Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible...Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L. in China. In total, 220 individuals from 12 populations in China and three populations outside China were analyzed, representing the largest number of populations studied by molecular markers to date. Nineteen haplotypes were produced and haplotype A was found in all populations. Populations in south-western China, including WC, JF, PX, and SP, contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.771 4 to 0.867 6. The TM population from China also showed a high genetic diversity （H = 0.848 5）. Most of the genetic variation existed within populations and the differentiation among populations was low （GsT = 0.2）. According to haplotype distribution and the historical record, we suggest that populations of G. biloba have been subjected to extensive human impact, which has compounded our attempt to infer glacial refugia for Ginkgo. Nevertheless, the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.展开更多
This study aims at identifying the microevolutionary processes responsible for the onset of the remarkable phylogeographic structure already recorded for the endangered giant clam Tridacna squamosa across its distribu...This study aims at identifying the microevolutionary processes responsible for the onset of the remarkable phylogeographic structure already recorded for the endangered giant clam Tridacna squamosa across its distribution range.For this purpose,the evolutionary,biogeographic and demographic histories of the species were comprehensively reconstructed in a mitochondrial dataset comprising nearly the whole available published cytochrome c oxidase 1 gene sequences of T.squamosa.Relatively higher level of genetic diversification was unveiled within T.squamosa,in comparison to earlier macro-geographic investigations,whereby five mitochondrial clusters were delineated.The resulting divergent gene pools in the Red Sea,western Indian Ocean,Indo-Malay Archipelago and western Pacific were found to be driven by Early Pleistocene glacial vicariance events among refugial lineages.Accentuated genetic diversification of the species across the Indo-Malay Archipelago was successively triggered by historical dispersal event during the Mid-Pleistocene MIS19c interglacial.This latter historical event might have also enabled genetically distinct giant clams from the Indo-Malay Archipelago to subsequently colonize the western Pacific,accounting for the genetic diversity hotspot detected within this region(comprising three divergent mitochondrial clusters).Late Pleistocene demographic expansion of T.squamosa,during the Last Interglacial period,could have contributed to forging spatial distribution of the so far delineated genetic entities across the Indo-Western Pacific.Overall,being resilient to major climate shifts during the Pleistocene through adaptation and consequent diversification,T.squamosa could be used as a model species to track the impact of climate change on genetic variability and structure of marine species.In particular,the new information,provided in this investigation,may help with understanding and/or predicting the consequences of ongoing global warming on genetic polymorphism of endangered coral reef species among which Tridacna sp.are listed as ecologically important.展开更多
第四纪气候波动以及地理和环境隔离深刻地影响了现代植物的遗传多样性、遗传结构和地理分布格局。该研究采用分子谱系地理学的研究方法对药用植物半夏19个居群共212个个体的3个叶绿体片段psb K-psb I、atp F-atp H和trn L-F进行分析,探...第四纪气候波动以及地理和环境隔离深刻地影响了现代植物的遗传多样性、遗传结构和地理分布格局。该研究采用分子谱系地理学的研究方法对药用植物半夏19个居群共212个个体的3个叶绿体片段psb K-psb I、atp F-atp H和trn L-F进行分析,探究半夏的遗传多样性、遗传结构、地理分布格局模式及成因,并探讨其居群历史动态。结果表明:(1)半夏总单倍型多样性H d为0.882,总核苷酸多样性π为1.23×10-3,在物种水平上表现出较高的遗传多样性。(2)分子方差分析(AMOVA)结果显示,半夏遗传变异主要发生在居群间,显著的遗传分化(F ST=0.909,P<0.001)和较低的种群内遗传多样性(H S=0.134);种群间遗传分化系数N ST=0.913>G ST=0.855(0.01<P<0.05),表明叶绿体单倍型具有明显的谱系地理结构。(3)中性检验结果显示,Tajima s D值、Fu and Li s D值以及Fu and Li s F值均为不显著正值,Fu s Fs值为不显著负值且失配分析曲线呈双峰,表明半夏居群整体没有经历过扩张事件。(4)单倍型地理分布显示,西南地区和中-东部地区具有单倍型多样性较高,并存在特有单倍型,故推测第四纪冰期时在这两个区域存在冰期避难所。总之,通过3个叶绿体基因对不同区域半夏的分析,阐明了其遗传多样性、遗传结构和地理分布格局,为半夏优良种源的分子筛选和保护提出了科学的建议和保护策略。展开更多
海洋植物谱系地理学虽然在国内受到的关注比较有限,但近年来的研究进展对了解环境变动如何影响物种的多样性结构、生态适应和进化潜力等亦提供了重要信息。本文首先对刊发海洋植物谱系地理研究最具代表性的两本国际期刊《Molecular Ecol...海洋植物谱系地理学虽然在国内受到的关注比较有限,但近年来的研究进展对了解环境变动如何影响物种的多样性结构、生态适应和进化潜力等亦提供了重要信息。本文首先对刊发海洋植物谱系地理研究最具代表性的两本国际期刊《Molecular Ecology》和《Journal of Biogeography》进行搜索和筛选,从研究团队的地域分布和研究对象的阶元等角度纵览全球范围内近20年间海洋植物谱系地理学研究的现状和特征。其后,本文从洋流如何驱动海洋植物谱系地理结构和多样性、入侵物种的种群遗传变异特征和路径重建、冰期避难所如何影响现今海洋植物遗传结构和地理变动、克隆繁殖和谱系多样化等四个方面概述了这一领域的主要成果进展。最后,本文还从岛屿地理模型、共生物种的谱系协同进化和高通量数据应用等三个方面对海洋植物谱系地理学的发展趋势进行了展望。展开更多
