Alpine biogeography of Parnassian butterflies during Quaternary climate cycles in North America

Growth of alpine glaciers during the Pleistocene had profound effects on montane landscapes in North America and the organisms now inhabiting alpine ecosystems. Biogeography of this region has often been viewed as a system of sky islands despite the fact that species richness patterns deviate from a strict island biogeographic model. One explanation is that alpine species are not in equilibrium because of late Quaternary geographic range shifts. Genetic data can provide evidence of nonequilibrium dynamics and the distributional shifts that occur during glaciation events in alpine landscapes. Using mitochondrial and nuclear sequence data, we examine the evolutionary history of butterflies in the Parnassius phoebus complex. We test explicit, alternative models of the biogeographic history of Parnassius smintheus and Parnassius behrii , including an equilibrium island model, ancestral radiation and fragmentation, an expanding alpine archipelago and an alpine archipelago refuge model. Our results support the alpine archipelago refuge model, in which alpine butterflies undergo population contraction during glacial climates followed by population expansion during interglacial phases. While butterflies can disperse between distant mountain ranges during glacial periods, gene flow is rare. We find evidence of recent connectivity between California and Colorado, population expansion events following deglaciation ∼20 000 years B.P., and small population sizes during the last glacial period. An analysis of lineage splitting suggests that morphological differences in P. smintheus and P. behrii are the result of late Pleistocene divergence (∼48 000 years B.P.) with limited gene flow. Our results demonstrate that spatially complex and nonequilibrium population dynamics influence alpine diversity patterns.     

Multilocus phylogeography of the sea snake Hydrophis curtus reveals historical vicariance and cryptic lineage diversity

The Indo‐Australian archipelago (IAA) supports the world's highest diversity of marine fish, invertebrates and reptiles. Many of the marine fish and invertebrates show congruent phylogeographic patterns, supporting a view that the region's complex geo‐climatic history has played an important role in generating its exceptional biodiversity. Here, we examine population genetic structure of the viviparous sea snake, Hydrophis curtus, to assess how past and present barriers to gene flow in the IAA have contributed to genetic and species diversity in a fully marine reptile. Mitochondrial and anonymous nuclear sequences and ten microsatellite loci were used to identify patterns of historical genetic structure and population expansion, reconstruct dated genealogies and assess levels of recent gene flow. These markers revealed strong concordant geographic structure within H. curtus with a prominent genetic break between populations broadly distributed in the Indian Ocean and the West Pacific. These populations were estimated to have diverged in the late Pliocene or early Pleistocene, and microsatellite admixture analyses suggested limited recent gene flow between them despite the current lack of barriers to dispersal, indicating possible cryptic species. Subsequent divergence in the mid–late Pleistocene was detected within the West Pacific clade among the populations in the Phuket‐Thailand region, South‐East Asia and Australia, and two of these populations also showed genetic signals of recent range expansions. Our results show that climatic fluctuations during the Plio‐Pleistocene generated high levels of cryptic genetic diversity in H. curtus, and add to similar findings for diverse other marine groups in the IAA.     

Phylogeography and conservation genetics of the Iowa pleistocene snail

The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.     

Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences

Shortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 10(1) to 10(4), but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty-nine mtDNA nucleotide-substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2-5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide-substitution haplotypes and length-variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once-glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five-region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units.     

Ir genes of different high responder haplotypes for staphylococcal nuclease are not allelic

The Ir gene controlling high responsiveness to staphylococcal nuclease in the H-2d haplotype has been mapped to the I-A subregion, in contrast to that in the H-2k and H-2a haplotypes, which maps in the I-B subregion. The nonallelic high responder genes also confer differences in fine specificity on the antibodies produced. This nonallelism of Ir genes for the same antigen in different haplotypes is consistent with Ir gene mechanisms involving associative recognition of antigen plus Ia by T lymphocytes. It further suggests that products of different subregions can perform the same function.     

