Extra-Mediterranean refugia: The rule and not the exception?

Hot spring oases in the periglacial desert as the Last Glacial Maximum refugia for temperate trees in Central Europe

Northern glacial refugia are a hotly debated concept. The idea that many temperate organisms survived the Last Glacial Maximum (LGM; ~26.5 to 19 thousand years) in several sites across central and northern Europe stems from phylogeographic analyses, yet direct fossil evidence has thus far been missing. Here, we present the first unequivocal proof that thermophilous trees such as oak (Quercus), linden (Tilia), and common ash (Fraxinus excelsior) survived the LGM in Central Europe. The persistence of the refugium was promoted by a steady influx of hydrothermal waters that locally maintained a humid and warm microclimate. We reconstructed the geological and palaeohydrological factors responsible for the emergence of hot springs during the LGM and argue that refugia of this type, allowing the long-term survival and rapid post-LGM dispersal of temperate elements, were not exceptional in the European periglacial zone.

A genetic atlas for the butterflies of continental Canada and United States

Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.

Evolutionary dynamics and geographical dispersal of Borrelia lusitaniae

Background

Borrelia lusitaniae is a species within the complex Borrelia burgdorferi sensu lato, associated with lizards as reservoirs and Ixodes ricinus as its main vector. Borrelia lusitaniae is predominantly distributed in Central and Southeast Europe, and in countries of the Mediterranean basin, such as Portugal, Morocco, Tunisia, and Italy where this spirochete appears to infect vector ticks more frequently than other genospecies. Evolution of this zoonotic tick-borne microparasite is shaped by different environmental factors. Comprehensive phylogenetic analysis may give insight into how B. lusitaniae spreads to new geographic locations.

Aim

We applied Bayesian statistical methods to B. lusitaniae multilocus sequence typing (MLST) data to study the migration routes of B. lusitaniae and its potential for further spread.

Results

The discrete phylogeographic analysis placed origins of B. lusitaniae in Southeast Europe and identified at least two introductions of B. lusitaniae from Europe to North Africa. Estimated effective reproductive potential (Re), as a key indicator for a pathogen spread, suggested potential for further spread.

Conclusion

The results of this study can provide beneficial information about the potential for further spread of B. lusitaniae in Europe and North Africa and estimation of necessity for the development of strategies to monitor and control Lyme borreliosis.

Reconstructing the post-glacial spread of the sand fly Phlebotomus mascittii Grassi, 1908 (Diptera: Psychodidae) in Europe

Phlebotomine sand flies (Diptera: Phlebotominae) are the principal vectors of Leishmania spp. (Kinetoplastida: Trypanosomatidae). In Central Europe, Phlebotomus mascittii is the predominant species, but largely understudied. To better understand factors driving its current distribution, we infer patterns of genetic diversity by testing for signals of population expansion based on two mitochondrial genes and model current and past climate and habitat suitability for seven post-glacial maximum periods, taking 19 climatic variables into account. Consequently, we elucidate their connections by environmental-geographical network analysis. Most analyzed populations share a main haplotype tracing back to a single glacial maximum refuge area on the Mediterranean coasts of South France, which is supported by network analysis. The rapid range expansion of Ph. mascittii likely started in the early mid-Holocene epoch until today and its spread possibly followed two routes. The first one was through northern France to Germany and then Belgium, and the second across the Ligurian coast through present-day Slovenia to Austria, toward the northern Balkans. Here we present a combined approach to reveal glacial refugia and post-glacial spread of Ph. mascittii and observed discrepancies between the modelled and the current known distribution might reveal yet overlooked populations and potential further spread.

Is there a massive glacial-Holocene flora continuity in Central Europe?

The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.

A new pseudoscorpion genus (Garypinoidea: Garypinidae) from the Eocene supports extinction and range contraction in the European paleobiota

During the Paleogene, the Holarctic experienced drastic climatic oscillations, including periods of extensive glaciation. These changes had a severe impact on both the flora and fauna causing widespread extinction and range shifts with some taxa retreating to refugia in the Mediterranean Basin. Here we provide evidence for this hypothesis using fossils from the pseudoscorpion family Garypinidae Daday, 1889 (Arachnida: Pseudoscorpiones). This family comprises 21 extant genera from all continents except Antarctica but is restricted to low mid-latitudes (<44°N) in the Northern Hemisphere. We provide the second record of garypinids from the European succinite ambers of the Eocene by describing the first extinct genus in Garypinidae, Baltamblyolpium gen. nov., which includes two species: Baltamblyolpium gizmotum sp. nov. from Baltic amber and Baltamblyolpium grabenhorsti sp. nov. from Bitterfeld amber. The new genus exhibits a morphology that closely resembles Neoamblyolpium Hoff, 1956 from western North America and the genus Amblyolpium Simon, 1898, which is widespread but includes taxa restricted to Mediterranean refugia in Europe. The discovery of a new fossil genus of Garypinidae from Europe confirms that the family was found at more northerly latitudes during the Eocene, however, extinction and range contraction resulted in their present-day relictual distribution in southern Europe like many other lineages that once thrived in the European "Baltic amber forest" of the Eocene.

