Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems.Recent phylogenomic studies based on large-scale data from plastid,mitochondri...Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems.Recent phylogenomic studies based on large-scale data from plastid,mitochondrial,or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants.However,owing to ancient rapid radiations,the interrelationships among the five lineages of Mesangiospermae,the vast majority of angiosperms,remain contentious.Here we show that,although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny,the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data.According to our Bayesian cross-validation and model test in a maximum likelihood framework,siteheterogeneous models(e.g.,CAT-GTR+G4,LG+C20+F+G)outperform site-homogeneous or partition models often used in previous studies.Under site-heterogeneous models,the approximately unbiased test favored our preferred tree recovered from various datasets:Ceratophyllales(coontails)are robustly recovered as sister to monocots,and they together are sister to the clade comprising magnoliids,Chloranthales,and eudicots.Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants.展开更多
Most described Mesozoic ants belong to stem groups that existed only during the Cretaceous period.Previously,the earliest known crown ants were dated to the Turonian(Late Cretaceous,ca.94-90 million years ago(Ma))depo...Most described Mesozoic ants belong to stem groups that existed only during the Cretaceous period.Previously,the earliest known crown ants were dated to the Turonian(Late Cretaceous,ca.94-90 million years ago(Ma))deposits found in the USA,Kazakhstan,and Botswana.However,the recent discovery of an alate male ant in Kachin amber from the earliest Cenomanian(ca.99 Ma),representing a new genus and species,Antiquiformica alata,revises the narrative on ant diversification.Antiquiformica can be distinctly differentiated from all known male stem ants by its geniculate antennae with elongated scape,extending far beyond the occipital margin of the head and half the length of the funiculus,as well as its partly reduced forewing venation.Furthermore,the combination of a one-segmented waist with a well-developed node,elongated scape extending beyond the occipital margin,and reduced forewing venation,particularly the completely reduced m-cu and rs-m crossveins and absence of rm and mcu closed cells,firmly places the fossil within the extant subfamily Formicinae.Fourier transform infrared spectroscopy(FTIR)confirmed that the amber containing Antiquiformica alata originated from the Kachin mines in Myanmar.This discovery significantly revises our understanding of the early evolution of Formicinae.The presence of Antiquiformica in Cenomanian amber indicates that the subfamily Formicinae emerged at least by the start of the Late Cretaceous,with crown ants likely originating earlier during the earliest Cretaceous or possibly the Late Jurassic,although paleontological evidence is lacking to support the latter hypothesis.展开更多
The aquatic plant Nymphaea,a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae,has been extensively studied.However,the availability of chloroplast genome data for this genus is inco...The aquatic plant Nymphaea,a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae,has been extensively studied.However,the availability of chloroplast genome data for this genus is incomplete,and phylogenetic relationships within the order Nymphaeales remain controversial.In this study,12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time.These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes,including 79 protein-coding genes,30 tRNA genes,and four rRNA genes.We also report on codon usage,RNA editing sites,microsatellite structures,and new repetitive sequences in this genus.Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers.Additionally,it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions.Furthermore,the phylogenetic tree showed the order Nymphaeales was divided into three families,and the genus Nymphaea can be divided into five(or three)subgenera,with the subgenus Nymphaea being the oldest.The divergence times of nymphaealean taxa were analyzed,with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years,respectively.The results of the phylo-genetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.展开更多
Twig mimicry among insects,whereby they imitate branches and twigs of plants to escape predation or enhance prey capture,is most common and diversified in Phasmatodea(stick and leaf insects),a group of iconic models f...Twig mimicry among insects,whereby they imitate branches and twigs of plants to escape predation or enhance prey capture,is most common and diversified in Phasmatodea(stick and leaf insects),a group of iconic models for understanding the evolution of camouflage and mimicry.Extant stick and leaf insects exhibit a wide array of exaggerated morphologies mimicking twigs,bark,fresh or dried leaves,ferns,and even moss[1].However,the Mesozoic lineages Susumaniidae and Pterophasmatidae,considered as stem groups to Phasmatodea s.str.,lack obvious characters relating to the familiar twig mimicry of the latter clade.展开更多
基金supported by the National Natural Science Foundation of China(42222201,42288201)。
文摘Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems.Recent phylogenomic studies based on large-scale data from plastid,mitochondrial,or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants.However,owing to ancient rapid radiations,the interrelationships among the five lineages of Mesangiospermae,the vast majority of angiosperms,remain contentious.Here we show that,although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny,the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data.According to our Bayesian cross-validation and model test in a maximum likelihood framework,siteheterogeneous models(e.g.,CAT-GTR+G4,LG+C20+F+G)outperform site-homogeneous or partition models often used in previous studies.Under site-heterogeneous models,the approximately unbiased test favored our preferred tree recovered from various datasets:Ceratophyllales(coontails)are robustly recovered as sister to monocots,and they together are sister to the clade comprising magnoliids,Chloranthales,and eudicots.Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants.
