Rivers influence the population genetic structure of bonobos (Pan paniscus)

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.     

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA

The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D‐loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high‐frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low‐frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.     

Genetic diversity and phylogeography of Daphnia similoides sinensis located in the middle and lower reaches of the Yangtze River

Geographical patterns, climate, and environmental change have important influences on the distribution and spread of aquatic organisms. However, the relationships between the geographical pattern and phylogenetics of Daphnia as well as environmental change are not well known. The genetic diversity and phylogeography of seven D. similoides sinensis populations located in the middle and lower reaches of the Yangtze River were investigated based on the combination of mitochondrial (COI gene) and nuclear (14 microsatellite primers) markers. Based on the mitochondrial gene markers, D. similoides sinensis from the middle and lower reaches of the Yangtze River had one ancestral haplotype and two evolutionary clades. In addition, D. similoides sinensis population deviated from neutral evolution, showing signs of a bottleneck effect followed by population expansion. Based on the microsatellite markers, the seven D. similoides sinensis populations formed three main groups. The dendrogram (NJ/ME) showed that D. similoides sinensis based on the mitochondrial genes marker were obviously clustered two main clades, whereas there were three clades based on the microsatellite markers. Our results suggested that the habitat fragmentation due to the barrier of the dams and sluices promoted the genetic differentiation and phylogeography of D. similoides sinensis populations in the middle and lower reaches of the Yangtze River.     

Phylogeography of the Southeast Asian stone oaks (Lithocarpus)

Abstract Aim To describe current geographical patterns of genetic diversity and infer the historical population dynamics of the stone oaks (Lithocarpus) in Southeast Asia. Location We sampled three populations in Indochina: (1) Yunnan province, China; (2) Pyin Oo Lwin area, Myanmar and (3) north‐western Vietnam; two in western Borneo: (1) South‐western Sarawak and (2) West Kalimantan, Indonesia; two in central Borneo: (1) north coastal Sarawak and (2) north‐eastern Sarawak, Malaysia; and two in northern Borneo: (1) Central Sabah and (2) Northern Sabah, Malaysia. Methods A phylogenetic reconstruction of chloroplast DNA sequence variation from numerous individuals of multiple species was used to determine geographical distribution of genetic diversity. A resampling scheme was used to determine the significance of these patterns at different hierarchical levels of the phylogeny. Results were compared with a previously published set of nuclear DNA sequence data. Results A high level of chloroplast sequence variation was found, which was divided equally between two major clades separated by four non‐homoplasious changes. One clade was confined to the island of Borneo, while the other was widespread. Strong geographical structure was observed in the chloroplast sequence variation. The Indo‐chinese populations were much more closely related than expected, comparable with the highly endemic and isolated population on the western coast of Borneo. Conversely, individuals from the Kelabit Highlands were found to be more distantly related than expected. The highest levels of genetic endemism were observed in western Borneo. More geographical structure was observed in the Bornean clade than in the Widespread clade, because of limited genetic diversity in the Widespread clade. Relatively weak geographical structure was found in the nuclear sequence variation: only populations in southern China and central Sabah were significantly related. Conclusions The high levels of chloroplast genetic diversity and the persistence of an ancestral haplotype that is a single step away from a haplotype found in Castanopsis indicates the continuous presence of tropical rain forest in Southeast Asia throughout the evolutionary history of the genus (c. 40 Myr). This conclusion is supported by the high frequency of numerous endemic types observed in every population and the relatively few number of ‘missing’ haplotypes. This situation suggests both limited migration and limited extinction. In contrast, the nuclear genetic diversity contained less geographical structure, indicating that our taxonomic sampling among populations was unbiased and that gene flow mediated through pollen is less geographically restricted and contains less geographical structure than purely seed‐mediated (chloroplast) gene flow. The most likely scenario suggested by the evidence involves four major patterns: (1) the widespread presence of an ancestral haplotype; (2) the large degree of separation (four non‐homoplasious base pairs) between the types found in the two major clades; (3) the concentration of derived types from both major clades found in central and northern Borneo; and (4) the molecular endemism found in each location. These patterns suggest four primary things about the population dynamics of Lithocarpus since the late Eocene: (1) populations have either spanned the entire region throughout much of the evolutionary history of the genus or substantial populations have persisted in both Indochina and Borneo with limited migration between them; (2) significant fragmentation has occurred subsequently between the Asian mainland and the Melasian island archipelago, leading to independent genetic diversification in both regions; (3) several locations possessing significant independent histories, have experienced little migration and have never gone completely extinct; and (4) that the central highlands of Borneo have been re‐invaded from the north and the west. The timing of these events is difficult to ascertain but probably predate the Quaternary Period, suggesting that although the recent ice ages might have affected the overall distribution of rain forest in Southeast Asia, it managed to persist in most regions even through the most dramatic drying events.     