Limited congruence in phylogeographic patterns observed for riverine predacious beetles sharing distribution along the mountain rivers

Riverine predacious beetles (RPB) (Carabidae, Staphylinidae) are highly diverse and numerous elements of riverine ecosystems. Their historical and contemporary distribution and diversity are highly dependent on natural flow regimes and topography of watercourses. Despite broad knowledge of their ecology, data on population genetic diversity and connectivity are lacking. This study aimed to fill this gap in order to solve two principal hypotheses assuming (i) congruence of phylogeographic patterns observed for RPB indicating that they share a common history and the ecological adaptations to the dynamic environment, (ii) genetic structuration of populations according to river basins. The Carpathian populations of four ground beetles and three rove beetles were examined using cytochrome oxidase and arginine kinase sequencing. There are substantial differences in RPB demographic history and current genetic diversity. Star-like phylogeny of Bembidion and complex haplotype networks of Paederus/Paederidus, with some haplotypes being drainage-specific and others found in distant populations, indicate a general lack of isolation by distance. Signs of recent demographic expansion were detected for most RPB with the latest population collapse for some rove beetles. To some extent, migration of examined species has to be limited by watersheds. Observed phylogeographic patterns are essential for correctly understanding RPB meta-population functioning.

Historical biogeography and local adaptation explain population genetic structure in a widespread terrestrial orchid

BACKGROUND AND AIMS

Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential.

METHODS

Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence.

KEY RESULTS

The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation.

CONCLUSIONS

Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.

Unexpected high species richness of Bythotrephes Leydig, 1860 (Branchiopoda: Cladocera: Cercopagididae) in subalpine Austrian lakes, with the description of new taxa

The presence of four taxa at the species and subspecies level was revealed based on morphological investigation of a small collection of the representatives of the genus Bythotrephes Leydig, 1860 from Austrian subalpine lakes. The presence of a new species, B. inexpectatus sp. nov. was revealed in two lakes and the presence of a new subspecies, B. longimanus austriacus ssp. nov., in six lakes. Specimens of the population from the Lake Halstättersee, distinguished by the presence of peculiar features, are provisionally assigned to the species B. brevimanus Lilljeborg, 1901 of which the main range is confined to Circumbaltic region. Few morphologically specific specimens from Wolfgangsee could not be accurately identified and therefore assigned to the taxon Bythotrephes sp. requiring further investigation. Previously described taxa from the region, B. styriacus Ischreyt, 1939 and B. longimanus var. carnica Ischreyt, 1939, were considered either required further taxonomic evaluation or having an unclear taxonomic status, respectively. In one lake, the co-occurrence of two species was recorded, which is a rather rare case for the representatives of the genus. The potential reasons for the high species richness of spiny waterfleas in Austrian subalpine lakes and their possible origin are briefly discussed.

Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history

European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and reassess the genetic consequences of natural and anthropogenic forces. We found that population fragmentation, inbreeding and recent hybridization with domestic pigs have caused the spatial genetic structure to be heterogeneous at the local scale. Underlying local anthropogenic signatures, we found a deep genetic structure in the form of an arch-shaped cline extending from the Dinaric Alps, via Southeastern Europe and the Baltic states, to Western Europe and, finally, to the genetically diverged Iberian peninsula. These findings indicate that, despite considerable anthropogenic influence, the deeper, natural continental structure is still intact. Regarding the glacial refugia, our findings show a weaker signal than generally assumed, but are nevertheless suggestive of two main recolonization routes, with important roles for Southern France and the Balkans. Our results highlight the importance of applying genomic resources and framing genetic results within a species' demographic history and geographic distribution for a better understanding of the complex mixture of underlying processes.

Strong intraspecific phylogenetic and karyotypic diversification in Isophya modestior (Orthoptera: Tettigoniidae: Phaneropterinae)

Isophya modestior (Orthoptera: Tettigoniidae) is a species distributed in central and south-eastern Europe, where its distribution is largely separated by two large rivers (Sava and Danube). Since previous studies on the song and morphology of the stridulatory file across its complete geographic range showed that the species is separated into two main groups, we decided to use phylogenetic and karyological analyses in order to evaluate the status of the previously analysed populations.

Phylogenetic analyses showed the existence of two major clades within I. modestior with very high bootstrap values and posterior probabilities—Clade A: present on the Balkan Peninsula, Slovenia (Inner Carniola), Italy, Pannonian Serbia (Vršac Mts and Deronje) and Austria (Burgenland and Lower Austria); Clade B: present in Slovenia (Upper Carniola), Croatia and Austria (Carinthia), Pannonian Serbia (Fruška Gora Mt.) and Hungary.

A comparison of chromosomes of 51 specimens revealed discrete differences between their karyotypes. The physical characteristics of the karyotypes included chromosome number (2n), sex chromosome (X) morphology and C-banding patterns. The standard chromosome complement of 50 specimens from different localities is characterized by 2n = 30 + X0 in males. In one male collected in Fruška Gora Mt. (Andrevlje), the chromosome number was reduced to 2n = 28 + neo-XY. Therefore, further cytogenetic studies involving larger samples, especially from Fruška Gora Mt., are needed in order to gain a more comprehensive view of the chromosome evolution in this group of Isophya species.

Evolutionary Potential of Parthenogenesis-Bisexual Lineages within Triploid Apomictic Thelytoky in Cacopsylla ledi (Flor, 1861) (Hemiptera, Psylloidea) in Fennoscandia

A widely accepted hypothesis is that parthenogenesis is an evolutionary dead end since it is selectively advantageous in the short term only but results in lowered diversification rates. Triploid apomictic parthenogenesis might represent an exception, as in favorable environments, triploid females are able to produce rare males and diploid females. The aim of the present study was to analyze the modes of reproduction and their evolutionary implications in the parthenogenetic psyllid Cacopsylla ledi (Flor, 1861) from Fennoscandia. The cytogenetic assessment of ploidy levels and the analysis of the COI haplotype revealed two geographically separated bisexual lineages implying genuine bisexual populations. The southern lineage occurring south of latitude 65° N in Finland showed a COI haplotype different from that of parthenogenetic triploids in the same population but identical to the haplotype of specimens in a genuine bisexual population in the Czech Republic. This allows us to suggest that bisexuals in southern Fennoscandia represent the original bisexual C. ledi. By contrast, in the northern bisexual lineage north of latitude 65° N, rare males and diploid females carried the same haplotype as triploids in the same population, having been produced by the triploids. In the Kola Peninsula, a genuine bisexual population of presumably rare male/diploid female origin was discovered. As this population is geographically isolated from populations of the ancestral bisexual C. ledi, it can develop into a new bisexual species through peripatric speciation during evolution. Our findings demonstrate that apomictic triploid parthenogenesis is not necessarily an evolutionary dead end but is able to lead to the emergence of a new bisexual species of parthenogenetic origin.

Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

Following the niche: the differential impact of the last glacial maximum on four European ungulates

Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.

European megafaunal ungulates living in open habitats over the last 50,000 years showed evidence for niche change, possibly driven by climatic change and extinction of competitors and predators

Phylogeography reveals the origin of the two phenological forms of large blue, Phengaris arion (Lepidoptera: Lycaenidae)

Our main goal was to investigate the phylogeography of the butterfly Phengaris arion to reveal the evolutionary origin of its ‘spring’ and ‘summer’ forms. Molecular analyses based on highly variable microsatellites, together with Wolbachia screening, were carried out on 34 populations in Europe. We found three well-defined genetic lineages of different origins: the Apennine, the central and the eastern. The highly distinct Apennine lineage is limited by the Alps and evaluated as an Evolutionary Significant Unit (ESU). Therefore, the taxon name ligurica, described from the Ligurian coast (Italy), should not be applied to denote the ‘summer form’ of the Pannonian region. The central lineage is limited by the Carpathians and the most eastern ranges of the Alps, and lacks major range fluctuations related to glaciations, although there is evidence for extra-Mediterranean refugia in the Carpathian Basin. The eastern clade could have had refugia in central Asia. Our results exclude the potential allopatric origin of the ‘spring’ and ‘summer’ arion, and support the hypothesis that the existence of the two forms could be a result of local adaptation to the distinctive phenology of host plant flowering which is manifested in the genetic differences between them. Wolbachia infection has been ruled out as a driver of sympatric speciation in P. arion.

Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations

Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmetric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.

Phylogeography and Wolbachia Infections Reveal Postglacial Recolonization Routes of the Parthenogenetic Plant Louse Cacopsylla myrtilli (W. Wagner 1947), (Hemiptera, Psylloidea)

To reveal the phylogeographic pattern of the parthenogenetic psyllid Cacopsylla myrtilli (W. Wagner 1947) (Hemiptera, Psylloidea), we sequenced a 638 bp fragment of the mitochondrial COI gene from 962 individuals. These insects originated from 46 sampling sites, which cover a significant part of the northern Palearctic distribution range of the species. The sequence data revealed 40 haplotypes, with three main (H1, H2, and H3) and 37 derived ones. The main haplotypes H1 or H2 or both were present at all sampling sites. The star-like shape of the haplotype networks indicated recent population expansion. In most cases, the derived haplotypes were specific for each country, suggesting that the main haplotypes H1 and H2 are of refugial origin, and the derived haplotypes have emerged after the postglacial recolonization process. Based on the haplotype sequences, we suggest H3 to represent the ancestral haplotype from which H1 and H2 have evolved. We suggest that the main haplotype H3 together with its derived haplotypes represents bisexual C. myrtilli, which shows a limited distribution on both sides of the border between Finland and Russia in northern Fennoscandia. The genetic diversity was the highest in Sjoa in southern Norway and also high in the White Sea region in northwest Russia. Higher diversity in Sjoa was attributed to both earlier recolonizations compared to that of the White Sea region and the absence of Wolbachia infection. We suggest that these sites were colonized from different Pleistocene refugia, i.e., from western and eastern refugia, respectively. From the White Sea region, recolonization continued eastwards to Ural Mountains and westwards to Finland and further north to Kola Peninsula. From northern Finland, recolonization continued to Finnmark, Norway, and further to Sweden and finally reached a secondary contact zone with colonizers from Norway in Central Sweden. The Caucasus and Siberian/Manchurian refugial regions have played an important role in the origin of C. myrtilli populations in Siberia and the Russian Far East.

Hidden in plain sight: novel molecular data reveal unexpected genetic diversity among paramphistome parasites (Digenea: Paramphistomoidea) of European water frogs

Parasites might represent a helpful tool in understanding the historical dispersion and phylogeography of their hosts. In order to reveal whether the migration routes and diversification of hosts can be traceable in the genetic structures of their parasites, we investigated the diversity of paramphistomoid trematodes of Pelophylax frogs in 2 geographically distant European regions. Water frogs belonging to the genus Pelophylax represent a striking example of a species with a high variety of ecological adaptations and a rich evolutionary history. The parasites were collected from 2 Balkan endemic species, P. epeiroticus and P. kurtmuelleri, and 2 species in Slovakia, P. esculentus and P. ridibundus. While in Slovakia, Pelophylax frogs harboured 2 species, the diplodiscid Diplodiscus subclavatus and the cladorchiid Opisthodiscus diplodiscoides, only the former was recorded in the south-western Balkans. Remarkably high genetic diversity (16 unique mitochondrial cox1 haplotypes, recognized among 60 novel sequences) was observed in D. subclavatus, and subsequent phylogenetic analyses revealed a strong population-genetic structure associated with geographical distribution. We also evidenced the existence of 2 divergent D. subclavatus cox1 haplogroups in the south-western Balkans, which might be associated with the historical diversification of endemic water frogs in the regional glacial microrefugia.

