Molecular phylogeny of <Emphasis Type="Italic">Pisolithus</Emphasis> species from Moroccan forest woodlands

The phylogenetic relationships among 200 Pisolithus basidiomata collected from pine, oak, and eucalypt forests and rockrose scrubs in Morocco were investigated. Using PCR-RFLP analysis of the internal transcribed spacer (ITS) of ribosomal DNA, this collection could be divided into 5 groups, by using PCR-RFLP analysis of the internal transcribed spacer (ITS) of ribosomal DNA. The ITS of a representative basidioma of each group was sequenced, and a phylogenetic analysis was performed. The dendrogram suggests that at least five Pisolithus species are present in Morocco. Pisolithus basidiomata collected in the Pinus and Quercus forests correspond to Pisolithus arrhizus and P. species 4 as previously described by Martin and colleagues in 2002. Those collected from the eucalyptus forests, under E. gomphocephala and E. camaldulensis, correspond to P. albus and P. microcarpus. Basidiomata collected from the rockrose scrubs, under Cistus crispus, C. monspeliensis or C. salviifolius, are all identified as Pisolithus species 3. Phylogenetic analyses showed that our different Pisolithus grouped well with Pisolithus specimens from other geographical origins.     

Cryptic species, native populations and biological invasions by a eucalypt forest pathogen

Human‐associated introduction of pathogens and consequent invasions is very evident in areas where no related organisms existed before. In areas where related but distinct populations or closely related cryptic species already exist, the invasion process is much harder to unravel. In this study, the population structure of the Eucalyptus leaf pathogen Teratosphaeria nubilosa was studied within its native range in Australia, including both commercial plantations and native forests. A collection of 521 isolates from across its distribution was characterized using eight microsatellite loci, resulting in 112 multilocus haplotypes (MLHs). Multivariate and Bayesian analyses of the population conducted in structure revealed three genetically isolated groups (A, B and C), with no evidence for recombination or hybridization among groups, even when they co‐occur in the same plantation. DNA sequence data of the ITS (n = 32), β‐tubulin (n = 32) and 27 anonymous loci (n = 16) were consistent with microsatellite data in suggesting that T. nubilosa should be considered as a species complex. Patterns of genetic diversity provided evidence of biological invasions by the pathogen within Australia in the states of Western Australia and New South Wales and helped unravel the pattern of invasion beyond Australia into New Zealand, Brazil and Uruguay. No significant genetic differences in pathogen populations collected in native forests and commercial plantations were observed. This emphasizes the importance of sanitation in the acquisition of nursery stock for the establishment of commercial plantations.     

Genetic evidence for the origins of range disjunctions in the Australian dry sclerophyll plant Hardenbergia violacea

Aim The distribution of genetic variation in the Australian dry sclerophyll plant Hardenbergia violacea (Fabaceae) is examined in the context of Pleistocene climate change in order to identify likely refugia. Particular consideration is given to the origin of range disjunctions in South Australia and Tasmania, and to determining whether the Tasmanian population is indigenous or recently introduced from mainland Australia. Location Southeastern Australian mainland and Tasmania. Methods A combination of chloroplast polymerase chain reaction–restriction fragment length polymorphism and genomic amplified fragment length polymorphism (AFLP) marker systems was used to examine the genetic structure of 292 individuals from 13 populations across the range of H. violacea in southeastern Australia. Results Hardenbergia violacea populations in Tasmania and southern Victoria were characterized by low, almost monotypic chloroplast diversity. New South Wales showed higher haplotype diversity and haplotype sharing among widely distributed populations. Principal coordinates analysis (PCoA) of the AFLP data found a strong latitudinal cline in AFLP variation from northern New South Wales south to Tasmania. The Tasmanian population formed an isolated and somewhat disjunct genetic cluster at one end of this cline. However, the South Australian population was an exception to the clinal variation shown by all other populations, forming a highly disjunct cluster in the PCoA. Within‐population genetic diversity was low in both disjunct populations. Main conclusions The genetic evidence indicates that the Tasmanian population is likely to be indigenous and probably the product of vicariance, which was followed by range contraction at the Last Glacial Maximum or an earlier glacial event. The deep phylogenetic disjunction in South Australia is evidence of a much earlier separation on mainland Australia. The chloroplast structure indicates that, during the Pleistocene, H. violacea underwent broad‐scale recolonization in southern Victoria and Tasmania, possibly from a large continental refugium in eastern New South Wales. We conclude that H. violacea, and presumably the sclerophyll communities in which it occurs, have undergone multiple range contractions to large continental refugia during different Pleistocene glaciations in southeastern Australia.     

