The impact of Pleistocene climate change on an ancient arctic-alpine plant: multiple lineages of disparate history in Oxyria digyna

The ranges of arctic-alpine species have shifted extensively with Pleistocene climate changes and glaciations. Using sequence data from the trnH-psbA and trnT-trnL chloroplast DNA spacer regions, we investigated the phylogeography of the widespread, ancient (>3 million years) arctic-alpine plant Oxyria digyna (Polygonaceae). We identified 45 haplotypes and six highly divergent major lineages; estimated ages of these lineages (time to most recent common ancestor, T(MRCA)) ranged from ～0.5 to 2.5 million years. One lineage is widespread in the arctic, a second is restricted to the southern Rocky Mountains of the western United States, and a third was found only in the Himalayan and Altai regions of Asia. Three other lineages are widespread in western North America, where they overlap extensively. The high genetic diversity and the presence of divergent major cpDNA lineages within Oxyria digyna reflect its age and suggest that it was widespread during much of its history. The distributions of individual lineages indicate repeated spread of Oxyria digyna through North America over multiple glacial cycles. During the Last Glacial Maximum it persisted in multiple refugia in western North America, including Beringia, south of the continental ice, and within the northern limits of the Cordilleran ice sheet. Our data contribute to a growing body of evidence that arctic-alpine species have migrated from different source regions over multiple glacial cycles and that cryptic refugia contributed to persistence through the Last Glacial Maximum.     

Population genomic evidence for plant glacial survival in Scandinavia

Quaternary glaciations have played a major role in shaping the genetic diversity and distribution of plant species. Strong palaeoecological and genetic evidence supports a postglacial recolonization of most plant species to northern Europe from southern, eastern and even western glacial refugia. Although highly controversial, the existence of small in situ glacial refugia in northern Europe has recently gained molecular support. We used genomic analyses to examine the phylogeography of a species that is critical in this debate. Carex scirpoidea Michx subsp. scirpoidea is a dioecious, amphi‐Atlantic arctic–alpine sedge that is widely distributed in North America, but absent from most of Eurasia, apart from three extremely disjunct populations in Norway, all well within the limits of the Weichselian ice sheet. Range‐wide population sampling and variation at 5,307 single nucleotide polymorphisms show that the three Norwegian populations comprise unique evolutionary lineages divergent from Greenland with high between‐population divergence. The Norwegian populations have low within‐population genetic diversity consistent with having experienced genetic bottlenecks in glacial refugia, and host private alleles that probably accumulated in long‐term isolated populations. Demographic analyses support a single, pre‐Weichselian colonization into Norway from East Greenland, and subsequent divergence of the three populations in separate refugia. Other refugial areas are identified in North‐east Greenland, Minnesota/Michigan, Colorado and Alaska. Admixed populations in British Columbia and West Greenland indicate postglacial contact. Taken together, evidence from this study strongly indicates in situ glacial survival in Scandinavia.     

The post‐Pleistocene population genetic structure of a western North American passerine: the chestnut‐backed chickadee Poecile rufescens

The population genetic structure of many high‐latitude species in North America was affected by the last glaciation, and current structure reflects isolation in refugia and colonisation patterns. Large ice‐free areas, both south of the ice sheets and in the north‐west, supported numerous flora and fauna throughout this period. Fossil evidence suggests additional western glacial refugia existed both on Haida Gwaii (the Queen Charlotte Islands) and in northern Idaho. The chestnut‐backed chickadee Poecile rufescens is a songbird found along the western edge of Canada and the United States, with a linear distribution along the coast, and an isolated interior population. Mitochondrial DNA sequence data (control region and ATPase 6–8) from 10 populations (n = 122) were used to test for population genetic structure. The data supported a general north/south separation. Haida Gwaii was found to be genetically distinct from the rest of the populations, and the two northern British Columbia populations separated from all but Alaska. The interior population showed evidence of both historical isolation and secondary colonisation by birds from coastal populations. Neutrality tests suggested a past population expansion in all populations from previously glaciated areas, and a stable population in areas believed to be unglaciated. This pattern supports the use of multiple glacial refugia by the chestnut‐backed chickadee. We could not reject the use of Haida Gwaii or the interior (i.e. Clearwater Basin) as glacial refugia.     