基金supported by the National Natural Science Foundation of China(32270467,32020103006)National Research Foundation of Ukraine(2020/02/0369 to A.G.R.)CONCYTEC through the PROCIENCIA“Interinstitutional Alliances for Doctorate Programs”(PE501084299-2023-PROCIENCIA-BM to M.S.E.)。
文摘Most described Mesozoic ants belong to stem groups that existed only during the Cretaceous period.Previously,the earliest known crown ants were dated to the Turonian(Late Cretaceous,ca.94-90 million years ago(Ma))deposits found in the USA,Kazakhstan,and Botswana.However,the recent discovery of an alate male ant in Kachin amber from the earliest Cenomanian(ca.99 Ma),representing a new genus and species,Antiquiformica alata,revises the narrative on ant diversification.Antiquiformica can be distinctly differentiated from all known male stem ants by its geniculate antennae with elongated scape,extending far beyond the occipital margin of the head and half the length of the funiculus,as well as its partly reduced forewing venation.Furthermore,the combination of a one-segmented waist with a well-developed node,elongated scape extending beyond the occipital margin,and reduced forewing venation,particularly the completely reduced m-cu and rs-m crossveins and absence of rm and mcu closed cells,firmly places the fossil within the extant subfamily Formicinae.Fourier transform infrared spectroscopy(FTIR)confirmed that the amber containing Antiquiformica alata originated from the Kachin mines in Myanmar.This discovery significantly revises our understanding of the early evolution of Formicinae.The presence of Antiquiformica in Cenomanian amber indicates that the subfamily Formicinae emerged at least by the start of the Late Cretaceous,with crown ants likely originating earlier during the earliest Cretaceous or possibly the Late Jurassic,although paleontological evidence is lacking to support the latter hypothesis.
基金supported by the National Natural Science Foundation of China(No.32370244)the Taishan Scholar Project(No.tsqn202306214)+1 种基金the Shandong Province Natural Science Foundation of China(No.ZR2023MC157)the State Key Laboratory of Pal-aeobiology and Stratigraphy(No.223123).
文摘The aquatic plant Nymphaea,a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae,has been extensively studied.However,the availability of chloroplast genome data for this genus is incomplete,and phylogenetic relationships within the order Nymphaeales remain controversial.In this study,12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time.These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes,including 79 protein-coding genes,30 tRNA genes,and four rRNA genes.We also report on codon usage,RNA editing sites,microsatellite structures,and new repetitive sequences in this genus.Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers.Additionally,it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions.Furthermore,the phylogenetic tree showed the order Nymphaeales was divided into three families,and the genus Nymphaea can be divided into five(or three)subgenera,with the subgenus Nymphaea being the oldest.The divergence times of nymphaealean taxa were analyzed,with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years,respectively.The results of the phylo-genetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.
基金supported by the National Natural Science Foundation of China(41688103,32020103006,and 31730087)registered under Zoo Bank LSID urn:lsid:zoobank.org:pub:221D9C8B-4091-4200-8784-5DD633CF1028。
文摘Twig mimicry among insects,whereby they imitate branches and twigs of plants to escape predation or enhance prey capture,is most common and diversified in Phasmatodea(stick and leaf insects),a group of iconic models for understanding the evolution of camouflage and mimicry.Extant stick and leaf insects exhibit a wide array of exaggerated morphologies mimicking twigs,bark,fresh or dried leaves,ferns,and even moss[1].However,the Mesozoic lineages Susumaniidae and Pterophasmatidae,considered as stem groups to Phasmatodea s.str.,lack obvious characters relating to the familiar twig mimicry of the latter clade.