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) from New Zealand

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct “cryptic” species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa.     

Identification and population genetic comparison of three ascidian species based on mtDNA sequences

Ascidians are sessile marine chordate invertebrates found along seashores worldwide and are typically regarded as invasive organisms. Knowledge concerning their global genetic structure and subsequent invasive potential is limited. Here, we identified three ascidians—Ciona robusta, Ciona savignyi, and Styela clava from the northeast region of China using morphological characteristics and mitochondrial cytochrome c oxidase subunit I (cox1) as genetic marker. We additionally used phylogenetics to aid in the identification of these three species. The results of a population genetic analysis showed that among the three species, the level of haplotype diversity was particularly high within C. savignyi, and nucleotide diversity varied moderately. We divided the three species separately into native and invasive populations using 170 cox1 sequences from global resources to explore population genetic structure and invasive potential. Although in the network analysis Ciona spp. formed haplogroups of native and invasive populations, some haplotypes were still shared. We found that the haplotypes did not cluster within the network of S. clava. Our AMOVA results also showed that Ciona spp. had a weak genetic structure, and less genetic differentiation was present in S. clava. These data suggest that there are extensive incursions of these three ascidians into different geographical regions. Global comparisons of ascidian populations will help in the understanding of their population genetic structure and invasive potential, hence providing important insights regarding conservation as well as management.     

Genetic differentiation of the Thorn‐tailed Rayadito Aphrastura spinicauda (Furnariidae: Passeriformes) revealed by ISSR profiles suggests multiple palaeorefugia and high recurrent gene flow

Nucleotide sequence data (cytochrome b) and ISSR genomic fingerprints were used to analyse the genetic variation and population differentiation in Thorn‐tailed Rayadito, a widespread Patagonian forest bird. We included samples from eight populations of Thorn‐tailed Rayadito covering most of the distribution range of the species: from fragmented patches of Olivillo forest in northern Chile to Isla Navarino forests in the extreme south of South America. Low levels of genetic diversity were found among populations, with a large within‐population molecular variance indicating high levels of gene flow. The multivariate and cluster analyses based on ISSR markers show that the subspecies bullocki (from Mocha Island) differs significantly from all other populations. The subspecies fulva (Chiloé Island) shows less differentiation than bullocki, sharing several alleles with continental populations. Bayesian analyses suggest that the Mocha Island population contributes most to the total genetic diversity observed in the species. Mantel tests revealed no significant correlation between geographical distance and pairwise genetic distance and cytochrome b sequence analyses failed to detect differentiation among subspecies. Mocha Island might have been a palaeorefuge and this population may have diversified by genetic drift after the last glacial maximum. There is also the possibility of a postglacial colonization of the Thorn‐tailed Rayadito from an austral palaeorefugium, supporting a multiple refugia hypothesis. This study illustrates the usefulness of the rarely used ISSR genomic fingerprint method in avian phylogeography.     