Phylogeography of the Japanese common sedge, Carex conica complex (Cyperaceae), based on chloroplast DNA sequence data and chromosomal variation

? Premise of the study: Genetic and chromosomal variations in plants are often reflected in the geographical distribution patterns. Therefore, identifying such phylogeographical patterns on population is important for understanding the process of plant diversification and speciation, and analyzing both molecular and cytological aspects is necessary. ? Methods: We investigated the phylogeographic pattern and genetic diversity of the widespread Japanese sedge, Carex conica complex, based on chloroplast DNA haplotypes and chromosomal variations. ? Key results: Sixteen distinct haplotypes were detected from 258 individuals in the C. conica complex inferred from the cpDNA sequences of intergenic spacer (IGS) between atpB and rbcL, IGS between trnT and trnL, trnL intron, and IGS between trnL and trnF. Most haplotypes showed distinct geographical structures. Phylogenetic analyses revealed two major clades, clades I and II, among 16 haplotypes of the complex. The haplotypes of clade I were mainly found in eastern Japan, while most haplotypes of clade II were found in western Japan. Four intraspecific aneuploids of 2n = 32, 34, 36, and 38, with forming normal bivalents in meiotic divisions, were also found in the complex. The geographical distribution of these intraspecific aneuploids corresponded well with those of the haplotypes. ? Conclusions: Our results suggest that the genetic diversity and chromosomal variations in the C. conica complex may have originated from contractions and expansions of geographical ranges affected by Quaternary climatic oscillations.     

Geographic differentiation of <Emphasis Type="Italic">Cobitis shikokuensis</Emphasis> inferred from mtDNA RFLP analysis

Mitochondrial DNA divergence among populations of the Japanese spinous loach Cobitis shikokuensis, endemic to Shikoku Island, was investigated by restricted fragment length polymorphism analysis. A total of 68 restriction sites on DNA fragments from the cytochrome b to D-loop regions and from the 12S rRNA to 16S rRNA regions, amplified by PCR, were analyzed. A total of 12 haplotypes (plus 6 in outgroups) were detected in 268 specimens collected from 19 localities in seven rivers (and 41 specimens from four localities in three rivers in outgroups). Three of the seven river populations of C. shikokuensis were shown to have unique haplotypes, and four of the seven river populations were monomorphic. The nested structure of the haplotype network for populations of C. shikokuensis exhibited two large clades corresponding to (1) populations from the Shimanto River and its neighbors and (2) two genetically divergent populations in the Shigenobu and Iwamatsu Rivers. The population from the Shimanto River, the largest river inhabited by C. shikokuensis, maintains great haplotype diversity as well as the allozyme diversity previously reported. On the other hand, populations from the Hiji River, the second largest river, which exhibited the highest allozyme diversity, were monomorphic in their mtDNA. The nested clade analysis (NCA) revealed that past fragmentation between the above two clades could occur in the initial distribution process of C. shikokuensis. The large genetic divergence of two river populations from the Shigenobu and Iwamatsu Rivers was inferred to be caused by a process of long distance colonization and fragmentation. MtDNA introgression into the Hiji River population from southern river populations was suggested. Taking genetic divergence into consideration, each river population of C. shikokuensis should be conserved separately as like a distinct species, and conservation programs for the small populations showing less genetic variability should be invoked as soon as possible.     

