History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20–rps12 intergenic spacer, the trnV intron and psbA‐trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species’ range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east–west split of cpDNA divergence was supported by an amova which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the ‘four‐refugia’ hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south‐eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold‐tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.     

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai–Tibetan Plateau

There are two long‐standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai–Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage‐specific habitat preferences.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Northern glacial refugia for the pygmy shrew Sorex minutus in Europe revealed by phylogeographic analyses and species distribution modelling

The southern European peninsulas (Iberian, Italian and Balkan) are traditionally recognized as glacial refugia from where many species colonized central and northern Europe after the Last Glacial Maximum (LGM). However, evidence that some species had more northerly refugia is accumulating from phylogeographic, palaeontological and palynological studies, and more recently from species distribution modelling (SDM), but further studies are needed to test the idea of northern refugia in Europe. Here, we take a rarely implemented multidisciplinary approach to assess if the pygmy shrew Sorex minutus, a widespread Eurasian mammal species, had northern refugia during the LGM, and if these influenced its postglacial geographic distribution. First, we evaluated the phylogeographic and population expansion patterns using mtDNA sequence data from 123 pygmy shrews. Then, we used SDM to predict present and past (LGM) potential distributions using two different training data sets, two different algorithms (Maxent and GARP) and climate reconstructions for the LGM with two different general circulation models. An LGM distribution in the southern peninsulas was predicted by the SDM approaches, in line with the occurrence of lineages of S. minutus in these areas. The phylogeographic analyses also indicated a widespread and strictly northern‐central European lineage, not derived from southern peninsulas, and with a postglacial population expansion signature. This was consistent with the SDM predictions of suitable LGM conditions for S. minutus occurring across central and eastern Europe, from unglaciated parts of the British Isles to much of the eastern European Plain. Hence, S. minutus likely persisted in parts of central and eastern Europe during the LGM, from where it colonized other northern areas during the late‐glacial and postglacial periods. Our results provide new insights into the glacial and postglacial colonization history of the European mammal fauna, notably supporting glacial refugia further north than traditionally recognized.     

Phylogeographic structure of Hippophae tibetana (Elaeagnaceae) highlights the highest microrefugia and the rapid uplift of the Qinghai‐Tibetan Plateau

The uplift of the Qinghai‐Tibetan Plateau (QTP) dramatically changed the topography and climate of Asia and affected the biodiversity of the plateau and its adjacent areas. However, the effects of the uplift on the dispersal, differentiation and adaptation of plants remain a puzzle when the date and processes of the uplift cannot be determined with certainty and the impacts of the Quaternary glaciations on plants on the QTP are unknown. To clarify the relationships among plants on the QTP with the plateau uplift and the Quaternary glaciations, the cpDNA trnT‐trnF regions of 891 individuals from 37 populations of Hippophae tibetana, endemic to the QTP, were sequenced in the present study. A total of 50 haplotypes were found and a strong phylogeographic structure was revealed (N_ST = 0.854, G_ST = 0.611, N_ST > G_ST, P < 0.01). The results show that three main lineages of the present populations of H. tibetana occupy the western, the middle, and the eastern geographical range, respectively, and their divergence time dates back to 3.15 Ma before present. Of 50 haplotypes, 33 (66%) are private haplotypes, which are restricted to single populations. These private haplotypes are scattered throughout the present geographical range of H. tibetana and originated from multiple differentiations in many lineages during more than 1.0 Ma period, strongly suggesting that multiple microrefugia of H. tibetana existed throughout the present geographical range during the last glacial maximum (LGM) and even earlier glaciations. Additionally, the average elevation of present populations is over 4500 m in the west and the equilibrium‐line of glaciers in the LGM was 500–300 m lower than present in the major interior part of the plateau suggesting that at most sites in the west, LGM microrefugia of H. tibetana may have been above 4000 m above sea level, the highest of all known refugia. Moreover, the divergence times among and within the three lineages and their distinct distributions as well as dispersal barriers support the theory of the recent and rapid uplift of the QTP. The rapid uplift of the plateau within the last 3.4 Ma and the associated environmental changes may have affected the dispersal and differentiation of H .tibetana and shaped its phylogeographic structure.     

The Quaternary evolutionary history,potential distribution dynamics,and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial,Anisodus tanguticus (Solanaceae)

Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai–Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well‐differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F_ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.     

