Leading-edge populations do not show low genetic diversity or high differentiation in a wind-pollinated tree

Climate changes can shift species’ ranges. Knowledge on genetic variation of the leading-edge populations provides critical information to understand responses and adaptation of plants to projected climate warming. To date, the research into genetic variation of leading-edge populations has been limited, particularly in the role of wind-mediated pollen flow in maintaining high genetic variation. Castanopsis sclerophylla (Fagaceae) is a wind-pollinated and gravity-dispersed tree. In the present study, we used seven polymorphic microsatellites to genotype 482 samples from five leading-edge and 12 non-edge populations. Significant effects of recent population bottleneck events were found in three of the five leading-edge populations, indicating that the leading-edge populations might have been recolonized after the Last Glacial Maximum. Genetic diversity was higher, though not significantly, in leading-edge than in non-edge populations. Relationship between genetic diversity and latitude indicated an increasing trend of genetic diversity towards leading-edge populations. No significant difference in genetic differentiation was found between leading-edge and non-edge populations. The inconsistence with the general predictions by leading-edge colonization model could be explained by high gene flow via pollen grains. Pollen-mediated gene flow could maintain high genetic diversity within and low differentiation among leading-edge populations. In response to climate warming, high genetic variation may provide leading-edge populations raw materials for evolutionary adaptation to future environmental conditions.     

Wild sunflower diversity in Argentina revealed by ISSR and SSR markers: an approach for conservation and breeding programmes

Wild sunflower Helianthus annuus originates from North America and has naturalised in Argentina where it is considered invasive. The present study attempts to assess the genetic diversity using two different molecular marker systems to study the wild genetic patterns and to provide data applicable to conservation and breeding uses. Ten natural populations sampled throughout the wild range and six inbred lines were studied using inter‐simple sequence repeat (ISSR) and simple sequence repeats (SSR) markers. A total of 64 ISSR bands and 29 SSR alleles were produced from 106 wild and cultivated plants. We found 9 ISSR private bands and 21 SSR private alleles in wild accessions, but no private bands/alleles were found in cultivated sunflowers. Molecular variability in wild populations was approximately 60% higher than in inbred lines. Local wild sunflowers kept considerable diversity levels in comparison with populations in the centre of origin (approximately 70%) and therefore they might possess a potential for adaptive evolutionary change. Analysis of molecular variance (AMOVA) indicated population structure with nearly 20% of genetic variability attributable to between‐population differentiation. Principal coordinate analyses (PCO) grouped wild populations from different geographic locations, and a Mantel test showed low congruence between genetic distance (GD) and geographic distances (GGD); hence, molecular data could not rule out multiple wild introduction events. Low correlations were found between ISSR and SSR GD at individual and population levels; thus, divergent evolutionary groups were not evident in local wild sunflowers. Several genetic diversity criteria were utilised to assign conservation value and certain wild populations emerged as interesting sites for more extensive sampling.     

Patterns of neutral diversity under general models of selective sweeps

Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best-investigated models of linked selection is the recurrent full-sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation. Here we develop a general model of recurrent selective sweeps in a coalescent framework, one that generalizes the recurrent full-sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, which under fairly general assumptions are unaffected by the subsequent fate of the selected allele. We also apply the theory to a simple model to investigate the impact of recurrent partial sweeps on levels of neutral diversity and find that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequencies rapidly achieved by the selected alleles. Consequently, recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. In fact, the limiting coalescent model under a high rate of sweeps to low frequency is identical to the standard neutral model. The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available.     

Genetic structure of endangered Emmenopterys henryi Oliv. based on ISSR polymorphism and implications for its conservation

Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of nine populations of Emmenopterys henryi Oliv., an endangered plant endemic to China. Relatively low genetic diversity was detected at population level (the percentage of polymorphic loci P=22.56%, the number of alleles per locus A=1.183+/-0.045, the effective number of alleles per locus A(E)=1.007+/-0.345, Nei's gene diversity h=0.071+/-0.017, Shannon information index I=0.104+/-0.025). However, the genetic diversity at species level was relatively high (P=56.05%; A=1.561+/-0.498, A(E)=1.325+/-0.371, h=0.191+/-0.199, I=0.287+/-0.284). Analysis of molecular variance showed that most of the ISSR variation (68.03%) in E. henryi occurred among populations. The estimated Nm from F (ST )was 0.235. It indicated that the fragmentation and isolation of populations might result from specific evolutionary history and anthropogenic activity. Consequently, genetic drift might play an important role in determining the genetic structure of E. henryi. Conservation strategies for this endangered species are proposed based on the genetic data.     