Phylogenetic Analysis of the Complete Mitochondrial Genomes in the Ten Rupicapra Subspecies and Implications for the Existence of Multiple Glacial Refugia in Europe

Simple Summary

The successive glaciations that took place during the Pleistocene shaped de distribution of temperate species in Europe, both plants and animals. Traditionally, it has been hypothesized that during the coldest periods, species took refuge in three areas of southern Europe (Iberian, Italian and Balkan peninsulas) and then recolonized the north when temperatures rose and conditions were more favorable. In the present work, the complete mitochondrial sequences of the ten described chamois populations have been analyzed to identify which areas of the continent have served as refuges for the species during the glaciations. The results of the present work are consistent with the existence of multiple glacial refugia across Europe, revealing a much more complex picture of the effect of glaciations on the genetics of temperate species than is commonly accepted, giving us a better understanding of how past events determine the present species.

Abstract

The current distribution of populations in Europe is marked by the effects of glaciations that occurred during the Pleistocene. Temperate species were isolated in glacial refugia that were the sources of postglacial recolonization. The traditional glacial refuge areas were the Iberian, the Italian and the Balkan peninsulas. Here we revisit the evolutionary history of chamois (Rupicapra genus) to evaluate other sites in continental Europe and Anatolia that have been suggested as potential refuges. We have obtained the complete mitochondrial sequence of seven chamois, including the subspecies parva, carpatica, caucasica, and asiatica whose mitochondrial genome had not been yet reported. These, together with the other fourteen sequences already in the GenBank, represent the different geographical populations of the Rupicapra genus. The phylogenetic analysis showed the three old clades, dating from the early Pleistocene, already reported: mtW in the Iberian Peninsula, mtC in the Appenines and the Massif of Chartreuse, and mtE comprising all the population from the Alps to the east. The genomes within each of the clades mtW and mtE, showed divergence times larger than 300 thousand years. From here, it can be argued that the present-day lineages across Europe are very old and their split dates back to the middle Pleistocene.

The mixed phylogenetic origin of northern pike (Esox lucius Linnaeus 1758) populations in the Middle Danubian drainage

BACKGROUND

Pikes, members of genus Esox, are widespread freshwater predators of the northern hemisphere, and important sport fish also. From the Carpathian basin only one species, the northern pike (E. lucius) is noted. At the same time the pike stocks living in this area show high level of phenotypic variance (e.g. various body pattern) and its growth varies highly both among and within populations. These features usually explained by the environmental diversity of the area. Whereas we think that genetic reasons -e.g. the appearance of other/new pike species in the area- may also be responsible for these observed features. Since as no detailed information have been published from the pike populations of this area, so far; we conducted phylogenetic and morphological assay on 88 pike specimens, collected from 49 Middle Danubian sampling sites.

RESULTS

Our phylogenetic surveys showed that the northern pike appear in the study area solely, but all the three of its major lineages (Northern, Circumpolar, Southern) were indicated. Only six specimens represent the Northern lineage, collected from the western part of the study area. The Circumpolar and Southern lineages were common in the Carpathian basin, but the Southern lineage showed higher levels of haplotype diversity than the Circumpolar clade. Which indicates that only the Southern lineage is native in the area, while the other two groups could have appeared in the Middle Danubian system either spontaneously or by human introduction. Moreover, the different clades appeared in the same populations, suggesting the opportunity of inter-lineage hybridisation. From the studied morphologicalal features, the number of scales on the lateral line and the head length showed significant differences among the lineages. At the same time the body pattern of the studied individuals seems to be rather influenced by the ontogenic changes than phylogeny.

CONCLUSIONS

The high phenotypic variability of Middle Danubian northern pike populations may be due that all of its three major clades appeared and came in secondary contact in the area. In the within watershed spread of the non-native lineages the human stocking/transfer may play a considerable role.

Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic

Pleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.

Fuzzy species borders of glacial survivalists in the Carpathian biodiversity hotspot revealed using a multimarker approach

The Carpathians are one of the key biodiversity hotspots in Europe. The mountain chain uplifted during Alpine orogenesis and is characterised by a complex geological history. Its current biodiversity was highly influenced by Pleistocene glaciations. The goal of the current study was to examine the phylogenetic and demographic history of Gammarus balcanicus species complex in the Carpathians using multiple markers as well as to delimit, using an integrative approach, and describe new species hidden so far under the name G. balcanicus. Results showed that divergence of the studied lineages reaches back to the Miocene, which supports the hypothesis of their survival in multiple micro refugia. Moreover, the increase of their diversification rate in the Pleistocene suggests that glaciation was the driving force of their speciation. The climatic changes during and after the Pleistocene also played a major role in the demography of the local Carpathian lineages. Comparison of diversity patterns and phylogenetic relationships of both, the mitochondrial and nuclear markers, provide evidence of putative hybridisation and retention of ancient polymorphism (i.e., incomplete lineage sorting). The morphological examination supported the existence of two morphological types; one we describe as a G. stasiuki sp. nov. and another we redescribe as a G. tatrensis (S. Karaman, 1931).

Demographic inferences and climatic niche modelling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale

Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within "sky islands". Here, we studied the genetic structure of the Apollo butterfly in five such sky islands (above 1,000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly unfavourable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya vs. 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a nonequilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely interconnected populations overtime according to a "metapopulation-pulsar" functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale.

Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles

The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.

