Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences

The present study explores the utility of mitochondrial COI gene sequences to reveal phylogenetic and phylogeographic relationships for the entire European freshwater crayfish genus Austropotamobius. The two traditional taxa, Austropotamobius pallipes and Austropotamobius torrentium, were monophyletic, showing similar genetic diversity, with 28 and 25 haplotypes, respectively, and an uncorrected average pairwise divergence of 0.059 and 0.041. A third distinct haplotype clade, in sister relation to A. torrentium, was discovered at the Upper Kolpa drainage in the northern Dinaric area. All populations north and west of the Alps are genetically impoverished (nucleotide diversity (pi)=0.000-0.001), while southern populations are more diverse (pi=0.001-0.034). A. pallipes reaches the highest diversity in the region of Istra, probably its primary center of radiation. The genetic diversity center for A. torrentium is the southern Balkan peninsula. Other potential glacial refugia were identified in Southern France, Northwestern Italy, the Apennine Peninsula, and in the northern Dinaric area. The Iberian Peninsula has been stocked artificially from Northern Italy. Three main periods of radiation were tentatively identified: late Miocene/early Pliocene for the divergence of species and main lineages, the Pleistocene for the divergence within populations south from Alps, and a postPleistocene expansion north and west from Alps.     

Haplotype richness in refugial areas: phylogeographical structure of <Emphasis Type="Italic">Saxifraga callosa</Emphasis>

This paper illustrates the phylogeographical structure of Saxifraga callosa in order to describe its genetic richness in refugial areas and to reconstruct its glacial history. S. callosa is a species spread throughout south-east France and Italy with a high distribution in the Maritime Alps. Four chloroplast microsatellite and AFLP markers were analyzed in populations of S. callosa. The size variants of all tested loci amount to 11 different haplotypes. Intrapopulational haplotype variation was found in two of the populations analyzed: on the Mt. Toraggio in the Maritime Alps, and in the Apuan Alps. On the other hand, no intrapopulational variation was found in 25 populations, most of which were sampled from isolated areas. Analysis of the haplotype distribution showed that population subdivision across all populations was high (G _ST = 0.899). Moreover, its genetic structure was studied using AMOVA and STRUCTURE analysis. The study legitimated inferred conclusions about the phylogeographical structure of the species and identified centers of diversity. Considerations concerning genetic structure and divergence among three major clades (Maritime Alps, Apuan Alps and Apennines), the patchy distribution of haplotypes, and the high number of private haplotypes support the proposal that S. callosa survived in some refugia within the Italian Peninsula refugium, and that mainly northern populations of refugia were involved in postglacial recolonization.     

Differentiation among Austrian populations of Norway spruce [Picea abies (L.) Karst.] assayed by mitochondrial DNA markers

Thirty-seven populations of Norway spruce [Picea abies (L.) Karst.] across the Austrian Alps and Bohemian Massif were sampled to elucidate the geographical pattern of genetic differentiation. Three polymorphic mitochondrial DNA (mtDNA) loci were surveyed. Two or three alleles were detected at each locus, resulting in seven multilocus mtDNA haplotypes (A–F). Western populations proved to be monomorphic, whereas eastern and central Austrian populations were slightly to highly polymorphic, respectively. As revealed by spatial analysis of molecular variance and Monmonier’s analysis, the two main haplotypes A and B are not randomly distributed. Haplotype A was restricted to central and eastern Austria, whereas haplotype B occurred in all Austrian populations but was the only haplotype identified in western populations. This pattern may be explained by different glacial refugia located in the Dinaric Alps and the Carpathian mountains.     

