Phylogeography and palaeodistribution modelling in the Patagonian steppe: the case of Mulinum spinosum (Apiaceae)

Aim An integrative study of the endemic, yet ubiquitous, Patagonian shrub Mulinum spinosum (Apiaceae) was performed: (1) to assess the historical processes that influenced its geographical pattern of genetic variation; (2) to test hypotheses of its survival in situ or in glacial refugia during glacial cycles; and (3) to model its extant and palaeoclimatic distributions to assess support for the phylogeographical patterns recovered. Location Chilean and Argentinian Andean region and Patagonian steppe. Methods Chloroplast DNA sequences, trnH–psbA, trnS–trnG and 3′trnV–ndhC, were obtained for 314 individuals of M. spinosum from 71 populations. The haplotype data matrix was analysed using nested clade analysis (NCA) to construct a network. Analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA) and neutrality tests were also used to test for genetic structure and range expansion in the species. The present potential geographical distribution of M. spinosum was modelled and projected onto a Last Glacial Maximum (LGM) model. Results Amongst the 29 haplotypes observed, one was widely distributed, but most were restricted to either northern or southern regions. The populations with highest haplotype diversity were found in southern Patagonia, the high Andean region, and northern Patagonia. AMOVA and SAMOVA showed latitudinal structure for Argentinian populations. NCA implied patterns of restricted gene flow or dispersal but with some long‐distance dispersal and also long‐distance colonization and/or past fragmentation. Neutrality tests did not support range expansions. The current distribution model was a fairly good representation of the extant geographical distribution of the species, and the distribution model for the LGM did not show important shifts of the extant range to lower latitudes, except for a shift towards the palaeoseashore. Main conclusions Based on agreement amongst phylogeographical patterns, distribution of genetic variability, equivocal evidence of putative refugia and palaeodistribution modelling, it is probable that glaciations did not greatly affect the distribution of Mulinum spinosum. Our results are consistent with the in situ survival hypothesis, and not with the latitudinal migration of plant communities to avoid adverse climate conditions during Pleistocene glaciations. It is possible that populations of northern Patagonia may have been isolated from the southern ones by the Chubut and Deseado basins.     

High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end‐glacial refugia

The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An important geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyse genetic diversity and colonization history of the bank vole (Myodes glareolus) throughout Europe (>800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land‐bridge route deriving from a “Carpathian” glacial refugium and one via a north‐eastern route from an “Eastern” glacial refugium near the Ural Mountains. Clustering of genome‐wide SNPs revealed high diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red‐backed voles (Myodes rutilus) took place in Fennoscandia just after end‐glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this emerging model species.     

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.     

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.     

Demographic inference and genetic diversity of <Emphasis Type="Italic">Octopus mimus</Emphasis> (Cephalopoda: Octopodidae) throughout the Humboldt Current System

Climatic and oceanographic events occurring during the last glacial cycle in the Humboldt Current System (HCS) have left genetic footprints in marine invertebrate populations. The objective of this study was to evaluate the effect of the glacial period on Octopus mimus populations found throughout the HCS. This species lays a large number of small eggs which hatch into planktonic paralarvae with the potential to undergo wide dispersal. We sequenced the COIII gene to perform phylogeographic analyses of 197 octopuses sampled from seven localities. The genetic diversity of Octopus mimus was low and decreased towards the southern end of the distribution range, which comprises a single population. The haplotype genealogy and Bayesian Skyride plot suggest that O. mimus underwent a demographic expansion after the last glacial maximum (LGM). This would imply a contraction of the range of this organism toward northern latitudes during the LGM followed by southward expansion and recolonization once the contemporary interglacial period began.     

Mitochondrial DNA variation and Quaternary range dynamics in the endangered Yellow Spotted Mountain Newt,Neurergus derjugini (Caudata,Salamandridae)

