Phylogenetic relations of twining chirality of Dioscorea sp.in China were analyzed based on the genes matK,rbcL and trnL;phylogenetic character of higher-level phylogeny of twining plants was analyzed at a high taxon ...Phylogenetic relations of twining chirality of Dioscorea sp.in China were analyzed based on the genes matK,rbcL and trnL;phylogenetic character of higher-level phylogeny of twining plants was analyzed at a high taxon level based on matK gene.A significant phylogenetic framework of chirality was found:(i)based on matK analysis,right-handed Dioscorea species in China congregate completely to form a monophyly;(ii)rbcL and trnL data sets also supported Chinese right-handed Dioscorea a monophyly,although with ex...展开更多
Phylogenetic relationships of the 'higher' hamamelids were estimated based on nucleotide sequences of the non-coding region of chloroplast trnL-F. Twenty-five species were sampled, representing 24 genera of al...Phylogenetic relationships of the 'higher' hamamelids were estimated based on nucleotide sequences of the non-coding region of chloroplast trnL-F. Twenty-five species were sampled, representing 24 genera of all eight families of the 'higher' hamamelids. A parsimony analysis of data set indicated that the 'higher' hamamelids formed a strongly supported clade with 100% bootstrap value in the strict consensus tree. Nothofagus was the basal lineage and the Fagaceae was sister to a well-supported core 'higher' hamamelids clade containing Myricaceae, Rhoipteleaceae, Juglandaceae, Casuarinaceae, Ticodendraceae and Betulaceae. Three clades were recognized in the core ' higher' hamamelids: (1) Casuatina ( Ticodendron, ( Betu-laceae)), (2) Juglandaceae-Rhoipteleaceae, and (3) Myricaceae. Compared with the previous studies, familial relationships of the 'higher' hamamelids were better resolved.展开更多
To reveal how a large gene family evolved in the highly organized genome, the present study sequenced 294 copies of 5S rRNA genes from six individuals of three populations of Ophiopogon xylorrhizus Wang et Dai, and 45...To reveal how a large gene family evolved in the highly organized genome, the present study sequenced 294 copies of 5S rRNA genes from six individuals of three populations of Ophiopogon xylorrhizus Wang et Dai, and 45 copies from its closest species, O. sylvicola Wang et Tang. Based on the sequences the gene-phylogeny was inferred through PAUP. The sequences were highly diversified. Of the 339 randomly cloned copies, only 13 pairs (3.8%) were identical, with length varied between 307 - 548 bp (average 438.6 bp). The sequence differentiation index (SDI) in O. xylorrhints was 0.078, in O. sylvicola was 0.032, and between these two species was 0.149. In the most parsimonious tree reconstructed, all of the 294 copies of O. xylorrhizus were grouped into one clade, and those of O. sylvicola were grouped into another clade with 100% bootstrap support. The result demonstrated that the copies of 5S rRNA genes originated from just one progenitor copy, 'founder copy', in both of the species respectively, followed by a series of proliferation, and little, if any, homogenization ever occurred in the copies. As the common ancestor of the two species must have home multiple copies of the genes, all the other copies were lost during or after the speciation. Additionally, the phylogeny clearly showed that the founder copy was proliferated continuously through time, not just once. O. xylorrhizus is an extremely endangered species in which high genetic diversity, selfing and depression on seedlings were observed previously. In our study the sequences from different populations or different individuals were mixed in the branches of the O. xylorrhizus clade, although they evolved independently. It is assumed that gene flow of the species happened much more frequently in the past, making the proliferated copies dispersed to different populations, and the species maintained an amount of genetic diversity. Therefore, the selfing and seedling depression would be the result of a recent event. We suggest that some changes in outer mechanisms, such as the pollinators or seed-dispersers, might cause the species selfed, depressed and, finally, endangered.展开更多
Inflorescences structures in context of their evolution have been conducted for 60 genera and 170 species of Celastrales （according to APG （Angiosperm Phylogeny Group） III 2009, almost 60% of genera and 15% of spec...Inflorescences structures in context of their evolution have been conducted for 60 genera and 170 species of Celastrales （according to APG （Angiosperm Phylogeny Group） III 2009, almost 60% of genera and 15% of species from this taxon of the world flora）. There are two big groups of inflorescences in Celastrales-intercalary （more often） and terminal. For many genera of Celastrales both types of inflorescences can be observed, although the frequency of their occurrence varies. There is an important difference between two types of inflorescences： character of completion of the main axis （the terminal flower present or absent）. Flower opening can be in basipetal （Celastraceae, Brexia） or acropetal （Stackhousiaceae） order. Partial inflorescence types included： simple, compound or umbrellate dichasia, spike, raceme, thyrse. Simple flowers of Parnassia are large, nested on long reproductive shoots, emerging from a rosette, with amplexicaule leaf.展开更多
Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For ac...Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.展开更多
基金Supported by the CAS Special Grant for Postgraduate Research,Innovation and Practice~~
文摘Phylogenetic relations of twining chirality of Dioscorea sp.in China were analyzed based on the genes matK,rbcL and trnL;phylogenetic character of higher-level phylogeny of twining plants was analyzed at a high taxon level based on matK gene.A significant phylogenetic framework of chirality was found:(i)based on matK analysis,right-handed Dioscorea species in China congregate completely to form a monophyly;(ii)rbcL and trnL data sets also supported Chinese right-handed Dioscorea a monophyly,although with ex...