Genetic diversity and population demography of narrow‐ridged finless porpoises from South Korea on the basis of mitochondrial DNA variation: Implications for its conservation in East Asia

The narrow‐ridged finless porpoise, Neophocaena asiaeorientalis, is a small cetacean inhabiting the coastal waters of Taiwan, East China, Korea, and Japan, and is threatened by anthropogenic pressures. We analyzed the mitochondrial control region of N. asiaeorientalis from Korean waters to better understand the genetic diversity, population structure, and demographic history through comparison with previously reported sequences from Japan and China. The network and phylogenetic analyses illustrated that few common haplotypes were centrally located, and that most of the unique haplotypes were on the edges of the branches. Moreover, the estimates of fixation indices and gene flow revealed significant genetic differentiation among the regions in East Asia. The mismatch distribution suggested a population expansion in the late Pleistocene. We propose that the current genetic variation in N. asiaeorientalis in East Asia was shaped by historical demographic expansion during the late Pleistocene. The N. asiaeorientalis of Korean waters has the highest diversity observed with the sampling available at this time. However, the abundance of N. asiaeorientalis in Korean waters has rapidly declined and the species needs protection from bycatch.     

Polyploidy,phylogeography and Pleistocene refugia of the rockfern Asplenium ceterach: evidence from chloroplast DNA

Chloroplast DNA sequences were obtained from 331 Asplenium ceterach plants representing 143 populations from throughout the range of the complex in Europe, plus outlying sites in North Africa and the near East. We identified nine distinct haplotypes from a 900 bp fragment of trnL-trnF gene. Tetraploid populations were encountered throughout Europe and further afield, whereas diploid populations were scarcer and predominated in the Pannonian-Balkan region. Hexaploids were encountered only in southern Mediterranean populations. Four haplotypes were found among diploid populations of the Pannonian-Balkans indicating that this region formed a northern Pleistocene refugium. A separate polyploid complex centred on Greece, comprises diploid, tetraploid and hexaploid populations with two endemic haplotypes and suggests long-term persistence of populations in the southern Mediterranean. Three chloroplast DNA (cpDNA) haplotypes were common among tetraploids in Spain and Italy, with diversity reducing northwards suggesting expansion from the south after the Pleistocene. Our cpDNA and ploidy data indicate at least six independent origins of polyploids.     

Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north-western Pacific

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested-clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial–interglacial cycles shaping genetic structure and population demography of S. ariakensis .     

Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum)

The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.     

基于线粒体COI基因序列的黄胫小车蝗不同地理种群的遗传分化及基因流分析

黄胫小车蝗Oedaleus infernalis Saussure是一种在我国分布广泛、 对农牧业生产危害严重的经济害虫。本文对黄胫小车蝗10个地理种群的线粒体COI基因序列进行测序和分析, 利用DnaSP 5.0和Arlequin 3.5.1.2软件对该蝗虫种群间的遗传多样性、 遗传分化程度、 基因流水平及分子变异进行了分析, 建立了单倍型贝叶斯系统发育进化树和单倍型网络图。结果表明： 在所分析的144个序列样本中, 共检测到21种单倍型, 其中1种单倍型为10个地理种群所共享。总群体的单倍型多样性指数为0.653, 各地理种群单倍型多样度范围在0.423~0.790之间。总群体和各种群的Tajima’s D检验结果皆不显著, 说明该种害虫在较近的历史上未经历群体扩张。总群体的遗传分化系数Gst为0.04436, 固定系数Fst为0.05255, 基因流Nm为9.01。AMOVA分子方差分析结果表明, 黄胫小车蝗的遗传分化主要来自种群内部, 种群间的遗传变异水平较低。各地理种群的遗传距离的大小与其地理距离间没有显著的相关性。贝叶斯系统发育进化树与单倍型网络图显示, 黄胫小车蝗各地理种群中的单倍型散布在不同的分布群中, 分布格局较为混杂, 未形成明显的系统地理结构。研究结果揭示, 黄胫小车蝗各种群间的基因交流并未受到地理距离的影响。     

Glacial vicariance and historical biogeography of rock ptarmigan (Lagopus mutus) in the Bering region

In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However, isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow. In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.     

Patterns of spatial genetic structuring in a hydropsychid caddisfly (Cheumatopsyche sp. AV1) from southeastern Australia

We assessed levels of mitochondrial genetic spatial structuring in the hydropsychid caddisfly Cheumatopsyche sp. AV1 in southeastern New South Wales, Australia. No significant spatial structuring was detected within or between catchments using analysis of molecular variance, and nested clade contingency analysis suggested no strong relationship between haplotypes and geographical location, at any clade level. However, tests for association among haplotypes incorporating geographical distance in the nested clade analysis, revealed patterns of historical range expansion and recent restricted gene flow. Most likely, population fragmentation preceded range expansion, although subsequent recontact and gene flow among the previously sundered populations has apparently obscured the geographical signature of the former fragmentation. Taken together, our analyses suggest that a number of populations fragmented during the Pleistocene evolved in isolation for a time and subsequently expanded into secondary contact. Since expansion, there has apparently been substantial (albeit somewhat restricted) dispersal and gene flow of adult female Cheumatopsyche sp. AV1, throughout the study area.     

Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism

We used molecular evidence to examine the roles that vicariance mechanisms (mountain-building and drainage changes during the Pleistocene) have played in producing phylogeographical structure within and among South American fish species of the temperate perch family Percichthyidae. The percichthyids include two South American genera, Percichthys and Percilia, each containing several species, all of which are endemic to southern Argentina and Chile (Patagonia). Maximum-likelihood phylogenies constructed using mitochondrial DNA (mtDNA) control region haplotypes and nuclear GnRH3-2 intron allele sequences support the current taxonomy at the genus level (both Percichthys and Percilia form strongly supported, monophyletic clades) but indicate that species-level designations need revision. Phylogeographical patterns at the mtDNA support the hypothesis that the Andes have been a major barrier to gene flow. Most species diversity occurs in watersheds to the west of the Andes, together with some ancient divergences among conspecific populations. In contrast, only one species (Percichthys trucha) is found east of the Andes, and little to no phylogeographical structure occurs among populations in this region. Mismatch analyses of mtDNA sequences suggest that eastern populations last went through a major bottleneck c. 188 000 bp, a date consistent with the onset of the penultimate and largest Pleistocene glaciation in Patagonia. We suggest that eastern populations have undergone repeated founder-flush events as a consequence of glacial cycles, and that the shallow phylogeny is due to mixing during recolonization periods. The area of greater diversity west of the Andes lies outside the northern limit of the glaciers. mtDNA mismatch analysis of the genus Percilia which is restricted to this area suggests a long-established population at equilibrium. We conclude that patterns of genetic diversity in these South American genera have been primarily influenced by barriers to gene flow (Andean orogeny, and to a lesser extent, isolation in river drainages), and by glacial cycles, which have resulted in population contraction, re-arrangement of some watersheds, and the temporary breakdown of dispersal barriers among eastern river systems.     

云南西花蓟马rDNA-ITS2遗传多态性及其种群扩张

应用rDNA-ITS2基因序列对云南各地理种群西花蓟马Frankliniella occidentalis(Pergande)的遗传结构和遗传分化程度进行初步研究。经过比对112条序列,共发现了59个变异位点,定义了30种单倍型。云南省西花蓟马的单倍型多态性较高(Hd=0.90219),而核酸多态性较低(Pi=0.00891)。各地理种群西花蓟马的遗传分化指数Fst为0.00810,基因流Nm为30.61,表明各地理种群间遗传分化程度非常低,种群间存在充分的基因交流。对群体进行中性检验、错配分析表明西花蓟马群体曾经历过近期的种群扩张。分子方差分析(AMOVA)表明,云南西花蓟马的遗传变异主要来自于种群内部,种群间的遗传变异水平还非常低。从分子生物学的角度上也证实了西花蓟马近期入侵云南的事实。     

Mitochondrial phylogeny, taxonomy and biogeography of the silvered langur species group (Trachypithecus cristatus)

With a distribution ranging from mainland Southeast Asia to the Sunda region, the silvered langur species group is the most widely distributed species complex of the genus Trachypithecus. However, the systematic classification of its members and the phylogenetic relationships among them are less understood, leading to different classification schemes and proposed distribution zones. To address these issues, we sequenced a 573 bp long fragment of the mitochondrial cytochrome b gene from 115 silvered langurs (68 individuals from known origin). According to our data, five monophyletic clades were detected, which refer to the five taxa auratus, cristatus, germaini, margarita and mauritius. The phylogenetic relationships among them are not well resolved, indicating a radiation-like splitting event, which was estimated to have occurred about 0.95-1.25 mya. Within T. cristatus, two major clades were detected, with one comprising specimens from Sumatra, Borneo and the Natuna archipelago, and the other solely individuals from the Malaysian peninsula. According to our findings, we propose to rank all five taxa as distinct species. While T. auratus, T. germaini, T. margarita and T. mauritius seem to be monotypic, T. cristatus should be split into two subspecies, with the Malaysian form being described as new form here. From a phylogeographic perspective, the species group most likely originated on Java. During the early Pleistocene, its range was expanded to the Malaysian peninsula and to the Southeast Asian mainland. Later on, the Malaysian form colonised further regions of the Sunda region, including Sumatra, Borneo and the Natuna archipelago.     