Gene flow among native bush rat,Rattus fuscipes (Rodentia: Muridae), populations in the fragmented subtropical forests of south‐east Queensland

Abstract Many natural populations in areas of continuous habitat exhibit some form of local genetic structure. Anthropogenic habitat fragmentation can also strongly influence the dynamics of gene flow between populations. We used eight microsatellite markers to investigate the population genetic structure of an abundant forest species, the Australian bush rat (Rattus fuscipes), in the subtropical forests of south‐east Queensland. Five sites were sampled, allowing pairwise comparisons within continuous habitat and across clearings. Weak, but significant population differentiation and a significant pattern of isolation by distance was detected over the small scale (<10 km) of this study. Fine‐scale analysis at a single site (<1 km) showed a significant correlation between individual female genetic distance and geographical distance, but no similar pattern among male individuals. There was no evidence of increased population differentiation across clearings relative to comparisons within continuous forest. This was attributed to dispersal within corridors of remnant and revegetated habitat between the forested areas. We concluded that an inherently restricted dispersal ability, female philopatry and natural habitat heterogeneity play an important part in the development of genetic structure among populations of R. fuscipes. It is important to understand the relationship between landscape features and the pattern of gene flow among continuous populations, as this allows us to predict the impact of fragmentation on natural populations.     

Crossing the Tasman Sea: Inferring the introduction history of Litoria aurea and Litoria raniformis (Anura: Hylidae) from Australia into New Zealand

Abstract The amphibian fauna of New Zealand consists of three native species (Leiopelma spp.), and three Litoria species introduced from Australia in the last 140 years. We conducted a molecular phylogeographical study that aimed to identify the Australian origins of two species, Litoria aurea and Litoria raniformis. We used partial sequences of the mitochondrial cytochrome oxidase I (cox1) gene from 59 specimens sampled from across the range of both species to identify the probable source populations for the New Zealand introductions, and to describe the current genetic diversity among New Zealand Litoria populations. Our genetic data suggest that L. aurea was introduced into the North Island of New Zealand from two regions in Australia, once from the northern part of coastal New South Wales and once from the southern part of coastal New South Wales. Our data indicate that L. raniformis introductions originated from the Melbourne region of southern Victoria and once established in the South Island of New Zealand, the species subsequently spread throughout both islands. In addition, we found a distinct haplotype in L. raniformis from Tasmania that strongly suggests, contrary to earlier reports, that this species was not introduced into New Zealand from Tasmania. Finally, we identified two very distinctive mitochondrial lineages of L. raniformis within the mainland Australia distribution, which may be previously unrecognized species.     

Polymorphic microsatellite markers of a Pisolithus sp. from a Eucalyptus plantation

We developed six polymorphic microsatellite markers for an ectomycorrhizal Pisolithus sp., which are associated with Eucalyptus camaldulensis in Thailand using a method starting with amplified fragments of intersimple sequence repeats (ISSR). The number of alleles per locus varied between two and five and expected heterozygosities ranged from 0.123 to 0.625. These loci are available for analysis of genetic structure and gene flow in Eucalyptus‐associated Pisolithus spp. populations.     

Genetic diversity of mitochondrial D-LOOP sequences in the spotted scat (Scatophagus argus) from different geographical populations along the northern coast of the South China Sea

The genetic diversity of 289 spotted scat (Scatophagus argus) from seven populations along the northern coast of the South China Sea was studied by analyzing the full-length sequences of the mitochondrial control region (D-LOOP). The S. argus D-LOOP sequence was 1,004–1,010 bp long and contained 156 variant sites. The seven studied S. argus populations had a high degree of genetic diversity (haplotype diversity [Hd] = 0.99135; nucleotide diversity (π) = 0.01313). There was no obvious genetic differentiation among the seven geographical populations and gene exchange was frequent (Fst = −0.01867–0.01117, p > .05). Four distinct mitochondrial lineages were identified in the phylogenetic tree and the haplotype network. The between-lineage Fst was 0.71690–0.84940 (p < .001), but these lineages showed no obvious phylogeographic pattern. Based on D-LOOP mutation rates, we estimated that the four lineages diverged approximately 513,800–93,600 years ago, during the Eocene ice age, at which time falling sea levels may have led to population segregation. We estimated that S. argus population expansion occurred approximately 2.29–0.68 million years ago, during the late Pleistocene. During this period, sea levels rose again, allowing previously separated lineages to come into sympatry, which eventually gave rise to a highly genetically diverse population without pyhlogeographic structure. Here, we characterized the genetic structure and differentiation of seven S. argus populations from the northern coast of the South China Sea. Our results suggested that the seven S. argus populations from the northern coast of the South China Sea have a relatively low level of genetic variation and can be considered a single unit for the purposes of fishery development, utilization, and management.     