The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences

The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species'' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent.     

Genetic diversity and population structure of Sepiella japonica (Mollusca: Cephalopoda: Decapoda) inferred by mitochondrial DNA (COI) variations

In order to describe the genetic diversity of five geographical populations of cuttlefish (Sepiella japonica) along with Chinese coast and determined their phylogenetic relationship, partial mitochondrial COI gene (681bp in length) was amplified from 96 individuals collected from these populations and sequenced. The 5 populations of cuttlefish inhabit Yellow Sea, East China Sea and South China Sea. Out of 22 polymorphic nucleotides identified, 8 were represented by a single sequence, 12 were parsimony informative, which defined 22 haplotypes. Haplotype and nucleotide diversity were low among populations. Of 22 haplotypes, 15 appeared only in a single population, 6 appeared in 2 or 3 populations and 1 was shared by all populations. The COI gene was monomorphic in Qingdao population. The haplotypes identified clustered into 2 clades, each covered individuals from 5 populations each. Pairwise F_ST were not proportional to the geographical distances. Among the 5 populations, relatively high level of genetic diversity was found in Ningde population which was recommended to be the best choice of germplasm resources for artificial releasing project.     

Genetic diversity,genetic structure and phylogeography of the Iberian endemic Gypsophila struthium (Caryophyllaceae) as revealed by AFLP and plastid DNA sequences: connecting habitat fragmentation and diversification

Iberian gypsum outcrops are highly fragmented and ecologically challenging environments for plant colonization. As gypsophytes occur exclusively in such habitats, they are ideal models for the study of both the effects of habitat fragmentation and selection on population genetic diversity and structure. In this study, we used amplified fragment length polymorphism (AFLP) and plastid DNA sequences to investigate the phylogeographical history of the Iberian plant Gypsophila struthium (Caryophyllaceae), a widespread endemic restricted to Iberian gypsum outcrops. Gypsophila struthium consists of two subspecies that differ in the architecture of their inflorescence and have mostly allopatric ranges. Gypsophila struthium subsp. struthium occurs in central, eastern and south‐eastern Iberia, whereas G. struthium subsp. hispanica occurs in northern and eastern areas. AFLPs revealed low but significant genetic differentiation between the subspecies, probably as a result of a recent diversification during the Pliocene–Pleistocene. In the geographical contact zone between the taxa, the Bayesian analyses revealed populations with mixed ancestries and genetic clusters predominantly of one or the other subspecies, indicating incomplete reproductive barriers between them. Plastid DNA haplotypes revealed strong geographical structure and testified to processes of isolation by distance and continuous range expansion for some haplotype clades. The Bayesian analyses of the population structure of AFLP data and nested clade phylogeographical analysis (NCPA) of plastid haplotypes revealed that the putative ancestral range corresponded to central and eastern populations of G. struthium subsp. struthium, with those lineages contributing through more recent expansion to increased genetic diversity and structure of the south‐eastern and eastern ranges of this subspecies and to the diversification of G. struthium subsp. hispanica in northern and eastern gypsum outcrops. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 654–675.     

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。     

Palaeo‐islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae)

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within‐island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable ‘palaeo‐islands’ of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra‐island levels of genetic diversity larger than those between‐islands. We argue that volcanic eruptions and landslides after the merging of the palaeo‐islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo‐islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.     

