In the present paper,the cladistics method is used to analyze the phylogenetic relationship of 16 genera of Tinginae (Hemiptera:Heteroptera:Tingidae) from northern China. 33 characters with 88 states were chosen based...In the present paper,the cladistics method is used to analyze the phylogenetic relationship of 16 genera of Tinginae (Hemiptera:Heteroptera:Tingidae) from northern China. 33 characters with 88 states were chosen based on the morphological comparison. The character matrix was formed through ingroup and outgroup analysis and computed using the computer programs MacClad (version 3 0 1), AutoDecay (version 3 0), PAUP (version 3 1 1) and Hennig 86 (version 1 5),and the same most parsimonious tree and Nelson consensus cladogram were obtained from both computation to explain the phylogenetic relationship among the genera (L=118,CI=0 454,RI=0 529). We categorized these genera involved in the analysis phylogenetically into 6 groups according to the results. They are Agramma group,Leptoypha group,Dictyla group,Catoplatus group,Physatocheila group and Derephysia group. The phylogenetic relationship among the involved genera is presented as (((((Derephysia group=( Lasiacantha ,( Acalypta ,( Galeatus ,( Dictyonota ,( Derephysia,Sphaerista ))))),Physatocheila group =(( Elasmotropis,Tingis ),(( Oncochila,Cochlochila ), Physatocheila ))),Catoplatus group= Catoplatus ),Dictyla group=( Monosteira,Dictyla )),Leptoypha group= Leptoypha ),Agramma group= Agramma ). These groups will not be regarded as higher classific taxa until more genera and data are available and further analysis are carried out.展开更多
A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial(COI,Cyt b and control region) and nuclear(5S rDNA) DNA sequence data in multigene perspective.A variety of phylogenetic analy...A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial(COI,Cyt b and control region) and nuclear(5S rDNA) DNA sequence data in multigene perspective.A variety of phylogenetic analytic methods were used to clarify the current taxonomic classification and to assess phylogenetic relationships and the evolutionary history of this genus.The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber.We confirmed that S.japonicus and S.colias were genetically distinct.Although morphologically and ecologically similar to S.colias,the molecular data showed that S.japonicus has a greater molecular affinity with S.australasicus,which conflicts with the traditional taxonomy.This phylogenetic pattern was corroborated by the mtDNA data,but incompletely by the nuclear DNA data.Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes supports an Atlantic origin for Scomber.The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus.The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events.In addition,our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution,from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.展开更多
Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been esta...Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lnc RNA catalogs(4,142–42,558 lnc RNAs) covering the major mammalian species. Compared to protein-coding RNAs, expression of lnc RNAs exhibits striking lineage specificity. Notably, although 30%–99% human lnc RNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lnc RNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes(48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lnc RNAs. Moreover, we constructed lnc RNA expression phylogenetic trees across nine mammals and demonstrated that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lnc RNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lnc RNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named Phylo NONCODE(http://www.bioinfo.org/phylo Noncode). Our work starts to place mammalian lnc RNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.展开更多
文摘In the present paper,the cladistics method is used to analyze the phylogenetic relationship of 16 genera of Tinginae (Hemiptera:Heteroptera:Tingidae) from northern China. 33 characters with 88 states were chosen based on the morphological comparison. The character matrix was formed through ingroup and outgroup analysis and computed using the computer programs MacClad (version 3 0 1), AutoDecay (version 3 0), PAUP (version 3 1 1) and Hennig 86 (version 1 5),and the same most parsimonious tree and Nelson consensus cladogram were obtained from both computation to explain the phylogenetic relationship among the genera (L=118,CI=0 454,RI=0 529). We categorized these genera involved in the analysis phylogenetically into 6 groups according to the results. They are Agramma group,Leptoypha group,Dictyla group,Catoplatus group,Physatocheila group and Derephysia group. The phylogenetic relationship among the involved genera is presented as (((((Derephysia group=( Lasiacantha ,( Acalypta ,( Galeatus ,( Dictyonota ,( Derephysia,Sphaerista ))))),Physatocheila group =(( Elasmotropis,Tingis ),(( Oncochila,Cochlochila ), Physatocheila ))),Catoplatus group= Catoplatus ),Dictyla group=( Monosteira,Dictyla )),Leptoypha group= Leptoypha ),Agramma group= Agramma ). These groups will not be regarded as higher classific taxa until more genera and data are available and further analysis are carried out.
基金Project(50621063)supported by the National Natural Science Foundation of ChinaProject(2004CB619204)supported by the National Basic Research Program of China
基金Supported by the International Cooperation and Exchange of the National Natural Science Foundation of China (No. 31061160187)Special Fund for Agro-scientific Research in the Public Interest(No. 200903005)
文摘A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial(COI,Cyt b and control region) and nuclear(5S rDNA) DNA sequence data in multigene perspective.A variety of phylogenetic analytic methods were used to clarify the current taxonomic classification and to assess phylogenetic relationships and the evolutionary history of this genus.The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber.We confirmed that S.japonicus and S.colias were genetically distinct.Although morphologically and ecologically similar to S.colias,the molecular data showed that S.japonicus has a greater molecular affinity with S.australasicus,which conflicts with the traditional taxonomy.This phylogenetic pattern was corroborated by the mtDNA data,but incompletely by the nuclear DNA data.Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes supports an Atlantic origin for Scomber.The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus.The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events.In addition,our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution,from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.
基金supported by Training Program of the Major Research Plan of the National Natural Science Foundation of China(91229120)
文摘Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lnc RNA catalogs(4,142–42,558 lnc RNAs) covering the major mammalian species. Compared to protein-coding RNAs, expression of lnc RNAs exhibits striking lineage specificity. Notably, although 30%–99% human lnc RNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lnc RNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes(48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lnc RNAs. Moreover, we constructed lnc RNA expression phylogenetic trees across nine mammals and demonstrated that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lnc RNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lnc RNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named Phylo NONCODE(http://www.bioinfo.org/phylo Noncode). Our work starts to place mammalian lnc RNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.