Evolutionary history of the scorpionfly Dicerapanorpa magna (Mecoptera,Panorpidae)

Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapted insects to Pleistocene climate changes in eastern Asia. The scorpionfly Dicerapanorpa magna (Chou), with cold temperate habitat preference and weak dispersal ability, provides a good model system to explore how climate changes have influenced the distribution and divergence of cold‐adapted insects in eastern Asia. This study reconstructed the demographic dynamics and evolutionary history of D. magna with phylogeographic approaches, and predicted the species’ suitable areas under the Last Glacial Maximum (LGM) and current scenarios with the ecological niche modelling analysis. The mitochondrial cytochrome c oxidase subunit I resolved three phylogenetic lineages in D. magna dating back to Pleistocene, corresponding well with the geographically isolated Qinling, Bashan and Minshan Mountains. The ecological niche modelling recovered the suitable habitats for D. magna were the Qinling and Bashan Mountains under LGM and current conditions. The three lineages of D. magna might be in a process of incipient speciation, and likely derived their current distribution from separate glacial origins, followed by vicariance and divergence.     

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool‐temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high‐latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.     

New insights on postglacial colonization in western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri)

Despite recent advances in the understanding of the interplay between a dynamic physical environment and phylogeography in Europe, the origins of contemporary Irish biota remain uncertain. Current thinking is that Ireland was colonized post-glacially from southern European refugia, following the end of the last glacial maximum (LGM), some 20 000 years BP. The Leisler''s bat (Nyctalus leisleri), one of the few native Irish mammal species, is widely distributed throughout Europe but, with the exception of Ireland, is generally rare and considered vulnerable. We investigate the origins and phylogeographic relationships of Irish populations in relation to those across Europe, including the closely related species N. azoreum. We use a combination of approaches, including mitochondrial and nuclear DNA markers, in addition to approximate Bayesian computation and palaeo-climatic species distribution modelling. Molecular analyses revealed two distinct and diverse European mitochondrial DNA lineages, which probably diverged in separate glacial refugia. A western lineage, restricted to Ireland, Britain and the Azores, comprises Irish and British N. leisleri and N. azoreum specimens; an eastern lineage is distributed throughout mainland Europe. Palaeo-climatic projections indicate suitable habitats during the LGM, including known glacial refugia, in addition to potential novel cryptic refugia along the western fringe of Europe. These results may be applicable to populations of many species.     

Phylogeography of the world's tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia

Aim There is a need for more Southern Hemisphere phylogeography studies, particularly in Australia, where, unlike much of Europe and North America, ice sheet cover was not extensive during the Last Glacial Maximum (LGM). This study examines the phylogeography of the south‐east Australian montane tree species Eucalyptus regnans. The work aimed to identify any major evolutionary divergences or disjunctions across the species’ range and to examine genetic signatures of past range contraction and expansion events. Location South‐eastern mainland Australia and the large island of Tasmania. Methods We determined the chloroplast DNA haplotypes of 410 E. regnans individuals (41 locations) based on five chloroplast microsatellites. Genetic structure was examined using analysis of molecular variance (AMOVA), and a statistical parsimony tree was constructed showing the number of nucleotide differences between haplotypes. Geographic structure in population genetic diversity was examined with the calculation of diversity parameters for the mainland and Tasmania, and for 10 regions. Regional analysis was conducted to test hypotheses that some areas within the species’ current distribution were refugia during the LGM and that other areas have been recolonized by E. regnans since the LGM. Results Among the 410 E. regnans individuals analysed, 31 haplotypes were identified. The statistical parsimony tree shows that haplotypes divided into two distinct groups corresponding to mainland Australia and Tasmania. The distribution of haplotypes across the range of E. regnans shows strong geographic patterns, with many populations and even certain regions in which a particular haplotype is fixed. Many locations had unique haplotypes, particularly those in East Gippsland in south‐eastern mainland Australia, north‐eastern Tasmania and south‐eastern Tasmania. Higher haplotype diversity was found in putative refugia, and lower haplotype diversity in areas likely to have been recolonized since the LGM. Main conclusions The data are consistent with the long‐term persistence of E. regnans in many regions and the recent recolonization of other regions, such as the Central Highlands of south‐eastern mainland Australia. This suggests that, in spite of the narrow ecological tolerances of the species and the harsh environmental conditions during the LGM, E. regnans was able to persist locally or contracted to many near‐coastal refugia, maintaining a diverse genetic structure.     