Streaked horned lark <Emphasis Type="Italic">Eremophila alpestris strigata</Emphasis> has distinct mitochondrial DNA

The Streaked Horned Lark (STHL; Eremophila alpestris strigata) is a federal candidate for listing under the Endangered Species Act. We evaluated the conservation status and level of genetic diversity of the STHL using the complete mitochondrial ND2 gene. We sampled 32 STHLs from the southern Puget Sound region, the Pacific coast, and Whites Island in the Columbia River of Washington, and additional 68 horned larks from Alaska, alpine and eastern Washington, Oregon, California, and Asia (outgroups). Our Maximum Likelihood analysis of 32 haplotypes identified three geographically concordant clades in Pacific coast states: Pacific Northwest (alpine and eastern Washington, Alaska), Pacific Coast (western Washington, California), and Great Basin (eastern Oregon). Each of the three clades was supported by bootstrap values ≥86%. The distance among them varied from 0.72 to 0.79% nucleotide divergence excluding intraclade variation. The relationship among the clades was not resolved. AMOVA also showed significant structuring of haplotypes among the three clades. Differences among clades accounted for 75.7% of sequence variation, differences among localities within clades accounted for 12.1%, and differences among individuals within localities accounted for the remaining 12.2%. Although STHL populations were closely related to the Californian sample, they appeared unique and isolated. All pairwise F _st values involving the STHL samples were significant (except between themselves). STHLs appear to have remarkably low genetic diversity; all 32 STHLs shared the same haplotype. Even with small sample sizes, all other localities had multiple haplotypes. Because the STHL appears to be unique and isolated, and to have little genetic diversity our data suggest it should be a conservation priority.     

长江中下游湖泊短颌鲚线粒体控制区遗传多样性分析

为探明长江中下游不同湖泊中短颌鲚(Coilia brachygnathus)遗传多样性水平和遗传分化程度,以洞庭湖、长湖、巢湖3个地理群体作为研究对象,采用线粒体控制区序列为分子标记,分别应用软件Dna SP 5.0、Arlequin3.1.1、MEGA5.0和Network 5.1进行了遗传参数统计和单倍型间分子变异分析(AMOVA),构建邻接系统树及单倍型网络图。对长江中下游短颌鲚野生群体的遗传多样性和遗传结构进行分析。结果显示,用来分析的1 236 bp D-loop区序列中共90个变异位点,54个简约信息位点。长江中下游3个地理群体中共发现58个单倍型,单倍型多样性(h)范围0.949~0.982,核苷酸多样性范围0.004 99~0.006 21,说明长江中下游3个湖泊短颌鲚地理群体具有较高的遗传多样性水平。3个短颌鲚地理群体遗传分化指数(Fst)为0.265 95,呈现出中等程度的分化水平,主要表现在巢湖群体与其他群体之间处于中等程度分化水平。依据遗传距离构建系统发育树及单倍型网络图也出现相类似结果。     

秦岭细鳞鲑群体遗传结构

秦岭细鳞鲑(Brachymystax lenok tsinlingensis)是秦岭地区特有鱼类,近年来由于环境恶化及人类活动的加剧,已对其造成严重影响,种群处于濒危状态,因此研究秦岭细鳞鲑的群体遗传结构、演化历史、分布动态等对其进行有效保护具有重要意义。本研究用线粒体D-loop区序列对秦岭地区6个群体(n=112)进行了遗传结构和群体演化分析。D-loop区扩增出的891bp序列在112个个体中,检测到42个变异位点,共26个单倍型;碱基序列总的单倍型多样度较高为0.883,核苷酸多样度为0.00799。AMOVA分析显示,60.05%的分子差异位于群体内,39.95%的分子差异位于群体间,Fst值统计检验表明,除那布大河群体与漳河群体和千河群体之间差异不显著之外,其余两两群体之间Fst值统计检验均为显著。系统树和单倍型网络图分析表明,6个地理群体的单倍型按照渭河上游和渭河中游两个河段形成两个大的类群,且5个群体共享一个单倍型H2,表明这些群体具有相同的演化历史,为同一个祖先群体演化而来。中性检验和歧点分布显示,秦岭细鳞鲑种群大小保持相对稳定,未经历明显的种群扩张。同时建议将渭河上游秦岭细鳞鲑群体作为一个整体进行重点保护。     

POPULATION GENETIC STRUCTURE OF FINLESS PORPOISES, NEOPHOCAENA PHOCAENOIDES, IN CHINESE WATERS, INFERRED FROM MITOCHONDRIAL CONTROL REGION SEQUENCES

