Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey

The genetic diversity and phylogeography of maternal lineages in Ursus arctos Linnaeus, 1758 (the brown bear) have been studied extensively over the last two decades; however, sampling has largely been limited to the northern Holarctic, and was possibly biased towards lineages that recolonized the vast expanses of the north as the Last Glacial Maximum (LGM) ended. Here we report the genetic diversity and phylogeography of U. arctos from Turkey based on 35 non‐invasive samples, including five from captive individuals. Bayesian phylogenetic analyses based on a 269‐bp fragment of the mitochondrial DNA control region revealed 14 novel haplotypes belonging to three major lineages. The most widespread lineage was found to be the Eastern clade 3a, whereas geographically more restricted Western and Middle Eastern lineages were reported for the first time in Turkey. A specimen from the Taurus mountain range carried a haplotype closely related to the presumably extinct bears in Lebanon. Moreover, we identify a unique new lineage that appears to have split early within the Middle Eastern clade. Despite limited sampling, our study reveals a high level of mitochondrial diversity in Turkish U. arctos, shows that the ranges of both European and Middle Eastern clades extend into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence. Obtaining these results with 35 samples also demonstrates the value of proper sampling from regions that have not been significantly affected by the LGM. © 2015 The Linnean Society of London     

Phylogenetic Relationships Among Quolls Revisited: The mtDNA Control Region as a Useful Tool

There has been a great deal of interest in determining phylogenetic relationships within the family Dasyuridae due to the widespread distribution, ecological diversity, and relative plesiomorphy of this taxon within the Australasian marsupial radiation. In the past, it has been extremely problematic to determine the phylogenetic relationships among species within Dasyurus, with numerous studies using both morphological and molecular characters providing different topologies. Here, the mitochondrial DNA (mtDNA) control region is used as a novel set of characters in an attempt to identify relationships among the six closely related extant species. Sequences were obtained from multiple individuals representing all extant species of quolls including, when possible, individuals from different geographical regions. Sequences were analyzed using both parsimony criteria and neighbor-joining methods. Results presented here concur with those of Krajewski et al. (1997) in (1) placing D. geoffroii in a highly supported clade with D. spartacus, (2) resolving a monophyletic group of D. albopunctatus + D. geoffroii + D. spartacus, and (3) placing D. hallucatus as the sister taxon to all other species of quolls. Results also show two highly supported and geographically distinct clades of D. maculatus (Tasmanian and mainland) that do not correspond to the currently used subspecific nomenclature. Preliminary results also indicate that there are different clades among geographic groups of D. hallucatus that warrant further investigation. The mtDNA control region is a highly variable locus and may be used in forensic tests for species identification in this genus.     

Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis

A fragment of mitochondrial DNA (mtDNA) control region (approximately 700 bp) was sequenced in 104 individuals from 20 breeds (three Chinese domestic breeds, five recently derived breeds and 12 introduced breeds) of domestic rabbits, Oryctolagus cuniculus. Nineteen sites were polymorphic, with 18 transitions and one insertion/deletion, and eight haplotypes (A1, A2, A3, A4, A5, A6, A7 and A8) were identified. Haplotype A1 was the most common and occurred in 89 individuals. In the 25 Chinese rabbits, only haplotype A1 was observed, while four haplotypes (A1, A3, A5 and A6) were found in 26 recently derived individuals. Haplotype A2 was shared by seven individuals among three introduced strains. The other six haplotypes accounted for 0.96-1.92% of the animals. Combined with the published sequences of European rabbits, a reduced median-joining network was constructed. The Chinese rabbit mtDNAs were scattered into two clusters of European rabbits. These results suggest that the (so-called) Chinese rabbits were introduced from Europe. Genetic diversity in Chinese rabbits was very low.     

三个黄颡鱼群体遗传多样性及亲缘关系的微卫星标记分析

利用微卫星标记技术对3个黄颡鱼群体(W S、TE和QF)的遗传多样性及亲缘关系进行研究。通过筛选的30个引物对3个黄颡鱼群体基因组DNA的扩增,获得了19个有效引物,其中有6个微卫星位点具有多态性,并计算出了3个黄颡鱼群体间的遗传相似系数和遗传距离,TE和QF群体间的遗传相似系数最大(0.8736),遗传距离最小(0.1790);W S和QF群体间的遗传相似系数最小(0.7284),遗传距离最大(0.2768)。同时运用聚类分析(UPGMA)的方法建立了3个黄颡鱼群体的系统发生树。     

Phylogenetic lineages of Monopterus albus (Synbranchiformes: Synbranchidae) in China inferred from mitochondrial control region