The freshwater molluscs of Serbia: Annotated checklist with remarks on distribution and protection status

We present a checklist of 86 valid freshwater mollusc species of Serbia (65 gastropods and 21 bivalves) belonging to 19 families (15 gastropods and four bivalves). The list is based on our latest research and includes data from published sources and personal communications. The most diverse family among gastropods is Planorbidae (16 species), while Sphaeriidae are most diverse within the bivalves (10 species). Ten species are local endemics (all of them gastropods), while eight are introduced species (three gastropods and five bivalves). The Danube River and its smaller tributaries harbour the most diverse gastropod community, with a total of 61 species (41 gastropods and 20 bivalves). The snail Theodoxus transversalis (Pfeiffer, 1828) and the bivalve Unio crassus Philipson, 1788 are listed as EN (endangered) on the global (IUCN) level, while the snail Plagigeyeria gladilini Kuer, 1937 and the bivalves Pseudanodonta complanata (Rossmssler, 1835) and Sphaerium rivicola (Lamarck, 1818) are considered as VU (vulnerable) species. Of those IUCN taxa, only U. crassus is listed as protected on the national level (along with 12 mostly local endemic gastropod species). In comparison with the previous checklist of gastropods by Karaman Karaman (2007), a total of seven species are added here: Belgrandiella serbica Gler 2008, Bythinella istoka Gler Pei 2014, B. nonveilleri Gler 2008, B. pesterica Gler 2008, Acroloxus lacustris (Linnaeus, 1758), Melanoides tuberculata (O.F. Mller, 1774) and Armiger crista (Linnaeus, 1758). In view of global and regional trends in taxonomy, ecology and invasive biology, an even richer diversity of the Serbian freshwater malocofauna can be expected.

Molecular biogeography of the fungus-dwelling saproxylic beetle Bolitophagus reticulatus indicates rapid expansion from glacial refugia

The geographical distributions of species associated with European temperate broadleaf forests have been significantly influenced by glacial–interglacial cycles. During glacial periods, these species persisted in Mediterranean and extra-Mediterranean refugia and later, during interglacial periods, expanded northwards. The widespread saproxylic beetle Bolitophagus reticulatus depends closely on European temperate broadleaf forests. It usually develops in the tinder fungus Fomes fomentarius, a major decomposer of broadleaf-wood. We sampled B. reticulatus in sporocarps from European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis) across Europe and the Caucasus region. We analysed mitochondrial gene sequences (cox1, cox2, cob) and 17 microsatellites to reconstruct the geographical distribution of glacial refugia and postglacial recolonization pathways. We found only marginal genetic differentiation of B. reticulatus, except for a significant split between populations of the Caucasus region and Europe. This indicates the existence of past refugia south of the Great Caucasus, and a contact zone with European populations in the Crimean region. Further potential refugia might have been located at the foothills of the Pyrenees and in the Balkan region. Our genetic data suggest a phalanx-wise recolonization of Europe, a reflection of the high mobility of B. reticulatus.

A dynamic history of admixture from Mediterranean and Carpathian glacial refugia drives genomic diversity in the bank vole

Understanding the historical contributions of differing glacial refugia is key to evaluating the roles of microevolutionary forces, such as isolation, introgression, and selection in shaping genomic diversity in present-day populations. In Europe, where both Mediterranean and extra-Mediterranean (e.g., Carpathian) refugia of the bank vole (Clethrionomys glareolus) have been identified, mtDNA indicates that extra-Mediterranean refugia were the main source of colonization across the species range, while Mediterranean peninsulas harbor isolated, endemic lineages. Here, we critically evaluate this hypothesis using previously generated genomic data (>6,000 SNPs) for over 800 voles, focusing on genomic contributions to bank voles in central Europe, a key geographic area in considering range-wide colonization. The results provide clear evidence that both extra-Mediterranean (Carpathian) and Mediterranean (Spanish, Calabrian, and Balkan) refugia contributed to the ancestry and genomic diversity of bank vole populations across Europe. Few strong barriers to dispersal and frequent admixture events in central Europe have led to a prominent mid-latitude peak in genomic diversity. Although the genomic contribution of the centrally located Carpathian refugium predominates, populations in different parts of Europe have admixed origins from Mediterranean (28%-47%) and the Carpathian (53%-72%) sources. We suggest that the admixture from Mediterranean refugia may have provisioned adaptive southern alleles to more northern populations, facilitating the end-glacial spread of the admixed populations and contributing to increased bank vole diversity in central Europe. This study adds critical details to the complex end-glacial colonization history of this well-studied organism and underscores the importance of genomic data in phylogeographic interpretation.

Mitochondrial DNA diversity of the alpine newt (Ichthyosaura alpestris) in the Carpathian Basin: evidence for multiple cryptic lineages associated with Pleistocene refugia

The phylogeography and molecular taxonomy of the Alpine newt, Ichthyosaura alpestris, has been intensively studied in the past. However, previous studies did not include a comprehensive sampling from the Carpathian Basin, possibly a key region in the evolution of the species. We used a 1251 bp long fragment of the mitochondrial genome to infer the species’ evolutionary history in central-eastern Europe by assigning isolated Carpathian Basin populations from 6 regions to previously defined mtDNA lineages. We also revised the morphology-based intraspecific taxonomy of the species in the light of new genetic data. Alpine newt populations from the Carpathian Basin represented two different mitochondrial lineages. The Mátra, Bükk and Zemplén Mts populations can be assigned to the Western lineage of the nominotypical subspecies. Bakony and Őrség populations showed high haplotype diversity and formed a separate clade within the Western lineage, suggesting that the Carpathian Basin might have provided cryptic refugia for Alpine newt populations in their cold-continental forest-steppe landscapes during the younger Pleistocene. Newts from Apuseni Mts were related to the Eastern lineage but formed a distinct clade within this lineage. Considering the morphological and genetic differentiation of the Bakony and Őrség populations, consistent with a long independent evolutionary history, we propose these populations be referred to as Ichthyosaura alpestris bakonyiensis (Dely, 1964). We provide a redescription of this poorly known subspecies.