Geographically congruent large‐scale patterns of plastid haplotype variation in the European herbs Silene dioica and S. latifolia (Caryophyllaceae)

The closely related dioecious herbs Silene latifolia and Silene dioica are widespread and predominantly sympatric in Europe. The species are interfertile, but morphologically and ecologically distinct. A study of large‐scale patterns of plastid DNA (polymerase chain reaction–restriction fragment length polymorphism) haplotypes in a sample of 198 populations from most of the European ranges of both species revealed extensive interspecific haplotype sharing. Four of the 28 detected haplotypes were frequent (found in > 40 populations) and widespread. Three of these frequent haplotypes occurred in both species and the geographic distribution of each haplotype was broadly congruent in both species. Each of these three, shared and widespread haplotypes is likely to have colonized central and/or northern Europe after the last glaciation from one or more of refugial areas in southern Europe. Interspecific hybridization and plastid introgression within refugial regions and/or during the early stages of postglacial expansion is the most plausible explanation for the broadly similar distribution patterns of the shared, frequent chloroplast haplotypes in the two species. The fourth frequent, widespread haplotype was absent from S. latifolia and almost entirely restricted to Nordic S. dioica. It is most likely that this haplotype spread into the Nordic countries from a central or northern European source or from a refugial area in Russia. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 153–170.     

Geographic distribution of chloroplast variation in Italian populations of beech (<Emphasis Type="Italic">Fagus sylvatica</Emphasis> L.)

The distribution of chloroplast DNA (cpDNA) variation in Italian beech (Fagus sylvatica L.) populations was studied using PCR-RFLP and microsatellite markers. In total, 67 populations were analysed, and 14 haplotypes were identified by combining the two marker types. A remarkable subdivision of cpDNA diversity in Italian beech was found, as indicated by a high level of genetic differentiation (G_st=0.855). The highest level of total haplotype diversity (h_t=0.822) was estimated for southern Italian populations. The highest number of haplotypes was found in the central-southern region of the peninsula. The nested clade analysis provided evidence for past fragmentation events that may have been occurred during the Quaternary glaciations and had a major role in defining the genetic structure of the central-southern Italian beech populations. Only one haplotype apparently spread towards the north of Italy along the Apennine chain and reached the Italian slope of the western part of the Alps (Maritime Alps, Liguria). All haplotypes found along the Apennines remained trapped in the Italian peninsula. Southern and central Italy represent hotspots of haplotype diversity for Italian beech.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by O. Savolainen     

Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host

The phylogeography of the bark beetle Ips typographus was assessed using five microsatellite markers. Twenty-eight populations were sampled throughout Europe on the host tree Picea abies . I. typographus showed very low levels of genetic diversity, and the study revealed a lack of genetic structure across Europe. No significant barrier to gene flow was found, even though P. abies has a fragmented distribution. A weak but significant effect of isolation by distance was found. These results suggest a high dispersal capacity of I. typographus , which leads to low genetic differentiation between populations. Its high dispersal capacity is likely to have prevented I. typographus from developing important local adaptations to its host, which would have influenced its genetic structure. The nuclear data was compared to previously published mitochondrial data that showed strong differentiation between Central–Northern European populations and Russian–Baltic populations, and a founder effect in Scandinavia, probably reflecting the postglacial history of I. typographus . Discrepancies between nuclear and mitochondrial markers could be due to the maternal inheritance of mitochondrial DNA, and to sex-biased dispersal in I. typographus . The overall low genetic diversity observed on both markers on a large geographical scale is discussed. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 239–246.     

Conservation genetics of small relic populations of silver fir (Abies alba Mill.) in the northern Apennines

Abstract

Small and isolated silver fir populations from the Emilian Apennines (northern Italy) were studied to assess their level of genetic variation and their relationship with Alpine populations. We investigated the variability of two chloroplast microsatellites to analyse the within‐population genetic variability of four peripheral and fragmented Apennine populations and to determine their phylogenetic relatedness to seven Alpine populations covering the entire distribution of silver fir in the Alps. Haplotypic richness and haplotype diversity as well as the fraction of private haplotypes were lower in Apennine populations, evidencing the genetic impoverishment of these stands. The among‐population genetic variability analysis revealed the genetic peculiarity of Apennine populations. Analysis of molecular variance showed that the highest level of the among‐population variation occurs between Alpine and Apennine regions. A neighbour‐joining dendrogram revealed a distinct Apennine cluster that included the closest Alpine population. Our genetic analysis supports a common origin for Emilian Apennine populations, suggesting that these populations are relicts of past large silver fir populations in the northern Apennines. Our results point to a relevant conservation value for these stands, to be considered in their management.     

Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations

Intraspecific phylogeographical patterns largely depend on the life history traits of a species. Especially species with a high degree of cold tolerance, limited requirements towards habitat preferences, and relatively low active dispersal capacities may have responded in a different way to the Pleistocene climatological fluctuations than the majority of taxa studied so far. To evaluate this possibility, we studied Arion fuscus (Muller, 1774), a common and widespread European terrestrial slug, from 88 locations (N = 964). Sequence variation was assessed for fragments of the mitochondrial 16S rDNA and COI genes by means of single-strand conformation polymorphisms (SSCP) and subsequent DNA sequencing. Additionally, eight allozyme loci were scored in 843 individuals. Phylogenetic analysis revealed the presence of two major evolutionary lineages, one in the Balkan region and another in the Alps and the rest of Europe. The sequence divergence between the two lineages was limited (3.3%), but gene flow between the regions was absent, suggesting that the two regions have been isolated since the late Pliocene or early Pleistocene. Allozyme differentiation among geographical regions and mitochondrial DNA (mtDNA) lineages was low. The geographical patterns observed in our data showed that (i) haplotype and nucleotide diversities are very low in northern Europe, suggesting that single haplotypes rapidly colonized large areas; (ii) recently expanded haplotype clades have restricted distribution ranges, suggesting that current gene flow is low; and (iii) genetic diversity in the Alps is much higher than in other regions and estimated past gene flow from the Eastern Alps to other regions was high, suggesting that this was a refugial zone during the Pleistocene. This full-range phylogeography suggests the existence of an alternative refugial zone, situated north of the refugial areas currently recognized in most other taxa.     

Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent‐wide lineage admixture

Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent‐wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear‐edge populations in the Mediterranean region more vulnerable to extinction due to climate change.     

Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpina

Our data on the intercontinental population biology of Letharia vulpina show an unexpected shift from a recombining North American population with unique haplotypes to genetically depauperate Swedish and Italian populations, each with many representatives of a single repeated haplotype. Analysis of eight loci in 47 individuals supported recombination in North American populations and showed almost no variation among European populations. We infer that a genetic bottleneck caused by limited long-distance dispersal accounts for the lack of genetic variation found in marginal populations. This lack of variation in the European populations makes it impossible to use population genetic means to distinguish clonal reproduction from self-fertilization or even outcrossing, but phenotype indicates that reproduction in the marginal populations is by clonal spread, via soredia and isidioid soredia.     

Inducibility of chemical defenses in Norway spruce bark is correlated with unsuccessful mass attacks by the spruce bark beetle

Secondary attraction to aggregation pheromones plays a central role in the host colonization behavior of the European spruce bark beetle Ips typographus. However, it is largely unknown how the beetles pioneering an attack locate suitable host trees, and eventually accept or reject them. To find possible biomarkers for host choice by I. typographus, we analyzed the chemistry of 58 Norway spruce (Picea abies) trees that were subsequently either (1) successfully attacked and killed, (2) unsuccessfully attacked, or (3) left unattacked. The trees were sampled before the main beetle flight in a natural Norway spruce-dominated forest. No pheromones were used to attract beetles to the experimental trees. To test the trees' defense potential, each tree was treated in a local area with the defense hormone methyl jasmonate (MeJ), and treated and untreated bark were analyzed for 66 different compounds, including terpenes, phenolics and alkaloids. The chemistry of MeJ-treated bark correlated strongly with the success of I. typographus attack, revealing major chemical differences between killed trees and unsuccessfully attacked trees. Surviving trees produced significantly higher amounts of most of the 39 analyzed mono-, sesqui-, and diterpenes and of 4 of 20 phenolics. Alkaloids showed no clear pattern. Differences in untreated bark were less pronounced, where only 1,8-cineole and (-)-limonene were significantly higher in unsuccessfully attacked trees. Our results show that the potential of individual P. abies trees for inducing defense compounds upon I. typographus attack may partly determine tree resistance to this bark beetle by inhibiting its mass attack.     

Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages

Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) and sequence analysis of noncoding regions of chloroplast DNA were used to investigate 37 populations of Eritrichium nanum covering its total distribution area, the European Alps. There was no haplotypic variation within the populations, and most haplotypes were restricted to single sites or to neighbouring populations, suggesting low levels of long distance gene flow via seeds. The present geographical distribution of haplotypes probably reflects an ancient geographical pattern within two regions in the intensely glaciated western and eastern central Alps identified as genetic hotspot areas. These two regions contained seven of the total of 11 haplotypes, including many of the most derived ones. The divergent haplotypes formed closely related groups, which supported a separate evolution of these haplotypes in these two regions and, more importantly, gave strong evidence for the in situ survival of these populations on nunataks within the western and eastern central Alps during Pleistocene glaciation. This result is in concordance with a previous study on E. nanum using nuclear markers. Only one haplotype was common and widespread throughout the distributional range of E. nanum. At the same time, it was the evolutionarily basal-most and all other haplotypes were best described as its descendants. This haplotype is hypothesized to be genetically identical to a Tertiary Alpine colonizing ancestor, whose distribution was secondarily fragmented and infiltrated by derived haplotypes originating through local mutations.     

Alpine crossroads or origin of genetic diversity? Comparative phylogeography of two sympatric microgastropod species

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa--Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae)--by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant 'hot-spot' for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.     

The genetic structure of the mountain forest butterfly Erebia euryale unravels the late Pleistocene and postglacial history of the mountain coniferous forest biome in Europe

The distribution of the mountain coniferous forest biome in Europe throughout time is not sufficiently understood. One character species of this habitat type is the large ringlet, Erebia euryale well reflecting the extension of this biome today, and the genetic differentiation of this species among and within mountain systems may unravel the late Pleistocene history of this habitat type. We therefore analysed the allozyme pattern of 381 E. euryale individuals from 11 populations in four different European mountain systems (Pyrenees, Alps, Carpathians, Rila). All loci analysed were polymorphic. The mean F(ST) over all samples was high (20%). Furthermore, the mean genetic distance among samples was quite high (0.049). We found four different groups well supported by cluster analyses, bootstraps and hierarchical variance analyses: Pyrenees, western Alps, eastern Alps and southeastern Europe (Carpathians and Rila). The genetic diversity of the populations was highest in the southeastern European group and stepwise decreased westwards. Interestingly, the populations from Bulgaria and Romania were almost identical; therefore, we assume that they were not separated by the Danube Valley, at least during the last ice age. On the contrary, the differentiation among the three western Alps populations was considerable. For all these reasons, we assume that (i) the most important refugial area for the coniferous mountain forest biome in Europe has been located in southeastern Europe including at least parts of the Carpathians and the Bulgarian mountains; (ii) important refugial areas for this biome existed at the southeastern edge of the Alps; (iii) fragments of this habitat types survived along the southwestern Alps, but in a more scattered distribution; and (iv) relatively small relicts have persisted somewhere at the foothills of the Pyrenees.     