In temperate regions of the Earth Pleistocene, climatic fluctuations significantly influenced distribution of species. However, little is known on how glacial and interglacial cycles affected range dynamics of the species occupying lower latitudes. In this study, we investigated mitochondrial DNA (mtDNA) variation and reconstructed the potential current and past (during the mid‐Holocene, 6 ka BP, and the Last Glacial Maximum, LGM, 21 ka BP) distribution of Neurergus derjugini, an endangered amphibian species endemic to the mid‐Zagros Mountains in Iran and Iraq. Six haplotypes identified in the control region (D‐loop) form a well‐supported monophyletic clade, distinct from other Neurergus species and revealing a sister relationship to Neurergus kaiseri. Nucleotide diversity quantifying mean divergence between the sequences is low and does not support the recognition of distinct evolutionary lineages in Neurergus derjugini. The landscape connectivity analysis and the haplotype parsimony network reveal higher gene flow rate between the breeding streams in the southern part of the range, while the northern populations are more isolated. The potential distribution of Neurergus derjugini is restricted to valleys close to mountain tops, wherein very high elevations and dry habitats appear to be unsuitable. During the mid‐Holocene and LGM conditions, the range of the species may have been more extended and shifted to lower elevations. These findings show retraction of the Neurergus derjugini range during the Quaternary and indicate that range dynamics of the species occupying lower latitudes may not follow a scenario of glacial retraction and postglacial expansion.     

Palaeodistribution modelling and genetic evidence highlight differential post‐glacial range shifts of a rain forest conifer distributed across a latitudinal gradient

Aim We examine the range expansion/contraction dynamics during the last glacial cycle of the late‐successional tropical rain forest conifer Podocarpus elatus using a combination of modelling and molecular marker analyses. Specifically, we test whether distributional changes predicted by environmental niche modelling are in agreement with (1) the glacial maximum contractions inferred from the southern fossil record, and (2) population genetic‐based estimates of range disjunctions and demographic dynamics. In addition, we test whether northern and southern ranges are likely to have experienced similar expansion/contraction dynamics. Location Eastern Australian tropical and subtropical rain forests. Methods Environmental niche modelling was completed for three time periods during the last glacial cycle and was interpreted in light of the known palynology. We collected 109 samples from 32 populations across the entire range of P. elatus. Six microsatellite loci and Bayesian coalescence analysis were used to infer population expansion/contraction dynamics, and five sequenced loci (one plastid and four nuclear) were used to quantify genetic structure/diversity. Results Environmental niche modelling suggested that the northern and southern ranges of P. elatus experienced different expansion/contraction dynamics. In the northern range, the habitat suitable for P. elatus persisted in a small refugial area during the Last Glacial Maximum (LGM, 21 ka) and then expanded during the post‐glacial period. Conversely, in the south suitable habitat was widespread during the LGM but subsequently contracted. These differential dynamics were supported by Bayesian analyses of the population genetic data (northern dispersal) and are consistent with the greater genetic diversity in the south compared with the north. A contact zone between the two genetically divergent groups (corresponding to the Macleay Overlap Zone) was supported by environmental niche modelling and molecular analyses. Main conclusions The climatic fluctuations of the Quaternary have differentially impacted the northern and southern ranges of a broadly distributed rain forest tree in Australia. Recurrent contraction/expansion cycles contributed to the genetic distinction between northern and southern distributions of P. elatus. By combining molecular and environmental niche modelling evidence, this unique study undermines the general assumption that broadly distributed species respond in a uniform way to climate change.     

Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza

Aim We perform a phylogeographical study of an endemic Patagonian herbaceous plant to assess whether geographical patterns of genetic variation correspond to in situ Pleistocene survival or to glacial retreat and post‐glacial expansion. We also seek to determine the locations of potential glacial refugia and post‐glacial colonization routes. Location Southern Andes and Patagonian steppe. Methods We used Calceolaria polyrhiza, a widely distributed Patagonian herbaceous plant that occurs mainly in the understorey of Nothofagus rain forests and in the arid Patagonian steppe, as our model system. The chloroplast intergenic spacer trnH–psbA was sequenced for 590 individuals from 68 populations. Sequence data were analysed using phylogenetic (maximum parsimony, maximum likelihood and Bayesian inference) and population genetic (spatial analyses of molecular variance, mismatch distributions and neutrality tests) methods. Nested clade phylogeographic analyses, and divergence time estimates using a calibrated molecular clock, were also conducted. Results A total of 27 haplotypes identified in the present study clustered into four primary genealogical lineages, revealing three significant latitudinal phylogeographical breaks. The two high Andean lineages probably split first, during the late Miocene, and the Patagonian lineage split around 4 Ma, coincident with the establishment of the Patagonian steppe. Within each haplogroup, major diversification occurred in the Pleistocene. The Patagonian groups show a pattern consistent with a rapid post‐glacial expansion and colonization of the Andean flanks, achieved independently by four lineages. The highest haplotype diversity was found along a longitudinal transect that is remarkably congruent with the limit of the ice‐sheet extension during the Greatest Patagonian Glaciation. A north‐east expansion is evident, which is probably associated with the ‘Arid Diagonal’ fluctuations. Main conclusions Glacial climate fluctuations had a substantial impact on the diversification, distribution and demography of the study species. A scenario of multiple periglacial Pleistocene refugia and subsequent multiple recolonization routes, from eastern Patagonia to the Andean flanks, may explain the phylogeographical patterns observed. However, current genetic structure also preserves the imprints of older events that probably occurred in the Miocene and Pliocene, providing evidence that multiple processes, operating at different spatial and temporal scales, have moulded biodiversity in Patagonia.     

Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae, Cichorieae)

We report the phylogeographic pattern of the Patagonian and Subantarctic plant Hypochaeris incana endemic to southeastern South America. We applied amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) analysis to 28 and 32 populations, respectively, throughout its distributional range and assessed ploidy levels using flow cytometry. While cpDNA data suggest repeated or simultaneous parallel colonization of Patagonia and Tierra del Fuego by several haplotypes and/or hybridization, AFLPs reveal three clusters corresponding to geographic regions. The central and northern Patagonian clusters (∼38–51° S), which are closer to the outgroup, contain mainly tetraploid, isolated and highly differentiated populations with low genetic diversity. To the contrary, the southern Patagonian and Fuegian cluster (∼51–55° S) contains mainly diploid populations with high genetic diversity and connected by high levels of gene flow. The data suggest that H. incana originated at the diploid level in central or northern Patagonia, from where it migrated south. All three areas, northern, central and southern, have similar levels of rare and private AFLP bands, suggesting that all three served as refugia for H. incana during glacial times. In southern Patagonia and Tierra del Fuego, the species seems to have expanded its populational system in postglacial times, when the climate became warmer and more humid. In central and northern Patagonia, the populations seem to have become restricted to favourable sites with increasing temperature and decreasing moisture and there was a parallel replacement of diploids by tetraploids in local populations.     

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central‐western and south‐eastern Patagonia, consistent with long‐term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.     

Climate control on ancestral population dynamics: insight from Patagonian fish phylogeography

Changes in lake and stream habitats during the growth and retreat of Pleistocene glaciers repeatedly altered the spatial distributions and population sizes of the aquatic fauna of the southern Andes. Here, we use variation in mtDNA control region sequences to infer the temporal dynamics of two species of southern Andean fish during the past few million years. At least five important climate events were associated with major demographic changes: (i) the widespread glaciations of the mid-Pliocene (c. 3.5 Ma); (ii) the largest Patagonian glaciation (1.1 Ma); (iii) the coldest Pleistocene glaciation as indicated by stacked marine delta(18)O (c. 0.7 Ma); (iv) the last southern Patagonian glaciation to reach the Atlantic coast (180 ka); and (v) the last glacial maximum (LGM, 23-25,000 years ago). The colder-water inhabitant, Galaxias platei, underwent a strong bottleneck during the LGM and its haplotype diversity coalesces c. 0.7 Ma. In contrast, the more warm-adapted and widely distributed Percichthys trucha showed continuous growth through the last two glacial cycles but went through an important bottleneck c. 180,000 years ago, at which time populations east of the Andes may have been eliminated. Haplotype diversity of the most divergent P. trucha populations, found west of the Andes, coalesces c. 3.2 Ma. The demographic timelines obtained for the two species thus illustrate the continent-wide response of aquatic life in Patagonia to climate change during the Pleistocene, but also show how differing ecological traits and distributions led to distinctive responses.     

