Chloroplast DNA phylogeography of the endangered Japanese red maple (Acer pycnanthum): the spatial configuration of wetlands shapes genetic diversity

Aim Japanese red maple (Acer pycnanthum K. Koch) is an endangered species which grows in discrete wetland ecosystems within a limited geographical range. It is an important relic of geologic time, an endemic of unique wetland ecosystems and an indicator of hotspots of plant species diversity. However, information on its genetic characteristics across its range is lacking. Our aim was to determine the genetic structure and diversity of the species and make recommendations for conservation. Location Wetlands in central Honshu Island, Japan. Methods We collected leaf samples from 400 individuals of A. pycnanthum in 30 populations, extracted total DNA from each and sequenced three non‐coding regions of chloroplast DNA. Results We identified nine haplotypes. High haplotype diversity (0.81) and the occurrence of rare haplotypes in eight distant populations suggest that wetlands provided multiple, adequate‐size refuges during the Last Glacial Maximum. We found only one to four haplotypes within populations. The high degree of differentiation (G_ST = 0.83) implies that gene flow by seeds among populations is restricted. Eight populations demonstrated a positive contribution to the total genetic diversity owing to occurrence of rare and private haplotypes. Such populations are concentrated in the south‐western part of the species distribution. According to the spatial autocorrelation analysis, there were significant spatial clusters of populations, which were characterized by similar haplotype composition. Using the haplotype distribution, samova and barrier detected nearly identical genetic boundaries. Main conclusion In spite of the species’ limited geographical range, we identified a relatively high number of haplotypes and a clear geographical structure. We propose six management units, which can be used for future conservation activities, such as introduction of new individuals for on‐site conservation projects and seed collection for ex situ conservation.     

High gene flow in Girella punctata (Perciformes,Kyphosidae) among the Japanese Islands inferred from partial sequence of the control region in mitochondrial DNA

Sequencing analysis of the partial control region (c. 450 bp) detected 88 haplotypes from 249 individuals of Girella punctata collected from coastal waters of nine locations in the Japanese Islands. A single haplotype was the most numerous at all sampling locations, and no significant genetic difference was found among G. punctata samples collected from various locations (F_ST=?0·0274 to 0·0247) with high haplotype diversity and low nucleotide diversity, suggesting that G. punctata population had experienced a bottleneck followed by rapid population growth around the Japanese Islands and might be affected by larval dispersal in association with warm currents.     

High Genetic Diversity and Population Differentiation in the Critically Endangered Plant Species Trailliaedoxa gracilis (Rubiaceae)

Trailliaedoxa gracilis W. W. Smith et Forrest (Rubiaceae), a Chinese endemic monotypic genus belonging to the Alberteae (Rubiaceae), exhibits a narrow distribution in the dry valleys of the Jinsha River and Red River drainage area in southwestern China. The few sites at which T. gracilis occurs are fragmented and isolated, and several are highly vulnerable to human disturbance. As T. gracilis is a protected plant with a second-degree national priority, the genetic diversity and structure of the populations of this species should be investigated to determine the most suitable conservation strategy. In this study, two chloroplast regions and one nuclear region were used to investigate the genetic diversity, genetic structure, and demographic history of T. gracilis. We observed a high total genetic diversity (H _T?=?0.952 and 0.966) and low average within-population diversity (H _S?=?0.07 and 0.489) based on cpDNA and nDNA analyses. Thus, a strong genetic structure (F _ST?=?0.98049 and 0.59731) was detected. A phylogeographic structure was detected by nuclear DNA analysis (N _ST?>?G _ST, P?<?0.05); however, the chloroplast data did not show a significant phylogeographic structure (N _ST?<?G _ST, P?>?0.05). The Bayesian skyline plot and isolation with migration analysis were used to estimate the demographic history of T. gracilis. The results indicated that a marked bottleneck effect occurred during the glacial-interglacial of the Pleistocene. Among the extant populations of T. gracilis, the population found in ChunJiang, LuQuan, and YuXi showed the highest haplotype diversity based on cpDNA sequences and should be given priority for protection. According to the nDNA analysis, every population presented a high level of diversity and a high content of private haplotypes. Therefore, every population should be protected.