GENETIC STRUCTURE OF THE AUSTRALIAN CYCAD,MACROZAMIA COMMUNIS (ZAMIACEAE)

Cycads have been the subject of a wide variety of botanical studies. However, nothing is known of the genetic structure of their populations. Seeds were collected from five populations of the common Australian cycad Macrozamia communis along a north to south transect through its 500-km-long range in eastern New South Wales. Leaf samples from seedlings grown from those seeds were the subject of isozyme analysis. Nine of the 18 isozyme loci studied were polymorphic. Levels of polymorphism varied among loci and among populations. The three southern-most populations were genetically similar to one another but well differentiated from the other two. The levels of species-wide genetic diversity observed for M. communis were relatively low compared with those of other gymnosperms and angiosperms. On the other hand, the levels of spatial differentiation were relatively high, especially compared with other gymnosperms.     

Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. In spite of geographical proximity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of isolation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation.     

Genetic diversity and structure of the invasive tree Miconia calvescens in Pacific islands

Aim This study investigates the amount and distribution of genetic variation within and among populations of the highly invasive tree, Miconia calvescens (Melastomataceae; hereafter miconia), in tropical island habitats that are differently impacted (distribution and spread) by this weed. Location Invasive populations were included from northern and southern Pacific islands including the Hawaiian Islands (Hawaii, Kauai and Maui), Marquesas Islands (Nuku Hiva), Society Islands (Tahiti, Tahaa, Moorea, Raiatea) and New Caledonia. Methods We used 9 codominant microsatellite and 77 highly variable dominant intersimple sequence repeat markers (ISSRs) to characterize and compare genetic diversity among and within invasive miconia populations. For the codominant microsatellite data we calculated standard population genetic estimates (heterozygosity, number of alleles, inbreeding coefficients, etc.) and described population genetic structure using AMOVA, Mantel tests (to test for isolation by distance), unweighted pair‐group method with arithmetic averages (UPGMA) cluster analysis and principal components analysis (PCA). We also tested for the presence of a population bottleneck and used a Bayesian analysis of population structure in combination with individual assignment tests. For the dominant ISSR data we used AMOVA, PCA, upgma and a Bayesian approach to investigate population genetic structure. Results Both markers types showed little to no genetic differentiation among miconia populations from northern and southern Pacific hemispheres (AMOVA: microsatellite, 3%; ISSR, 0%). Bayesian and frequency‐based analysis also failed to support geographical genetic structure, confirming considerable low genetic differentiation throughout the Pacific. Molecular data furthermore showed that highly successful miconia populations throughout the Pacific are currently undergoing severe bottlenecks and high levels of inbreeding (f = 0.91, ISSR; F_IS = 0.27, microsatellite). Main conclusions The lack of population genetic structure is indicative of similar geographical sources for both hemispheres and small founding populations. Differences in invasive spread and distribution among Pacific islands are most likely the result of differences in introduction dates to different islands and their accompanying lag phases. Miconia has been introduced to relatively few tropical islands in the Pacific, and the accidental introduction of a few or even a single seed into favourable habitats could lead to high invasive success.     

