Holocene re‐colonisation,central–marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species

Corynephorus canescens (L.) P.Beauv. is an outbreeding, short‐lived and wind‐dispersed grass species, highly specialised on scattered and disturbance‐dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post‐glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance‐driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation‐by‐distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re‐colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re–)colonisation histories and range centre–margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre–periphery gradients.     

Hitchhiking with forests: population genetics of the epiphytic lichen Lobaria pulmonaria in primeval and managed forests in southeastern Europe

Availability of suitable trees is a primary determinant of range contractions and expansions of epiphytic species. However, switches between carrier tree species may blur co‐phylogeographic patterns. We identified glacial refugia in southeastern Europe for the tree‐colonizing lichen Lobaria pulmonaria, studied the importance of primeval forest reserves for the conservation of genetically diverse populations and analyzed differences in spatial genetic structure between primeval and managed forests with fungus‐specific microsatellite markers. Populations belonged to either of two genepools or were admixed. Gene diversity was higher in primeval than in managed forests. At small distances up to 170 m, genotype diversity was lower in managed compared with primeval forests. We found significant associations between groups of tree species and two L. pulmonaria genepools, which may indicate “hitchhiking” of L. pulmonaria on forest communities during postglacial migration. Genepool B of L. pulmonaria was associated with European Beech (Fagus sylvatica) and we can hypothesize that genepool B survived the last glaciation associated within the refuge of European Beech on the Coastal and Central Dinarides. The allelic richness of genepool A was highest in the Alps, which is the evidence for a northern refuge of L. pulmonaria. Vicariant altitudinal distributions of the two genepools suggest intraspecific ecological differentiation.     

Scattered late‐glacial and early Holocene tree populations as dispersal nuclei for forest development in north‐eastern European Russia

Aim Concepts about patterns and rates of post‐glacial tree population migration are changing as a result of the increasing amount of palaeobotanical information being provided by macroscopic plant remains. Here we combine macrofossil, pollen and stomata records from five sites in north‐eastern European Russia and summarize the results for the late‐glacial–early Holocene transition. The late‐glacial–early Holocene transition encompasses the first indications of trees (tree‐type Betula, Picea abies, Abies sibirica and Larix sibirica) and subsequent forest development. Considerable time‐lags between the first macrobotanical and/or stomata finds of spruce (Picea abies) and the establishment of a closed forest are reconsidered. Location Pechora basin, north‐eastern European Russia. Methods We used plant macrofossil, stomata, pollen and radiocarbon analyses to reconstruct late‐glacial and early Holocene tree establishment and forest development. The data were derived from lake sediment and peat archives. Results Palaeobotanical data reveal an early Holocene presence (11,500–10,000 cal. yr bp ) of arboreal taxa at all five sites. One site presently located in the northernmost taiga zone, shows the presence of spruce and reproducing tree birch during the late‐glacial. Given the current view of post‐glacial population dynamics and migration rates, it seems likely that the source area of these early tree populations in north‐eastern European Russia was not located in southern Europe but that these populations had local origins. Results thus support the emerging view that the first post‐glacial population expansions in non‐glaciated regions at high latitudes do not reflect migration from the south but were a result of an increase in the size and density of small persisting outlying tree populations. Main conclusions Results suggest that the area east of the margin of the Scandinavian ice sheet to the Ural Mountains had isolated patches of trees during the late‐glacial and early Holocene and that these small populations acted as initial nuclei for population expansion and forest development in the early Holocene.     