Refugial persistence and postglacial recolonization of North America by the cold-tolerant herbaceous plant Orthilia secunda

Previous phylogeographical and palaeontological studies on the biota of northern North America have revealed a complex scenario of glacial survival in multiple refugia and differing patterns of postglacial recolonization. Many putative refugial regions have been proposed both north and south of the ice sheets for species during the Last Glacial Maximum, but the locations of many of these refugia remain a topic of great debate. In this study, we used a phylogeographical approach to elucidate the refugial and recolonization history of the herbaceous plant species Orthilia secunda in North America, which is found in disjunct areas in the west and east of the continent, most of which were either glaciated or lay close to the limits of the ice sheets. Analysis of 596 bp of the chloroplast trnS-trnG intergenic spacer and five microsatellite loci in 84 populations spanning the species' range in North America suggests that O. secunda persisted through the Last Glacial Maximum (LGM) in western refugia, even though palaeodistribution modelling indicated a suitable climate envelope across the entire south of the continent. The present distribution of the species has resulted from recolonization from refugia north and south of the ice sheets, most likely in Beringia or coastal regions of Alaska and British Columbia, the Washington/Oregon region in the northwest USA, and possibly from the region associated with the putative 'ice-free corridor' between the Laurentide and Cordilleran ice sheets. Our findings also highlight the importance of the Pacific Northwest as an important centre of intraspecific genetic diversity, owing to a combination of refugial persistence in the area and recolonization from other refugia.     

The coastal-disjunct mesic flora in the inland Pacific Northwest of USA and Canada: refugia, dispersal and disequilibrium

Aim Understanding the history of the mesic‐adapted plant species of eastern British Columbia and northern Idaho, disjunct from their main coastal distribution, may suggest how biotas reorganize in the face of climate change and dispersal barriers. For different species, current evidence supports establishment of the disjunction via an inland glacial refugium, via recent dispersal from the coast, or via a combination of both. In this study, the modern distributions of the coastal‐disjunct vascular plants are analysed with respect to modern climate to examine how refugia and/or dispersal limitation control regional patterns in species richness. Location North‐west North America. Methods The distributions of nine tree and 58 understorey species with a coastal‐disjunct pattern were compiled on a 50‐km grid. The relationship between species richness and an estimate of available moisture was calculated separately for formerly glaciated and unglaciated portions of the coastal and inland regions. Growth habit and dispersal mode were assessed as possible explanatory variables for species distributions. Results Species richness shows a strong relationship to climate in coastal‐unglaciated areas but no relationship to climate in inland‐glaciated areas. In inland‐glaciated areas, richness is c. 70% lower than that expected from climate. Species with animal‐dispersed seeds occupy a larger portion of coastal and inland regions than species with less dispersal potential. Main conclusions Modern patterns of diversity are consistent with both refugia and dispersal processes in establishing the coastal‐disjunct pattern. The inland glacial refugium is marked by locally high diversity and several co‐distributed endemics. In the inland‐glaciated area, dispersal limitation has constrained diversity despite the nearby refugia. Onset of mesic climate within only the last 3000 years and the low dispersal capacity of many species in the refugium may explain this pattern. This study suggests that vascular plant species will face significant challenges responding to climate change on fragmented landscapes.     

Inferring long-distance dispersal and topographic barriers during post-glacial colonization from the genetic structure of red maple (Acer rubrum L.) in New England

Aim  This study aims to assess the role of long-distance seed dispersal and topographic barriers in the post-glacial colonization of red maple ( Acer rubrum L.) using chloroplast DNA (cpDNA) variation, and to understand whether this explains the relatively higher northern diversity found in eastern North American tree species compared with that in Europe.
Location  North-eastern United States.
Methods  The distribution of intraspecific cpDNA variation in temperate tree populations has been used to identify aspects of post-glacial population spread, including topographic barriers to population expansion and spread by long-distance seed dispersal. We sequenced c.  370 cpDNA base pairs from 221 individuals in 100 populations throughout the north-eastern United States, and analysed spatial patterns of diversity and differentiation.
Results  Red maple has high genetic diversity near its northern range limit, but this diversity is not partitioned by topographic barriers, suggesting that the northern Appalachian Mountains were not a barrier to the colonization of red maple. We also found no evidence of the patchy genetic structure that has been associated with spread by rare long-distance seed dispersal in previous studies.
Main conclusions  Constraints on post-glacial colonization in eastern North America seem to have been less stringent than those in northern Europe, where bottlenecks arising from long-distance colonization and topographic barriers appear to have strongly reduced genetic diversity. In eastern North America, high northern genetic diversity may have been maintained by a combination of frequent long-distance dispersal, minor topographic obstacles and diffuse northern refugia near the ice sheet.     

Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.     

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

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

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.     

Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)

Eastern North American plant biogeography has traditionally focused on two primary issues: (i) the location of temperate Pleistocene refugia and their proximity to the southern margin of the ice sheet during the last glacial maximum, and (ii) the origin of the temperate element of northern Latin America. While numerous population genetic and phylogeographical studies have focused on the first issue, few (if any) have considered the second. We addressed these issues by surveying 117 individuals from 24 populations of Liquidambar styraciflua (American sweetgum; Altingiaceae) across the southeastern USA, eastern Mexico, and Guatemala, using more than 2200 bp of chloroplast DNA sequence data. To specifically address the issue of timing, we estimated intraspecific divergence times on the basis of multiple fossil-based calibration points, using taxa from Altingiaceae ( Liquidambar and Altingia ) and Hammamelidaceae ( Hamamelis ) as outgroups. More than half of the sampled localities exhibited multiple haplotypes. Remarkably, the greatest variation was observed within the USA, with Mexico and Guatemala sharing widespread haplotypes with Texas, Mississippi, Kentucky, Ohio, and northern Virginia. This lack of differentiation suggests shared ancestral polymorphisms, and that the genetic signal we observed is older than the disjunction itself. Our data provide support for previously proposed hypotheses of Pleistocene refugia in peninsular Florida and along the eastern Atlantic, but also for deeper divergences (~8 million years ago) within the USA. These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study.     

A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer

Jack pine (Pinus banksiana Lamb.) is a broadly distributed North American conifer and its current range was covered by the Laurentian ice sheet during the last glacial maximum. To infer about the history and postglacial colonization of this boreal species, range-wide genetic variation was assessed using a new and highly variable minisatellite-like marker of the mitochondrial genome. Among the 543 trees analysed, 14 distinct haplotypes were detected, which corresponded to different repeat numbers of the 32-nucleotide minisatellite-like motif. Several haplotypes were rare with limited distribution, suggesting recent mutation events during the Holocene. At the population level, an average of 2.6 haplotypes and a mean haplotype diversity (H) of 0.328 were estimated. Population subdivision of genetic diversity was quite high with G(ST) and R(ST) values of 0.569 and 0.472, respectively. Spatial analyses identified three relatively homogeneous groups of populations presumably representative of genetically distinct glacial populations, one west and one east of the Appalachian Mountains in the United States and a third one presumably on the unglaciated northeastern coastal area in Canada. These results indicate the significant role of the northern part of the US Appalachian Mountains as a factor of vicariance during the ice age. A fourth distinct group of populations was observed in central Québec where the continental glacier retreated last. It included populations harbouring haplotypes present into the three previous groups, and it had higher level of haplotype diversity per population (H = 0.548) and lower population differentiation (G(ST) = 0.265), which indicates a zone of suture or secondary contact between the migration fronts of the three glacial populations. Introgression from Pinus contorta Dougl. var. latifolia Engelm. was apparent in one western population from Alberta. Altogether, these results indicate that the mitochondrial DNA variation of jack pine is geographically highly structured and it correlates well with large-scale patterns emerging from recent phylogeographical studies of other tree boreal species in North America.     

HOT SPOTS OF GENETIC DIVERSITY DESCENDED FROM MULTIPLE PLEISTOCENE REFUGIA IN AN ALPINE UNGULATE

Species that inhabit naturally fragmented environments are expected to be spatially structured and exhibit reduced genetic diversity at the periphery of their range. Patterns of differentiation may also reflect historical processes such as recolonization from glacial refugia. We examined the relative importance of these factors in shaping the spatial patterns of genetic differentiation across the range of an alpine specialist, the North American mountain goat (Oreamnos americanus). Contrary to fossil evidence that suggests a single southern refugium, we detected evidence for additional refugia in northern British Columbia and the Alaskan coast using both mitochondrial and microsatellite DNA. A core area of elevated genetic diversity characterized both regions, and molecular dating suggested a recent Pleistocene split was followed by demographic expansion. Across their range, mountain goats were highly genetically structured and displayed the expected pattern of declining diversity toward the periphery. Gene flow was high within contiguous mountain ranges, but cross‐assignments paradoxically suggest that long‐distance contemporary dispersal movements are not uncommon. These results improve our understanding of how historical vicariance and contemporary fragmentation influence population differentiation, and have implications for conserving the adaptive potential of alpine populations and habitat.     

Investigating cytoskeletal function in chloroplast protrusion formation in the arctic-alpine plant Oxyria digyna

Arctic and alpine plants like Oxyria digyna have to face enhanced environmental stress. This study compared leaves from Oxyria digyna collected in the Arctic at Svalbard (78 degrees N) and in the Austrian Alps (47 degrees N) at cellular, subcellular, and ultrastructural levels. Oxyria digyna plants collected in Svalbard had significantly thicker leaves than the samples collected in the Austrian Alps. This difference was generated by increased thickness of the palisade and spongy mesophyll layers in the arctic plants, while epidermal cells had no significant size differences between the two habitats. A characteristic feature of arctic, alpine, and cultivated samples was the occurrence of broad stroma-filled chloroplast protrusions, 2 - 5 microm broad and up to 5 microm long. Chloroplast protrusions were in close spatial contact with other organelles including mitochondria and microbodies. Mitochondria were also present in invaginations of the chloroplasts. A dense network of cortical microtubules found in the mesophyll cells suggested a potential role for microtubules in the formation and function of chloroplast protrusions. No direct interactions between microtubules and chloroplasts, however, were observed and disruption of the microtubule arrays with the anti-microtubule agent oryzalin at 5 - 10 microM did not alter the appearance or dynamics of chloroplast protrusions. These observations suggest that, in contrast to studies on stromule formation in Nicotiana, microtubules are not involved in the formation and morphology of chloroplast protrusions in Oxyria digyna. The actin microfilament-disrupting drug latrunculin B (5 - 10 microM for 2 h) arrested cytoplasmic streaming and altered the cytoplasmic integrity of mesophyll cells. However, at the ultrastructural level, stroma-containing, thylakoid-free areas were still visible, mostly at the concave sides of the chloroplasts. As chloroplast protrusions were frequently found to be mitochondria-associated in Oxyria digyna, a role in metabolite exchange is possible, which may contribute to an adaptation to alpine and arctic conditions.     

Zoogeographical implications of variation in mitochondrial DNA of Arctic grayling (Thymallus arcticus)

Most of the northern half of North America's freshwater fish survived the last glacial period in unfrozen refugia peripheral to the ice sheets. In our study, the question of which refugia Arctic grayling ( Thymallus arcticus ) inhabited during the Wisconsinan Ice Age, and how they subsequently dispersed to their present geographical range, was examined using mitochondrial DNA (mtDNA) analysis. mtDNA from 12 T. arcticus populations was analysed by direct sequencing and restriction fragment length polymorphism analysis (RFLP). Our data support the hypotheses that T. arcticus had a large refugial population in the Bering Refuge (shown by high mtDNA diversity in extant Alaskan populations) and that British Columbia was colonized from the Bering Refuge (shown by mtDNA haplotype similarities). Our data also show that a disjunct southern set of populations in Montana is significantly different from the northern grayling, in terms of restriction haplotype frequency and distinguishing sequence characteristics. Sequence results yielded an estimated divergence time of 370 000 years between the northern and Montana grayling haplotypes. We conclude that T. arcticus survived the Wisconsinan glaciation in at least two refugia: (i) the Bering Refuge north of the ice sheets; and (ii) either the Upper Missouri or the southwest Alberta Refuge, south of the ice sheet.     