栓皮栎天然群体SSR遗传多样性研究

利用微卫星(SSR)标记对我国4个省内的5个栓皮栎（Quercus variabilis Bl.）天然群体的遗传多样性进行了研究。16对SSR标记揭示了栓皮栎丰富的遗传多样性：等位基因数（A）平均8.4375个,有效等位基因数(Ne)平均为5.9512个,平均期望杂合度(He)0.8059,Nei多样性指数(h)为0.8041。栓皮栎自然分布区中心地带的群体具有较高的遗传多样性,而人为对森林的破坏将降低林木群体的遗传多样性。栓皮栎群体的变异主要来源于群体内,群体间分化较小,遗传分化系数仅为0.0455。此外,栓皮栎群体间的遗传距离与地理距离之间存在显著的正相关。这些遗传信息为栓皮栎遗传多样性的保护和利用提供了一定依据。Abstract: Genetic diversity of five Quercus variabilis natural populations in four provinces of China was studied with microsatellite (SSR) markers. A relatively high level of genetic diversity was detected in Q. variabilis species with 16 polymorphic microsatellite loci. Average number of alleles (A) and effective number of alleles (Ne) were 8.4375 and 5.9512 respectively. The mean expected heterozygosity (He) was 0.8059 and Nei diversity index (h) was 0.8041. Higher diversity was found with the populations from the central range of the species in contrast to those from peripheral areas and human activities might decrease the genetic diversity of populations. The majority of genetic variation occurred within populations, which could be concluded from the low coefficient of genetic differentiation (Fst=0.0455). In addition, significant correlation was found between geographical distance and genetic distance. All these results present a basis to the conservation and utilization of genetic diversity of Quercus variabilis.     

Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers

The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population.     

Survival of the endangered butterfly Lycaena helle in a fragmented environment: Genetic analyses over 15 years

Temporal changes in allele frequencies are often assumed in studies addressing the history of populations affected by different anthropogenic and natural impacts at different time scales. Yet, few studies directly compare the genetic composition of populations over time spans of more than 10 years. Therefore, to test the genetic effects of 15 years of population isolation in the butterfly Lycaena helle, we analysed 472 individuals from 27 samples, of which nine were collected in 1991 and 18 in 2006. Sampling was performed in five mountain regions (Pyrenees, Massif Central, Jura, Vosges and Ardennes). Genetic analyses were performed using five polymorphic microsatellites. Old and new samples of identical or neighbouring populations revealed similar genetic differentiations among these five mountain regions. A comparatively strong genetic differentiation among populations combined with a high amount of private alleles for each mountain area was detected, but mountain‐specific alleles were in most cases identical in 1991 and 2006. Nevertheless, the obtained data also indicate moderate changes between 1991 and 2006 in the species’ genetic structure – genetic differentiation among local populations increased marginally and allele frequencies showed corresponding modifications. A significant decline in genetic diversity was not detectable, and nine private alleles exclusive to a single mountain region were only detected in samples from the year 1991, whereas eleven were only observed in the individuals collected in 2006. These observations might indicate the results of genetic drift within isolated populations.     

Genetic structure of an endangered plant, Antirrhinum microphyllum (Scrophulariaceae): allozyme and RAPD analysis

Thirteen allozyme loci and 68 random amplified polymorphic DNA (RAPD) markers were analyzed to assess the genetic diversity and population structure of threatened Antirrhinum microphyllum (Scrophulariaceae), a narrow endemic of central Spain known from only four populations. According to allozyme data, species genetic diversity (p = 46.15%, A = 2.61, and H(e) = 0.218), as well as within-population genetic diversity (p = 44.23%, A = 2.10, and H(e) = 0.204), were high when compared to average estimates for other narrowly distributed plant species. Ninety-four percent of species genetic diversity corresponded to within-population genetic diversity. Nevertheless, significant differences were found among populations in allele frequencies of four of the six polymorphic loci, and three private alleles were detected. Inbreeding coefficients (F(IS)) suggest that populations are structured in genetic neighborhoods. The RAPDs also showed high levels of genetic diversity (p = 89.71% and H(e) = 0.188 at the species level, and p = 67.65% and H(e) = 0.171 at the population level). Nei's genetic distances estimated both from allozymes and RAPDs indicated low differentiation among populations. In spite of this, the low frequencies of certain alleles and the presence of private alleles indicate that efforts should be made to conserve all four remaining populations.     

Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite‐mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing‐selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts.     

中华猕猴桃和美味猕猴桃自然居群遗传结构及其种间杂交渐渗

 利用9对SSR引物对中华猕猴桃（Actinidia chinensis）和美味猕猴桃（A. deliciosa）两近缘种的5个同域分布复合体和各自1个非同域分布居群进行了遗传多样性、居群遗传结构的分析以及种间杂交渐渗的探讨。结果表明：1）两物种共有等位基因比例高达81.13%,物种特有等位基因较少（中华猕猴桃：13.27%,美味猕猴桃：5.61%）,但共享等位基因表型频率在两近缘种间存在差异,而且与各同域复合体中两物种样本的交错程度或间距存在关联;2）两种猕猴桃均具有极高遗传多样性,美味猕猴桃的遗传多样性（H_o＝0 .749, PIC＝0.818）都略高于中华猕猴桃（H_o＝0.686,PIC＝0.799）;3）两猕 猴桃物种均具有较低的Nei’s居群遗传分化度,但AMOVA分析结果揭示种内异域居群间（F_ST=0.091 5）和同域复合体种间（F_ST=0.111 5）均存在一定程度的遗传分化;中华猕猴桃居群遗传分化（G_ST=0.086; F_ST=0.212 1）高于美味猕猴桃（G_ST= 0.080;F_ST=0.142 0）;4）同域分布复合体两物种间的遗传分化（G_ST=0.020）低于物种内异域居群间的遗传分化（中华猕猴桃：G_ST=0.086; 美味猕猴桃：G_ST=0.080）,同域复合体物种间的基因流（N_m＝7.89 -29.75）远远高于 同种异域居群间（中华猕猴桃：N_m =2.663; 美味猕猴桃：N_m=2.880）; 5）居群UPGMA聚类揭示在同一地域的居群优先聚类,个体聚类结果显示多数个体聚在各自居群组内,但各地理居群并不按地理距离的远近聚类,这与Mantel相关性检测所揭示的居群间遗传距离与地理距离没有显著性相关的结果一致。进一步分析表明两种猕猴桃的遗传多样性和居群遗传结构不仅受其广域分布、远交、晚期分化等生活史特性的影响,同时还与猕猴桃的染色体基数高 (x=29)、倍性复杂和种间杂交等因素密切相关,其中两种猕猴桃的共享祖先多态性和同域分布种间杂交基因渗透对两猕猴桃的居群遗传结构产生了重要影响。     

Impact on Reindeer (Rangifer tarandus) Genetic Diversity from Two Parallel Population Bottlenecks Founded from a Common Source

Population bottlenecks and founder events reduce genetic diversity through stochastic processes associated with the sampling of alleles at the time of the bottleneck, and the recombination of alleles that are identical by descent. At the same time bottlenecks and founder events can structure populations through the stochastic distortion of allele frequencies. Here we undertake an empirical assessment of the impact of two independent bottlenecks of known size from a known source, and consider inference about evolutionary process in the context of simulations and theoretical expectations. We find a similar level of reduced variation in the parallel bottleneck events, with the greater impact on the population that began with the smaller number of females. The level of diversity remaining was consistent with model predictions, but only if re-growth of the population was essentially exponential and polygeny was minimal at the early stages. There was a high level of differentiation seen compared to the source population and between the two bottlenecked populations, reflecting the stochastic distortion of allele frequencies. We provide empirical support for the theoretical expectations that considerable diversity can remain following a severe bottleneck event, given rapid demographic recovery, and that populations founded from the same source can become quickly differentiated. These processes may be important during the evolution of population genetic structure for species affected by rapid changes in available habitat.     