Breeding structure of Glossina pallidipes populations evaluated by mitochondrial variation

Mitochondrial DNA diversity was studied at four loci in six natural populations of the tsetse fly Glossina pallidipes from Zimbabwe, Mozambique, Kenya, and Ethiopia. Single-locus diversity varied from 0.39 at 12S to 0.65 at COII. A total of 32 haplotypes was found with a mean of 6.4 +/- 2.9 per locus. To study breeding structure, diversity at two loci, COII and 16S2, was evaluated in 18 populations sampled from an area of approximately 1,611,000 km2 and in three laboratory cultures. Twenty-six haplotypes were detected at the two loci and mean haplotype diversity over all natural populations was 0.63. A high degree of population subdivision was detected within and among the Ethiopian and Kenya populations. The Zimbabwe and Zambia populations showed much less variation and differentiation than the northern populations. A population in Mozambique showed high levels of haplotype variation and affinities closest to populations in eastern Kenya, some 1700 km to the north. Analysis of variance of haplotype frequencies showed that 51.5% of the total lay within populations, 13% among populations within five nested groups, and 35.5% among the five groups. Wright's FST was 0.485, Nei's GST was 0.33, and Weir and Cunningham's theta = 0.45. Ecological data show that G. pallidipes is highly vagile. The large amount of genetic differentiation may be explained by genetic drift that occurred in scattered, relict populations during the rinderpest panzootic of the late 19th and early 20th centuries.     

Genetic diversity of Dinaric brown bears (Ursus arctos) in Croatia with implications for bear conservation in Europe

Brown bears have lost most of their range on the European continent. The remaining western populations are small, isolated and highly endangered. The Dinaric-Pindos brown bear population is the western-most stable population and the fourth largest in Europe. It has been recognized as a potential source for recolonization of populations whose survival is at risk. Indeed, several translocations of Dinaric bears to Italy, Austria and France have recently been made. Despite the importance of the Dinaric bear population, its genetic status remains poorly understood. Using tissue samples from 156 hunted or accidentally killed Dinaric bears in Croatia, this study analysed genetic diversity at 12 microsatellite loci, as well as population structure and past reductions in size. In addition, a subset of 59 samples was used to assess diversity of the mitochondrial DNA control region. The results indicate that Dinaric bears have high nuclear genetic diversity, as compared to other extant brown bear populations, despite genetic evidence of a bottleneck caused by past persecutions. However, haplotype diversity was low, probably as a result of male-biased dispersal and female philopatry. Not surprisingly, no evidence of population sub-structure was found using nuclear markers, as the bear habitat has remained continuous and the highway network has been built only recently. Management should focus on maintaining habitat connectivity and keeping the effective population size as large as possible. In addition, when removing individuals, care should be taken not to further deplete the population of rare haplotypes. A coordinated transboundary management of the entire Dinaric-Pindos brown bear population should be a priority for its long-term conservation.     

Testing for recombination in a short nuclear DNA sequence of the European meadow grasshopper, Chorthippus parallelus

Single-copy nuclear DNA sequences have high potential as a source of genetic markers for population analyses. However, the difficulties that arise when haplotypes that are the product of recombinational rearrangements are present require additional consideration. Two statistical methods for identifying potential recombinants by detecting anomalies in the distribution of variable sites along sequences were used to screen sequences from a single-copy nuclear DNA fragment, cpnl-1, of the European meadow grasshopper (Chorthippus parallelus). Five of the 71 haplotypes in the cpnl-1 data set showed nonrandom distribution of polymorphic sites using both methods. The second method pinpointed an additional four haplotypes. Estimates of the rate of recombination in the entire data set were obtained using standard methods. It is concluded that cpnl-1 haplotypes have been involved in recombination or gene conversion events at a rate more than twice the mutation rate. This confirms that recombination and gene conversion are significant factors in the generation of haplotype variation in nuclear gene sequences. The cpnl-1 haplotypes identified by the tests were present only in populations that have had recent contact; the Balkan and Turkish refugial populations and their post-glacial colonies to the north. This is discussed in relation to the phylogenetic inferences drawn from the same data in a previous report.     

