity of currently recognized subspecies.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

Traversing the Great Lakes: Post‐glacial colonization by a widespread terrestrial salamander

AbstractAimsGlacial retreat at the end of the Pleistocene epoch opened vast expanses of emergent habitat in the northern hemisphere that were colonized by opportunistic taxa. However, species that undergo post‐glacial expansion may have originated from one or several glacial refugia. We inferred the post‐glacial expansion history of the Eastern Red‐backed Salamander (Plethodon cinereus), a fully terrestrial species with a vast distribution despite severe dispersal limitations. Previous studies indicated populations south of the glacial boundary at the eastern and western limits of the distribution were closely related, suggesting either multiple refugia or an extraordinary post‐glacial expansion event.LocationEastern North America.Taxon Plethodon cinereus (Green, 1818), Caudata: Plethodontidae.MethodsWe collected ddRAD‐seq data from 106 individuals throughout the distribution of P. cinereus. We estimated phylogeographic structure, including finer‐scale structure among the post‐glacial populations. To test the origins and routes of colonization, we used ecological niche modelling, population trees and analyses of directional range expansion.ResultsAnalyses supported our hypothesis of a southeastern glacial refugium, with northward expansion along the Eastern Seaboard prior to westward invasion into the Great Lakes region, including southwestern expansion into unglaciated areas at the western end of the distribution. However, a distinct subgroup in the northwestern portion of the range raises the possibility of a second refugium near the ice‐free Driftless Area.Main ConclusionsBased on our results, we hypothesize a southeastern refugium from which most of today's northern populations undertook extensive post‐glacial colonization. Our results indicate a geographically non‐linear colonization history for P. cinereus.

Molecular phylogeography and historical demography of a widespread herbaceous species from eastern North America, Podophyllum peltatum.

Glacial/interglacial cycles and topographic complexity are both considered to have shaped today's diverse phylogeographic patterns of taxa from unglaciated eastern North America (ENA). However, few studies have focused on the phylogeography and population dynamics of wide-ranging ENA herbaceous species occurring in forest understory habitat. We examined the phylogeographic pattern and evolutionary history of Podophyllum peltatum L., a widely distributed herb inhabiting deciduous forests of ENA. Using chloroplast DNA (cpDNA) sequences and nuclear microsatellite loci, we investigated the population structure and genetic diversity of the species. Molecular dating, demographic history analyses, and ecological niche modeling were also performed to illustrate the phylogeographic patterns. Our cpDNA results identified three main groups that are largely congruent with boundaries along the Appalachian Mountains and the Mississippi River, two major geographic barriers in ENA. Populations located to the east of the Appalachians and along the central Appalachians exhibited relatively higher levels of genetic diversity. Extant lineages may have diverged during the late Miocene, and range expansions of different groups may have happened during the Pleistocene glacial/interglacial cycles. Our findings indicate that geographic barriers may have started to facilitate the population divergence in P. peltatum before the Pleistocene. Persistence in multiple refugia, including areas around the central Appalachians during the Quaternary glacial period, and subsequent expansions under hospitable climatic condition, especially westward expansion, are likely responsible for the species' contemporary genetic structure and phylogeographic pattern.

Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change

Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5939 and 11 513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We (1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, (2) test the validity of multiple sub-species designations, (3) provide spatial and temporal historical biogeographic perspectives, and (4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however, nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting the interpretation of ongoing evolutionary processes, particularly in southern portions of the species’ range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.

High-mountain phylogeography in the Balkan Peninsula: isolation pattern in a species of alpine siliceous grasslands and its possible background

