Velocity of climate change algorithms for guiding conservation and management

The velocity of climate change is an elegant analytical concept that can be used to evaluate the exposure of organisms to climate change. In essence, one divides the rate of climate change by the rate of spatial climate variability to obtain a speed at which species must migrate over the surface of the earth to maintain constant climate conditions. However, to apply the algorithm for conservation and management purposes, additional information is needed to improve realism at local scales. For example, destination information is needed to ensure that vectors describing speed and direction of required migration do not point toward a climatic cul‐de‐sac by pointing beyond mountain tops. Here, we present an analytical approach that conforms to standard velocity algorithms if climate equivalents are nearby. Otherwise, the algorithm extends the search for climate refugia, which can be expanded to search for multivariate climate matches. With source and destination information available, forward and backward velocities can be calculated allowing useful inferences about conservation of species (present‐to‐future velocities) and management of species populations (future‐to‐present velocities).     

Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe

The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic–continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range‐wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial–interglacial dynamic. The EGS is a steppe‐inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial–interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.     

Has past climate change affected cold‐specialized species differentially through space and time?

Quaternary climate change has been strongly linked to distributional shifts and recent species diversification. Montane species, in particular, have experienced enhanced isolation and rapid genetic divergence during glacial fluctuations, and these processes have resulted in a disproportionate number of neo‐endemic species forming in high‐elevation habitats. In temperate montane environments, a general model of alpine population history is well supported, where cold‐specialized species track favourable climate conditions downslope during glacial episodes and upslope during warmer interglacial periods, which leads to a climate‐driven population or species diversification pump. However, it remains unclear how geography mediates distributional changes and whether certain episodes of glacial history have differentially impacted rates of diversification. We address these questions by examining phylogenomic data in a North American clade of flightless, cold‐specialized insects, the ice crawlers (Insecta: Grylloblattodea: Grylloblattidae: Grylloblatta). These low‐vagility organisms have the potential to reveal highly localized refugia and patterns of spatial recolonization, as well as a longer history of in situ diversification. Using continuous phylogeographic analysis of species groups, we show that all species tend to retreat to nearby low‐elevation habitats across western North America during episodes of glaciation, but species at high latitude exhibit larger distributional shifts. Lineage diversification was examined over the course of the Neogene and Quaternary periods, with statistical analysis supporting a direct association between climate variation and diversification rate. Major increases in lineage diversification appear to be correlated with warm and dry periods, rather than with extreme glacial events. Finally, we identify substantial cryptic diversity among ice crawlers, leading to high endemism across their range. This diversity provides new insights into highly localized glacial refugia for cold‐specialized species across western North America.     

The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate‐driven vicariant diversification across an island archipelago

A primary goal of biogeography is to understand how large‐scale environmental processes, like climate change, affect diversification. One often‐invoked but seldom tested process is the “species‐pump” model, in which repeated bouts of cospeciation are driven by oscillating climate‐induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea‐level changes associated with glacial cycles. This repeated climate‐driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full‐likelihood, Bayesian model‐choice framework to test for shared divergence times among the pairs. Our results provide support against the species‐pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate‐driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago.     

Quaternary refugia are associated with higher speciation rates in mammalian faunas of the Western Palaearctic