How climate,migration ability and habitat fragmentation affect the projected future distribution of European beech

Recent efforts to incorporate migration processes into species distribution models (SDMs) are allowing assessments of whether species are likely to be able to track their future climate optimum and the possible causes of failing to do so. Here, we projected the range shift of European beech over the 21st century using a process‐based SDM coupled to a phenomenological migration model accounting for population dynamics, according to two climate change scenarios and one land use change scenario. Our model predicts that the climatically suitable habitat for European beech will shift north‐eastward and upward mainly because (i) higher temperature and precipitation, at the northern range margins, will increase survival and fruit maturation success, while (ii) lower precipitations and higher winter temperature, at the southern range margins, will increase drought mortality and prevent bud dormancy breaking. Beech colonization rate of newly climatically suitable habitats in 2100 is projected to be very low (1–2% of the newly suitable habitats colonised). Unexpectedly, the projected realized contraction rate was higher than the projected potential contraction rate. As a result, the realized distribution of beech is projected to strongly contract by 2100 (by 36–61%) mainly due to a substantial increase in climate variability after 2050, which generates local extinctions, even at the core of the distribution, the frequency of which prevents beech recolonization during more favourable years. Although European beech will be able to persist in some parts of the trailing edge of its distribution, the combined effects of climate and land use changes, limited migration ability, and a slow life‐history are likely to increase its threat status in the near future.     

Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans‐Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans‐Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans‐Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post‐glacial trans‐Atlantic secondary contact, contrasting with low European ancestry genome‐wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large‐scale intraspecific variation in genomic architecture of northern species.     

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.     

Potential source and sink locations for climate‐driven species range shifts in Europe since the Last Glacial Maximum

Aim To identify potential source and sink locations for climate‐driven species range shifts in Europe since the Last Glacial Maximum (LGM). Location Europe. Methods We developed a new approach combining past‐climate simulations with the concept of analogous climate space. Our index gives a continuous measure of the potential of a location to have acted as a source or a sink for species that have shifted their ranges since the LGM. High glacial source potential is indicated by LGM climatic conditions that are widespread now; high post‐glacial sink potential is indicated by current climatic conditions that were widespread at the LGM. The degree of isolation of source and sink areas was calculated as the median distance to areas with analogous climate conditions. Results We identified areas of high glacial source potential in the previously recognized refugial areas in the southern European peninsulas, but also in large areas in central‐western Europe. The most climatically isolated source areas were located in northern Spain, in north‐western Europe and in eastern Turkey. From here species would have had to cover substantial distances to find current climate conditions analogous to LGM conditions of these areas. Areas with high post‐glacial sink potential were mainly located in Fennoscandia and in central and south‐eastern Europe. Some of the most isolated sink areas were located in the Spanish highlands and around the Baltic Sea. Main conclusions Our species‐independent approach successfully identified previously recognized glacial refugial areas with high source potential for species range shifts in southern Europe and in addition highlighted other potential source areas in central Europe. This study offers new insights into how the distribution of past and current climatic conditions may have influenced past species range shifts and current large‐scale biodiversity patterns.     

Climatic limits for the present distribution of beech (Fagus L.) species in the world