Distribution and population structure of the anther smut Microbotryum silenes‐acaulis parasitizing an arctic–alpine plant

Cold‐adapted organisms with current arctic–alpine distributions have persisted during the last glaciation in multiple ice‐free refugia, leaving footprints in their population structure that contrast with temperate plants and animals. However, pathogens that live within hosts having arctic–alpine distributions have been little studied. Here, we therefore investigated the geographical range and population structure of a fungus parasitizing an arctic–alpine plant. A total of 1437 herbarium specimens of the plant Silene acaulis were examined, and the anther smut pathogen Microbotryum silenes‐acaulis was present throughout the host's geographical range. There was significantly greater incidence of anther smut disease in more northern latitudes and where the host locations were less dense, indicating a major influence of environmental factors and/or host demographic structure on the pathogen distribution. Genetic analyses with seven microsatellite markers on recent collections of 195 M. silenes‐acaulis individuals revealed three main genetic clusters, in North America, northern Europe and southern Europe, likely corresponding to differentiation in distinct refugia during the last glaciation. The lower genetic diversity in northern Europe indicates postglacial recolonization northwards from southern refugia. This study combining herbarium surveys and population genetics thus uniquely reveals the effects of climate and environmental factors on a plant pathogen species with an arctic–alpine distribution.     

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.     

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.     

Chloroplast DNA phylogeography of the arctic-montane species Saxifraga hirculus (Saxifragaceae)

The genetic structure of populations of an arctic-montane herb, Saxifraga hirculus (Saxifragaceae), was analysed by means of chloroplast restriction fragment-length polymorphism. Sampled populations were distributed across Europe and North America (Alaska and Colorado). There was no evidence for geographically structured genetically divergent lineages, and although no haplotypes were shared between North America and Europe, the haplotypes from different continents were intermixed on a minimum spanning tree. European populations were much more highly differentiated and had much lower levels of haplotype diversity than their Alaskan counterparts. Centres of haplotype diversity were concentrated in those Alaskan populations located outside the limits of the last (Wisconsin) glaciation, suggesting that they may have acted as refugia during the Pleistocene. It was not possible to identify putative migration routes or corresponding refugia in the European genepool. One British population, from the Pentland Hills, was genetically very distant from all the others, for reasons that are as yet unknown.     

A taxonomic study of campylopus schimperi and C. subulatus (Bryopsida: Dicranaceae) in North America

Campylopus schimperi is known in North America from Oaxaca, Colorado, British Columbia, Yukon, Alaska, Baffin Island, Gaspé Peninsula, and Newfoundland, and reported from Greenland. No specimens of the previously reported C. subulatus were found from North America and this species should be excluded from the North American bryophyte flora. A quantitative study and critical review of the characters distinguishing these two species indicate that leaf laminal cell shape and length, and costal anatomy are the most definitive taxonomic features. The distributional range of C. schimperi in North America suggests a close association with unglaciated areas and hypothesized glacial refugia.     

The importance of Anatolian mountains as the cradle of global diversity in Arabis alpina, a key arctic-alpine species

Background and Aims

Anatolia is a biologically diverse, but phylogeographically under-explored region. It is described as either a centre of origin and long-term Pleistocene refugium, or as a centre for genetic amalgamation, fed from distinct neighbouring refugia. These contrasting hypotheses are tested through a global phylogeographic analysis of the arctic–alpine herb, Arabis alpina.

Methods

Herbarium and field collections were used to sample comprehensively the entire global range, with special focus on Anatolia and Levant. Sequence variation in the chloroplast DNA trnL-trnF region was examined in 483 accessions. A haplotype genealogy was constructed and phylogeographic methods, demographic analysis and divergence time estimations were used to identify the centres of diversity and to infer colonization history.

Key Results

Fifty-seven haplotypes were recovered, belonging to three haplogroups with non-overlapping distributions in (1) North America/Europe/northern Africa, (2) the Caucuses/Iranian Plateau/Arabian Peninsula and (3) Ethiopia–eastern Africa. All haplogroups occur within Anatolia, and all intermediate haplotypes linking the three haplogroups are endemic to central Anatolia and Levant, where haplotypic and nucleotide diversities exceeded all other regions. The local pattern of haplotype distribution strongly resembles the global pattern, and the haplotypes began to diverge approx. 2·7 Mya, coinciding with the climate cooling of the early Middle Pleistocene.

Conclusions

The phylogeographic structure of Arabis alpina is consistent with Anatolia being the cradle of origin for global genetic diversification. The highly structured landscape in combination with the Pleistocene climate fluctuations has created a network of mountain refugia and the accumulation of spatially arranged genotypes. This local Pleistocene population history has subsequently left a genetic imprint at the global scale, through four range expansions from the Anatolian diversity centre into Europe, the Near East, Arabia and Africa. Hence this study also illustrates the importance of sampling and scaling effects when translating global from local diversity patterns during phylogeographic analyses.