Habitat fragmentation and the structure of genetic diversity within disjunct isolates of Anthericum ramosum L. (Anthericaceae) in Scandinavia

The lilioid herb, Anthericum ramosum , occurs in four geographically-isolated regions (Sjælland, Skåne, Öland and Gotland) in Denmark and southern Sweden. We investigated allozyme variation at nine polymorphic loci in A. ramosum from 16 sites (33 populations) in the four regions. There was no clear overall geographic pattern of differentiation between the regions, but the southernmost Gotland and the Öland populations had similar allele frequencies, suggesting that they have had a common history. The total genetic diversity (H_10t) was 0.458 and the between-region, site- and population components of diversity accounted, respectively, for 13%, 10% and 2% of the total diversity. The species is restricted to grassland habitats. Such habitats have become increasingly rare in the Sjælland and Skåne regions, where A. ramosum now has a highly fragmented distribution. Within three of the regions (Sjælland, Skane and Öland) there was a negative relationship between the extent of grassland habitat and the between-site components of genetic diversity. Öland, with its extensive grassland habitats and low levels of population disjunction, showed litde allelic differentiation between sites and the lowest between-site component of diversity (3%), suggesting that there is (or has been) extensive gene flow between sites. The between-site components of diversity were higher within Skåne (7%) and Sjaelland (12%). The high within-region G_ST (25%) for the fourth region, Gotland, cannot be explained in terms of recent habitat disjunction but is, instead, interpreted in terms of the restricted distribution of limestone bedrock on Gotland and the fact that die southern and northern Godand populations appear to have had different origins.     

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within-population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter-patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.     

Primula farinosa in Denmark; genetic diversity and population management

During the past centuries Danish populations of Primula farinosa have seriously declined in number. We investigated the genetic structure and genetic diversity of plants of seven populations from two different regions, Zealand and Bornholm in Denmark, using three AFLP markers. Two populations from nearby Scania, Sweden were included as reference. We found 54 unambiguously polymorphic loci. The genetic structure analysis suggested division of the 268 plants into three distinct groups, to a large extent matching the geographical distribution of the populations. Analysis of molecular variance (AMOVA) indicated significant genetic differentiation of 67% within populations and 33% among the populations. Our results suggest that genetic differentiation among regions and unique local genetic diversity should carefully be considered in future conservation attempts if we are to maintain as much genetic variation as possible. We present a historical overview of the decline in Danish populations and discuss conservation management and restoration strategies.     

Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks

Comparisons of neutral marker and quantitative trait divergence can provide important insights into the relative roles of natural selection and neutral genetic drift in population differentiation. We investigated phenotypic and genetic differentiation among Fennoscandian threespine stickleback (Gasterosteus aculeatus) populations, and found that the highest degree of differentiation occurred between sea and freshwater habitats. Within habitats, morphological divergence was highest among the different freshwater populations. Pairwise phenotypic and neutral genetic distances among populations were positively correlated, suggesting that genetic drift may have contributed to the morphological differentiation among habitats. On the other hand, the degree of phenotypic differentiation (PST) clearly surpassed the neutral expectation set by FST, suggesting a predominant role for natural selection over genetic drift as an explanation for the observed differentiation. However, separate PST/FST comparisons by habitats revealed that body shape divergence between lake and marine populations, and even among marine populations, can be strongly influenced by natural selection. On the other hand, genetic drift can play an important role in the differentiation among lake populations.     

广西红树植物桐花树种群遗传多样性分析

采用RAPD-PCR方法探讨广西3个不同生境下桐花树种群的遗传多样性和遗传分化。结果表明:3个不同生境桐花树RAPD扩增多态百分率为20.2%,3个不同生境桐花树种群两两之间的遗传距离分别为0.195、0.169、0.26,平均遗传距离为0.208。同一种群不同个体的扩增多态百分率最高为37.28%,其次为20.93%,最小的为19.32%。Shannon’s遗传多样性指数3个种群分别为0.331、0.225和0.17,其大小顺序与多态百分率的结果一致。种群内遗传多样性比率为62.3%,种群间遗传多样性比率为37.7%。说明广西3个不同生境的桐花树种群的遗传变异大部分存在种群内,种群间遗传变异较小。     

Allelic diversity associated with aridity gradient in wild emmer wheat populations

The association between allelic diversity and ecogeographical variables was studied in natural populations of wild emmer wheat [ Triticum turgidum ssp. dicoccoides (Körn.) Thell.], the tetraploid progenitor of cultivated wheat. Patterns of allelic diversity in 54 microsatellite loci were analyzed in a collection of 145 wild emmer wheat accessions representing 25 populations that were sampled across naturally occurring aridity gradient in Israel and surrounding regions. The obtained results revealed that 56% of the genetic variation resided among accessions within populations, while only 44% of the variation resided between populations. An unweighted pair-group method analysis (UPGMA) tree constructed based on the microsatellite allelic diversity divided the 25 populations into six major groups. Several groups were comprised of populations that were collected in ecologically similar but geographically remote habitats. Furthermore, genetic differentiation between populations was independent of the geographical distances. An interesting evolutionary phenomenon is highlighted by the unimodal relationship between allelic diversity and annual rainfall ( r  = 0.74, P  < 0.0002), indicating higher allelic diversity in populations originated from habitats with intermediate environmental stress (i.e. rainfall 350–550 mm year⁻¹). These results show for the first time that the 'intermediate-disturbance hypothesis', explaining biological diversity at the ecosystem level, also dominates the genetic diversity within a single species, the lowest hierarchical element of the biological diversity.     

Genetic variability in natural populations of Arabidopsis thaliana in northern Europe

Ten populations of the model plant Arabidopsis thaliana were collected along a north-south gradient in Norway and screened for microsatellite polymorphisms in 25 loci and variability in quantitative traits. Overall, the average levels of genetic diversity were found to be relatively high in these populations, compared to previously published surveys of within population variability. Six of the populations were polymorphic at microsatellite loci, resulting in an overall proportion of polymorphic loci of 18%, and a relatively high gene diversity for a selfing species (HE = 0.06). Of the overall variability, 12% was found within populations. Two of six polymorphic populations contained heterozygous individuals. Both FST and phylogenetic analyses showed no correlation between geographical and genetic distances. Haplotypic diversity patterns suggested postglacial colonization of Scandinavia from a number of different sources. Heritable variation was observed for many of the studied quantitative traits, with all populations showing variability in at least some traits, even populations with no microsatellite variability. There was a positive association between variability in quantitative traits and microsatellites within populations. Several quantitative traits exhibited QST values significantly less than FST, suggesting that selection may be acting to retard differentiation for these traits.     

Macrogeographic population structure of the tsetse fly, Glossina pallidipes (Diptera: Glossinidae)

Tsetse flies are confined to sub-Saharan Africa where they occupy discontinuous habitats. In anticipation of area-wide control programmes, estimates of gene flow among tsetse populations are necessary. Genetic diversities were partitioned at eight microsatellite loci and five mitochondrial loci in 21 Glossina pallidipes Austin populations. At microsatellite loci, Nei's unbiased gene diversity averaged over loci was 0.659 and the total number of alleles was 214, only four of which were shared among all populations. The mean number of alleles per locus was 26.8. Random mating was observed within but not among populations (fixation index FST=0.18) and 81% of the genetic variance was within populations. Thirty-nine mitochondrial variants were detected. Mitochondrial diversities in populations varied from 0 to 0.85 and averaged 0.42, and FST=0.51. High levels of genetic differentiation were characteristic, extending even to subpopulations separated by tens and hundreds of kilometres, and indicating low rates of gene flow.     

Genetic structure,allozyme-habitat associations and reproductive fitness in Gypsophila fastigiata (Caryophyllaceae)

Relationships between allozyme differentiation, habitat variation and individual reproductive success were examined in local populations of a perennial herb, Gypsophila fastigiata, on the Baltic island of Öland (Sweden). Relatively little (c. 2%) of the total allozyme diversity in this largely outcrossing species is explained by differentiation between sites tens of kilometres apart. The low level of geographic differentiation suggests that gene flow between sites is, or has recently been, extensive. Yet the component of allozyme diversity due to differentiation between plots (only tens of meters apart) within sites is 3 times larger than the between-site component of diversity. Allozyme variation, especially at the Pgi-2 locus, is significantly associated with habitat variation within sites. Different allele x habitat combinations for the Pgi-2 locus are associated with differences in individual reproductive fitness. Differential selection in different local habitats may thus contribute to the fine-scale structuring of genetic diversity within sites.     

Habitat differentiation vs. isolation-by-distance: the genetic population structure of Elymus athericus in European salt marshes

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt-marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt-marsh species, we were interested in population differentiation through isolation-by-distance, and among strongly divergent habitats (low and high marsh) in this wind- and water-dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross-species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation-by-distance was present only on larger scales (60-443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation-by-distance) effects among six sites 2.5-443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection-mediated restrictions to gene flow simultaneously.     

A comparison of the genetic diversity in Dipteronia sinensis Oliv. and Dipteronia dyeriana Henry

Dipteronia is an endemic genus to China and includes only two species, Dipteronia sinensis and D.dyeriana.Based on random amplified polymorphic DNA (RAPD) markers,a comparative study of the genetic diversity and genetic structure of Dipteronia was performed.In total,128 and 103 loci were detected in 17 D.sinensis populations and 4 D.dyeriana populations,respectively,using 18 random primers.These results showed that the proportions of polymorphic loci for the two species were 92.97% and 81.55%,respectively,indicating that the genetic diversity of D.sinensis was higher than that of D.dyeriana.Analysis,based on similarity coefficients,Shannon diversity index and Nei gene diversity index,also confirmed this result.AMOVA analysis demonstrated that the genetic variation of D.sinensis within and among populations accounted for 56.89% and 43.11% of the total variation,respectively,and that of D.dyeriana was 57.86% and 42.14%,respectively.The Shannon diversity index and Nei gene diversity index showed similar results.The abovementioned characteristics indicated that the genetic diversity levels of these two species were extremely similar and that the interpopulational genetic differentiation within both species was relatively high.Analysis of the genetic distance among populations also supported this conclusion.Low levels of interpopulational gene flow within both species were believed to be among the leading causes for the above-mentioned phenomenon.The correlation analysis between genetic and geographical distances showed the existence of a remarkably significant correlation between the genetic distance and the longitudinal difference among populations of D.sinensis (p＜0.01),while no significant correlation was found between genetic and geographical distances among populations of D.dyeriana.This indicated that genetic distance was correlated with geographical distances on a large scale rather than on a small scale.This result may be related to differences in the selection pressure on species by their habitats with different distribution ranges.We suggest that in situ conservation efforts should focus on establishing more sites to protect the natural populations and their habitats.Ex situ conservation efforts should focus on enhancing the exchange of seeds and seedlings among populations to facilitate gene exchange and recombination,and to help conserve genetic diversity.     

A study on population genetic structure of Oryza meyeriana (Zoll. et Mor. ex Steud.) Baill. from Yunnan and its in situ conservation significance

In order to determine genetic diversity of Oryza meyeriana (Zoll. et Mor. ex Steud. ) Baill., 12 enzyme systems encoded by 17 loci were electrophoretically analyzed in 164 individuals of seven populations from Simao Prefecture, Yunnan Province, China. In comparison with those seed plants with the same life history and breeding systems, as well as the other species in the genus Oryza, the species shows rather low levels of genetic diversity (A = 1.1, P = 8.0%, Ho = 0.004 and He = 0. 015) within populations and high genetic differentiation among populations. FST was up to 0. 649, suggesting that 64. 9% of total genetic variability exists among populations. Considering high genetic differentiation among populations from a limited geographic region, most of the populations of the species are worth being protected, and therefore, great natural protection regions should theoretically be established in which a great deal of populations should be involved for developing in situ conservation management. Meanwhile     

Population genetic diversity of the clonal plant Geum reptans (Rosaceae) in the Swiss Alps

In the alpine landscape most plant populations are spatially isolated due to extreme patchiness and strong natural fragmentation. We used RAPD-PCR (randomly amplified polymorphic DNA polymerase chain reaction) for a study of the genetic diversity within and among 20 populations of Geum reptans, an outcrossing clonal plant species in the Swiss Alps. Populations were sampled at different altitudes, in early-, medium- and late-successional habitats (population origin) using a spatially hierarchical design, with distances among populations ranging from 0.2 to 208 km. Seed and pollen dispersibility was estimated by direct measurements. Seed dispersibility by wind was low with only 0.015% of the seeds flying over 100 m. Observed pollen flow was even more restricted. Molecular diversity within populations was irrespective of population origin (H(e) = 0.22 ± 0.004) and similar to the average of other RAPD studies. Contrary to our expectation, populations were only moderately differentiated (G(st) = 0.14). However, there was a clear spatial genetic structure and a positive relationship between pairwise genetic and geographic distances. Our results indicate considerable gene flow among populations within the same regional area, and we found no indication for genetic depletion during succession or in peripheral habitats. We conclude that, despite the high natural fragmentation and the importance of vegetative reproduction in this alpine plant, gene flow and repeated seedling recruitment during succession might be more frequent than commonly suggested.     

金钱槭和云南金钱槭遗传多样性比较研究

金钱槭属(Dipteronia)是我国特有少种属,属下仅金钱槭(D. sinensis)和云南金钱槭(D. dyeriana)两种。该文用RAPD标记揭示了金钱槭的遗传多样性和遗传结构,并与云南金钱槭的RAPD研究结果进行了比较。同时,对两物种遗传距离与地理距离的相关性进行了分析,结果有助于阐释该属植物遗传变异的产生机制。研究显示,18条随机引物在17个金钱槭居群(226个个体)中检测到128个扩增位点,物种水平的多态位点比率为92.97%,在4个云南金钱槭居群(45个个体)中则检测到103个扩增位点,物种水平的多态位点比率为81.55%,金钱槭的多态位点比率高于云南金钱槭。相似性系数值、Shannon多样性指数和Nei基因多样性指数分析反映了与多态位点比率相一致的结果。AMOVA(Analysis of molecular variance)分析结果显示,金钱槭居群内、居群间的遗传变异分别占总变异量的56.89%和43.11%。云南金钱槭居群内、居群间的遗传变异分别占总变异量的57.86 %和42.14%。Shannon多样性指数、Nei基因多样性指数的分析结果与AMOVA分析结果趋势相同。上述特征值揭示,金钱槭和云南金钱槭居群间的遗传分化均已达到较高水平,推测居群间低水平的基因流可能是导致上述现象产生的原因之一。遗传距离与地理距离的相关分析结果显示,金钱槭居群间的遗传距离与经度差异存在极显著水平的相关性(p<0.01),云南金钱槭居群间的遗传距离与地理隔离则无显著相关关系。说明在大尺度上遗传距离与地理距离相关而在小范围内则无上述关系,该结果可能与位于不同分布区内的物种所承受的生境选择压力不同有关。建议在对该属植物进行就地保护时,应设立多个保护点,保护自然居群及其周围生境;在迁地保护时,应通过加大居群间种子和幼苗的交换,人为创造基因交流和重组的条件,保存该属植物的遗传多样性。     

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.     

基于线粒体控制区的序列变异分析青海东部甘肃鼢鼠遗传多样性

甘肃鼢鼠(Myospalax cansus)是一种终年营地下独居生活的小型掘土类动物。本文通过测定mt DNA的控制区部分序列(530 bp)变异,分析青海东部地区8个甘肃鼢鼠地理种群遗传多样性与遗传结构。158个样本共发现26个变异位点,定义了39种单倍型,整体的平均单倍型多样性高(h=0.953 2)、核苷酸多样性低(π=0.006 36)。歧点分布和中性检验均说明青海东部甘肃鼢鼠种群在历史上存在着快速扩张的事件。基于邻接法构建的网络关系图中,单倍型呈星状分布,没有按地理位置形成对应类群。基因流(Nm)数据显示多数地理种群间基因交流贫乏,AMOVA结果显示种群内与种群间遗传变异分别为48.82%和51.18%,遗传分化明显。IBD分析表明,甘肃鼢鼠的遗传分化与地理距离呈正相关,说明距离隔离对甘肃鼢鼠种群分化具有重要作用。甘肃鼢鼠的这种遗传多样性与种群遗传结构特点,可能是地下生活方式靠挖掘迁移带来的较小扩散能力的结果。     

Loss of genetic variation in geographically marginal populations of Atriplex tatarica (Chenopodiaceae)

BACKGROUND AND AIMS: Genetic variability was estimated for Atriplex tatarica from 25 populations in the Czech Republic. Since its north-western range margin is in central Europe, a relationship between marginality and low within-population genetic diversity was tested in accordance with the Central-Marginal Model. METHODS: Population genetic diversity was expressed by assessing patterns of variation at 13 putatively neutral allozyme loci (comprising 30 putative alleles) within and between 25 natural populations of A. tatarica along a north-west-south-east transect in the Czech Republic. KEY RESULTS: Atriplex tatarica is a species of human-made habitats with a mixed mating system and wide geographic distribution. Overall, A. tatarica displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of loci that were polymorphic was 47.1%, with average values of 1.55, 0.151 and 0.155 for the average number of alleles per polymorphic locus (A), observed heterozygosity (Ho) and expected heterozygosity (He), respectively. There was only weak evidence of inbreeding within populations (FIS=0.031) and significant population differentiation (FST=0.214). Analysis of the data provides no evidence for isolation-by-distance for the whole study area. However, Mantel tests were highly significant for the marginal Bohemian region and non-significant for the central Moravian region. While northern populations of A. tatarica showed significantly lower allelic richness (A=1.462) than populations from the southern part of the study area (A=1.615), they did not differ in observed heterozygosity (Ho), gene diversity (HS), inbreeding within populations (FIS) or population differentiation (FST), despite generally lower values of particular genetic measurements in the marginal region. CONCLUSIONS: Genetic diversity, with the exception of allelic richness, was not significantly lower at the margins of the species' range. This, therefore, provides only weak support for the predictions of the Central-Marginal Model.     

Contrasting genetic diversity and differentiation of populations of two successional stages in a Neotropical pioneer tree (Eremanthus erythropappus, Asteraceae)

Eremanthus erythropappus, commonly known as "candeia", is an abundant pioneer tree species, forming dense populations known as "candeial", but it is also found in forests at middle stages of succession. Trees from forests are bigger and occur in lower density than in the "candeial". The objectives of the present study were to investigate if the decrease in population density during successional process is accompanied by 1) changes in within-population genetic diversity, and 2) differentiation of populations. Eight populations, four of early successional stage ("candeial") and four of middle successional stages (forest), were analyzed with RAPD markers. The genetic diversity found was high compared to other tree species analyzed with RAPD markers. AMOVA revealed that most of the genetic variations of E. erythropappus were found within populations (85.7%), suggesting that this species is predominantly outcrossing. The relatively low differentiation among the populations can be attributed to small distances among the populations analyzed (0.2 to 10.8 km). No indication that populations from middle successional habitats show lower genetic variation than populations from early successional stages was found. The percentage of polymorphic fragments (82.8 and 84.8%) and the Shannon indexes (0.442 and 0.455) were similar in "candeial" and forest, respectively. These results suggest that if an increase in selection intensity occurred during succession, it did not result in a decrease in genetic diversity or that the selection effect was balanced by other factors, such as gene flow. Higher significant differentiation among E. erythropappus populations from "candeial" in relation to that among populations from forest was also not detected.     

Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Mahogany (Swietenia macrophylla, Meliaceae) is the most valuable and intensively exploited Neotropical tree. No information is available regarding the genetic structure of mahogany in South America, yet the region harbours most of the unlogged populations of this prized hardwood. Here we report on the genetic diversity within and the differentiation among seven natural populations separated by up to 2100 km along the southern arc of the Brazilian Amazon basin. We analysed the variation at eight microsatellite loci for 194 adult individuals. All loci were highly variable, with the number of alleles per locus ranging from 13 to 27 (mean = 18.4). High levels of genetic diversity were found for all populations at the eight loci (mean HE = 0.781, range 0.754-0.812). We found moderate but statistically significant genetic differentiation among populations considering both estimators of FST and RST, theta = 0.097 and rho = 0.147, respectively. Estimates of theta and rho were significantly greater than zero for all pairwise population comparisons. Pairwise rho-values were positively and significantly correlated with geographical distance under the isolation-by-distance model. Furthermore, four of the populations exhibited a significant inbreeding coefficient. The finding of local differentiation among Amazonian mahogany populations underscores the need for in situ conservation of multiple populations of S. macrophylla across its distribution in the Brazilian Amazon. In addition, the occurrence of microgeographical genetic differentiation at a local scale indicates the importance of maintaining populations in their diverse habitats, especially in areas with mosaics of topography and soil.     

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.