     

Genetic diversity and population structure in the mtDNA control region of Liza haematocheilus (Temminck & Schlegel, 1845)

The redlip mullet (Liza haematocheilus) is a commercial marine species widespread in the Northwestern Pacific. The genetic diversity and population structure of the redlip mullet collected from 2007 to 2010 along Chinese and Japanese coastal regions, were investigated by mitochondrial DNA. A total of 82 L. haematocheilus individuals were collected from five locations and 41 haplotypes were obtained. A pattern of distribution of genetic variability with high level of haplotype diversity (0.9642 ± 0.0104) and moderate nucleotide diversity (0.0162 ± 0.0085) was detected. The minimum spanning tree constructed with 41 haplotypes showed three divergent clades, corresponding to those defined in the NJ tree. Analyses of molecular variance and the population statistic F_ST also revealed significant genetic structures among populations of L. haematocheilus. The demographic history of L. haematocheilus was examined using neutrality tests and mismatch distribution analysis, which indicated a Pleistocene epoch population expansion. Comparisons of the Hakodate and Qingdao populations in different years demonstrated that marginal but significant (P < 0.05) differences exist in the two Qingdao populations, but with no significant difference (P > 0.05) in the Hakodate populations. Knowledge of their genetic diversity and genetic structure is crucial to establishing appropriate fishery management for the species.     

Microsatellite genetic variation in the Chinese endemic Eucommia ulmoides (Eucommiaceae): implications for conservation

Eucommia ulmoides, a traditional Chinese medicinal plant, is endangered as a consequence of long‐term and widespread harvest in the late 20th century. It has been widely cultivated as a source of herbal medicine and for use in the organic chemical industry in China. In this study, eight microsatellite markers were applied to investigate genetic diversity in E. ulmoides. Three hundred individuals from one semi‐wild population and nine cultivated populations across its main production area were collected. A high level of genetic diversity at population levels (H_E = 0.716) was observed. The highly outcrossed mating system, high longevity of E. ulmoides and seed admixture may be responsible for high genetic variation within populations. A genetic bottleneck was observed in one population. Populations were only slightly differentiated from one another (F_ST = 0.063); this was also supported by AMOVA, which revealed that 94.05% of the total variation resided within populations. This is probably attributable to long‐distance gene flow mediated by the exchange of seeds by local farmers. Implications of these results for the conservation of genetic resources of E. ulmoides are discussed. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 775–785.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215‐bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite F_ST = 0.205, P < 0.001; global mitochondrial control region Φ_ST = 0.399, P < 0.001). Microsatellite‐based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human‐mediated introductions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

青藏高原濒危植物唐古特大黄的遗传多样性

唐古特大黄(Rheum tanguticum)是中国传统的中藏药材,近几年由于生境的严重破坏,已濒临灭绝,并被列入濒危植物名单。为了探索唐古特大黄物种濒危的原因并保护其野生资源,本研究采集了9个居群87个个体的唐古特大黄样本,基于该物种的叶绿体基因trn S-G序列对其进行了遗传多样性研究。结果表明,唐古特大黄物种具有较高的遗传多样性水平(Ht=0.694),其中95.97%的遗传分化来自于居群间(G_(ST)=0.960),4.03%的遗传分化来自于居群内(Hs=0.028)。AMOVA分析也显示唐古特大黄居群间基因流较小(N_m=0.01),存在较高的遗传分化(F_(ST)=0.9631)。唐古特大黄较高的遗传多样性水平可能与该物种较长的进化史和生活史有关,居群间较高的遗传分化可能与高山地区特殊的地理环境和人类活动有关。根据研究结果,建议对唐古特大黄所有野生居群进行就地保护,同时收集种质资源开展异地繁殖工作,以保护物种的遗传多样性,维持其进化潜力。     