Aim Beech (Fagus L., Fagaceae) species are representative trees of temperate deciduous broadleaf forests in the Northern Hemisphere. We focus on the distributional limits of beech species, in particular on identifying climatic factors associated with their present range limits. Location Beech species occur in East Asia, Europe and West Asia, and North America. We collated information on both the southern and northern range limits and the lower and upper elevational limits for beech species in each region. Methods In total, 292 lower/southern limit and 310 upper/northern limit sites with available climatic data for all 11 extant beech species were collected by reviewing the literature, and 13 climatic variables were estimated for each site from climate normals at nearby stations. We used principal components analysis (PCA) to detect climatic variables most strongly associated with the distribution of beech species and to compare the climatic spaces for the different beech species. Results Statistics for thermal and moisture climatic conditions at the lower/southern and upper/northern limits of all world beech species are presented. The first two PCA components accounted for 70% and 68% of the overall variance in lower/southern and upper/northern range limits, respectively. The first PCA axis represented a thermal gradient, and the second a moisture gradient associated with the world‐wide distribution pattern of beech species. Among thermal variables, growing season warmth was most important for beech distribution, but winter low temperature (coldness and mean temperature for the coldest month) and climatic continentality were also coupled with beech occurrence. The moisture gradient, indicated by precipitation and moisture indices, showed regional differences. American beech had the widest thermal range, Japanese beeches the most narrow; European beeches occurred in the driest climate, Japanese beeches the most humid. Climatic spaces for Chinese beech species were between those of American and European species. Main conclusions The distributional limits of beech species were primarily associated with thermal factors, but moisture regime also played a role. There were some regional differences in the climatic correlates of distribution. The growing season temperature regime was most important in explaining distribution of Chinese beeches, whilst their northward distribution was mainly limited by shortage of precipitation. In Japan, distribution limits of beech species were correlated with summer temperature, but the local dominance of beech was likely to be dependent on snowfall and winter low temperature. High summer temperature was probably a limiting factor for southward extension of American beech, while growing season warmth seemed critical for its northward distribution. Although the present distribution of beech species corresponded well to the contemporary climate in most areas, climatic factors could not account for some distributions, e. g., that of F. mexicana compared to its close relative F. grandifolia. It is likely that historical factors play a secondary role in determining the present distribution of beech species. The lack of F. grandifolia on the island of Newfoundland, Canada, may be due to inadequate growing season warmth. Similarly, the northerly distribution of beech in Britain has not reached its potential limit, perhaps due to insufficient time since deglaciation to expand its range.     

Resilient forest faunal communities in South Africa: a legacy of palaeoclimatic change and extinction filtering?

Aim To examine the influence of climatic extinction filtering during the last glacial maximum (LGM; c. 18,000 yr bp ) and of the subsequent recolonization of forest faunas on contemporary assemblage composition in southern African forests. Location South Africa, Mozambique, Swaziland, Zimbabwe. Methods Data comprised presence/absence by quarter‐degree grid cell for forest‐dependent and forest‐associated birds, non‐volant mammals and frogs. Twenty‐one forest subregions were assigned to one of three previously identified forest types: Afrotemperate, scarp, and Indian Ocean coastal belt. Differences among forest types were examined through patterns and gradients of species richness and endemism, assemblage similarity, species turnover, and coefficients of species dispersal direction. The influence of contemporary environment on assemblage composition was investigated using partial canonical correspondence analysis. Several alternative biogeographical hypotheses for the recolonization of forest faunas were tested. Results Afrotemperate faunas are relatively species‐poor, have low species turnover, and are unsaturated and infiltrated by generalist species. In northern and central regions, communities are supplemented by recolonization from scarp forest refugia, and among frogs by autochthanous speciation in localized refugia. Scarp faunas are relatively species‐rich, contain many forest‐dependent species, have high species turnover, and overlap with coastal and Afrotemperate faunas. Coastal forests are relatively species‐rich with high species turnover. Main conclusions Afrotemperate communities were affected most by climatic extinction filtering events. Scarp forests were Afrotemperate refugia during the LGM and are a contemporary overlap zone between Afrotemperate and coastal forest. Coastal faunas derive from post‐LGM colonization along the eastern seaboard from tropical East African refugia. The greatest diversity is achieved in scarp and coastal forest faunas in northern KwaZulu–Natal province. This historical centre of diversity has influenced the faunal diversity of nearly all other forests in South Africa. The response of vertebrate taxa to large‐scale, historical processes is dependent on their relative mobility: forest birds best illustrate patterns resulting from post‐glacial faunal dispersal, while among mammals and frogs the legacy of climatic extinction filtering remains stronger.     

Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum-Mediterranean oak gallwasp Andricus quercustozae

Many studies have addressed the latitudinal gradients in intraspecific genetic diversity of European taxa generated during postglacial range expansion from southern refugia. Although Asia Minor is known to be a centre of diversity for many taxa, relatively few studies have considered its potential role as a Pleistocene refugium or a potential source for more ancient westward range expansion into Europe. Here we address these issues for an oak gallwasp, Andricus quercustozae (Hymenoptera: Cynipidae), whose distribution extends from Morocco along the northern coast of the Mediterranean through Turkey to Iran. We use sequence data for a fragment of the mitochondrial gene cytochrome b and allele frequency data for 12 polymorphic allozyme loci to answer the following questions: (1) which regions represent current centres of genetic diversity for A. quercustozae? Do eastern populations represent one refuge or several discrete glacial refugia? (2) Can we infer the timescale and sequence of the colonization processes linking current centres of diversity? Our results suggest that A. quercustozae was present in five distinct refugia (Iberia, Italy, the Balkans, southwestern Turkey and northeastern Turkey) with recent genetic exchange between Italy and Hungary. Genetic diversity is greatest in the Turkish refugia, suggesting that European populations are either (a) derived from Asia Minor, or (b) subject to more frequent population bottlenecks. Although Iberian populations show the lowest diversity for putatively selectively neutral markers, they have colonized a new oak host and represent a genetically and biologically discrete entity within the species.     

Leaf morphological variation in beech (Fagus sylvatica L.) populations in Greece and its relation to their post‐glacial origin

Diversity in leaf morphological traits was assessed in 38 Greek Fagus sylvatica populations, covering the distribution of the species in the country. The relationship between the post‐glacial origin of these populations and leaf morphology was investigated. The results showed a complex and geographically continuous morphological diversity pattern, influenced mainly by traits expressing leaf size, leaf shape and petiole length. Two simultaneous trends appeared to be responsible for the existing diversity pattern. One was geographical, with leaf types resembling F. sylvatica subsp. sylvatica occurring in the western part of the distribution of beech in Greece and types resembling F. sylvatica subsp. orientalis being dominant in the eastern part. A second trend seemed to be connected with the post‐glacial origin of the populations, as described by previous plastid DNA haplotype studies of the same trees. The genetic background and the possible adaptation of beech populations to different environmental conditions have resulted in a complex morphological pattern, especially in areas in which different post‐glacial lineages appear to meet. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 422–436.     

Ice age distributions of European small mammals: insights from species distribution modelling

Aim In addition to the traditionally recognized Last Glacial Maximum (LGM, 21 ka) refuge areas in the Mediterranean region, more northerly LGM distributions for temperate and boreal taxa in central and eastern Europe are increasingly being discussed based on palaeoecological and phylogeographical evidence. Our aim was to investigate the potential refuge locations using species distribution modelling to estimate the geographical distribution of suitable climatic conditions for selected rodent species during the LGM. Location Eurasia. Methods Presence/absence data for seven rodent species with range limits corresponding to the limits of temperate or boreal forest or arctic tundra were used in the analysis. We developed predictive distribution models based on the species present‐day European distributions and validated these against their present‐day Siberian ranges. The models with the best predictors of the species distributions across Siberia were projected onto LGM climate simulations to assess the distribution of climatically suitable areas. Results The best distribution models provided good predictions of the present‐day Siberian ranges of the study species. Their LGM projections showed that areas with a suitable LGM climate for the three temperate species (Apodemus flavicollis, Apodemus sylvaticus and Microtus arvalis) were largely restricted to the traditionally recognized southern refuge areas, i.e. mainly in the Mediterranean region, but also southernmost France and southern parts of the Russian Plain. In contrast, suitable climatic conditions for the two boreal species (Clethrionomys glareous and Microtus agrestis) were predicted as far north as southern England and across southern parts of central and eastern Europe eastwards into the Russian Plain. For the two arctic species (Lemmus lemmus and Microtus oeconomus), suitable climate was predicted from the Atlantic coast eastward across central Europe and into Russia. Main conclusions Our results support the idea of more northerly refuge areas in Europe, indicating that boreal species would have found suitable living conditions over much of southern central and eastern Europe and the Russian Plain. Temperate species would have primarily found suitable conditions in the traditional southern refuge areas, but interestingly also in much of the southern Russian Plain.     