Although the Balkan Peninsula belongs to the most mountainous regions of Europe, phylogeographic structure of its alpine flora remains insufficiently understood, especially for species distributed both in the western and eastern parts of the Peninsula. We analyzed Campanula orbelica, a Balkan endemic typical of high-mountain siliceous grasslands, based on the population genetic structure, climatic niche modeling at the species- and intraspecific level, and niche hindcasting back to the Last Glacial Maximum (LGM; 20 kya). Our data reveal a clear phylogeographic pattern with three geographically coherent genetic groups: (i) the most divergent and spatially restricted lineage of the Pirin mountains (east), (ii) neighboring Rila mountains and other eastern Balkan massifs (Rhodopes, Stara Planina, Vitoša), and (iii) the most geographically disjunct mountains of the Scardo-Pindhic range (Šar Planina and Korab) in the west. This pattern indicates multiple refugia and isolated evolutionary centers within the Balkan Peninsula mountains, with the eastern part of the range as likely ancestral area, and an early dispersion into the western region, which formed the main geographical disjunction. The genetic divergence was only partly correlated with geographical isolation, clear dispersal barriers, or climatic niche shifts, suggesting contrasting isolation/dispersal dynamics in various parts of the range. Climatic niche overlap was low among eastern vs. western groups, which correlates with the longest spatial distance and significant genetic divergence, while niche characteristic of the Pirin lineage was a subset of the adjacent Rila lineage niche. High genetic divergence of the Pirin populations was also not correlated with persistent gaps in potential distributions but hypothetically may have been triggered by diversified (limestone/silicate) bedrock conditions. Our results highlight the need for high-mountain phylogeographic surveys in the eastern part of the Balkan Peninsula, to assess the biogeographical relevance of isolation patterns and definition of evolutionarily important units in the high-mountain flora.

Ecological niche modeling of the Macedonian mouse, Mus macedonicus (Mammalia, Rodentia), under climate change conditions

Abstract Mus macedonicus Petrov & Ružic, 1983, also known as the Macedonian mouse or Balkan short-tailed mouse, lives in the southern Balkans and the Middle East. While this species is common in Mediterranean ecosystems and is listed as “least concern” by the IUCN, little is known about how its distribution may shift with climate change. This study explores the ‘species’ potential distribution in three different periods: during the Last Glacial Maximum (LGM) and under current and future climate scenarios, using Maximum Entropy modelling. Modelling was based on 137 georeferenced occurrence records from Macedonia, Bulgaria, Greece, Turkey, Syria, Lebanon, Israel, Iran, Georgia, and Russia and ten bioclimatic variables from the WorldClim database. We show that a combination of precipitation and temperature variables appear to shape the geographical range of the Macedonian mouse and that its predicted distribution during the LGM is consistent with its survival in multiple refugia, as suggested by previous genetic studies. Modelled future distributions are subtly but significantly different from the current, with population losses and gains in different regions. Our results provide a sound framework for future studies on this model species’ range dynamics, suggesting that the overall geographical range of M. macedonicus is relatively stable in the long term.

Phylogeographical breaks and limited connectivity among multiple refugia in a pan‐Antarctic moss species

AbstractAimThe historical biogeography of the Antarctic terrestrial flora remains poorly studied and understood. Long‐term in situ persistence of mosses was demonstrated but region‐wide phylogeographical patterns and processes which shaped extant ranges remain largely unknown. Based on a circum‐Antarctic phylogeography, we aim to explore the location of glacial refugia, especially the possibility of their existence in the continent, patterns of possible connections between extant discrete populations, local colonisation routes and barriers to gene flow, hence relative importance of connectivity and isolation.LocationAntarctica, South America, Australia and New Zealand.TaxonSyntrichia sarconeurum Ochyra & R.H.Zander (Pottiaceae).MethodsWe used a range‐wide, taxonomically informed sampling and multilocus sequencing of nuclear and chloroplast DNA regions. The temporal evolutionary framework, spatial genetic structure and regional diversification were assessed using phylogenetic reconstruction (maximum likelihood and Bayesian inference), molecular dating, phylogeographical analyses and reconstruction of ancestral areas.ResultsWe found a striking genetic structure of the Antarctic Syntrichia sarconeurum populations that deviates from previous reports on mosses. The presence of two allopatric cpDNA haplotypes indicated a long‐term isolation of the continental populations. Nuclear ITS revealed three major lineages with a main genetic break largely consistent with plastid data. Significant phylogeographical structure was further supported by NST/FST comparison, raggedness index and mismatch analyses. Diversification of the Antarctic lineages occurred within the Pleistocene, since about 1.36 Ma.Main ConclusionsThe genetic break genetic break revealed in the phylogeographical structure coincides with the Gressit line, a biogeographical separation area between the biota of the Antarctic Peninsula and the main continental Antarctica. It indicates limited connectivity of populations and suggests that S. sarconeurum has survived in multiple refugia both in the peripheral areas of the Antarctic and within the continent over several glacial periods. Differences in genetic diversity observed between these areas may hypothetically reflect asymmetric changes in reproductive mode in the past.