Quaternary climate changes have contributed to shape the biogeographic distribution of extant species. The combination of climatic niche conservatism and glacial‐interglacial cycles forced many species to retract their range limits for surviving under the advance of Pleistocene ice‐sheets. Refugia offered geographical opportunities for species to retreat, persist and, later on, begin recolonization processes under favourable environmental conditions. Here we explore the hypothesis that refugia have been not only crucial for the survival of multiple species but also acted as speciation centres for Western Palaearctic mammals. We define ‘recurrent massive refugia’ as those geographical regions that have historically accumulated the highest levels of co‐occurring species for several Quaternary cycles. Our assemblage‐level analyses identify the existence of refugia within the Iberian Peninsula and the Atlantic French margin that were recurrently selected by most mammals. The topographic heterogeneity, climatic stability and microhabitat availability of these refugial areas may have offered suitable habitat conditions for multiple species during different climatic events over time. Using a Bayesian analysis of macroevolutionary mixtures we detected that the higher level of divergence and accumulative evolutionary changes in mammals of the Western Palaearctic are found in refugia. The continuous retractions and expansions of species’ ranges during the Pleistocene promoted temporal changes in the composition and richness of communities in this biogeographic region. The reorganization of ecological composition driven by cyclical climatic events may have favoured the emergence of biotic interactions and ecological responses conducive to novel selective pressures. Our findings suggest, first, that multiple climatic changes in the form of glacial‐interglacial transitions during the Quaternary have left a detectable imprint on the observed geographical patterns of species richness in mammalian faunas of the Western Palaearctic, and second, highlight the importance of refugia for the preservation of species (‘museums’) and as centers of speciation and endemism (‘cradles’) as well.     

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

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

CLIMATE‐DRIVEN DIVERSIFICATION AND PLEISTOCENE REFUGIA IN PHILIPPINE BIRDS: EVIDENCE FROM PHYLOGEOGRAPHIC STRUCTURE AND PALEOENVIRONMENTAL NICHE MODELING

Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current‐day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep‐water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long‐term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate‐induced refugia acted in concert to produce great species diversity and endemism in the Philippines.     

Genetic consequences of interglacial isolation in a steppe bird

In response to climate changes that have occurred during Pleistocene glacial cycles, taxa associated to steppe vegetation might have followed a pattern of historical evolution in which isolation and fragmentation of populations occurred during the short interglacials and expansion events occurred during the long glacial periods, in contrast to the pattern described for temperate species. Here, we use molecular genetic data to evaluate this idea in a steppe bird with Palaearctic distribution, the little bustard (Tetrax tetrax). Overall, extremely low genetic diversity and differentiation was observed among eight little bustard populations distributed in Spain and France. Mismatch distribution analyses showed that most little bustard populations expanded during cooling periods previous to, and just after, the last interglacial period (127,000-111,000 years before present), when steppe habitats were widespread across Europe. Coalescent-based methods suggested that glacial expansions have resulted in substantial admixture in Western Europe due to the existence of different interglacial refugia. Our results are consistent with a model of evolution and genetic consequences of Pleistocene cycles with low between-population genetic differentiation as a result of short-term isolation periods during interglacials and long-term exchange during glacial periods.     

Glacial and interglacial refugia within a long-term rainforest refugium: The Wet Tropics Bioregion of NE Queensland, Australia

An artificial neural network is used to classify environments, including climate, terrain and soil variables, according to their suitability for fifteen structural/environmental forest classes in the Wet Tropics Bioregion of north-east Queensland. We map the environments characteristic of these forest classes in four climate regimes (the present and three past climate scenarios), quantify the changes in area of these environments in response to past regional changes in climate and identify areas that would have been environmentally suitable for rainforests at last glacial maximum (glacial refugia). We also identify areas that would have been suitable for upland and highland rainforest classes during the warmest parts of the interglacial (interglacial refugia) and map locations that consistently remain favourable to specific forest classes despite large changes in climate.In the climate of the last glacial maximum (LGM), rainforest environments are predicted in three relatively distinct refugia in the northern, central and southern Wet Tropics. Only three percent of the total area contains lowland, Mesophyll Vine Forest and the majority of the area of the rainforest refugia supports upland rainforest classes. In the cool, wet climate of the Pleistocene/Holocene transition (PHT), rainforest environments expand to form a more or less continuous block from the northern limits of the region to the Walter Hill Range, except for discontinuous patches extending through the Seaview and Paluma Ranges in the south. During the Holocene climatic optimum (HCO), rainforest environments become more fragmented, especially in the south. Lowland rainforest environments are very extensive in this climate while upland rainforest classes are restricted to what we term “interglacial refugia”.Estimated distributions and stable locations (consistently predicted in all four climate scenarios) for the various rainforest environment classes are our main, novel contribution. Each forest environment responds individualistically to climate change. Our results confirm the highly dynamic nature of the Wet Tropics landscape and present a much more detailed picture of landscape change since the late Pleistocene than previously has been available. This mapping exercise should be useful in the future for analyses of present-day biogeographic patterns. We argue that empirical modelling approaches have an important role in palaeoecology and global change research that is complementary to the developing mechanistic methods.     