Genetic diversity and evolutionary history of four closely related Aquilegia species revealed by 10 nuclear gene fragments

The genus Aquilegia is emerging as the new model system for plant development, ecology, and evolution studies. Previous research showed that pollinator shift might drive the diversification of North American Aquilegia species, and natural selection on the length of petal nectar spur might play a crucial role. In this genus, A. ecalcarata Maxim. is the only taxon that has lost nectar spurs. Previous phylogenetic results indicated that A. ecalcarata, A. yabeana Kitag., A. oxysepala var. kansuensis Bruhl., and A. rockii Munz comprised a monophyletic group. However, their pattern of genetic diversity remains unknown. In addition, little is known about the evolutionary relationship among the four species on the population level. We carried out a population genetics study with 21 representative populations based on 10 single-copy nuclear gene fragments and found that: (i) A. yabeana conserved the highest genetic diversity (both π_sil and θ_sil) and A. oxysepala var. kansuensis had the lowest level; (ii) A. ecalcarata split into two groups, with one population clustered with A. rockii and the other five populations clustered with A. oxysepala var. kansuensis; and (iii) the allele frequency spectrum showed an excess of low frequency alleles in all four species, implying that they may undergo the mutation-drift equilibrium. Our findings provide the first investigation of genetic diversity and evolutionary relationships in A. yabeana, A. oxysepala var. kansuensis, A. rockii, and A. ecalcarata. They lay the foundation for future evolutionary studies, such as speciation mediated by pollinators.     

Large mainland populations of South Island robins retain greater genetic diversity than offshore island refuges

For conservation purposes islands are considered safe refuges for many species, particularly in regions where introduced predators form a major threat to the native fauna, but island populations are also known to possess low levels of genetic diversity. The New Zealand archipelago provides an ideal system to compare genetic diversity of large mainland populations where introduced predators are common, to that of smaller offshore islands, which serve as predator-free refuges. We assessed microsatellite variation in South Island robins (Petroica australis australis), and compared large mainland, small mainland, natural island and translocated island populations. Large mainland populations exhibited more polymorphic loci and higher number of alleles than small mainland and natural island populations. Genetic variation did not differ between natural and translocated island populations, even though one of the translocated populations was established with five individuals. Hatching failure was recorded in a subset of the populations and found to be significantly higher in translocated populations than in a large mainland population. Significant population differentiation was largely based on heterogeneity in allele frequencies (including fixation of alleles), as few unique alleles were observed. This study shows that large mainland populations retain higher levels of genetic diversity than natural and translocated island populations. It highlights the importance of protecting these mainland populations and using them as a source for new translocations. In the future, these populations may become extremely valuable for species conservation if existing island populations become adversely affected by low levels of genetic variation and do not persist.     

Allozyme diversity in natural populations of Viola palmensis Webb & Berth. (Violaceae) from La Palma (Canary Islands): implications for conservation genetics

Genetic diversity was measured by allozyme electrophoresis in eight natural populations of the threatened Canarian endemic Viola palmensis Webb & Berth. (Violaceae). Nineteen alleles corresponding to 11 gene loci were detected. High levels of genetic diversity were found, ranging from 36.3 to 45.4 % for the percentage of polymorphic loci (P), from 1.45 to 1.60 for the average number of alleles per locus (A) and from 0.128 to 0.200 for the expected heterozygosity (H(e)). Between 85.5 and 96.6 % of genetic variability was apportioned within populations. As a whole, populations were not at Hardy-Weinberg equilibrium, with a deficit of heterozygous individuals attributable to the existence of genetic structuring in the populations analysed. The levels of interpopulation genetic differentiation were low (mean F(ST) = 0.100), while genetic identity pair-wise comparisons were high (mean I = 0.973) suggesting considerable levels of gene flow among populations. No relationship was detected between genetic differentiation and geographical distances between populations. An outcrossing insect-mediated breeding system might contribute to pollen dispersion of this species. For conservation genetics we suggest in situ preservation areas are defined that are free of disturbance and that include populations with the highest genetic diversity.     

Microsatellite variation within and among recently fragmented populations of the golden lion tamarin (Leontopithecus rosalia)

Four variable microsatellite loci were used toexamine the genetic diversity and differentiation of golden lion tamarins (Leontopithecus rosalia) in four populations recently isolated by habitat fragmentation. Using Rst estimates of genetic differentiation, a considerable genetic divergence was detected among these populations, with an averagedifferentiation of 31%. Significant differences in allele number among these populations were found. However, the heterozygosity among these populations was not statistically different. These results suggestthat loss in allele diversity was faster than loss in heterozygosity. Conservation implications, particularly for golden lion tamarins, are then discussed. Loss of allelic diversity might be as serious a concern to endangered species as heterozygosity or inbreeding.     