Phylogenetic inference of mitochondrial control region (501 bp) of 167 individuals from 12 regional populations revealed that Chinese swamp eels fell into five genetic lineages, Lineage A, B, C, D and E. Lineage A was speculated to share the same mitochondrial ancestors with the populations from Taiwan Island. Lineage C harboured most of the haplotypes (39/60) of populations and may have experienced population expansion. The distribution pattern of Lineage C from east to west regions may have resulted from the occurrence of the major glaciation and inter‐regional introduction. Lineage A, B and E inhabiting coastline regions were immune from the expansion of Lineage C due to isolation from inland areas blocking gene flow between inland and coastal populations. On the other hand, Chinese swamp eels were revealed to be maintaining substantially differentiated population structures, while three populations from the Sichuan basin (MY, LC and YA) were genetically closely related. This was attributed to the geographical isolation of Sichuan populations from other populations, facilitating gene flow among the three populations from the Sichuan basin.     

Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)

In the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.     

栓皮栎天然群体SSR遗传多样性研究

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

Phylogenetic analysis of chinese rhesus macaques (Macaca mulatta) based on mitochondrial control region sequences

Between one and six subspecies of Chinese rhesus macaques (Macaca mulatta) have been proposed based on morphological differences and/or their geographic distribution. In this study, a 489 base pair fragment of the mitochondrial control region was amplified from 230 DNA samples collected from rhesus macaques in the Sichuan province in Western China. The fragment was then sequenced and aligned with 208 sequences from wild rhesus macaques, sampled throughout the species' geographic range in China downloaded from GenBank. Phylogenetic analysis of the 182 unique sequences identified among these samples divided Chinese rhesus macaques into two western haplogroups (haplogroups A and B) and three older eastern haplogroups (haplogroups C, D, and E), whose differentiation probably occurred during the penultimate glacial event. During the warming after the penultimate glacial event, haplogroups A, B, and E rapidly expanded and a relatively young subhaplogroup of haplogroup E, E', limited to Southern China but shared with Vietnamese rhesus macaques, was reintroduced from Indochina during the last glacial event. One haplotype most closely related to subhaplogroup E' probably represents the isolation of Hainan Island, to where it is restricted, from the mainland by the formation of the Qiongzhou Strait approximately 8,500 years ago. The distribution of haplogroups both informs the phylogeographic history of dispersal of Chinese rhesus macaques and has implications for their suitability as animal models in biomedical research.     

华南地区黒眶蟾蜍的遗传变异和地理分化

黒眶蟾蜍Bufo melanostictus(Anura,Bufonidae)是亚洲常见的蟾蜍,广泛分布于中国华南地区。由于华南地区分布着众多的大陆架岛屿及其地貌的复杂性与多样性,因而不同地区的黑眶蟾蜍种群可能存在地理上的遗传变异。本文首次采用DNA序列分析方法,检测了采自我国华南6个省市地区(福建、广东、广西、海南、香港、台湾),包括4个主要大陆架岛屿(海南岛、大屿山、南澳岛、台湾岛)的12个黑眶蟾蜍种群共84个个体,获得mtDNA控制区序列长956bp的片段,共有75个变异位点(26.3%为单个多态位点,73.7%为简约信息位点),12个插入/缺失。所获得的44个单倍型中有5个为种群间共享的单倍型。华南地区黒眶蟾蜍较高的的遗传多样性(单倍型多样性h=0.977)不但表现为海岛种群内普遍具有较高的遗传变异,而且遗传分化指数(FST)、基因流(Nm)、Amova和Samova等分析均表明种群之间已经发生了明显的遗传分化。从Amova分析和分子系统发育分析结果来看,华南地区分布于大陆与分布于海岛的种群之间并未发生明显的遗传分化,说明由陆缘浅海造成的阻隔作用(isolation by barrier)并不能很好地解释华南地区黑眶蟾蜍种群之间遗传分化的原因。遗传距离与地理距离的低度相关(Mantel测试R=0.192,P<0.001)说明华南地区黑眶蟾蜍的种群分化並不完全符合距离决定分化(isolation by distance)的假说。Samova的结果表明华南沿海大陆东部的3个种群(广东汕头、福建莆田和东山)与其它地区9个种群之间的变异最大(FCT=0.35097),因此,推测黑眶蟾蜍这2个地理区域组之间应该存在着其它地理隔离屏障,对两地黑眶蟾蜍的迁移有一定的阻隔作用,产生此隔离效应的天然地理屏障可能为莲花山脉。黑眶蟾蜍种群在历史上曾发生多次局部扩张,时间大约在距今0.025MYA左右,这与最后一次冰期结束的时间相吻合,而位于我国华南大陆周边的4个主要大陆架岛屿(海南岛、大屿山、南澳岛、台湾岛)可能是华南地区黒眶蟾蜍在第四纪冰期的"避难所"。南澳岛种群所存在的特殊单倍型验证了这一岛屿避难所的存在。本研究揭示的地理种群之间的遗传变异和分化,对进一步了解华南地区乃至亚洲的黒眶蟾蜍的生物地理关系有重要意义。     

Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish,rock carp (Procypris rabaudi) in upper Yangtze River drainage

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, π = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit.     