Determinants of species richness, endemism and turnover in European longhorn beetles

This study assessed the diversity patterns of a large family of beetles, Cerambycidae, in Europe and tested the following hypotheses: 1) richness gradients of this hyperdiverse taxon are driven by water and energy variables; 2) endemism is explained by the same factors, but variation between areas also reflects post‐glacial re‐colonization processes; and 3) faunal composition is determined by the same climatic variables and, therefore, beta diversity (species turnover) is related to richness gradients. Species richness, endemism and beta diversity were modelled using inventories of 37 European territories, built from a database containing the distributions of 609 species. Area, spatial position, and nine topographical and climatic variables were used as predictors in regression and constrained analysis of principal coordinates modelling. Species richness was mostly explained by a temperature gradient, which produced a south‐to‐north decreasing richness gradient. Endemism followed the same pattern, but was also determined by longitudinal variation, peaking in the southwestern and southeastern corners of the continent. Faunal turnover was explained by an important purely spatial pattern and a spatially structured environmental gradient. Thus, contrary to other groups, cerambycid richness was mostly explained by environmental energy, but not by water availability. Endemism was concentrated in the Iberian and Greek peninsulas, but not in Italy. Thus, the latter area may have been the major source of post‐glacial re‐colonization for European longhorn beetles or, otherwise, a poor refuge during glaciations. Turnover patterns were independent of the richness gradient, because northern faunas are nested in southern ones. Turnover, in contrast to richness, was driven by both the independent effects of climate and geographic constraints that might reflect dispersal limitation or stochastic colonization events, suggesting that richness gradients are more environmentally deterministic phenomena than turnover patterns.     

A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences

Here, palaeobotanical and genetic data for common beech (Fagus sylvatica) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread. Four large datasets are presented, including over 400 fossil-pollen sites, 80 plant-macrofossil sites, and 450 and 600 modern beech populations for chloroplast and nuclear markers, respectively. The largely complementary palaeobotanical and genetic data indicate that: (i) beech survived the last glacial period in multiple refuge areas; (ii) the central European refugia were separated from the Mediterranean refugia; (iii) the Mediterranean refuges did not contribute to the colonization of central and northern Europe; (iv) some populations expanded considerably during the postglacial period, while others experienced only a limited expansion; (v) the mountain chains were not geographical barriers for beech but rather facilitated its diffusion; and (vi) the modern genetic diversity was shaped over multiple glacial-interglacial cycles. This scenario differs from many recent treatments of tree phylogeography in Europe that largely focus on the last ice age and the postglacial period to interpret genetic structure and argue that the southern peninsulas (Iberian, Italian and Balkan) were the main source areas for trees in central and northern Europe.     

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.     

Glacial refugia of mammals in Europe: evidence from fossil records

• 1 Glacial refugia were core areas for the survival of temperate species during unfavourable environmental conditions and were the sources of postglacial recolonizations. Unfortunately, the locations of glacial refugia of animals and plants are usually described by models, without reference to facts about real geographical ranges at that time.
• 2 Careful consideration of the faunal assemblages of archaeological sites from the Younger Palaeolithic, which are precisely dated to the Last Glacial Maximum (LGM), gives indications about the distribution of species during the LGM (23 000–16 000 bp ) and provides evidence for the locations of glacial refugia for mammalian species in Europe.
• 3 In Europe, 47 LGM sites, dating from 23 000 to 16 000 bp and containing typical temperate mammal species, have been described. The geographical range of these archaeological sites clearly shows a distribution which differs from the hypothesized traditional refuge areas of the temperate fauna. A considerable number of sites situated in the Dordogne in south‐western France and the Carpathian region contain records of red deer Cervus elaphus, roe deer Capreolus capreolus, wild boar Sus scrofa and red fox Vulpes vulpes.
• 4 The faunal composition of the majority of the evaluated Palaeolithic sites in the southern European peninsulas (with the exception of Greece), as well as France and the Carpathian region, indicates the co‐occurrence of these temperate species with cold‐adapted faunal elements such as mammoth Mammuthus primigenius and/or reindeer Rangifer tarandus.
• 5 The survival of species in Central European refugia would have significant consequences for phylogeography and would be revealed by the dominant distribution of haplotypes, originating from this region. A Carpathian refuge could also be the reason for the very early records of small mammals or mustelids from the Late‐Glacial or Interstadials before the LGM in regions like southern Germany.