Projected climate changes threaten ancient refugia of kelp forests in the North Atlantic

Intraspecific genetic variability is critical for species adaptation and evolution and yet it is generally overlooked in projections of the biological consequences of climate change. We ask whether ongoing climate changes can cause the loss of important gene pools from North Atlantic relict kelp forests that persisted over glacial–interglacial cycles. We use ecological niche modelling to predict genetic diversity hotspots for eight species of large brown algae with different thermal tolerances (Arctic to warm temperate), estimated as regions of persistence throughout the Last Glacial Maximum (20,000 YBP), the warmer Mid‐Holocene (6,000 YBP), and the present. Changes in the genetic diversity within ancient refugia were projected for the future (year 2100) under two contrasting climate change scenarios (RCP2.6 and RCP8.5). Models predicted distributions that matched empirical distributions in cross‐validation, and identified distinct refugia at the low latitude ranges, which largely coincide among species with similar ecological niches. Transferred models into the future projected polewards expansions and substantial range losses in lower latitudes, where richer gene pools are expected (in Nova Scotia and Iberia for cold affinity species and Gibraltar, Alboran, and Morocco for warm‐temperate species). These effects were projected for both scenarios but were intensified under the extreme RCP8.5 scenario, with the complete borealization (circum‐Arctic colonization) of kelp forests, the redistribution of the biogeographical transitional zones of the North Atlantic, and the erosion of global gene pools across all species. As the geographic distribution of genetic variability is unknown for most marine species, our results represent a baseline for identification of locations potentially rich in unique phylogeographic lineages that are also climatic relics in threat of disappearing.     

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.     

Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica

Climate warming is predicted to increase the frequency of invasions by pathogens and to cause the large-scale redistribution of native host species, with dramatic consequences on the health of domesticated and wild populations of plants and animals. The study of historic range shifts in response to climate change, such as during interglacial cycles, can help in the prediction of the routes and dynamics of infectious diseases during the impending ecosystem changes. Here we studied the population structure in Europe of two Microbotryum species causing anther smut disease on the plants Silene latifolia and Silene dioica. Clustering analyses revealed the existence of genetically distinct groups for the pathogen on S. latifolia, providing a clear-cut example of European phylogeography reflecting recolonization from southern refugia after glaciation. The pathogen genetic structure was congruent with the genetic structure of its host species S. latifolia, suggesting dependence of the migration pathway of the anther smut fungus on its host. The fungus, however, appeared to have persisted in more numerous and smaller refugia than its host and to have experienced fewer events of large-scale dispersal. The anther smut pathogen on S. dioica also showed a strong phylogeographic structure that might be related to more northern glacial refugia. Differences in host ecology probably played a role in these differences in the pathogen population structure. Very high selfing rates were inferred in both fungal species, explaining the low levels of admixture between the genetic clusters. The systems studied here indicate that migration patterns caused by climate change can be expected to include pathogen invasions that follow the redistribution of their host species at continental scales, but also that the recolonization by pathogens is not simply a mirror of their hosts, even for obligate biotrophs, and that the ecology of hosts and pathogen mating systems likely affects recolonization patterns.     

Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains

Climate change during the Quaternary played an important role in the differentiation and evolution of plants. A prevailing hypothesis is that alpine and arctic species survived glacial periods in refugia at the periphery of glaciers. Though the Rocky Mountains, south of the southernmost extent of continental ice, served as an important glacial refuge, little is known about how climate cycles influenced populations within this region. We inferred the phylogeography of Sedum lanceolatum (Crassulaceae) within the Rocky Mountain refugium to assess how this high-elevation plant responded to glacial cycles. We sequenced 884 base pairs (bp) of cpDNA intergenic spacers (tRNA-L to tRNA-F and tRNA-S to tRNA-G) for 333 individuals from 18 alpine populations. Our highly variable markers allowed us to infer that populations persisted across the latitudinal range throughout the climate cycles, exhibited significant genetic structure, and experienced cycles of range expansion and fragmentation. Genetic differentiation in S. lanceolatum was most likely a product of short-distance elevational migration in response to climate change, low seed dispersal, and vegetative reproduction. To the extent that Sedum is a good model system, paleoclimatic cycles were probably a major factor preserving genetic variation and promoting divergence in high-elevation flora of the Rocky Mountains.     

The effects of the Late Quaternary glacial–interglacial cycles on Anatolian ground squirrels: range expansion during the glacial periods?

The present study aimed to understand how Anatolian ground squirrels, Spermophilus xanthoprymnus (Bennett, 1835), have responded to global climate changes through the Late Quaternary glacial–interglacial cycles. Accordingly, ecological niche modelling was used, together with molecular phylogeography. Using species occurrence data compiled from field observations and relevant sources and the maximum entropy machine learning algorithm in MAXENT, an ecological niche model was developed to predict the potential geographical distribution of S. xanthoprymnus under reconstructed past (the Last Interglacial, approximately 130 000–116 000 years ago and the Last Glacial Maximum, 21 000 years ago) and present (1950–2000) bioclimatic conditions. In addition, using cytochrome b mitochondrial DNA sequences deposited in GenBank and the Bayesian skyline plot in BEAST, demographic events (population fluctuations) were further assessed over the history of Anatolian ground squirrels. Combined ecological niche modelling and molecular phylogeography revealed that S. xanthoprymnus, itself also a temperate (mid‐latitude) species, has responded to global climate changes through the Late Quaternary glacial–interglacial cycles in a fashion converse to that of most temperate (mid‐latitude) species: its range expanded rather than contracted during the glacial periods and contracted rather than expanded during the interglacial periods. In other words, Anatolian ground squirrels have been in refugia during the interglacial periods, suggesting that the classical paradigm of glacial range contraction and interglacial range expansion for temperate species may not be as general as previously assumed. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 19–32.     

Interglacial genetic diversification of Moussonia deppeana (Gesneriaceae), a hummingbird‐pollinated,cloud forest shrub in northern Mesoamerica

Recent empirical work on cloud forest‐adapted species supports the role of both old divergences across major geographical areas and more recent divergences attributed to Pleistocene climate changes. The shrub Moussonia deppeana is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling throughout the species range and employing plastid and nuclear markers, we (i) test whether the fragmented distribution is correlated with main evolutionary lineages, (ii) reconstruct its phylogeographical history to infer the history of cloud forest in northern Mesoamerica and (iii) evaluate a set of refugia/vicariance scenarios for the region and demographic patterns of the populations whose ranges expanded and tracked cloud forest conditions during the Last Glacial Maximum. We found a deep evolutionary split in M. deppeana about 6–3 Ma, which could be consistent with a Pliocene divergence. Comparison of variation in plastid and nuclear markers revealed several lineages mostly congruent with their isolated geographical distribution and restricted gene flow among groups. Results of species distribution modelling and coalescent simulations fit a model of multiple refugia diverging during interglacial cycles. The demographic history of M. deppeana is not consistent with an expanding–contracting cloud forest archipelago model during the Last Glacial Maximum. Instead, our data suggest that populations persisted across the geographical range throughout the glacial cycles, and experienced isolation and divergence during interglacial periods.     