Seven hundred and twenty base pairs (bp) of the mitochondrial control region from 73 finless porpoises, Neophocaena phocaenoides , in Chinese waters were sequenced. Thirteen variable sites were determined and 17 haplotypes were defined. Of these, 5 and 7 were found only in the Yellow Sea population and the South China Sea population, respectively, whereas no specific haplo-type was found in the Yangtze River population. Phylogenetic analyses using NJ and ML algorithm did not divide the haplotypes into monophyletic clades representing recognized geographic populations of finless porpoises in Chinese waters, suggesting the existence of migration and gene flow among populations. Analysis of molecular variance showed the obvious population genetic structure (φ_st= 0.41, P < 0.05); however, the structure was mainly between either the Yangtze River population or the Yellow Sea population and the South China Sea population. The genetic diversity (nucleotide diversity and haplotypic diversity) of the Yellow Sea population was significantly higher than those of the Yangtze River population and the South China Sea population, suggesting the relatively later divergence of the latter two populations and supporting the Yellow Sea population as the original center of Neophocaena .     

Phylogeography and genetic structure of the orchid Himantoglossum hircinum (L.) Spreng. across its European central–marginal gradient

Aim This study aims to link demographic traits and post‐glacial recolonization processes with genetic traits in Himantoglossum hircinum (L.) Spreng (Orchidaceae), and to test the implications of the central–marginal concept (CMC) in Europe. Location Twenty sites covering the entire European distribution range of this species. Methods We employed amplified fragment length polymorphism (AFLP) markers and performed a plastid microsatellite survey to assess genetic variation in 20 populations of H. hircinum located along central–marginal gradients. We measured demographic traits to assess population fitness along geographical gradients and to test for correlations between demographic traits and genetic diversity. We used genetic diversity indices and analyses of molecular variance (AMOVA) to test hypotheses of reduced genetic diversity and increased genetic differentiation and isolation from central to peripheral sites. We used Bayesian simulations to analyse genetic relationships among populations. Results Genetic diversity decreased significantly with increasing latitudinal and longitudinal distance from the distribution centre when excluding outlying populations. The AMOVA revealed significant genetic differentiation among populations (F_ST = 0.146) and an increase in genetic differentiation from the centre of the geographical range to the margins (except for the Atlantic group). Population fitness, expressed as the ratio N_R/N, decreased significantly with increasing latitudinal distance from the distribution centre. Flower production was lower in most eastern peripheral sites. The geographical distribution of microsatellite haplotypes suggests post‐glacial range expansion along three major migratory pathways, as also supported by individual membership fractions in six ancestral genetic clusters (C1–C6). No correlations between genetic diversity (e.g. diversity indices, haplotype frequency) and population demographic traits were detected. Main conclusions Reduced genetic diversity and haplotype frequency in H. hircinum at marginal sites reflect historical range expansions. Spatial variation in demographic traits could not explain genetic diversity patterns. For those sites that did not fit into the CMC, the genetic pattern is probably masked by other factors directly affecting either demography or population genetic structure. These include post‐glacial recolonization patterns and changes in habitat suitability due to climate change at the northern periphery. Our findings emphasize the importance of distinguishing historical effects from those caused by geographical variation in population demography of species when studying evolutionary and ecological processes at the range margins under global change.     

Mitochondrial DNA variation and the phylogeography of the grey partridge (Perdix perdix) in Europe: from Pleistocene history to present day populations