Genetic structure of the Danish red deer (Cervus elaphus)

The red deer (Cervus elaphus) population in Denmark became almost extinct in recent historical times due to over‐hunting. The species has subsequently recovered within remote areas, but non‐Danish individuals have been introduced at several localities. To assess genetic structure, past demographic history, and the possibility of a still existing original stock, we analysed 349 specimens from 11 geographically separate areas and from three enclosed areas, genotyping 11 microsatellite loci. Moreover, an 826‐bp fragment of the control region of the mitochondrial DNA was sequenced for 116 recent specimens and seven museum specimens. There was a significant difference in mean expected heterozygosity (H_E) between the three enclosed areas and the 11 unenclosed areas. Significant departures from Hardy–Weinberg equilibrium were observed in the three enclosed areas and in nine of the unenclosed areas. The overall degree of genetic differentiation among all 14 areas was significant (F_ST = 0.09, P < 0.01), primarily because the mean pairwise F_ST for the three enclosed areas was significantly higher than that for the 11 unenclosed areas. A Bayesian clustering procedure detected three genetically distinct populations and indicated reduced gene flow between the enclosed and unenclosed areas. The individuals in the unenclosed areas show genotypic mixture, presumably as a result of gene flow among them. Markov Chain Monte Carlo simulations, based on the genealogical history of the microsatellite alleles, suggest a drastic decline in the effective population size of the enclosed areas some 188–474 years ago. Mitochondrial DNA analysis of the recent specimens showed seven haplotypes. Individuals from the enclosed Jægersborg Dyrehave contain haplotypes that occur all over Denmark and also are found in Western Europe. A close relationship between Scandinavian and Western European red deer is most likely. Only individuals from the unenclosed Lindenborg Estate and the enclosed Tofte Skov did not group with any other Danish individuals. As six of seven museum specimens had haplotypes also found in modern Danish samples, the current population of red deer in Denmark is genetically close to the original Danish red deer. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 688–701.     

Is life history a barrier to dispersal? Contrasting patterns of genetic differentiation along an oceanographically complex coast

Extreme variation in early life‐history strategies is considered a moderately good predictor of genetic subdivision and hence dispersal for a range of marine species. In reality, however, a good deal of population differentiation must reflect historical effects, more subtle variation in life histories, and, particularly, the interaction of larvae with oceanographic processes. Using a combination of allozyme and microsatellite markers, we show that the large‐scale genetic structure of populations of three species (direct and planktonically developing cushion stars and a planktonic developing sea anemone that is also asexually viviparous) varies consistently, in line with the predicted capacity for dispersal within three geographic regions. We detected high levels of genetic subdivision for the direct developing cushion star (F_ST = 0.6), low levels for the planktonically developing cushion star (F_ST = 0.009), and intermediate levels for the sexual/asexual sea anmone (F_ST = 0.19). These patterns are exhibited despite the highly variable patterns of current movement and the presence of biogeographic barriers. Our results suggest that, although there is large scale genetic differentiation for two species, patterns of population connectivity are remarkably consistent within major regions and do not reflect variation in major oceanographic processes or genetic discontinuity coincident with biogeographic boundaries. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 106–116.     

Population structure,diversity, and phylogeography in the near‐threatened Eurasian black vultures Aegypius monachus (Falconiformes; Accipitridae) in Europe: insights from microsatellite and mitochondrial DNA variation

The Eurasian black vulture (Aegypius monachus) has experienced a severe decline during the last two centuries and is globally classified as near‐threatened. This has led to the extinction of many traditional breeding areas in Europe and resulted in the present patchy distribution (Iberian and Balkan peninsulas) in the Western Palearctic. In the present study, we describe the current genetic status of the European populations using both mitochondrial cytochrome b sequences and nuclear microsatellite markers, comparing with those found in Asia (Mongolia and Caucasus region). Although, mitochondrial (mt)DNA revealed a relatively low genetic variability (haplotype diversity), no evidence of genome‐wide genetic erosion exists because nuclear diversity exhibits normal levels and strong differentiation. A highly philopatric dispersal behaviour must be invoked to explain the existence of a clear pattern that revealed by the phylogeographic analysis, which indicates a sharp East–West clinal distribution and an allopatric differentiation. The distribution of mtDNA haplotypes one in the Iberian population and two in Balkan population and the significance divergence at nuclear loci fulfill the definitions of those populations as evolutionary significant units. We discuss how management strategies should aim at the maintenance (or increase) of current genetic variability levels, suggesting that independent conservation plans are urgently required to protect these two breeding European populations from extinction. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 859–872.     

中国湛江市和哈尔滨市褐家鼠种群遗传结构及其年度变化特征

为探索褐家鼠Rattus norvegicus地理种群的遗传结构及其年度变化特点,本研究以广东省湛江市的褐家鼠指名亚种和黑龙江省哈尔滨市的褐家鼠东北亚种为主要研究对象,结合我国及世界其他褐家鼠种群的D-loop序列分析这2个褐家鼠地理种群间D-loop序列的遗传分化情况及系统进化关系,重点分析2008—2015年褐家鼠湛江种群和哈尔滨种群D-loop单倍型的年度频率变化特点。结果表明,褐家鼠湛江种群和哈尔滨种群共有32种不同的单倍型,其中有11种单倍型是2个种群共有的,有4种单倍型仅在湛江种群中出现,有17种单倍型仅在哈尔滨种群中出现。褐家鼠湛江种群D-loop区的核苷酸多态性为0.005,有27个变异位点,单倍型多态性为0.695,褐家鼠哈尔滨种群D-loop区的核苷酸多态性比湛江种群略高,为0.008,有35个变异位点,单倍型多态性为 0.793。褐家鼠湛江种群和哈尔滨种群没有经历过暴发性的扩增。褐家鼠湛江、哈尔滨和湖北3个地理种群的D-loop序列之间发生了明显的遗传分化,其中湛江种群和哈尔滨种群之间的分化程度最高,遗传分化系数F_st为0.245。褐家鼠湛江种群和哈尔滨种群的单倍型数目和主单倍型频率都发生明显波动,推测主要原因可能是由于灭鼠剂的大量使用或其他灭鼠活动导致种群出现瓶颈或更替的现象。     

Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history

Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (G_ST = 0.215; N_ST = 0.256) and nuclear DNA (G_ST = 0.146; N_ST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.     

Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in Taiwan

Aim The purpose of this paper was to study the patterns of genetic variation, demographic history, haplotype relationships and potential location of diversity centres of two closely related species, Machilus thunbergii and Machilus kusanoi. Location The phylogeography of M. thunbergii and M. kusanoi was examined by sampling 110 and 106 individuals from 25 and 16 sampling sites, respectively, across their distributional range in Taiwan. Machilus thunbergii is distributed on the Asian mainland, South Korea, southern Japan, the Ryukyus, Taiwan and the Philippines, whereas M. kusanoi is endemic to Taiwan. These two species are closely related, and both are widely distributed in Taiwan but occupy different altitudinal zones and habitats. Methods The range‐wide variation of M. thunbergii and M. kusanoi in Taiwan was studied using chloroplast DNA (cpDNA) variations. A haplotype network was constructed with the computer program tcs . Nested clade analysis was conducted with the computer program ceodis , and various parameters of genetic diversity were calculated and neutrality tested by the computer program Dna SP. Population differentiation was estimated using the programs arlequin and hapstep . The contribution of the populations to gene diversity and to allelic richness was calculated using the software contrib . The level of divergence for each population from the remaining populations was calculated as the mean value of pairwise F_ST for each population against the rest of the populations. Results Extremely low levels of genetic differentiation were found for both species. This result suggested that these two species probably survived in multiple relict refugia with different population sizes throughout the island during low‐temperature periods of the Pleistocene. In addition, nested clade analysis (NCA) of cpDNA haplotypes indicated that restricted gene flow with isolation‐by‐distance characterized the recolonization after the Pleistocene by Tashueshan and Shiouhluan populations of M. thunbergii in the north‐central area west of the Central Mountain Range (CMR). In contrast, NCA analysis indicated that a major diversity centre on the southern tip of the island (Kending population) and contiguous range expansion characterized the recolonization by M. kusanoi of northern areas along the east side of the CMR. The major diversity centres found for the two species examined were further supported by the results of the mean F_ST for individual populations in comparison with other populations, and of the contribution of the divergence component to the total diversity. Main conclusions This research supports the multiple relict refugia hypothesis for both species investigated. Populations of M. thunbergii at Shiouhluan and Tashueshan in the north‐central area west of the CMR represent a diversity centre currently expanding its size. A diversity centre at the southern‐edge population of M. kusanoi, and a contiguous range expansion from Kending, were found. These results indicate that the M. thunbergii populations at Tashueshan and Shiouhluan and the M. kusanoi population at Kending, and even Soukar, are evolutionarily significant units for conservation programmes.     

Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas

We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise F_ST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise F_ST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.     

Genetic population structure of the paper wasp Polistes olivaceus (Hymenoptera: Vespidae) in Bangladesh

Dispersal triggers gene flow, which in turn strongly affects the ensuing genetic population structure of a species. Using nuclear microsatellite loci and mitochondrial DNA (mtDNA), we estimated the genetic population structure of the wasp Polistes olivaceus throughout Bangladesh. The level of population differentiation using nuclear markers (F _ST) appeared to be much lower than that estimated using mtDNA haplotype sequences (Ф_ST), even after correcting for effective population size differences between the two markers. These results suggest a philopatric tendency, in which gynes disperse less than males. We observed no isolation by distance among the study populations at either the nuclear or mtDNA level, suggesting nonequilibrium between gene flow and drift as a result of very frequent interpopulation movement. For the nuclear markers, an individual assignment test showed no genetically and geographically distinct groups. Instead, phylogenetic analyses as well as a minimum spanning network using mtDNA haplotypes consistently revealed two distinct lineages. The distribution of haplotypes indicated western populations with a single lineage and offered clear evidence for restricted gene flow across the Jamuna–Padma–Upper Meghna river system. Mismatch distributions exhibited a unimodal distribution, which along with a starlike haplotype network, suggested a population expansion in lineage I but not in lineage II. Overall, these results suggest that gene flow among populations of P. olivaceus was affected by both female philopatry and a major river system across Bangladesh.     

Phylogeography of Podocarpus matudae (Podocarpaceae): pre‐Quaternary relicts in northern Mesoamerican cloud forests

Aim Cloud forests of northern Mesoamerica represent the northern and southern limit of the contact zone between species otherwise characteristic of North or South America. Several phylogeographic studies featuring temperate conifer species have improved our understanding of species responses to environmental changes. In contrast, conifer species that presumably colonized northern Mesoamerica from South America are far less studied. A phylogeographic study of Podocarpus matudae (Podocarpaceae) was conducted to identify any major evolutionary divergences or disjunctions across its range and to determine if its current distribution is associated with pre‐Quaternary climatic and/or long‐distance dispersal events. Location Northern Mesoamerica (Mexico and Guatemala). Methods Sixteen populations (157 individuals) of P. matudae were screened for variation at two plastid DNA markers. The intra‐specific phylogenetic relationships among haplotypes were reconstructed using Bayesian inference. Population genetic analyses were undertaken to gain insight into the evolutionary history of these populations. To test whether genetic divergence among populations occurred at different time‐scales plastid DNA sequence data and fossil‐ and coalescent‐based calibrations were integrated. Results The combination of plastid markers yielded 11 haplotypes. Differentiation among populations based on DNA variation (G_ST) (0.707, SE 0.0807) indicated a clear population structure in P. matudae. Differentiation for ordered alleles (N_ST) (0.811, SE 0.0732) was higher than that for G_ST, indicating phylogeographical structure in P. matudae. Most of the total variation (81.3%, P < 0.0001) was explained by differences among populations. The estimated divergence time between the unique haplotypes from a Guatemalan population and the two most common haplotypes from the Sierra Madre Oriental in Mexico was between 10 and 20 Ma, and further haplotype divergence in the poorly resolved clade of the Sierra Madre Oriental occurred between 3 and 0.5 Ma. Main conclusions Divergence estimations support the hypothesis that extant Podocarpus matudae populations are pre‐Quaternary relicts. This finding is consistent with fossil and pollen data that support a Miocene age for temperate floristic elements in Mesoamerican cloud forests, whereas further haplotype divergence within the Sierra Madre Oriental, Chiapas and Guatemala occurred more recently, coinciding with Pleistocene cloud forest refugia.     