We conducted molecular phylogenetic analyses of Japanese Rhacophorus species, especially of R. schlegelii and R. arboreus from the mainland, based on samples encompassing their known distribution ranges, and discussed...We conducted molecular phylogenetic analyses of Japanese Rhacophorus species, especially of R. schlegelii and R. arboreus from the mainland, based on samples encompassing their known distribution ranges, and discussed about evolutionary history of Rhacophorus species within Japan. The common ancestor of Japanese Rhacophorus, except for R. owstoni from southern Ryukyus, was estimated to have diverged from a lineage occurring mainly in China about 7 MYBP. Both R. schlegelii and R. arboreus are genetically largely divergent between regions of eastern and western Japan, and this seems to have been promoted mainly by retreat to refugia. Retreats of the two species to different refugia sometimes in the past seem to have led restricted distribution of R. schlegelii in eastern and R. arboreus in western Japan, and brought their intraspecific variation patterns in morphology and breeding habit.展开更多
To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau （QTP） responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the ge...To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau （QTP） responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades （A, B and C）. Analysis of molecular variance （AMOVA） revealed that most of the genetic variability was found within populations （0.693）, while differentiations between populations were obviously distinct （Fst -- 0.307）. Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago （kya） were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu＇s Fs values and ＇g＇ tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum （LGM） and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages.展开更多
Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may ...Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin's biota.We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network.Populations from the northern and eastern Tarim Basin shared a similar history,as did those from the western and southern regions.Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations.The distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,which corresponded to known interglacial periods.Given the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the east.The absence of water likely forced the species into refugia,and this differed from other Pleistocene biogeographical drivers.The demographical and historical patterns have important implications for conservation.展开更多
The history of the Qinghai-Tibetan Plateau and the Himalayas(QTPH)region makes it a‘living laboratory'for understanding how the Earth's abiotic evolution has shaped regional biotas.However,no studies to date ...The history of the Qinghai-Tibetan Plateau and the Himalayas(QTPH)region makes it a‘living laboratory'for understanding how the Earth's abiotic evolution has shaped regional biotas.However,no studies to date have attempted to investigate general macro-scale biogeographical patterns and biogeographical affinities of the QTPH terrestrial fauna in a global context.Based on the analyses of the global distributions of QTPH Aphidomorpha species,we examined generalized distribution patterns for them and investigated the biogeographical affinities between the QTPH and other regions.Track analysis and cluster analysis of the global distributions of 298 Aphidomorpha species in the QTPH identified seven generalized biogeographical tracks and eight general distribution patterns.Both approaches detected similarly generalized distribution patterns.Four marginal areas where the generalized tracks intersect,i.e.the eastern Himalayas,the western Himalayas,the Hengduan Mountains,and the northeastern QTPH,were identified as biogeographical nodes.The generalized distribution patterns indicate the biogeographical affinities between the QTPH and other regions and suggest the complex nature of the QTPH fauna.A spatial congruence between the nodes and diversity centres detected by previous studies indicates the four marginal areas have been key areas in fauna evolution as centres for faunal exchange as well as glacial refugia.Based on the biogeographical patterns,the geological history of the QTPH and the evolutionary history of Aphidomorpha,we propose an evolutionary scenario for the evolution of the QTPH aphid fauna in which faunal exchanges,vicariance due to the uplift of geographical barriers,environmental heterogeneity and Quarternary glaciations have shaped the diversity patterns and fauna in the QTPH.展开更多
基金the National Basic Research Program of China (973 Program2007CB411605)the National Natural Science Foundation of China(30670139, 30300020).
文摘Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L. in China. In total, 220 individuals from 12 populations in China and three populations outside China were analyzed, representing the largest number of populations studied by molecular markers to date. Nineteen haplotypes were produced and haplotype A was found in all populations. Populations in south-western China, including WC, JF, PX, and SP, contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.771 4 to 0.867 6. The TM population from China also showed a high genetic diversity （H = 0.848 5）. Most of the genetic variation existed within populations and the differentiation among populations was low （GsT = 0.2）. According to haplotype distribution and the historical record, we suggest that populations of G. biloba have been subjected to extensive human impact, which has compounded our attempt to infer glacial refugia for Ginkgo. Nevertheless, the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.
文摘This study aims at identifying the microevolutionary processes responsible for the onset of the remarkable phylogeographic structure already recorded for the endangered giant clam Tridacna squamosa across its distribution range.For this purpose,the evolutionary,biogeographic and demographic histories of the species were comprehensively reconstructed in a mitochondrial dataset comprising nearly the whole available published cytochrome c oxidase 1 gene sequences of T.squamosa.Relatively higher level of genetic diversification was unveiled within T.squamosa,in comparison to earlier macro-geographic investigations,whereby five mitochondrial clusters were delineated.The resulting divergent gene pools in the Red Sea,western Indian Ocean,Indo-Malay Archipelago and western Pacific were found to be driven by Early Pleistocene glacial vicariance events among refugial lineages.Accentuated genetic diversification of the species across the Indo-Malay Archipelago was successively triggered by historical dispersal event during the Mid-Pleistocene MIS19c interglacial.This latter historical event might have also enabled genetically distinct giant clams from the Indo-Malay Archipelago to subsequently colonize the western Pacific,accounting for the genetic diversity hotspot detected within this region(comprising three divergent mitochondrial clusters).Late Pleistocene demographic expansion of T.squamosa,during the Last Interglacial period,could have contributed to forging spatial distribution of the so far delineated genetic entities across the Indo-Western Pacific.Overall,being resilient to major climate shifts during the Pleistocene through adaptation and consequent diversification,T.squamosa could be used as a model species to track the impact of climate change on genetic variability and structure of marine species.In particular,the new information,provided in this investigation,may help with understanding and/or predicting the consequences of ongoing global warming on genetic polymorphism of endangered coral reef species among which Tridacna sp.are listed as ecologically important.
文摘第四纪气候波动以及地理和环境隔离深刻地影响了现代植物的遗传多样性、遗传结构和地理分布格局。该研究采用分子谱系地理学的研究方法对药用植物半夏19个居群共212个个体的3个叶绿体片段psb K-psb I、atp F-atp H和trn L-F进行分析,探究半夏的遗传多样性、遗传结构、地理分布格局模式及成因,并探讨其居群历史动态。结果表明:(1)半夏总单倍型多样性H d为0.882,总核苷酸多样性π为1.23×10-3,在物种水平上表现出较高的遗传多样性。(2)分子方差分析(AMOVA)结果显示,半夏遗传变异主要发生在居群间,显著的遗传分化(F ST=0.909,P<0.001)和较低的种群内遗传多样性(H S=0.134);种群间遗传分化系数N ST=0.913>G ST=0.855(0.01<P<0.05),表明叶绿体单倍型具有明显的谱系地理结构。(3)中性检验结果显示,Tajima s D值、Fu and Li s D值以及Fu and Li s F值均为不显著正值,Fu s Fs值为不显著负值且失配分析曲线呈双峰,表明半夏居群整体没有经历过扩张事件。(4)单倍型地理分布显示,西南地区和中-东部地区具有单倍型多样性较高,并存在特有单倍型,故推测第四纪冰期时在这两个区域存在冰期避难所。总之,通过3个叶绿体基因对不同区域半夏的分析,阐明了其遗传多样性、遗传结构和地理分布格局,为半夏优良种源的分子筛选和保护提出了科学的建议和保护策略。
基金Supported by the National Natural Science Foundation of China, Grant Nos. 30470125, 40671066the Knowledge Innovation Project of Chinese Academy of Sciences, Grant No. KSCX2-SW-132.