The role of waterholes as 'refugia' in sustaining genetic diversity and variation of two freshwater species in dryland river systems (Western Queensland, Australia)

1. Episodic floods and extended low or no flow periods characterise dryland river systems in Western Queensland, Australia. During protracted intervals between floods, rivers consist of a series of isolated waterholes, which serve as ‘refugia’ for aquatic species and much of the channel is dry. We categorised these waterholes into ‘main waterholes’, which are located in the main part of the river channel and ‘satellite waterholes’, which are located in distributary river channels. 2. We used mitochondrial sequences and allozymes to investigate levels of genetic diversity and patterns of connectivity among waterholes for two obligate freshwater species: Macrobrachium australiense (Decapoda: Palaemonidae) and Notopala sublineata (Gastropoda: Viviparidae). 3. We sampled 31 waterholes for M. australiense and 12 for N. sublineata. Based on a 505‐bp fragment of cytochrome oxidase subunit I, we identified 54 haplotypes in a sample of 232 individuals for M. australiense and based on a 457‐bp fragment of the same gene, 36 haplotypes in a sample of 145 individuals for N. sublineata. 4. Both nuclear and mitochondrial genetic data sets indicated that estimates of genetic diversity were not different in populations inhabiting main and satellite waterholes for either species. Also, there was generally very limited genetic differentiation among populations at any site. 5. We suggest that levels of connectivity among populations inhabiting waterholes at most sites are higher than expected. High levels of connectivity may help to maintain overall high levels of genetic diversity as well as low levels of genetic differentiation among waterholes within sites.     

线粒体控制区在鱼类种内遗传分化中的意义

线粒体DNA（mtDNA）作为分子标记已被广泛应用于各物种系统发生的研究。mtDNA控制区序列（D-Loop）以其较高的突变积累对于研究物种种内的遗传分化具有重要价值。鱼类是脊椎动物中最原始但在种属数量上又最占优势的类群,其物种繁多,分布广泛,起源复杂,研究其系统发生历来是令人饶有兴趣的课题。D-Loop在研究鱼类种内遗传分化中具有多方面的重要意义。近年来,已有越来越多的研究工作将D-Loop作为分子标记来探讨各种鱼类的种内遗传分化,并且获得了许多有启发性的结果。青海湖是我国内陆最大的咸水湖,湖中主要鱼类为青海湖裸鲤（Gymnocypris przewalskii）,D-Loop分析初步结果显示青海湖及其周围河流中的裸鲤似乎没有新的种内遗传分化现象。      

Allozyme Variation and Phylogenetic Relationships in Picea jezoensis (Pinaceae) Populations of the Russian Far East

Genetic variation and differentiation of 12 populations of Picea jezoensis from the Russian Far East were studied using 20 allozyme loci. The mean number of alleles per locus was 2.63, the percent of polymorphic loci was 88.1%, the observed heterozygosity was 0.181, and the mean value of expected heterozygosity amounted to 0.189. The values of expected heterozygosity of the northern and central mainland populations were higher than in the southern part of the natural range. A significant bias of Hardy–Weinberg heterozygosity to equilibrium heterozygosity (H_eq) suggests that most of the mainland populations have recently experienced a severe expansion in population size while populations from Kamchatka Peninsula have undergone a reduction in population size. Unbiased Nei’s genetic distance values were low within and between the mainland and Sakhalin Island populations (D_N=0.008). The largest values (D_N=0.063) were found between the mainland/Sakhalin and Kamchatka Peninsula populations. Based on genetic distance, P. jezoensis and P. kamtschatkensis could be considered as distinct taxa, but P. ajanensis, P. microsperma, and P. komarovii do not warrant taxonomic recognition.     

Genetic diversity and multilocus structure in sexual Otiorhynchus alpicola populations (Goleoptera: Gurculionidae)

Otiorhynchus alpicola Boh. (Coleoptera: Curculionidae) is distributed on high mountains of central, southern and south-eastern Europe. On the Balkan peninsula, this species is patchily distributed on mountain peaks at heights over 1800 m. To examine the organization of isoenzyme variation of the ten sexual (diploid) populations, starch gel electrophoresis of enzymes was used. The average heterozygosity over 14 gene loci was 0.11. For diploid O. alpicola, F-statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other insects, this high-altitude weevil species is genetically very differentiated (the average F _ST= 0.35). In addition, gene-flow among populations was extremely low (the estimates of N_em from Wright's F _ST and Slatkin private-allele methods were 0.47 and 0.83, respectively). Pairwise linkage disequilibrium (LD) parameters were estimated from zygotic frequencies using Burrows' method. The average rate of significant LD in analysed populations of O. alpicola was about 27%. The pattern of LD over the diploid populations indicates that stochastic factors might be a primary cause of the observed multilocus associations.     