The Origin of Isolated Populations of the Mountain Weevil, Liparus glabrirostris-The Flagship Species for Riparian Habitats

Liparus glabrirostris is one of the largest European weevils, and it has been recently proposed as the flagship species for threatened riparian habitats in the mountains. For effective conservation of its populations (and associated habitats), it is crucial to understand its history, contemporary distribution, genetic diversity and predict changes in the range, including its highly isolated populations on the Baltic coast. Here, we examined numerous populations of L. glabrirostris across almost the entire species range using phylogeography and species niche modeling (SNM) approaches. Analyses of mtDNA and nucDNA markers revealed the existence of 2 major mitochondrial lineages generally separated between 1) the Alpine region and 2) the Bohemian Massif, the Carpathians, and the Baltic coast areas. Genetic diversity in nuclear genes was more complicated with no clear division between populations. The origin of Baltic populations was derived from the Carpathians, but there were probably multiple expansion events to the north. SNM suggested the existence of glacial refugia for L. glabrirostris, mainly in the Alps and the Southern Carpathians. Current predictions of species range were found to be generally congruent with zoogeographic data; however, the Baltic coast was not really supported as a suitable area for L. glabrirostris. An important prediction of future distribution (2050-2070 CE) suggests a shrinkage of the L. glabrirostris range and extinction of some of its populations (particularly those isolated on lower altitudes). Based on the aforementioned data, proposals for the protection of this species are proposed, including the designation of several evolutionary units of conservation importance.

Geographical disjunction and environmental conditions drive intraspecific differentiation in the chalk-hill blue butterfly

Drivers of evolution are often related to geographical isolation and/or diverging environmental conditions. Spatial variation in neutral genetic markers mostly reflects past geographical isolation, i.e. long-lasting allopatry, whereas morphology is often driven by local environmental conditions, resulting in more rapid evolution. In Europe, most thermophilic species persisted during the past glacial periods in geographically disjunct refugia, representing long-lasting isolates, frequently with diverging environmental conditions. This situation has driven the evolution of intraspecific signatures in species. Here, we analysed wing shape and wing pigmentation of the chalk-hill blue butterfly, Polyommatus coridon, across its entire distribution range restricted to the western Palaearctic. In addition, we compiled abiotic environmental parameters for each sampling site. Wing colour patterns differentiated a western and an eastern lineage. These lineages might represent two main Pleistocene refugia and differentiation centres, one located on the Italian Peninsula and the other in the Balkan region. The two lineages showed evidence of hybridization across Central Europe, from the Alps and across Germany. The intraspecific differentiation was strongest in the width of the brown band on the outer margin of the wings. The morphological structures obtained are in line with genetic signatures found in previous studies, but the latter are more fine-grained. Current environmental conditions, such as mean temperatures, were only marginally correlated with colour patterns. Our study underlines that Pleistocene range shifts, often resulting in allopatric isolation, shape intraspecific phenotypic structures within species; that pigmentation responds in a more sensitive manner to spatial disjunction than wing shape; and that morphometric and genetic structures in P. coridon provide concordant patterns and thus support identical biogeographical conclusions.

Stability in the Balkans: phylogeography of the endemic Greek stream frog, Rana graeca

We still have little knowledge concerning the phylogeography of amphibians and reptiles from the Balkan Peninsula compared with the other two Mediterranean peninsulas. This raises concerns for endemic taxa from these peninsulas, because it might interfere with further conservation efforts. Here we focus on the endemic Greek stream frog (Rana graeca) and reconstruct its biogeography and evolutionary history. Using four genetic markers (Cytb, 16S, COI and BDNF) in &gt; 350 sequences covering the whole distribution range, we conducted phylogenetic, demographic and ecological niche analyses, which revealed the phylogeography of this species. Surprisingly, this examination of R. graeca reveals a very shallow level of intraspecific genetic variability through the Balkans, with two main, statistically supported lineages having a partly sympatric distribution. The most variable marker was Cytb, which showed 19 haplotypes in 123 analysed sequences in the whole species distribution area. Here presented genetic data, together with the environmental niche projection and demographic analyses suggest that R. graeca was probably affected only marginally by climatic oscillations, with the Hellenides as the most suitable area for the occurrence of the species in different geological periods. This is consistent with the observed genetic diversity, which is mostly related to these mountains. Although the species shows a certain level of phenotypic variability and ecological preferences, this might be related to species plasticity affected by the micro-climatic conditions in small areas, which merits further research. Comparing phylogeography of other amphibian and reptile species in the Balkans, we showed that the observed pattern represents a new view on the phylogeography of the Balkan herpetofauna.

Increased spatial resolution of sampling in the Carpathian basin helps to understand the phylogeny of central European stream-dwelling gudgeons

Background

Phylogenetic studies of widespread European fish species often do not completely cover their entire distribution area, and some areas are often excluded from analyses than others. For example, Carpathian stocks are often omitted from these surveys or are under-represented in the samples. However, this area served as an extra-Mediterranean refugia for many species; therefore, it is assumed that fish stocks here may show special phylogenetic features. For this reason, increased spatial resolution of sampling, namely revealing genetic information from unexamined Carpathian areas within the range of doubtful taxa, may help us better understand their phylogenetic features. To test this hypothesis, a phylogenetic investigation using a partial mtCR sequence data was conducted on 56 stream-dwelling freshwater fish (Gobio spp.) individuals collected from 11 rivers of the data-deficient Southeastern Carpathian area. Moreover, we revieved the available phylogenetic data of Middle-Danubian stream-dwelling gudgeon lineages to delineate their distribution in the area.