Genetic implications of phylogeographical patterns in the conservation of the boreal wetland butterfly Colias palaeno (Pieridae)

The boreo‐montane wetland butterfly species Colias palaeno has a European distribution from the Alps to northern Fennoscandia. Within its European range, the species’ populations have shrunk dramatically in recent historical times. Therefore, detailed baseline knowledge of the genetic makeup of the species is pivotal in planning potential conservation strategies. We collected 523 individuals from 21 populations across the entire European range and analyzed nuclear (20 allozyme loci) and mitochondrial (600 bp of the cytochrome c oxidase subunit I gene) genetic markers. The markers revealed contrasting levels of genetic diversity and divergence: higher in allozymes and lower in mitochondrial sequences. Five main groups were identified by allozymes: Alps, two Czech groups, Baltic countries, Fennoscandia, and Poland. The haplotype mitochondrial network indicates a recent range expansion. The most parsimonious interpretation for our results is the existence of a continuous Würm glacial distribution in Central Europe, with secondary disjunction during the Last Glacial Maximum into a south‐western and a north‐eastern fragment and subsequent moderate differentiation. Both groups present signs of postglacial intermixing in the Czech Republic. However, even a complete extinction in this region would not considerably affect the species’ genetic basis, as long as the source populations in the Alps and in northern Europe, comprising the most relevant evolutionary units for conservation, are surviving.     

Average height of adolescents in the Dinaric Alps

This study contributes to an update of average heights among European populations. Our investigation covering 2705 boys and 2842 girls aged 17 years, shows that, contrary to the general belief, adolescents of the Dinaric Alps are, on average, the tallest in Europe. With an average height of 185,6 cm, they are taller than Dutch adolescents (184 cm on average). Above all, the density of very tall subjects appears to be characteristic of the Dinaric Alps, since 28% measure 190 cm or more in height, as opposed to only 20% in Holland and 1.5% in France. Although our information is not complete, adolescent girls in the Dinaric Alps, with an average height of 171 cm come a close second to girls in Holland.     

A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling

Background and Aims A worldwide increase in tree decline and mortality has been linked to climate change and, where these represent foundation species, this can have important implications for ecosystem functions. This study tests a combined approach of phylogeographic analysis and species distribution modelling to provide a climate change context for an observed decline in crown health and an increase in mortality in Eucalyptus wandoo, an endemic tree of south-western Australia.Methods Phylogeographic analyses were undertaken using restriction fragment length polymorphism analysis of chloroplast DNA in 26 populations across the species distribution. Parsimony analysis of haplotype relationships was conducted, a haplotype network was prepared, and haplotype and nucleotide diversity were calculated. Species distribution modelling was undertaken using Maxent models based on extant species occurrences and projected to climate models of the last glacial maximum (LGM).Key Results A structured pattern of diversity was identified, with the presence of two groups that followed a climatic gradient from mesic to semi-arid regions. Most populations were represented by a single haplotype, but many haplotypes were shared among populations, with some having widespread distributions. A putative refugial area with high haplotype diversity was identified at the centre of the species distribution. Species distribution modelling showed high climatic suitability at the LGM and high climatic stability in the central region where higher genetic diversity was found, and low suitability elsewhere, consistent with a pattern of range contraction.Conclusions Combination of phylogeography and paleo-distribution modelling can provide an evolutionary context for climate-driven tree decline, as both can be used to cross-validate evidence for refugia and contraction under harsh climatic conditions. This approach identified a central refugial area in the test species E. wandoo, with more recent expansion into peripheral areas from where it had contracted at the LGM. This signature of contraction from lower rainfall areas is consistent with current observations of decline on the semi-arid margin of the range, and indicates low capacity to tolerate forecast climatic change. Identification of a paleo-historical context for current tree decline enables conservation interventions to focus on maintaining genetic diversity, which provides the evolutionary potential for adaptation to climate change.