The integration of multiple independent data reveals an unusual response to Pleistocene climatic changes in the hard tick Ixodes ricinus

In the last few years, improved analytical tools and the integration of genetic data with multiple sources of information have shown that temperate species exhibited more complex responses to ice ages than previously thought. In this study, we investigated how Pleistocene climatic changes affected the current distribution and genetic diversity of European populations of the tick Ixodes ricinus, an ectoparasite with high ecological plasticity. We first used mitochondrial and nuclear genetic markers to investigate the phylogeographic structure of the species and its Pleistocene history using coalescent‐based methods; then we used species distribution modelling to infer the climatic niche of the species at last glacial maximum; finally, we reviewed the literature on the I. ricinus hosts to identify the locations of their glacial refugia. Our results support the scenario that during the last glacial phase, I. ricinus never experienced a prolonged allopatric divergence in separate glacial refugia, but persisted with interconnected populations across Southern and Central Europe. The generalist behaviour in host choice of I. ricinus would have played a major role in maintaining connections between its populations. Although most of the hosts persisted in separate refugia, from the point of view of I. ricinus, they represented a continuity of ‘bridges’ among populations. Our study highlights the importance of species‐specific ecology in affecting responses to Pleistocene glacial–interglacial cycles. Together with other cases in Europe and elsewhere, it contributes to setting new hypotheses on how species with wide ecological plasticity coped with Pleistocene climatic changes.     

Identifying refugia from climate change

This article highlights how the loose definition of the term ‘refugia’ has led to discrepancies in methods used to assess the vulnerability of species to the current trend of rising global temperatures. The term ‘refugia’ is commonly used without distinguishing between macrorefugia and microrefugia, ex situ refugia and in situ refugia, glacial and interglacial refugia or refugia based on habitat stability and refugia based on climatic stability. It is not always clear which definition is being used, and this makes it difficult to assess the appropriateness of the methods employed. For example, it is crucial to develop accurate fine‐scale climate grids when identifying microrefugia, but coarse‐scale macroclimate might be adequate for determining macrorefugia. Similarly, identifying in situ refugia might be more appropriate for species with poor dispersal ability but this may overestimate the extinction risk for good dispersers. More care needs to be taken to properly define the context when referring to refugia from climate change so that the validity of methods and the conservation significance of refugia can be assessed.     

Postglacial colonization of Europe by the barbastelle bat: agreement between molecular data and past predictive modelling

The barbastelle (Barbastella barbastellus) is a rare forest bat with a wide distribution in Europe. Here, we combine results from the analysis of two mtDNA fragments with species distribution modelling to determine glacial refugia and postglacial colonization routes. We also investigated whether niche conservatism occurs in this species. Glacial refugia were identified in the three southern European peninsulas: Iberia, Italy and the Balkans. These latter two refugia played a major role in the postglacial colonization process, with their populations expanding to England and central Europe, respectively. Palaeo‐distribution models predicted that suitable climatic conditions existed in the inferred refugia during the last glacial maximum (LGM). Nevertheless, the overlap between the current and the LGM distributions was almost inexistent in Italy and in the Balkans, meaning that B. barbastellus populations were forced to shift range between glacial and interglacial periods, a process that probably caused some local extinctions. In contrast, Iberian populations showed a ‘refugia within refugium’ pattern, with two unconnected areas containing stable populations (populations that subsisted during both glacial and interglacial phases). Moreover, the match between LGM models and the refugial areas determined by molecular analysis supported the hypothesis of niche conservatism in B. barbastellus. We argue that geographic patterns of genetic structuring, altogether with the modelling results, indicate the existence of four management units for conservation: Morocco, Iberia, Italy and UK, and Balkans and central Europe. In addition, all countries sampled possessed unique gene pools, thus stressing the need for the conservation of local populations.     

Long‐term in situ persistence of biodiversity in tropical sky islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long‐term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high‐elevation plant species from an archipelago of tropical sky islands (the Trans‐Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.     

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.