Results

Seven out of the nine detected haplotypes were newly described, suggesting the studied area hosts distinct and diverse Gobio stocks. Two valid species (G. obtusirostris, G. gobio), and a haplogroup with doubtful phylogenetic position” G. sp. 1" were detected in the area, showing a specific spatial distribution pattern. The distribution of the detected lineages in the Middle-Danubian area correspond with recent and paleo hydrogeographic features, at the same time mainly on their bordering areas show considerable overlap.

Conclusions

Despite the relatively limited geographic range of the study, our results provide important information which contributes to a better understanding of the phylogenetic, taxonomic and distribution features of Central European gudgeons. The genetically confirmed distribution data of the indicated lineages corresponds well with the recent and near-recent hydrogeographic features of the area, and assumes several hybrid zones in the Carpathian Basin. Additionally, the results show that the middle and lower Danubian watershed cannot be excluded from the range of G. gobio. Moreover, the” G. sp. 1", is slightly differentiated but phylogenetically distinct entity, and is the only Gobio taxa thus far detected in the middle and lower Tisza-basin. However, further investigations are necessary to clarify the taxonomic position of this group.

Species distribution modelling sheds light on the widespread distribution of Sphingonotus (Sphingonotus) rubescens (Orthoptera: Acrididae: Oedipodinae)

Sphingonotus (Sphingonotus) rubescens (Walker, 1870) occurs from the Atlantic Islands to central and southern Asia, but its ecological preferences and the potential drivers that shaped its currently extensive distribution remain unknown. We review the known occurrence data for S. rubescens and reconstruct its current and palaeoclimatic niche (Last Glacial Maximum and mid-Holocene) using species distribution modelling (SDM). We examine how climatic suitability might have created potential past migratory pathways shaping its current distribution. Moreover, we test the utility of SDM approaches to flag dubious records detected in the assembled dataset. The results reveal new distributional records from four countries. Climatic models indicate high levels of overlap between current and palaeoclimatic models, with stability of large suitable areas through time. Furthermore, we observe that suitability values associated with dubious records are lower than the distribution of suitability values within the known distribution of S. rubescens. Climatic stability of suitable areas through time for S. rubescens might have aided the expansion and maintenance of its current wide distribution. Furthermore, our results support previous studies indicating the usefulness of SDM tools for the detection of doubious occurrences.

Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies

The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.

Reconstruction of forest dynamics in the Western Palaearctic based on phylogeographic analysis of the ringlet butterfly Erebia aethiops

Glacial refugia are centers of high biodiversity. Therefore, knowledge on their locations and reactions of associated populations and landscapes to climatic changes is crucial for conservation management. We here investigated the biogeography of a butterfly species linked to open forest habitats. Using mitochondrial and nuclear markers in combination with Bayesian simulations, we analyzed the location and age of potential glacial refugia of the species. We identified five putative refugia in Europe. Considering the ecological needs of our study species, tree density within these refugial areas, in contrast to earlier assumptions, must have exceeded the level of individually scattered trees. Our results also provide evidence that especially the refuge areas in the Carpathians were previously underestimated regarding their age: the refugia in the Southern Carpathians presented suitable conditions throughout several glacial cycles, probably since the Mindel or Riss cycles. Additionally, our analyses provided support for a forest refugium near the Tatra Mountains persisting the last glacial maximum. Our results underline the usefulness of this and probably other butterfly species as indicators of forest refugia.

The origins and spread of domestic horses from the Western Eurasian steppes

Domestication of horses fundamentally transformed long-range mobility and warfare¹. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling^2-4 at Botai, Central Asia around 3500 BC³. Other longstanding candidate regions for horse domestication, such as Iberia⁵ and Anatolia⁶, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association⁷ between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC^8,9 driving the spread of Indo-European languages¹⁰. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture^11,12.

Ancient divergence, a crisis of salt and another of ice shaped the evolution of the west Mediterranean butterfly Euchloe tagis

The Mediterranean region is an extremely complex hotspot where, since the Miocene, extensive geological, habitat and climate changes have taken place, alternating between warm and cold periods. These phenomena have taken a toll on the genetic composition of species, and surviving lineages have often adapted locally and diverged to the point of (complete) speciation. To study these phenomena, in this study we used one of the most enigmatic butterflies, the Portuguese dappled white, Euchloe tagis, a west Mediterranean endemic with fragmented, morphologically differentiated populations whose status have long been disputed. Even its affiliations with other Anthocharidini are largely unresolved. We used mitochondrial and nuclear markers under a phylogenetic and phylogeographical framework to evaluate its placement among relatives and population differentiation, reconstructing its evolutionary history. We found that this species had a Miocene origin ~15 Mya and was nearest to Euchloe s.s. and Elphinstonia. Its populations showed high genetic diversity but all coalesced to 5.3 Mya, when European and all but one African population diverged. Our multiple findings concerning the evolution of E. tagis through a changing, narrow habitable area might provide a more general perspective on how species survive within this hotspot of paramount importance.

Successful post-glacial colonization of Europe by single lineage of freshwater amphipod from its Pannonian Plio-Pleistocene diversification hotspot

Gammarus roeselii Gervais, 1835 is a morphospecies with a wide distribution range in Europe. The Balkan Peninsula is known as an area of pre-Pleistocene cryptic diversification within this taxon, resulting in at least 13 Molecular Operational Taxonomic Units (MOTUs). The morphospecies diversified there during Neogene and has probably invaded other parts of the continent very recently, in postglacial or even historical times. Thus, the detailed goals of our study were to (1) identify which lineage(s) colonized Central-Western Europe (CWE), (2) determine their possible geographical origin, (3) verify, whether the colonisation was associated with demographic changes. In total, 663 individuals were sequenced for the cytochrome oxidase I (COI) barcoding fragment and 137 individuals for the internal transcribed spacer II (ITS2). We identified two MOTUs in the study area with contrasting Barcode Index Number and haplotype diversities. The Pannonian Basin (PB) appeared to be a potential ice age refugium for the species, while CWE was colonised by a single lineage (also present in PB), displaying low genetic diversity. Our results suggest that G. roeselii is a relatively recent coloniser in CWE, starting demographic expansion around 10 kya.

