Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the e...Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms.However,the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages.Here,we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches,character coding schemes,and data filtering criteria.We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages.Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone.Cytonuclear discordance was also observed among the five Mesangiospermae lineages,likely resulting from ancient hybridization.Furthermore,systematic errors in species network inference cannot be excluded.Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors,particularly pervasive ancient hybridization.展开更多
Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monoco...Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.展开更多
基金supported by the National Natural Science Foundation of China(32370228 and W2511024)(B.Z.)the Natural Science Foundation of Jiangsu Province(BK20250004)(B.Z.)+3 种基金the Collaborative Innovation Center for Modern Crop Production co-sponsored by the Province and Ministry(B.Z.)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)(B.Z.)the Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation(CPSF)(GZC20240730)(X.M.)the Jiangsu Funding Program for Excellent Postdoctoral Talent(2024ZB023)(X.M.).
文摘Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms.However,the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages.Here,we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches,character coding schemes,and data filtering criteria.We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages.Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone.Cytonuclear discordance was also observed among the five Mesangiospermae lineages,likely resulting from ancient hybridization.Furthermore,systematic errors in species network inference cannot be excluded.Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors,particularly pervasive ancient hybridization.
基金This study is supported by the National Natural Science Foundation of China(no.31970229,no.31570219,and no.91531301)the Young Elite Scientists Sponsorship Program of Jiangsu Province,the State Key Laboratory of Paleobiology and Stratigraphy(Nanjing Institute of Geology and Paleontology,CAS)and the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.