     

Northern richness and southern poverty: contrasting genetic footprints of glacial refugia in the relictual tree Sciadopitys verticillata (Coniferales: Sciadopityaceae)

Sciadopitys verticillata is amongst the most relictual of all plants, being the last living member of an ancient conifer lineage, the Sciadopityaceae, and is distributed in small and disjunct populations in high rainfall regions of Japan. Although mega‐fossils indicate the persistence of the species within Japan through the Pleistocene glacial–interglacial cycles, how the species withstood the colder and drier climates of the glacials is not well known. The present study utilized phylogeography and palaeodistribution modelling to test whether the species survived within pollen‐based coastal temperate forest glacial refugia or within previously unidentified refugia close to its current range. Sixteen chloroplast haplotypes were found that displayed significant geographical structuring. Unexpectedly, northern populations in central Honshu most distant from coastal refugia had the highest chloroplast diversity and were differentiated from the south, a legacy of glacial populations possibly in inland river valleys close to its current northern range. By contrast, populations near putative coastal refugia in southern Japan, harboured the lower chloroplast diversity and were dominated by a single haplotype. Fragment size polymorphism at a highly variable and homoplasious mononucleotide repeat region in the trnT‐trnL intergenic spacer reinforced the contrasting patterns of diversity observed between northern and southern populations. The divergent histories of northern and southern populations revealed in the present study will inform the management of this globally significant conifer. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 108 , 263–277.     

Molecular markers provide evidence for a broad‐fronted recolonisation of the widespread calcareous grassland species Sanguisorba minor from southern and cryptic northern refugia

• Calcareous grasslands belong to the most species‐rich and endangered habitats in Europe. However, little is known about the origin of the species typically occurring in these grasslands. In this study we analysed the glacial and post‐glacial history of Sanguisorba minor, a typical plant species frequently occurring in calcareous grasslands.
• The study comprised 38 populations throughout the whole distribution range of the species across Europe. We used molecular markers (AFLP) and applied Bayesian cluster analysis as well as spatial principal components analysis (sPCA) to identify glacial refugia and post‐glacial migration routes to Central Europe.
• Our study revealed significant differences in the level of genetic variation and the occurrence of rare fragments within populations of S. minor and a distinct separation of eastern and western lineages. The analyses uncovered traditional southern but also cryptic northern refugia and point towards a broad fronted post‐glacial recolonisation.
• Based on these results we postulate that incomplete lineage sorting may have contributed to the detected pattern of genetic variation and that S. minor recolonised Central Europe post‐glacially from Iberia and northern glacial refugia in France, Belgium or Germany. Our results highlight the importance of refugial areas for the conservation of intraspecific variation in calcareous grassland species.

     

The legacy of ice ages in mountain species: post‐glacial colonization of mountain tops rather than current range fragmentation determines mitochondrial genetic diversity in an endemic Pyrenean rock lizard