Bumblebees take the high road: climatically integrative biogeography shows that escape from Tibet,not Tibetan uplift,is associated with divergences of present‐day Mendacibombus

Many claims that uplift of the Qinghai‐Tibetan plateau (QTP) drove the divergences of extant high‐elevation biota have recently been challenged. For Mendacibombus bumblebees, high‐elevation specialists with distributions centred on the QTP, we examine broader explanations. We extend integrative biogeography to cover multiple contributing factors by using a framework of sequential filters: 1) molecular evidence from four genes is used to estimate phylogenetic relationships, with time calibration from a published estimate; 2) spatial evidence from current distributions is combined with the phylogeny and constrained by a model of short‐distance dispersal along mountain corridors to estimate ancestral distributions by both S‐DIVA and S‐DEC analysis; 3) geological evidence from the literature is used to constrain when high mountain ranges were uplifted to become potential corridors; and 4) climatological evidence from Mendacibombus niche‐evolution reconstructions and from palaeoclimate simulations is used to constrain when habitat was suitable in key gaps within corridors. Explanations for Mendacibombus distributions can be identified that require only short‐distance dispersal along mountain corridors, commensurate with the limited dispersal ability observed for bumblebees. These explanations depend on the timing of uplift of mountain ranges, regional climate change, and climate‐niche evolution. The uplift of the QTP may have contributed to the initial Oligocene divergence of the common ancestor of Mendacibombus from other bumblebees, but for the first two thirds of the history of Mendacibombus, only a single lineage has present‐day descendants. Divergence of multiple extant Mendacibombus lineages coincided with the Late Miocene–Pliocene uplift of externally connecting mountains, combined with regional climate cooling. These changes provided greater connectivity of suitable habitat, allowing these bumblebees to disperse out of the western QTP via new high bridges, escaping along the mountain corridors of the Tian Shan and Hindu Kush ranges, reaching eventually far to the west (Iberian Peninsula) and to the north‐east (Kamchatka).     

Investigating past range dynamics for a weed of cultivation,Silene vulgaris

Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.     

Across the southern Andes on fin: glacial refugia,drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re‐colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro‐glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic → Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.     

Persistent genetic signatures of historic climatic events in an Antarctic octopus

Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase 1 gene to examine genetic structure in the direct‐developing, endemic Southern Ocean octopod Pareledone turqueti sampled from a broad range of areas that circumvent Antarctica. We find that, unusually for a species with poor dispersal potential, P. turqueti has a circumpolar distribution and is also found off the islands of South Georgia and Shag Rocks. The overriding pattern of spatial genetic structure can be explained by hydrographic (with ocean currents both facilitating and hindering gene flow) and bathymetric features. The Antarctic Peninsula region displays a complex population structure, consistent with its varied topographic and oceanographic influences. Genetic similarities between the Ross and Weddell Seas, however, are interpreted as a persistent historic genetic signature of connectivity during the hypothesized Pleistocene West Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two major lineages within P. turqueti, a continental lineage and a sub‐Antarctic lineage, that diverged in the mid‐Pliocene with no subsequent gene flow. Both lineages survived subsequent major glacial cycles. Our data are indicative of potential refugia at Shag Rocks and South Georgia and also around the Antarctic continent within the Ross Sea, Weddell Sea and off Adélie Land. The mean age of mtDNA diversity within these main continental lineages coincides with Pleistocene glacial cycles.     

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range‐wide genetic diversity based on nuclear microsatellite data and detected four well‐differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra‐ and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.     

Phylogeographic analysis of North American populations of the parasitic herbaceous plant Monotropa hypopitys L. reveals a complex history of range expansion from multiple late glacial refugia

Aim We carried out a phylogeographic study across the range of the herbaceous plant species Monotropa hypopitys L. in North America to determine whether its current disjunct distribution is due to recolonization from separate eastern and western refugia after the Last Glacial Maximum (LGM). Location North America: Pacific Northwest and north‐eastern USA/south‐eastern Canada. Methods Palaeodistribution modelling was carried out to determine suitable climatic regions for M. hypopitys at the LGM. We analysed between 155 and 176 individuals from 39 locations spanning the species’ entire range in North America. Sequence data were obtained for the chloroplast rps2 gene (n = 168) and for the nuclear ITS region (n = 158). Individuals were also genotyped for eight microsatellite loci (n = 176). Interpolation of diversity values was used to visualize the range‐wide distribution of genetic diversity for each of the three marker classes. Minimum spanning networks were constructed showing the relationships between the rps2 and ITS haplotypes, and the geographical distributions of these haplotypes were plotted. The numbers of genetic clusters based on the microsatellite data were estimated using Bayesian clustering approaches. Results The palaeodistribution modelling indicated suitable climate envelopes for M. hypopitys at the LGM in both the Pacific Northwest and south‐eastern USA. High levels of genetic diversity and endemic haplotypes were found in Oregon, the Alexander Archipelago, Wisconsin, and in the south‐eastern part of the species’ distribution range. Main conclusions Our results suggest a complex recolonization history for M. hypopitys in North America, involving persistence in separate eastern and western refugia. A generally high degree of congruence between the different marker classes analysed indicated the presence of multiple refugia, with at least two refugia in each area. In the west, putative refugia were identified in Oregon and the Alexander Archipelago, whereas eastern refugia may have been located in the southern part of the species’ current distribution, as well as in the ‘Driftless Area’. These findings are in contrast to a previous study on the related species Orthilia secunda, which has a similar disjunct distribution to M. hypopitys, but which appears to have recolonized solely from western refugia.     