A low-latitude species pump: Peripheral isolation, parapatric speciation and mating-system evolution converge in a marine radiation.

Geologically recent radiations can shed light on speciation processes, but incomplete lineage sorting and introgressive gene flow render accurate evolutionary reconstruction and interpretation challenging. Independently evolving metapopulations of low dispersal taxa may provide an additional level of phylogeographic information, given sufficiently broad sampling and genome-wide sequencing. Evolution in the marine brown algal genus Fucus in the south-eastern North Atlantic was shaped by Quaternary climate-driven range shifts. Over this timescale, divergence and speciation occurred against a background of expansion-contraction cycles from multiple refugia, together with mating-system shifts from outcrossing (dioecy) to selfing hermaphroditism. We tested the hypothesis that peripheral isolation of range edge (dioecious) F. vesiculosus led to parapatric speciation and radiation of hermaphrodite lineages. Species tree methods using 876 single-copy nuclear genes and extensive geographic coverage produced conflicting topologies with respect to geographic clades of F. vesiculosus. All methods, however, revealed a new and early diverging hermaphrodite species, Fucus macroguiryi sp. nov. Both the multispecies coalescent and polymorphism-aware models (in contrast to concatenation) support sequential paraphyly in F. vesiculosus resulting from distinct evolutionary processes. Our results support (1) peripheral isolation of the southern F. vesiculosus clade prior to parapatric speciation and radiation of hermaphrodite lineages-a "low-latitude species pump". (2) Directional introgressive gene flow into F. vesiculosus around the present-day secondary contact zone (sympatric-allopatric boundary) between dioecious/hermaphrodite lineages as hermaphrodites expanded northwards, supported by concordance analysis and statistical tests of introgression. (3) Species boundaries in the extensive sympatric range are probably maintained by reproductive system (selfing in hermaphrodites) and reinforcement.

Population genetic analysis of the Humboldt’s flying squirrel using high-throughput sequencing

Abstract The San Bernardino flying squirrel (Glaucomys oregonensis californicus) is thought to be the southernmost population of the Humboldt’s flying squirrel (G. oregonensis) and is restricted to the San Bernardino and San Jacinto Mountains in California. However, recent surveys indicate they have been extirpated from the latter locality. In this study, we characterized the intraspecific genetic structure and diversity of G. oregonensis. We amplified and sequenced at least 300 bp of the mitochondrial cytochrome-b gene and 11 nuclear microsatellites to provide baseline genetic data for this species and subspecies, investigate G. oregonensis genetic structure with a focus on the subspecies distributed in California, and finally evaluate the genetic diversity within G. o. californicus. Population and phylogenetic analyses were performed on a total of 147 samples (tissue, hair, and museum specimen) using the Illumina high-throughput sequencing (HTS) platform, thereby bioinformatically coding microsatellite alleles using established pipelines. Our results indicate reduced genetic diversity in G. o. californicus and highlight genetic distinctiveness of the San Jacinto population. In addition, the differences in genetic diversity between the mitochondrial and nuclear markers suggest sex-biased dispersal and historic separation of the species in multiple refugia followed by more recent gene flow among subpopulations in northern California. This study contributes valuable information toward understanding the genetic variation within G. oregonensis, provides information for future conservation decisions for G. o. californicus, and has novel implications for HTS genotyping-by-sequencing.