Aim The genetic impact of Quaternary climatic fluctuations on mountain endemic species has rarely been investigated. The Pyrenean rock lizard (Iberolacerta bonnali) is restricted to alpine habitats in the Pyrenees where it exhibits a highly fragmented distribution between massifs and between habitats within massifs. Using mitochondrial DNA markers, we set out: (1) to test whether several evolutionary units exist within the species; (2) to understand how the species persisted through the Last Glacial Maximum and whether the current range fragmentation originates from distribution shifts after the Last Glacial Maximum or from more ancient events; and (3) to investigate whether current mitochondrial diversity reflects past population history or current habitat fragmentation. Location The Pyrenees in south‐western France and northern Spain. Methods We used variation in the hypervariable left domain of the mitochondrial control region of 146 lizards collected in 15 localities, supplemented by cytochrome b sequences downloaded from GenBank to cover most of the species’ distribution range. Measures of population genetic diversity were contrasted with population isolation inferred from topography. Classical (F‐statistics) and coalescence‐based methods were used to assess the level of gene flow and estimate divergence time between populations. We used coalescence‐based simulations to test the congruence of our genetic data with a scenario of simultaneous divergence of current populations. Results Coalescence‐based analyses suggested that these peripheral populations diverged simultaneously at the end of the last glacial episode when their habitats became isolated on mountain summits. High mitochondrial diversity was found in peripheral, isolated populations, while the populations from the core of the species’ range were genetically impoverished. Where mitochondrial diversity has been retained, populations within the same massif exhibited high levels of genetic differentiation. Main conclusions As suggested for many other mountain species, the Pyrenean rock lizard survived glacial maxima through short‐distance range shifts instead of migration or contraction in distant southern refugia. Most of the main Pyrenean range has apparently been re‐colonized from a single or a few source populations, resulting in a loss of genetic diversity in re‐colonized areas. As a result, current levels of intra‐population mitochondrial diversity are better explained by post‐glacial population history than by current habitat fragmentation. Genetic population differentiation within massifs implies severe reduction in female‐mediated gene flow between patches of habitats.     

Species persistence in northerly glacial refugia of Europe: a matter of chance or biogeographical traits?

Aim The southern European peninsulas (Iberian, Italian and Balkan) are considered to have been refugia for many European species of plants and animals during the climatic extremes of the Pleistocene ice ages. A number of recent studies (fossil and genetic), however, have provided evidence for full‐glacial survival of some species beyond these peninsulas. Here we explore the biogeographical traits of these species, and ask whether they possessed certain characteristics that enabled them to persist in more northerly refugia. Location Europe. Methods Fossil and genetic evidence for refugial localities of species that survived in Europe during the last full‐glacial was obtained from the literature (totalling 90 species: 34 woody plants and 56 vertebrates). Forty‐seven of these species (23 woody plants and 24 vertebrates) had fossil evidence, whereas the remaining 43 species (11 woody plants and 32 vertebrates) had only genetic evidence. All species were scored according to their present geographical distribution, habitat preference and life‐history traits. The species were classified on the basis of these traits using hierarchical cluster analysis. Analysis of similarities was used to examine differences in vertebrate and woody plant species groups that survived only in southerly refugia and those that also persisted in more northerly locations. Non‐metric multi‐dimensional scaling was used to examine patterns observed between and within groups. Results Results from our analysis of species with fossil and genetic evidence for survival in refugia reveal that species that survived only in southerly refugia were large‐seeded trees or thermophilous vertebrates. In contrast, species that had a full‐glacial distribution, including more northerly locations, were wind‐dispersed, habitat‐generalist trees with the ability to reproduce vegetatively, and habitat‐generalist mammals with present‐day northerly distributions. Main conclusions Analysis of the geographical distribution, habitat preference and life‐history traits of the species studied suggests that underlying biogeographical traits may have determined their response to Pleistocene glaciation. The traits most commonly found in present populations with a northerly distribution in Europe enabled the same species to exist much farther north than the southern European peninsulas during the full‐glacial. It is possible that many of these species are now in restricted populations, within the ‘warm‐stage’ refugia of the current interglacial. The northerly full‐glacial survival of a number of woody plants and vertebrate species has significant implications for understanding migration rates of these species in response to climate change. It also has important implications for understanding current patterns of genetic diversity of European species. We suggest that both fossil and genetic evidence should be used to identify and prioritize for conservation of refugial localities in southern and northern Europe.