Species status and population structure of the Australian Eucalyptus pest Paropsis atomaria Olivier (Coleoptera: Chrysomelidae)

1 Paropsis atomaria Olivier represents an emergent pest of Eucalyptus plantations in Queensland and New South Wales, Australia. Most prior studies on the biology and control of P. atomaria have centred on populations from Canberra in the Australian Capital Territory, but the biological relationship between beetles from Canberra and those from up to 1500 km further north are unknown. 2 DNA markers were used to determine whether P. atomaria from Canberra are the same biological species as those from Eucalyptus forestry plantations in northern New South Wales and Queensland, where the beetle has become an important pest. Using the mitochondrial gene, cytochrome c oxidase I (COI), individuals collected from across the distribution of P. atomaria were investigated for haplotype diversity and levels of mitochondrial divergence. 3 Within P. atomaria, genetic distance averaged 0.5% across 23 unique haplotypes for 93 individuals, with an average of 14% difference between P. atomaria and the outgroup species, Paropsis obsoleta. Significant genetic structure was observed relative to geographical distribution, but not with respect to host plant species of origin. Greatest divergence was between the southern‐most sample site (Canberra) and northern sites in New South Wales and Queensland, indicating reduced gene flow between these regions. 4 Individuals from across eastern Australia belong to the same genetic species with population substructuring evident. Consequently, there is no evidence to suggest cryptic species complexes exist within the currently defined taxon. Continued implementation of control strategies for P. atomaria across its distribution is appropriate.     

Major biogeographic barriers in eastern Australia have shaped the population structure of widely distributed Eucalyptus moluccana and its putative subspecies

We have investigated the impact of recognized biogeographic barriers on genetic differentiation of grey box (Eucalyptus moluccana), a common and widespread tree species of the family Myrtaceae in eastern Australian woodlands, and its previously proposed four subspecies moluccana, pedicellata, queenslandica, and crassifolia. A range of phylogeographic analyses were conducted to examine the population genetic differentiation and subspecies genetic structure in E. moluccana in relation to biogeographic barriers. Slow evolving markers uncovering long term processes (chloroplast DNA) were used to generate a haplotype network and infer phylogeographic barriers. Additionally, fast evolving, hypervariable markers (microsatellites) were used to estimate demographic processes and genetic structure among five geographic regions (29 populations) across the entire distribution of E. moluccana. Morphological features of seedlings, such as leaf and stem traits, were assessed to evaluate population clusters and test differentiation of the putative subspecies. Haplotype network analysis revealed twenty chloroplast haplotypes with a main haplotype in a central position shared by individuals belonging to the regions containing the four putative subspecies. Microsatellite analysis detected the genetic structure between Queensland (QLD) and New South Wales (NSW) populations, consistent with the McPherson Range barrier, an east‐west spur of the Great Dividing Range. The substructure was detected within QLD and NSW in line with other barriers in eastern Australia. The morphological analyses supported differentiation between QLD and NSW populations, with no difference within QLD, yet some differentiation within NSW populations. Our molecular and morphological analyses provide evidence that several geographic barriers in eastern Australia, including the Burdekin Gap and the McPherson Range have contributed to the genetic structure of E. moluccana. Genetic differentiation among E. moluccana populations supports the recognition of some but not all the four previously proposed subspecies, with crassifolia being the most differentiated.     

Genetic structure and putative selective sweep in the pioneer tree,Zanthoxylum ailanthoides

Zanthoxylum ailanthoides Siebold & Zucc. is one of the most frequently encountered pioneer trees in Japanese warm–temperate evergreen oak forests. Our previous study in one region of Japan suggested high levels of population differentiation and putative natural selection acting on one of the nuclear loci analyzed. Here, we extend our analysis to study the genetic structure of 10 populations of Z. ailanthoides across Japan using 9 simple sequence repeat (SSR) loci for a better understanding of its genetic structure. First, the southernmost population (Kagoshima) in the samples was found to have the highest genetic diversity, suggesting there was a glacial refugium at or near the location of the population. Second, relatively strong genetic differentiation was found among populations, and there was a positive correlation between genetic distances and geographic distances (Mantel test; P < 0.001). Based on this information, we analyzed nucleotide variation at the putatively selected locus homologous to the gene encoding the ADP-glucose pyrophosphorylase large subunit (agpL). Despite the strong genetic differentiation among populations suggested by the SSR loci, the agpL locus was monomorphic in almost all populations analyzed. The results of this study strongly supported the possibility of a selective sweep at or near the agpL locus.     