Population Genetic Structure of the Wild Boar (Sus scrofa) in the Carpathian Basin

In the Carpathian Basin the wild boar (Sus scrofa) belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different (p < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an F_st value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations’ genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces’ having been preserved from both the last ice age and the period before the Hungarian water regulation.

Past, current, and potential future distributions of unique genetic diversity in a cold-adapted mountain butterfly

AIM

Climatic changes throughout the Pleistocene have strongly modified species distributions. We examine how these range shifts have affected the genetic diversity of a montane butterfly species and whether the genetic diversity in the extant populations is threatened by future climate change.

LOCATION

Europe.

TAXON

Erebia epiphron Lepidoptera: Nymphalidae.

METHODS

We analyzed mtDNA to map current genetic diversity and differentiation of E. epiphron across Europe to identify population refugia and postglacial range shifts. We used species distribution modeling (SDM) to hindcast distributions over the last 21,000 years to identify source locations of extant populations and to project distributions into the future (2070) to predict potential losses in genetic diversity.

RESULTS

We found substantial genetic diversity unique to specific regions within Europe (total number of haplotypes = 31, number of unique haplotypes = 27, H d = 0.9). Genetic data and SDM hindcasting suggest long-term separation and survival of discrete populations. Particularly, high rates of unique diversity in postglacially colonized sites in England (H d = 0.64) suggest this population was colonized from a now extinct cryptic refugium. Under future climate change, SDMs predict loss of climate suitability for E. epiphron, particularly at lower elevations (<1,000 meters above sea level) equating to 1 to 12 unique haplotypes being at risk under climate scenarios projecting 1°C and 2-3°C increases respectfully in global temperature by 2070.

MAIN CONCLUSIONS

Our results suggest that historical range expansion and retraction processes by a cold-adapted mountain species caused diversification between populations, resulting in unique genetic diversity which may be at risk if distributions of cold-adapted species shrink in future. Assisted colonizations of individuals from at-risk populations into climatically suitable unoccupied habitat might help conserve unique genetic diversity, and translocations into remaining populations might increase their genetic diversity and hence their ability to adapt to future climate change.

Potential impact of chemical stress on freshwater invertebrates: A sensitivity assessment on continental and national scale based on distribution patterns, biological traits, and relatedness

Current chemical risk assessment approaches rely on a standard suite of test species to assess toxicity to environmental species. Assessment factors are used to extrapolate from single species to communities and ecosystem effects. This approach is pragmatic, but lacks resolution in biological and environmental parameters. Novel modelling approaches can help improve the biological resolution of assessments by using mechanistic information to identify priority species and priority regions that are potentially most impacted by chemical stressors. In this study we developed predictive sensitivity models by combining species-specific information on acute chemical sensitivity (LC50 and EC50), traits, and taxonomic relatedness. These models were applied at two spatial scales to reveal spatial differences in the sensitivity of species assemblages towards two chemical modes of action (MOA): narcosis and acetylcholinesterase (AChE) inhibition. We found that on a relative scale, 46% and 33% of European species were ranked as more sensitive towards narcosis and AChE inhibition, respectively. These more sensitive species were distributed with higher occurrences in the south and north-eastern regions, reflecting known continental patterns of endemic macroinvertebrate biodiversity. We found contradicting sensitivity patterns depending on the MOA for UK scenarios, with more species displaying relative sensitivity to narcotic MOA in north and north-western regions, and more species with relative sensitivity to AChE inhibition MOA in south and south-western regions. Overall, we identified hotspots of species sensitive to chemical stressors at two spatial scales, and discuss data gaps and crucial technological advances required for the successful application of the proposed methodology to invertebrate scenarios, which remain underrepresented in global conservation priorities.

Genetic analysis of Bromus tectorum (Poaceae) in the Mediterranean region: biogeographical pattern of native populations

Genetic diversity within and among 42 native populations of Bromus tectorum (cheatgrass) was characterized within two regions, the eastern Mediterranean and the western Mediterranean. Two hypotheses were tested for the genetic diversity of these populations: (1) populations from the eastern Mediterranean are more genetically diverse compared with populations to the west, a potential consequence of the species' westward dispersal with the spread of agriculture, and (2) populations across the Mediterranean contain comparable genetic diversity but display high genetic differentiation, a potential consequence of both regions having served as refugia during glacial advances in the late Quaternary Period. Populations in the eastern Mediterranean possess 16 polymorphic loci and 37 multilocus genotypes. In contrast, populations from the western Mediterranean include a subset of these polymorphic loci (9) and fewer multilocus genotypes (19), consistent with the dispersal of B. tectorum with the east-west Holocene spread of agriculture. Among the 19 multilocus genotypes identified in populations from the western Mediterranean, 13 are undetected among eastern Mediterranean populations. Average genetic diversity within populations from the eastern Mediterranean is nonetheless comparable to the genetic diversity in populations from the Iberian Peninsula, whereas diversity is the lowest in the populations from southern France. Our results suggest a prominent role for agriculture in the grass's western spread, although glacial history and environmental heterogeneity also could have influenced the grass's genetic diversity. The exceptionally high level of self-pollination (>99%) in B. tectorum has contributed to preserving the genetic signature associated with the species' biogeographical history across the Mediterranean region.