Genetic signature of recent glaciation on populations of a near-shore marine fish species (Syngnathus leptorhynchus)

Continental glaciation has played a major role in shaping the present-day phylogeography of freshwater and terrestrial species in the Northern Hemisphere. Recent work suggests that coastal glaciation during ice ages may have also had a significant impact on marine species. The bay pipefish, Syngnathus leptorhynchus , is a near-shore Pacific coast fish species with an exceptionally wide latitudinal distribution, ranging from Bahia Santa Maria, Baja California to Prince William Sound, Alaska. Survey data indicate that S. leptorhynchus is experiencing a range expansion at the northern limit of its range, consistent with colonization from southern populations. The present study uses six novel microsatellite markers and mitochondrial DNA (mtDNA) sequence data to study the present-day population genetic structure of four coastal populations of S. leptorhynchus . Deficits in mtDNA and nuclear DNA diversity in northern populations from regions glaciated during the last glacial maximum (LGM) [ c . 18 000 years before present ( bp )] suggest that these populations were effected by glacial events. Direct estimates of population divergence times derived from both isolation and isolation-with-migration models of evolution are also consistent with a postglacial phylogenetic history of populations north of the LGM. Sequence data further indicate that a population at the southern end of the species range has been separated from the three northern populations since long before the last interglacial event ( c . 130 000 years bp ), suggesting that topographical features along the Pacific coast may maintain population separation in regions unimpacted by coastal glaciation.     

Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.     

‘What's larvae got to do with it?’ Disparate patterns of post‐glacial population structure in two benthic marine gastropods with identical dispersal potential

In marine environments, many species have apparently colonized high latitude regions following the last glacial maximum (LGM) yet lack a life-history stage, such as a free-living larva, that is clearly capable of long-distance dispersal. Two hypotheses can explain the modern high latitude distributions of these marine taxa: (1) survival in northern refugia during the LGM or (2) rapid post-glacial dispersal by nonlarval stages. To distinguish these two scenarios, I characterized the genetic structure of two closely related northeastern Pacific gastropods that lack planktonic larvae but which have distributions extending more than 1000 km north of the southern limit of glaciers at the LGM. Despite having identical larval dispersal potential, these closely related species exhibit fundamentally different patterns of genetic structure. In Nucella ostrina, haplotype diversity among northern populations (British Columbia and Alaska) is low, no pattern of isolation by distance exists and a coalescent-based model of population growth indicates that during the LGM population size was reduced to less than 35% of its current size. In the congeneric and often sympatric N. lamellosa, northern populations harbour a diversity of ancient private haplotypes, significant evidence of isolation by distance exists and regional subdivision was found between northern (Alaska) and southern (southern British Columbia, Washington and Oregon) populations. Estimates of coalescent parameters indicate only a modest reduction in population size during the LGM and that northern and southern populations of N. lamellosa split approximately 50 Kyr before the LGM. The patterns are consistent with the hypothesis that N. ostrina recently reinvaded the northeastern Pacific but N. lamellosa survived the LGM in a northern refuge. A comparison of similar studies in this region indicates that depleted levels of genetic variation at high latitudes--evidence suggestive of recent colonization from a southern refuge--is more common among intertidal species that live relatively high on the shore, where exposure times to cold stress in air are longer than for species living lower on the shore. These data suggest that for some faunas, ecological differences between taxa may be more important than larval dispersal potential in determining species' long-term biogeographical responses to climate change.     

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.     

Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen

Norway spruce (Picea abies [L.] Karst.) is a broadly distributed European conifer tree whose history has been intensively studied by means of fossil records to infer the location of full‐glacial refugia and the main routes of postglacial colonization. Here we use recently compiled fossil pollen data as a template to examine how past demographic events have influenced the species’ modern genetic diversity. Variation was assessed in the mitochondrial nad1 gene containing two minisatellite regions. Among the 369 populations (4876 trees) assayed, 28 mitochondrial variants were identified. The patterns of population subdivision superimposed on interpolated fossil pollen distributions indicate that survival in separate refugia and postglacial colonization has led to significant structuring of genetic variation in the southern range of the species. The populations in the northern range, on the other hand, showed a shallow genetic structure consistent with the fossil pollen data, suggesting that the vast northern range was colonized from a single refugium. Although the genetic diversity decreased away from the putative refugia, there were large differences between different colonization routes. In the Alps, the diversity decreased over short distances, probably as a result of population bottlenecks caused by the presence of competing tree species. In northern Europe, the diversity was maintained across large areas, corroborating fossil pollen data in suggesting that colonization took place at high population densities. The genetic diversity increased north of the Carpathians, probably as a result of admixture of expanding populations from two separate refugia.     

Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory

We aimed to reveal the effects of range expansion and subsequent lineage admixture from separated glacial refugia on genetic diversity of Kalopanax septemlobus in Japan, by combining nuclear microsatellite data and ecological niche modelling. Allelic richness and gene diversity were compared at the population and regional level. We also statistically examined these indices as a function of population accessibility to the last glacial maximum (LGM) palaeodistribution reconstructed by ecological niche modelling to test a simple range expansion scenario from glacial refugia. Genetic diversity was highest in the populations of southern Japan and gradually decreased towards the north. However, an additional centre of genetic diversity, when measured as gene diversity, was found in northern Honshu Island, where distinct lineages were shown to be in contact. Positive effects of population accessibility to the LGM range were detected in both diversity indices at different spatial scales. The combined data support independent postglacial range expansions towards the north from the edge populations on the exposed coastal shelf of Pacific and Sea of Japan in northern Honshu during the LGM, which subsequently resulted in markedly low genetic diversity in the northernmost extant range, Hokkaido. The regional increase in gene diversity in northern Honshu is likely to be the result of postglacial lineage admixture. Relative difference in the spatial scales best relating population genetic diversity with the LGM distribution can be explained by a higher rate of allelic richness diversity loss during range expansions and stronger effects of lineage admixture on gene diversity.     

Late‐glacial recolonization and phylogeography of European red deer (Cervus elaphus L.)

The Pleistocene was an epoch of extreme climatic and environmental changes. How individual species responded to the repeated cycles of warm and cold stages is a major topic of debate. For the European fauna and flora, an expansion–contraction model has been suggested, whereby temperate species were restricted to southern refugia during glacial times and expanded northwards during interglacials, including the present interglacial (Holocene). Here, we test this model on the red deer (Cervus elaphus) a large and highly mobile herbivore, using both modern and ancient mitochondrial DNA from the entire European range of the species over the last c. 40 000 years. Our results indicate that this species was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (LGM) haplogroups restricted today to South‐East Europe and Western Asia reached as far west as the UK. During the LGM, red deer was mainly restricted to southern refugia, in Iberia, the Balkans and possibly in Italy and South‐Western Asia. At the end of the LGM, red deer expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, Scandinavia, Germany, Poland and Belarus. Ancient DNA data cannot rule out refugial survival of red deer in North‐West Europe through the LGM. Had such deer survived, though, they were replaced by deer migrating from Iberia at the end of the glacial. The Balkans served as a separate LGM refugium and were probably connected to Western Asia with genetic exchange between the two areas.     

Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae)

Aim Based on extensive range‐wide sampling, we address the phylogeographical history of one of the most widespread and taxonomically complex sedges in Europe, Carex nigra s. lat. We compare the genetic structure of the recently colonized northern areas (front edge) and the long‐standing southern areas (rear edge), and assess the potential genetic basis of suggested taxonomic divisions at the rank of species and below. Location Amphi‐Atlantic, central and northern Europe, circum‐Mediterranean mountain ranges, central Siberia, Himalayas. Methods A total of 469 individuals sampled from 83 populations, covering most of the species’ range, were analysed with amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) markers. Bayesian clustering, principal coordinates analysis, and estimates of diversity and differentiation were used for the analysis of AFLP data. CpDNA data were analysed with statistical parsimony networks and maximum parsimony and Bayesian inference of phylogenetic trees. Results Overall genetic diversity was high, but differentiation among populations was limited. Major glacial refugia were inferred in the Mediterranean Basin and in western Russia; in addition, there may have been minor refugia in the North Atlantic region. In the southern part of the range, we found high levels, but geographically quite poorly structured genetic diversity, whereas the levels of genetic diversity varied among different areas in the north. North American populations were genetically very similar to the European populations. Main conclusions The data are consistent with extensive gene flow, which has obscured the recent history of the taxon. The limited differentiation in the south probably results from the mixing of lineages expanding from several local refugia. Northward post‐glacial colonization resulted in a leading‐edge pattern of low diversity in the Netherlands, Belgium, Scotland and Iceland, whereas the observed high diversity levels in Fennoscandia suggest broad‐fronted colonization from the south as well as from the east. The patterns found in the American populations are consistent with post‐glacial colonization, possibly even with anthropogenic introduction from Europe. Our data also suggest that the tussock‐forming populations of C. nigra, often referred to as a distinct species (Carex juncella), represent an ecotype that has originated repeatedly from different populations with creeping rhizomes.     

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.