North‐south population subdivision of Juniperus seravschanica in Kyrgyzstan revealed through novel plastid DNA markers

Abstract Junipers are main components of semiarid forests in Central Asia. Conservation of these plant genetic resources should be based on an understanding of factors that have shaped species‐level genetic variation. We used Juniperus seravschanica Kom. as a model species to investigate patterns and processes that may be associated with these factors. Novel plastid DNA markers (two minisatellites, one transversion, one indel) were identified and applied to investigate haplotype diversity and population structure in Kyrgyzstan. In total, 540 individuals from 15 populations were analyzed and 11 haplotypes detected. Strong divergence between populations from northern and southern Kyrgyzstan was evident from the haplotype distribution. Gene diversity within populations ranged from 0.083 to 0.765, and was on average higher in southern (0.687) than in northern populations (0.540). A similar pattern was detected in allelic richness. Analysis of molecular variance (AMOVA) revealed that 11.9% of the total genetic variation was due to differences among regions, 1.5% among populations, and 86.6% within populations. N_ST was not significantly different from G_ST (0.125), suggesting no evidence of a phylogeographic pattern. A Mantel test detected a weak but significant isolation‐by‐distance pattern for the whole dataset and southern populations separately. These results suggest that the north of Kyrgyzstan was relatively recently colonized by migrants from southern populations, probably associated with favorable conditions during the early Holocene. The humid Fergana Valley and Fergana Range are probable ecological barriers to gene flow between northern and southern populations.     

Genetic diversity and population structure of the endangered ripon barbel,Barbus altianalis (Boulenger, 1900) in Lake Victoria catchment,Kenya based on mitochondrial DNA sequences

Approximately 850 bp of the mitochondrial control region was used to assess the genetic diversity, population structure and demographic expansion of the endangered cyprinid Barbus altianalis, a species known to be potamodramous in the Lake Victoria drainage system. The 196 samples taken from the four main rivers draining the Lake Victoria catchment (Nzoia, Yala, Nyando and Sondu–Miriu) yielded 49 mitochondrial DNA haplotypes; 83.7% thereof were private haplotypes restricted to particular rivers. The overall mean haplotype diversity was high (0.93663 ± 0.008) and ranged between 0.566 (Sondu – Miriu) and 0.944 (Nzoia). The overall mean nucleotide diversity was low (0.01322 ± 0.00141), ranging from 0.0342 (Sondu – Miriu) to 0.0267 (Nzoia). Population differentiation tests revealed strong and highly significant (P ≤ 0.001) segregation of populations in the four river basins. F_ST values among the four river‐based populations ranged from 0.05202 to 0.44352. The samples formed two main haplotype networks based on a 95% parsimony criterion, each exhibiting a strong signature of past population expansion. The smaller network was restricted to the River Nzoia, whereas the larger network contained representatives from all four rivers; within this the central haplotypes were found in more than one river, whereas the peripheral haplotypes tended to be river‐specific. The degree of population differentiation and the number of river‐specific haplotypes are too high to be explained by recent anthropogenic impacts alone and suggest that the species has probably existed in the Lake Victoria catchment as two populations: the now ‘extinct’ migratory population and the extant river restricted non‐migratory populations.