中国大陆黑斑侧褶蛙基于mtDNA控制区序列的种群遗传结构

用分子遗传数据研究了黑斑侧褶蛙 (Pelophylaxnigromaculata)种群的遗传结构和分化。标本采自中国大陆的 12个地点 ,每个种群测定 10只或少于 10只蛙的mtDNA控制区 5′端 6 85bp的序列。 112只蛙的序列经比对后 ,共发现 111个变异位点 ,定义了 6 7种单元型 ,其中 7种单元型为地方种群间共享单元型 ,多数单元型为地方种群内特有。 12个地方种群合并成一个大种群分析时表明 ,中国大陆黑斑侧褶蛙的线粒体单元型多样性相当高 (h=0 98± 0 0 0 5 ) ,总体核苷酸多样性也较高 (π =0 0 30 3± 0 0 0 2 9)。这样高的单元型多样性和核苷酸多样性与黑斑侧褶蛙作为古北界和东洋界的广布种、种群大是相应的。基于最大简约法的单元型系统发生树和基于邻接法的地方种群系统发生分析中 ,吉林通化和辽宁辽阳种群与中国大陆其他地方种群构成姐妹群。分子变异分析表明 ,吉林和辽宁种群代表的吉辽组和其余 10个地方种群代表的综合组间出现了显著的种群分化 (Φ CT=0 80 9,P <0 0 0 1) ,各地方种群间成对的FST及种群间的核苷酸歧异度也均表明两者之间出现了显著的遗传分化。吉辽组与综合组间的遗传分化最可能的原因就是受第四纪冰川的影响     

Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

Aim  Middle East brown bears ( Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species.
Location  Middle East region of south-western Asia.
Methods  We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed.
Results  Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals.
Main conclusion  This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.     

Genetic homogeneity of the Sedgling Nehalennia speciosa (Odonata: Coenagrionidae) indicates a single Würm glacial refugium and trans‐Palaearctic postglacial expansion

The phylogeographic structures of taiga species often support the hypothesis of East Palaearctic refugia for these taxa, but the phylogeographic structures of northern temperate and southern boreal bog species are still poorly understood. Therefore, we analysed the genetic diversity and differentiation of a stenotopic damselfly, Nehalennia speciosa, across its trans‐Palaearctic range by means of sequencing two mitochondrial gene fragments, 16S rRNA‐ND1 and cytochrome c oxidase II. Only four single nucleotide polymorphisms were detected over the 1130 sequenced nucleotides. This low genetic diversity and differentiation and thus the lack of phylogeographic structure imply postglacial expansion from a single Würm Ice Age refugium, most likely located in the Far East of Asia, i.e. Manchurian refugium. From here, the species could have colonized large parts of the Palaearctics, including Europe, during the postglacial.     

Patterns of differentiation among wild rabbit populations Oryctolagus cuniculus L. in arid and semiarid ecosystems of north-eastern Australia

Feral rabbit populations in Australia have generally been managed using localized control procedures. While these procedures may result in local extinctions, persistence of populations will depend on the probability of recolonization. Genetic markers developed using temperature gradient gel electrophoresis (TGGE) combined with heteroduplex analysis (HA) of mitochondrial DNA (mtDNA) were used to characterize the degree of subdivision and extent of gene flow within and among rabbit populations distributed over large distances (up to 1000 km) in southern Queensland (QLD) and north-west New South Wales (NSW), Australia. TGGE analyses revealed significant heterogeneity in mtDNA control region haplotype frequencies. From heterogeneity χ² tests, it was evident that the differentiation observed was largely attributable to five sites which were located in the semiarid eastern region, whereas haplotype frequencies were homogeneous throughout the arid western region. These results suggest that there are independent population systems within the study area. The extent of gene flow among local populations within each system is related to the spatial configuration of acceptable habitat patches and the persistence of the populations is determined by the probability of recolonization following local extinction. These data suggest that to provide better overall control of rabbit populations, different management strategies may be necessary in arid and semiarid ecosystems. In arid south-west QLD and north-west NSW, where extensive gene flow occurs over large distances, rabbit populations should be managed at a regional level. In semiarid eastern QLD, where gene flow is restricted and populations are more isolated, localized control procedures may provide effective short-term relief. These results indicate that in nonequilibrium systems with patchy distribution of individuals, the interpretation of migration rate from estimates of gene flow obtained using existing genetic models must include an understanding of the spatial and temporal scales over which population processes operate.