Linked selection, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence in Quercus dentata

AbstractMultiple evolutionary forces contribute to heterogeneous genomic landscapes; however, disentangling their relative contributions is challenging. We sampled nine populations across the distribution of Quercus dentata, a dominant forest tree in East Asia, and used whole‐genome sequencing data to investigate mechanisms underlying divergence. We identified two genetic groups (north and south) that diverged ~1.84 million years ago, consistent with the uplift of the Qinling Mountains during the Pleistocene. The north group experienced a bottleneck during the middle–late Pleistocene and expanded from multiple refugia. The south group experienced a more severe bottleneck and showed high population differentiation, probably due to long‐term isolation and habitat fragmentation. We detected genomic islands with elevated relative differentiation (FST) scattered across the genome. Among these, 65.9% showed reduced absolute divergence (dXY) consistent with linked selection, while the remaining (34.1%) showed elevated dXY suggestive of divergent sorting of ancient polymorphisms. The recombination rate in genomic islands was lower than background, suggesting the importance of genome structure in shaping the genomic landscape. We detected 108 single nucleotide polymorphisms significantly associated with environmental factors, 12 of which clustered in a region of ~500 kb. This region showed multiple signals of positive selection in the north group, including the enrichment of XP‐extended haplotype homozygosity scores, an elevated population branch statistic, and an excess of high‐frequency derived alleles. In addition, we found that linkage disequilibrium was low and derived haplotypes declined rapidly in this region, indicating selection on standing variation. Our results clarify the evolutionary processes driving genomic divergence in Q. dentata.

Phylogeographic pattern of a cryptoviviparous mangrove, Aegiceras corniculatum, in the Indo-West Pacific, provides insights for conservation actions.

This study identified the historical geoclimatic factors which caused low genetic diversity and strong phylogeographic structure in a cryptoviviparous mangrove. The phylogeographic pattern was used to suggest conservation actions. Phylogeographic studies are used to understand the spatial distribution and evolution of genetic diversity, and have major conservation implications, especially for threatened taxa like the mangroves. This study aimed to assess the phylogeographic pattern of Aegiceras corniculatum, a cryptoviviparous mangrove, across its distribution range in the Indo-West Pacific (IWP) region. We genotyped 398 samples, collected from 37 populations, at four chloroplast DNA (cpDNA) loci, and identified the influence of historical processes on the contemporary population structure of the species. Low genetic diversity at the population level was observed. The evolutionary relationship between 12 cpDNA haplotypes suggested a strong phylogeographic structure, which was further validated by the clustering algorithms and proportioning of maximum variation among hierarchical population groups. The magnitude and direction of historical gene flow indicated that the species attained its wide distribution from its likely ancestral area of the Malay Archipelago. The divergence time estimates of the haplotypes indicated that the geoclimatic changes during the Pleistocene, especially the glacial sea-level changes and emergence of landmasses, hindered genetic exchange and created genetic differentiation between the phylogenetic groups. The species overwintered the last glacial maxima in multiple refugia in the IWP, as identified by the environmental niche modelling. Overall, our findings indicated that ancient glacial vicariance had influenced the present genetic composition of A. corniculatum, which was maintained by the current demographic features of this region. We discussed how these findings can be used to prioritize areas for conservation actions, restore disturbed habitats and prevent further genetic erosion.

European common frog (Rana temporaria) recolonized Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes.

The high mountain ranges of Western Europe had a profound effect on the biotic recolonization of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonization from multiple refugia in northern Italy. Here, we investigate the effect of the European Alps on the phylogeographic history of the European common frog Rana temporaria. Based on partial cytochrome b and COXI sequences from Switzerland, we find two mitochondrial lineages roughly north and south of the Alpine ridge, with contact zones between them in eastern and western Switzerland. The northern haplogroup falls within the previously identified Western European haplogroup, while the southern haplogroup is unique to Switzerland. We find that the lineages diverged ~110 kya, at approximately the onset of the last glacial glaciation; this indicates that they are from different glacial refugia. Phylogenetic analyses suggest that the northern and southern haplogroups colonized Switzerland via trans‐ and circum‐Alpine routes from at least two separate refugia in northern Italy. Our results illustrate how a complex recolonization history of the central European Alps can arise from the semi‐permeable barrier created by high mountains.