Conservation of genetic diversity in British populations of the diploid endemic Coincya monensis ssp monensis (Isle of Man Cabbage): the risk of hybridisation with the tetraploid alien, Coincya monensis ssp cheiranthos

Coincya monensis is represented in the British flora by two, cytologically distinct subspecies. Coincya monensis ssp monensis is an endemic diploid with a coastal sand dune distribution that includes a number of isolated populations. Coincya monensis ssp cheiranthos is a tetraploid alien, well established in South Wales in early successional habitats. Both subspecies share similar life form traits, flowering times and pollinators. Cluster analysis and phylogenetic reconstruction based on sequences of the mitochondrial nad4 gene confirmed the distinction between alien and endemic taxa. Tetraploid populations carry more polymorphic RAPDs loci and their genetic diversity is partitioned more within than among populations. In contrast, C. monensis ssp monensis has a distinct population genetic structure. Analysis of the multilocus genetic data confirmed a structure of genetically isolated, endemic population clusters in Scotland, Arran, the Isle of Man and South Wales. Experimental hybridisation showed the two subspecies are interfertile. Multivariate analysis of RAPDs data resolved hybrids between alien and endemic clusters and hybrids contained a proportion of alien-specific polymorphic loci. Hybrids of alien maternal parentage contained the mitochondrial nad4 sequence characteristic of the alien subspecies. Since the alien subspecies can invade mobile sand dune communities from urban sites and compete for pollinators, there is a risk that alien and endemic populations will mix and introgress. Conservation of endemic genetic diversity in Britain will require protection for all C. monensis ssp monensis populations. Currently, the most disjunct endemic population in South Wales is most at risk from introgression.     

Variation in the chloroplast DNA of Swiss stone pine (Pinus cembra L.) reflects contrasting post-glacial history of populations from the Carpathians and the Alps

Aim To characterize the genetic structure and diversity of Pinus cembra L. populations native to two disjunct geographical areas, the Alps and the Carpathians, and to evaluate the rate of genetic differentiation among populations. Location The Swiss Alps and the Carpathians. Methods We screened 28 populations at three paternally inherited chloroplast simple sequence repeats (cpSSRs) for length variation in their mononucleotide repeats. Statistical analysis assessed haplotypic variation and fixation indices. Hierarchical analysis of molecular variance (AMOVA), Mantel test, spatial analysis of molecular variance (SAMOVA) and barrier analyses were applied to evaluate the geographical partitioning of genetic diversity across the species’ range. Results Haplotypic diversity was generally high throughout the natural range of P. cembra, with the mean value substantially higher in the Carpathians (H = 0.53) than in the Alps (H = 0.35). The isolated Carpathian populations showed the highest haplotype diversity among the populations originating from the High Tatras (Velka Studena Dolina) and South Carpathians (Retezat Mountains). AMOVA revealed that only 3% of the total genetic variation derived from genetic differentiation between the two mountain ranges. Differentiation among Carpathian populations was higher (F_ST = 0.19) than among Alpine populations (F_ST = 0.04). Low, but significant, correlation was found between the geographical and genetic distances among pairs of populations (r = 0.286, P < 0.001). SAMOVA results revealed no evident geographical structure of populations. barrier analysis showed the strongest differentiation in the eastern part of the species’ range, i.e. in the Carpathians. Main conclusions The populations of P. cembra within the two parts of the species’ range still share many cpDNA haplotypes, suggesting a common gene pool conserved from a previously large, continuous distribution range. Carpathian populations have maintained high haplotypic variation, even higher than Alpine populations, despite their small population sizes and spatial isolation. Based on our results, we emphasize the importance of the Carpathian populations of Swiss stone pine for conservation. These populations comprise private haplotypes and they may represent a particular legacy of the species’ evolutionary history.