Phylogeography of the Asian lesser white-toothed shrew, <Emphasis Type="Italic">Crocidura shantungensis</Emphasis>, in East Asia: role of the Korean Peninsula as refugium for small mammals

Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp). A Bayesian tree for 98 haplotypes detected in 228 C. shantungensis specimens from East Asia revealed the presence of three major groups with at least 5 subgroups. Most haplotypes were distributed according to their geographic proximity. Pairwise F_ST’s and analysis of molecular variance (AMOVA) revealed a high degree of genetic differentiation and variance among regions as well as among populations within region, implying little gene flow among local populations. Genetic evidence from South Korean islands, Jeju-do Island of South Korea, and Taiwan leads us to reject the hypothesis of recent population expansion. We observed unique island-type genetic characteristics consistent with geographic isolation and resultant genetic drift. Phylogeographic inference, together with estimates of genetic differentiation and diversity, suggest that the southern most part the Korean Peninsula, including offshore islands, played an important role as a refugium for C. shantungensis during the Pleistocene. However, the presence of several refugia on the mainland of northeast Asia is also proposed.     

羚牛的遗传多样性及其种群遗传结构分析

羚牛是亚洲大陆一种特有的大型珍稀动物,目前正面临着栖息地丧失、片段化和人类活动的严重威胁。为了有效地保护这种濒危动物,全面了解羚牛的种群结构、进化历史和整个分布区内遗传多样性的分布是至关重要的。本研究以mtDNA D-loop330bp基因片段为分子标记,比较分析了来自陕西秦岭、甘肃南部、四川岷山、邛崃山和云南贡山的40个样品的序列差异,根据分布特点将所采集到的羚牛分为3个地理单元,即秦岭、四川和云南。结果表明,在3个地理单元中存在4种单倍型,且地理单元间不存在共享单倍型,相互单倍型之间的平均序列差异为1.66％。进一步分析表明,3个地理单元间的基因流较低,存在着显的遗传分化 ,说明羚牛具有明显的系统地理分布格局。同时提出应将分布于秦岭山区、唐家河青川地区、天全以及云南贡山地区作为独立的管理单元分别加以保护。     

Distinguishing between primary and secondary intergradation among morphologically differentiated populations of Anolis marmoratus

Distinguishing between primary and secondary intergradation among differentiated populations, and the relative importance of drift and selection, are persistent problems in evolutionary biology. An historical perspective on population interactions can provide insight into the nature of contacts, and thus help resolve these questions. Continuously distributed populations of Anolis marmoratus from the island of Basse Terre in the Guadeloupean archipelago of the Lesser Antilles show a striking degree of geographic variation in morphology. Initial surveys of mtDNA variation from throughout the Guadeloupean Archipelago revealed one case where levels of sequence difference and phylogenetic relationships of alleles from morphologically differentiated populations from the east coast of Basse Terre were consistent with primary intergradation. In this paper, I examine the genetic population structure of a series of populations spanning this north-south cline in morphological variation to test the hypothesis of primary intergradation. Sequences of the mitochondrial cytochrome-b gene from 50 individuals representing five populations spanning the cline were obtained and fourteen unique haplotypes (differing by 2% or less) were detected. Patterns of nucleotide substitution among haplotypes do not deviate from neutral expectation indicating no effect of selection at the level of mtDNA sequences. Estimates of population structure and gene flow were made using both summary statistics for nucleotide diversity (N_at) and cladistic methods. The results are sensitive to the choice of gene flow model, and this is discussed in detail. Mitochondrial variation in the northern populations may not be at equilibrium, and the phylogeny of alleles is consistent with a recent increase in effective population size. Estimates of nucleotide diversity, gene flow, and the phylogenetic relationships of haplotypes indicate that the southern-most population (representing the extreme of morphological variation along this cline) has been relatively isolated from populations to the north and has experienced a reduced effective population size. The apparent clinal variation between the southern population and the others may therefore reflect secondary contact and introgression rather than primary intergradation.     

Colonization, dispersal, and hybridization influence phylogeography of North Atlantic sea urchins (Strongylocentrotus droebachiensis)

We used frequency-based and coalescent-based phylogeographic analysis of sea urchin (Strongylocentrotus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans-Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back-migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans- Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.