Mid-Pleistocene Transition as a trigger for diversification in the Irano-Anatolian region: Evidence revealed by phylogeography and distribution pattern of the eastern three-lined lizard

Past climatic events are one of the major drivers for divergence of species that could shape the present biodiversity and species dispersal patterns. Irano-Anatolian region is one of the biodiversity hotspots in the world. This region is predicted to serve various refugia during Quaternary glaciations. The eastern three-lined lizard ( Lacerta media media ) is a medium-sized lacertid species, which is originated from central Anatolian and is currently distributed almost across Irano-Anatolian region. In this study, the phylogeography, demographic history of the subspecies using mtDNA genes (cyt b , 12S and 16S) along with the species distribution models (SDMs) under past-present-future scenarios have been investigated. The results revealed that four distinct clades are well-established within the L. m. media which may intensely diverge during Pleistocene climatic fluctuations since the Mid-Pleistocene Transition (MPT). The past climate oscillations may isolate the population in various refugia throughout the Irano-Anatolian region which has been led to this divergence. The results of SDMs also indicates several localities with suitable climate conditions for eastern three-lined lizard in the region since LGM (21 thousand years ago) until the current date. This suitability can be expanded under future climate scenarios considering the existence of various low and high altitude refugia. Some conservation implications arise from the results that emphasize the importance of the region and its multiple refugia in preserving biodiversity. It can be suggested that, future conservation practices should be focused on the obtained biogeographical units such as central Anatolia, west and northwestern Iran, which encompass high levels of diversity including distinct clades within the eastern three-lined lizard.

Long‐term continuity of steppe grasslands in eastern Central Europe: Evidence from species distribution patterns and chloroplast haplotypes

AbstractAimThe steppe grasslands of eastern Central Europe are exceptionally species rich and valuable from a nature conservation point of view. However, their historical biogeography is still poorly understood. Here we use the regional diversity of habitat specialists and chloroplast DNA data to investigate potential long‐term refugia of steppe species in this region.LocationPannonian Basin and adjacent regions; SW Russia.TaxonVascular plants.MethodsAfter identifying habitat specialists of the three main steppe types (meadow steppes, grass steppes and rocky steppes), we compiled their regional presence–absence in grid cells of 75 km × 75 km. We analysed the dependency of habitat specialist diversity to climate, topographic heterogeneity and geographical distance to potential refugia. For genetic analysis, we sampled three or four habitat specialists of each steppe type and used cpDNA markers to investigate intraspecific diversity and geographical distribution of haplotypes. We also tested for correspondence between the number of habitat specialists and haplotype diversity.ResultsClimate and topography explained between 40% and 63% of the variance in habitat specialist diversity. Adding geographical distance to potential refugia increased the explained variance in the models for all steppe types. Chloroplast haplotypes featured a complex pattern across the study area. Several species showed a strong geographical differentiation, suggesting migration waves from multiple refugia with only limited subsequent genetic intermixture. Maximum haplotype diversity in a region showed a better correlation with the number of habitat specialists per steppe type than mean haplotype diversity.Main conclusionsWe can clearly reject the scenario of a late‐Holocene immigration of steppe species from areas outside the Pannonian Basin. Most species must have been present in the region since at least the early Holocene, highlighting the importance of the lower mountain ranges surrounding the Pannonian Basin as long‐term refugia for European steppe species. Dispersal limitation and resulting migration lags seem to have a strong influence on the distribution of steppe species in Central Europe.

Phylogeography of the stoneflyKamimuria tibialis: multiple glacial refugia and sympatric occurrence of different lineages in the southern islands of Japan

AbstractTo elucidate the effect of Pleistocene climatic fluctuations on the historical distribution and geographical genetic structure of temperate Japanese species, we performed phylogeographical and demographic analyses using mitochondrial gene sequences obtained from the stonefly species Kamimuria tibialis, sampled from four main islands of the Japanese Archipelago (i.e. Hokkaido, Honshu, Shikoku and Kyushu) and Tsushima Island. We detected three main clades with distinct geographical distributions, including the Tsushima, Kyushu and Hokkaido–Honshu–Shikoku phylogroups. These groups were estimated to have diverged from one another 0.54–2.02 Mya, suggesting they have undergone several glacial cycles in different refugia. Our results showed that during the glacial epochs and with a fall in sea-level, gene flow was limited among Tsushima and Kyushu, and among Hokkaido and Honshu, probably because the straits between these islands are deep. The population in Kyushu and Shikoku, the southernmost islands, exhibited high genetic diversity, with two distinct haplotype lineages occurring sympatrically. These results suggest that the population division into multiple refugia and the existence of stable southern refugia have contributed to the high genetic diversity of the species in this region.