蒙古沙葱萤叶甲种群遗传多样性的微卫星分析

【目的】沙葱萤叶甲 Galeruca daurica (Joannis)是一种近年来在内蒙古草原上猖獗成灾的新害虫,本研究旨在明确内蒙古沙葱萤叶甲不同地理种群间的遗传分化和基因交流程度。【方法】应用5对微卫星引物分析了沙葱萤叶甲8个地理种群的遗传多样性、基因流和遗传分化。【结果】5个位点等位基因数为10~18,有效等位基因数为9.2796~16.0388,多态信息含量值为0.6760~0.8985,期望杂合度为0.3430~0.5284,说明所选5个微卫星位点均为高度多态性位点。8个种群的期望杂合度为0.2216~0.3701,平均值为0.2680;种群间遗传分化系数为0.1244~0.4116,平均值为0.2521;种群间基因流为0.3574~1.7596,平均值为0.9622。8个地理种群根据遗传距离聚为3个分支,遗传距离与地理距离呈显著的正相关关系 (r=0.4854,P=0.0180)。【结论】沙葱萤叶甲种群遗传多样性低,不同地理种群之间基因流较小,遗传分化程度高;沙葱萤叶甲迁移能力弱和地理阻碍可能是限制其基因交流和导致遗传高度分化的主要原因。     

Simple allelic-phenotype diversity and differentiation statistics for allopolyploids

The analysis of genetic diversity within and between populations is a routine task in the study of diploid organisms. However, population genetic studies of polyploid organisms have been hampered by difficulties associated with scoring and interpreting molecular data. This occurs because the presence of multiple alleles at each locus often precludes the measurement of genotype or allele frequencies. In allopolyploids, the problem is compounded because genetically distinct isoloci frequently share alleles. As a result, analysis of genetic diversity patterns in allopolyploids has tended to rely on the interpretation of phenotype frequencies, which loses information available from allele composition. Here, we propose the use of a simple allelic-phenotype diversity statistic (H') that measures diversity as the average number of alleles by which pairs of individuals differ. This statistic can be extended to a population differentiation measure (F'ST), which is analogous to FST. We illustrate the behaviour of these statistics using coalescent computer simulations that show that F'ST behaves in a qualitatively similar way to FST, thus providing a useful way to quantify population differentiation in allopolyploid species.     

Global diversity and genetic contributions of chicken populations from African,Asian and European regions

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (F_ST) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour‐Net genetic clustering and structure analysis revealed two main groups of Asian and north‐west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north‐west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds.     

Postglacial colonisation of western Central Europe by Polyommatus coridon (Poda 1761) (Lepidoptera: Lycaenidae): evidence from population genetics

The genetic population structure of Polyommatus coridon (Poda 1761) over large regions of France, Italy and Germany was studied by allozyme electrophoresis. The genetic diversity within populations was high for all parameters analysed (number of alleles 2.72; observed and expected heterozygosity 19.6% and 20.3%, respectively; percentage of polymorphic loci: total: 76.4% and, with polymorphism if the frequency of the commonest allele is below 95%: 53.1%), whereas genetic differentiation between populations was comparatively low (FST = 0.021 +/- 0.002). The mean number of alleles declined significantly from southern to northern populations (r = -0.53, P = 0.0005). Similar effects were found also for other parameters of genetic diversity. This is interpreted as a loss of genetic diversity during postglacial expansion. However, samples from France and Italy had similar patterns of genetic diversity indicating no significant loss in this region. Populations from southern Germany were genetically uniform, well differentiated from French populations and showed a significant loss of genetic diversity. Probably, this is due to a bottleneck during passing through the Burgundian Gap, which is a migration corridor from north-eastern France to southern Germany. In contrast to southern German populations, western German populations were not well differentiated from French populations. Nevertheless, they were genetically impoverished, probably as a result from local bottlenecks and post-expansion phenomena.     

Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak

Understanding the factors determining genetic diversity and structure in peripheral populations is a long‐standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter‐population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak.