The genus Trachypithecus is the most diverse langur taxon,distributed in southwestern China,south and southeastern Asia.In this study,we include 16 recognized Trachypithecus species to reconstruct the phylogeny with p...The genus Trachypithecus is the most diverse langur taxon,distributed in southwestern China,south and southeastern Asia.In this study,we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of T.phayrei using multiple genes.Our results support a sister-relationship between T.p.phayrei and T.p.shanicus.However,the mitochondrial CYT B gene supported T.p.crepuscula as a distinct species,but the nuclear PRM1 gene suggested a closer relationship between T.p.crepuscula and T.p.phayrei.The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred,a fact that would benefit from re-examination using multiple unlinked nuclear genes.展开更多
Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based o...Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided展开更多
Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitut...Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.展开更多
谱系年代学是结合化石记录和分子钟方法计算"生命树"(Tree of Life)上各分歧点时间的一个新兴交叉学术领域。由于化石记录的不完整性,各类生物的起源年代和支系分化时间的确定可借助于部分化石记录和通过计算现生生物类群之...谱系年代学是结合化石记录和分子钟方法计算"生命树"(Tree of Life)上各分歧点时间的一个新兴交叉学术领域。由于化石记录的不完整性,各类生物的起源年代和支系分化时间的确定可借助于部分化石记录和通过计算现生生物类群之间的遗传距离转换得出的相对分歧时间相结合的办法进行讨论。化石记录可代表部分生物类群起源时间的保守估计值,而分子钟方法可为那些不易保存为化石的生物类群与其姊妹群的分化时间提供依据。如果使用得当的话,两者可进行相互验证。在分子谱系年代分析中,正确使用化石校准方案是获得准确分歧时间的关键,这需要:1)正确确定化石物种在谱系树上的位置;2)正确解释化石记录所代表的时间含义(最小值、确定值、最大值及其标准差)。分子钟估算分歧时间的技术在不断改进,目前常用的分子分歧时间估算法(宽松分子钟法,如贝叶斯法、补偿性似然法等)包容分子演化速率在谱系间和随时间的变化。随着谱系年代研究的不断深入,长期困扰人们的化石记录时间与分子钟计算结果悬殊的问题正在逐渐趋于和谐并得到正确诠释。文中还讨论了有关动物起源与早期分化时间以及早期陆生节肢动物的谱系年代学研究进展。我们强调,化石记录和分子钟分析可以优势互补,两者的整合无疑将提高生物演化历史时间格架的准确度和精度,以利更好地将生命演化事件置于地球系统科学及地球环境演化史之中。展开更多
The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny wi...The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of Z phayrei using multiple genes. Our results support a sister-relationship between Z p. phayrei and T p. shanicus. However, the mitochondrial CYT B gene supported T. p. crepuscula as a distinct species, but the nuclear PRMI gene suggested a closer relationship between T p. crepuscula and T p. phayrei. The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred, a fact that would benefit from re-examination using multiple unlinked nuclear genes.展开更多
The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptati...The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed mo-lecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed diver-gence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.展开更多
基金the Fund of State Key Laboratory of Genetics Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences(GREKF12-06)。
文摘The genus Trachypithecus is the most diverse langur taxon,distributed in southwestern China,south and southeastern Asia.In this study,we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of T.phayrei using multiple genes.Our results support a sister-relationship between T.p.phayrei and T.p.shanicus.However,the mitochondrial CYT B gene supported T.p.crepuscula as a distinct species,but the nuclear PRM1 gene suggested a closer relationship between T.p.crepuscula and T.p.phayrei.The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred,a fact that would benefit from re-examination using multiple unlinked nuclear genes.
文摘Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided
基金supported,in part,by the National Science Foundation (USA)-Emerging Frontiers,Assembling the Tree of Life,Collaborative Research:Gymnosperms on the Tree of Life:Resolving the Phylogeny of Seed Plants (Grant No. EF-0629657 to SMI-B)supported by the Swedish Research Council (grants to CR)
文摘Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions （amphitropical range）. Great heterogeneity in the substitution rates of Gnetales （Ephedra, Gnetum, and Welwitschia） has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species （and 7736 aligned nucleotides） to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long-distance dispersal, but finer-scale studies are needed to test this hypothesis.
文摘谱系年代学是结合化石记录和分子钟方法计算"生命树"(Tree of Life)上各分歧点时间的一个新兴交叉学术领域。由于化石记录的不完整性,各类生物的起源年代和支系分化时间的确定可借助于部分化石记录和通过计算现生生物类群之间的遗传距离转换得出的相对分歧时间相结合的办法进行讨论。化石记录可代表部分生物类群起源时间的保守估计值,而分子钟方法可为那些不易保存为化石的生物类群与其姊妹群的分化时间提供依据。如果使用得当的话,两者可进行相互验证。在分子谱系年代分析中,正确使用化石校准方案是获得准确分歧时间的关键,这需要:1)正确确定化石物种在谱系树上的位置;2)正确解释化石记录所代表的时间含义(最小值、确定值、最大值及其标准差)。分子钟估算分歧时间的技术在不断改进,目前常用的分子分歧时间估算法(宽松分子钟法,如贝叶斯法、补偿性似然法等)包容分子演化速率在谱系间和随时间的变化。随着谱系年代研究的不断深入,长期困扰人们的化石记录时间与分子钟计算结果悬殊的问题正在逐渐趋于和谐并得到正确诠释。文中还讨论了有关动物起源与早期分化时间以及早期陆生节肢动物的谱系年代学研究进展。我们强调,化石记录和分子钟分析可以优势互补,两者的整合无疑将提高生物演化历史时间格架的准确度和精度,以利更好地将生命演化事件置于地球系统科学及地球环境演化史之中。
文摘The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of Z phayrei using multiple genes. Our results support a sister-relationship between Z p. phayrei and T p. shanicus. However, the mitochondrial CYT B gene supported T. p. crepuscula as a distinct species, but the nuclear PRMI gene suggested a closer relationship between T p. crepuscula and T p. phayrei. The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred, a fact that would benefit from re-examination using multiple unlinked nuclear genes.
基金the National Basic Research Program of China (Grant No. 2007CB411600) the National Natural Science Foundation of China (Grant No. 30530120)
文摘The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed mo-lecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed diver-gence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.
基金supported by the National Natural Science Foundation of China(NSFC)key project(30830016)the Program for New Century Excellent Talents in University(NCET-07-0445)the Ministry of Education of China,and the major project of the Natural Science Foundation of the Jiangsu Higher Education Institutions of Jiangsu Province,China(07KJA18016)