Evolutionary history of the Dactylorhiza maculata polyploid complex (Orchidaceae)

Taxonomic complexity may be associated with migration history and polyploidy. We used plastid and nuclear DNA markers to investigate the evolutionary history of the systematically challenging Dactylorhiza maculata polyploid complex. A total of 1833 individuals from 298 populations from throughout Europe were analysed. We found that gene flow was limited between the two major taxa, diploid ssp. fuchsii (including ssp. saccifera) and tetraploid ssp. maculata. A minimum of three autotetraploid lineages were discerned: (1) southern/western ssp. maculata; (2) northern/eastern ssp. maculata; and (3) Central European ssp. fuchsii. The two ssp. maculata lineages, which probably pre‐date the last glaciation, form a contact zone with high genetic diversity in central Scandinavia. Intermediate plastid haplotypes in the contact zone hint at recombination. Central Europe may have been a source area for the postglacial migration for the southern/western lineage of ssp. maculata, as well as for ssp. fuchsii. The northern/eastern lineage of ssp. maculata may have survived the LGM in central Russia west of the Urals. The tetraploid lineage of ssp. fuchsii is indistinguishable from diploid ssp. fuchsii, and is probably of postglacial origin. The Mediterranean region and the Caucasus have not contributed to the northward migration of either ssp. fuchsii or ssp. maculata. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 503–525.     

East Asian allopatry and north Eurasian sympatry in Long‐tailed Tit lineages despite similar population dynamics during the late Pleistocene

Eurasia is a large continent characterized by heterogeneous environments. Glacial cycles during the late Pleistocene have had variable impacts on the avifauna across Eurasia. Bird populations from South‐East Asia show stability through the Last Glacial Maximum (LGM), while populations from Europe exhibit evidence of post‐LGM expansion. We investigated the phylogeography of the Long‐tailed Tit (Aegithalos caudatus), which spans the longitudinal breadth of Eurasia to test how climatic history and regional topographical complexity affected populations and diversification within the species complex. Our results show that two lineages from central and southern China (lineages C and D) segregate geographically, while lineages across northern Eurasia (lineage A and B) show substantial sympatry. Bayesian estimates for the timing of diversification suggest that the four lineages diverged during the middle Pleistocene, splitting in parallel and undergoing concurrent demographic histories since divergence. A. caudatus lineages experienced similar and synchronous population size dynamics during glacial cycles before the LGM. We conclude that the difference in geo‐topologic complexity may be an important factor that led to the variation in secondary admixture between northern Eurasian and eastern Asian lineages.     

A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species

The phylogeographic architecture of the common vole, Microtus arvalis, has been well‐studied using mitochondrial DNA and used to test hypotheses relating to glacial refugia. The distribution of the five described cytochrome b (cyt b) lineages in Europe west of Russia has been interpreted as a consequence of postglacial expansion from both southern and central European refugia. A recently proposed competing model suggests that the ‘cradle’ of the M. arvalis lineages is in western central Europe from where they dispersed in different directions after the Last Glacial Maximum. In the present study, we report a new cyt b lineage of the common vole from the Balkans that is not closely related to any other lineage and whose presence might help resolve these issues of glacial refugia. The Balkan phylogroup occurs along the southern distributional border of M. arvalis in central and eastern Bosnia and Herzegovina, Montenegro, and eastern Serbia. Further north and west in Slovenia, Bosnia and Herzegovina, and Serbia, common voles belong to the previously‐described Eastern lineage, whereas both lineages are sympatric in one site in Bosnia and Herzegovina. The Balkan phylogroup most reasonably occupied a glacial refugium already known for various Balkan endemic species, in contrast to the recently proposed model. South‐east Europe is an absolutely crucial area for understanding the postglacial colonization history of small mammals in Europe and the present study adds to the very few previous detailed phylogeographic studies of this region. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 788–796.