Abstract For a phylogeographical analysis of European grey partridge (Perdix perdix) we sequenced 390 nucleotides of the 5′ end of the mitochondrial control region (CR) of 227 birds from several localities. The birds were divided into two major clades (western and eastern) which differed in control region 1 (CR1) by 14 nucleotide substitutions (3.6%). For estimation of the time of divergence, the whole CR of 14 specimens was sequenced. The major clades differed by 2.2%, corresponding to an estimated coalescence time of c. 1.1 million years. On CR1, 45 haplotypes were found. Western clade haplotypes were found in France, England, Germany, Poland, Italy and Austria. Eastern clade haplotypes were found in Finland, Bulgaria, Greece, and Ireland. One Finnish population and all Bulgarian and Irish populations were mixed, but only in Bulgaria was the mixing assumed to be natural. Nucleotide and haplotype diversities varied between populations, and both clades showed geographical structuring. The distribution of pairwise nucleotide differences in the eastern clade fitted the expectations of an expanding population. About 80% of the genetic structure in the grey partridge could be explained by the clades. The western clade presumably originates on the Iberian Peninsula (with related subtypes in Italy), and the eastern clade either on the Balkan or Caucasian refugia. Large‐scale hand‐rearing and releasing of western partridges have introduced very few mtDNA marks into the native eastern populations in Finland.     

Mitochondrial DNA variation and biogeography of eastern gorillas

Mitochondrial DNA variation in 109 individuals from four populations of wild living gorillas in East Africa was ascertained by sequencing the first hypervariable segment of the control region, or 'd-loop', amplified from noninvasively collected hair and faeces. D-loop haplotypes from eastern gorillas fell into two distinct clades, each with low levels of genetic diversity; most observed haplotypes within each clade differing by only one or two mutations. Both clades show evidence of population bottlenecks in the recent past, perhaps concomitant with the tropical forest reduction and fragmentation brought on by global cooling and drying associated with the last glacial maximum.     

Phylogeographic structure and postglacial evolutionary history of water voles (Arvicola terrestris) in the United Kingdom

The phylogeographic pattern of mitochondrial DNA variation in water voles (Arvicola terrestris) from 57 localities across the United Kingdom and representative samples from Spain, France, Switzerland and Finland was determined from sequence variation in the central portion of the control region. Twenty-seven different haplotypes were resolved which formed two distinct phylogenetic clades. This major division separated haplotypes found in Scotland from those found in England and Wales. Nested clade analysis of haplotypes indicated that such a division was a consequence of allopatric fragmentation. The haplotypes found in Switzerland, France and Spain clustered with Scottish haplotypes, whereas the haplotype from Finland clustered with the English/Welsh haplotypes. These patterns indicate that contemporary Scottish populations are derived from an Iberian glacial refugium, whereas English and Welsh populations are derived from an eastern European refugium. As such, the postglacial recolonization of the United Kingdom must have involved two colonization events, either in different localities with no subsequent contact, or as two waves separated over time, with the second wave of colonizers displacing the first. An analysis of molecular variance (AMOVA) identified significant population genetic divergence within both the major clades, indicative of restricted gene flow and regional population isolation. The implications of both phylogeographical and population genetic structure are discussed in context with the conservation of water voles in Britain.     

赤水河半鳆的遗传多样性和种群历史动态分析

在赤水河的水潦、茅台、二合、太平、赤水市5个样点共采集了168尾半鰐Hemiculterella sauvagei, 通过线粒体DNA的细胞色素b (Cyt b)基因序列分析了半鰐种群遗传多样性和种群历史动态。获得序列长度为1137 bp, 其中包含42个变异位点, 13个单突变位点, 29个简约信息位点。168条序列共检测到38种单倍型, 单倍型多样性(H_d)和核苷酸多样性(P_i)分别为0.895±0.012和0.00487±0.00695。分子方差分析(Analysis of Molecular Variance, AMOVA)显示: 遗传变异主要来源于种群内部(80.95%)。F_st值统计表明, 赤水市种群与茅台、二合、水潦种群之间存在高度分化, 与太平镇种群之间存在中度分化, 其他种群之间无显著差异, 这表明分布在赤水市和其他4个地理种群的半鰐应作为不同的管理单元(MU)进行保护。Mega 6.0 软件计算5个种群之间的平均净遗传距离范围为0.004—0.006。中性检验结果为水潦、太平和赤水市的F_s值为负值, 表明这3个地理种群的半鰐曾发生过种群扩张。采用1% per Myr的突变速率推算出半鰐水潦种群扩张时间大约在0.43百万年前, 太平镇种群大约在0.40百万年前, 赤水市种群大约在0.37百万年前。