文摘Phylogenetic relationships of the 'higher' hamamelids were estimated based on nucleotide sequences of the non-coding region of chloroplast trnL-F. Twenty-five species were sampled, representing 24 genera of all eight families of the 'higher' hamamelids. A parsimony analysis of data set indicated that the 'higher' hamamelids formed a strongly supported clade with 100% bootstrap value in the strict consensus tree. Nothofagus was the basal lineage and the Fagaceae was sister to a well-supported core 'higher' hamamelids clade containing Myricaceae, Rhoipteleaceae, Juglandaceae, Casuarinaceae, Ticodendraceae and Betulaceae. Three clades were recognized in the core ' higher' hamamelids: (1) Casuatina ( Ticodendron, ( Betu-laceae)), (2) Juglandaceae-Rhoipteleaceae, and (3) Myricaceae. Compared with the previous studies, familial relationships of the 'higher' hamamelids were better resolved.
文摘To reveal how a large gene family evolved in the highly organized genome, the present study sequenced 294 copies of 5S rRNA genes from six individuals of three populations of Ophiopogon xylorrhizus Wang et Dai, and 45 copies from its closest species, O. sylvicola Wang et Tang. Based on the sequences the gene-phylogeny was inferred through PAUP. The sequences were highly diversified. Of the 339 randomly cloned copies, only 13 pairs (3.8%) were identical, with length varied between 307 - 548 bp (average 438.6 bp). The sequence differentiation index (SDI) in O. xylorrhints was 0.078, in O. sylvicola was 0.032, and between these two species was 0.149. In the most parsimonious tree reconstructed, all of the 294 copies of O. xylorrhizus were grouped into one clade, and those of O. sylvicola were grouped into another clade with 100% bootstrap support. The result demonstrated that the copies of 5S rRNA genes originated from just one progenitor copy, 'founder copy', in both of the species respectively, followed by a series of proliferation, and little, if any, homogenization ever occurred in the copies. As the common ancestor of the two species must have home multiple copies of the genes, all the other copies were lost during or after the speciation. Additionally, the phylogeny clearly showed that the founder copy was proliferated continuously through time, not just once. O. xylorrhizus is an extremely endangered species in which high genetic diversity, selfing and depression on seedlings were observed previously. In our study the sequences from different populations or different individuals were mixed in the branches of the O. xylorrhizus clade, although they evolved independently. It is assumed that gene flow of the species happened much more frequently in the past, making the proliferated copies dispersed to different populations, and the species maintained an amount of genetic diversity. Therefore, the selfing and seedling depression would be the result of a recent event. We suggest that some changes in outer mechanisms, such as the pollinators or seed-dispersers, might cause the species selfed, depressed and, finally, endangered.
文摘Inflorescences structures in context of their evolution have been conducted for 60 genera and 170 species of Celastrales （according to APG （Angiosperm Phylogeny Group） III 2009, almost 60% of genera and 15% of species from this taxon of the world flora）. There are two big groups of inflorescences in Celastrales-intercalary （more often） and terminal. For many genera of Celastrales both types of inflorescences can be observed, although the frequency of their occurrence varies. There is an important difference between two types of inflorescences： character of completion of the main axis （the terminal flower present or absent）. Flower opening can be in basipetal （Celastraceae, Brexia） or acropetal （Stackhousiaceae） order. Partial inflorescence types included： simple, compound or umbrellate dichasia, spike, raceme, thyrse. Simple flowers of Parnassia are large, nested on long reproductive shoots, emerging from a rosette, with amplexicaule leaf.
基金supported by the National Natural Science Foundation of China (31270269,30800059,30990241)the Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-Z-2)
文摘Correct combination of plastid(cp)and nuclear(nr)DNA data for plant phylogenetic reconstructions is not a new issue,but with an increasing number of nrDNA loci being used,it is of ever greater practical concern.For accurately reconstructing the phylogeny and evolutionary history of plant groups,correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data.We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011.Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets,or did not address in detail possible reasons for incongruence between the two data sets.By reviewing various methods,we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data,which includes four steps:identifying significant incongruence,determining conflicting taxa,providing possible interpretations for incongruence,and reconstructing the phylogeny after treating incongruence.Particular attention is given to explanation of the cause of incongruence.We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data.
