Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red rive...Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.展开更多
Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence ...Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography （BPP） is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation （= unguided species delimitation）. We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and ＊BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities [Current Zoology 61 （5）： 866-873, 2015].展开更多
Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about l...Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals （representing 24 genera and 73 species） of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine, a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.展开更多
文摘Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.
基金We thank the authors of species delimitation studies listed in Table 1 for permission to use their datasets in our study. We also thank J. Grummer for providing feedback on an earlier draft of the manuscript. This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington. I.W.C.S. was supported by a graduate scholarship from the Consejo Nacional de Ciencia y Tecnologia （CONACYT）, and N.M.B was supported by the National Science Foundation Graduate Research Fellowship （NSF-GRFP）.
文摘Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography （BPP） is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation （= unguided species delimitation）. We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and ＊BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities [Current Zoology 61 （5）： 866-873, 2015].
基金Great thanks to Rick Winterbottom for his hard work on improving this manuscript and Abebe Getahun for graciously providing a part of his dissertation. We thank LN Du, MN He, WS Jiang, JH Lan, R Min, B Yang and J Yang for sample collection. GH Cui provided information on collection localities. L Jia and WY Wang helped with laboratory work. GH Yu and YF Huang provided advice on the study. This study was supported by the National Natural Science Foundation of China （30730017, 31201707）, National Basic Research Program of China （2007CB411600, 2008GA001）, Western Light Doctor Programme of Chinese Academy of Sciences, and Yunnan Provincial Science and Technology Program （2009CC008）.
文摘Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals （representing 24 genera and 73 species） of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine, a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.