Pleistocene climate fluctuations as the major driver of genetic diversity and distribution patterns of the Caspian green lizard, Lacerta strigata Eichwald, 1831.

Green lizards of the genus Lacerta have served as excellent models for studying the impact of Pleistocene climatic oscillations on genetic structures. The Caspian green lizard, Lacerta strigata, occupies various habitats across the Caucasus and the South Caspian Sea, with the Hyrcanian Forests and north of the Alborz Mountains forming the core of the range. This study aimed to re‐examine the phylogenetic relationships of L. strigata with other congeneric members and to assess the genetic structure and historical demography of the species. Furthermore, Species Distribution Models (SDMs) were performed to infer the species' potential habitat suitability and were then projected on climate scenarios reflecting current and past (6 ky and 21 ky before present) conditions. A total of 39 individuals collected from most of the distribution range, together with additional lacertid species sequences from the GenBank database, were examined using mtDNA (Cyt b and 12S ribosomal RNA) and nuclear (C‐mos and β‐fibrinogen) sequence data. Based on the phylogenetic analyses, L. strigata was found to be a sister taxon to all other members of the genus. The species included two main clades (regional western and eastern) that diverged in a period between the Early and Middle Pleistocene. Based on the BBM and S‐Diva analyses, both dispersal and vicariance events explained the phylogeographic structure of the species in the Hyrcanian Forests. The historical demographic analyses using Bayesian skyline plots showed a mild increase in the effective population size from about 120 Kya for the western regional clade. According to phylogeographic structures and SDMs evidence, as in other species within the region, it appears that the south of the Caspian Sea (Hyrcanian Forests), and the Alborz Mountains acted as multiple refugia during cold periods and promoted expansion outwards amid the warm periods. Overall, the results provided evidence that the genetic structure of the species has been influenced by the Pleistocene climatic fluctuations.

Comparative phylogeography of bromeliad species: effects of historical processes and mating system on genetic diversity and structure

Abstract A fundamental challenge in population genetics is to understand the role of ecological and historical processes in shaping genetic diversity patterns within and among species. Based on a set of nuclear microsatellite loci, we conducted a comparative study of the genetic diversity and structure of two epiphytic plant species: Vriesea simplex and V. scalaris (Bromeliaceae), endemic to the Brazilian Atlantic Rainforest. The results showed contrasting genetic diversity and structure patterns according to variation in reproductive systems of these species. High genetic diversity, high effective population sizes and low genetic differentiation were observed in the mainly outcrossing V. simplex populations. In contrast, low genetic diversity, low effective population sizes and high genetic differentiation were detected in the mainly selfing V. scalaris populations. Accordingly, the isolation-by-distance indicated stronger population structures in V. scalaris than in V. simplex. Both species showed a similar phylogeographic north-south split across the Atlantic Rainforest, suggesting possible multiple refugia in this biome. Historical climatic changes during the Pleistocene were possible determinants of the genetic diversity and structure of these species in the Atlantic Rainforest. Divergent mating systems (selfing vs. outcrossing), genetic drift and colonization history influenced the genetic diversity and structure of these Neotropical plant species.

Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog,Hyla andersonii(Anura: Hylidae)

AbstractRange fragmentation poses challenges for species persistence over time and can be caused by both historical and contemporary processes. We combined genomic data, phylogeographical model testing and palaeoclimatic niche modelling to infer the evolutionary history of the Pine Barrens tree frog (Hyla andersonii), a seepage bog specialist, in eastern North America to gain a better understanding of the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species range: Alabama/Florida (AF), the Carolinas (CL) and New Jersey (NJ). Phylogenetic relationships within H. andersonii were consistent between the nuclear species tree and mitochondrial analyses, indicating divergence between AF and CL/NJ (Atlantic clade) ~0.9 Mya and divergence of the NJ clade ~0.15 Mya. Several predictions of north-eastern expansion along the Atlantic coast were supported by phylogeographical analyses. Model testing using genome-wide single nucleotide polymorphism data and species distribution models both provided evidence for multiple disjunct refugia. This comprehensive phylogeographical study of H. andersonii demonstrates a long history of range fragmentation within an endemic coastal plain species and highlights the influence of historical climate change on the current distribution of species and their genetic diversity.