文摘海洋植物谱系地理学虽然在国内受到的关注比较有限,但近年来的研究进展对了解环境变动如何影响物种的多样性结构、生态适应和进化潜力等亦提供了重要信息。本文首先对刊发海洋植物谱系地理研究最具代表性的两本国际期刊《Molecular Ecology》和《Journal of Biogeography》进行搜索和筛选,从研究团队的地域分布和研究对象的阶元等角度纵览全球范围内近20年间海洋植物谱系地理学研究的现状和特征。其后,本文从洋流如何驱动海洋植物谱系地理结构和多样性、入侵物种的种群遗传变异特征和路径重建、冰期避难所如何影响现今海洋植物遗传结构和地理变动、克隆繁殖和谱系多样化等四个方面概述了这一领域的主要成果进展。最后,本文还从岛屿地理模型、共生物种的谱系协同进化和高通量数据应用等三个方面对海洋植物谱系地理学的发展趋势进行了展望。
基金partly supported by Grants-in-Aid from the Monbukagakusho through the JSPS (Nos. 10041166, 20405013, and 23405014)a grant from The U. S. National Geographic Society (No. 4505-91) to MM
文摘We conducted molecular phylogenetic analyses of Japanese Rhacophorus species, especially of R. schlegelii and R. arboreus from the mainland, based on samples encompassing their known distribution ranges, and discussed about evolutionary history of Rhacophorus species within Japan. The common ancestor of Japanese Rhacophorus, except for R. owstoni from southern Ryukyus, was estimated to have diverged from a lineage occurring mainly in China about 7 MYBP. Both R. schlegelii and R. arboreus are genetically largely divergent between regions of eastern and western Japan, and this seems to have been promoted mainly by retreat to refugia. Retreats of the two species to different refugia sometimes in the past seem to have led restricted distribution of R. schlegelii in eastern and R. arboreus in western Japan, and brought their intraspecific variation patterns in morphology and breeding habit.
基金Supported by the Frontier Project of the Knowledge Innovation Program of Northwest Plateau Institute of Biology of the Chinese Academy of Sciences,National Natural Science Foundation of China (30725004)the Programfor New Century Excellent Talents,Ministry of Education of China (NCET-05-0886)a Grant-in Aid for Scientific Research (A) from the Ministry of Education,Culture,Sports,Science and Technology,Government of Japan(18255004)
文摘To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau （QTP） responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades （A, B and C）. Analysis of molecular variance （AMOVA） revealed that most of the genetic variability was found within populations （0.693）, while differentiations between populations were obviously distinct （Fst -- 0.307）. Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago （kya） were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu＇s Fs values and ＇g＇ tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum （LGM） and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages.
基金supported by the National Key Basic Research Program of China (2007CB411600)the National Natural Science Foundation of China (30500061 and 31060152)+1 种基金the Research Start-up Fund of Xinjiang Uighur Autonomous Region for Young Teachers in University (XJEDU2008S03)the College-University United Project of Xinjiang University (XY080117)
文摘Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin's biota.We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network.Populations from the northern and eastern Tarim Basin shared a similar history,as did those from the western and southern regions.Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations.The distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,which corresponded to known interglacial periods.Given the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the east.The absence of water likely forced the species into refugia,and this differed from other Pleistocene biogeographical drivers.The demographical and historical patterns have important implications for conservation.
基金supported by the National Natural Sciences Foundation of China(Grant numbers:32270499,30900133)。
文摘The history of the Qinghai-Tibetan Plateau and the Himalayas(QTPH)region makes it a‘living laboratory'for understanding how the Earth's abiotic evolution has shaped regional biotas.However,no studies to date have attempted to investigate general macro-scale biogeographical patterns and biogeographical affinities of the QTPH terrestrial fauna in a global context.Based on the analyses of the global distributions of QTPH Aphidomorpha species,we examined generalized distribution patterns for them and investigated the biogeographical affinities between the QTPH and other regions.Track analysis and cluster analysis of the global distributions of 298 Aphidomorpha species in the QTPH identified seven generalized biogeographical tracks and eight general distribution patterns.Both approaches detected similarly generalized distribution patterns.Four marginal areas where the generalized tracks intersect,i.e.the eastern Himalayas,the western Himalayas,the Hengduan Mountains,and the northeastern QTPH,were identified as biogeographical nodes.The generalized distribution patterns indicate the biogeographical affinities between the QTPH and other regions and suggest the complex nature of the QTPH fauna.A spatial congruence between the nodes and diversity centres detected by previous studies indicates the four marginal areas have been key areas in fauna evolution as centres for faunal exchange as well as glacial refugia.Based on the biogeographical patterns,the geological history of the QTPH and the evolutionary history of Aphidomorpha,we propose an evolutionary scenario for the evolution of the QTPH aphid fauna in which faunal exchanges,vicariance due to the uplift of geographical barriers,environmental heterogeneity and Quarternary glaciations have shaped the diversity patterns and fauna in the QTPH.
