The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylo...The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylogeny-based trait evolution.However,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear discordant.Here,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent“phylogenetic discordance”between different morphological traits and probable species phylogeny in the Allium subg.Cyathophora.Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the KS distribution.However,GTD was high across the genomes of subg.Cyathophora:~27%e38.9%of the SCG trees were in conflict with the species tree.Plasmid and nuclear incongruence was also present.Our coalescent simulations indicated that such GTD was mainly a product of ILS.Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg.Cyathophora phylogeny may have caused the character transition,as well as the anomalous cpDNA tree.Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.展开更多
A new species of Phoenicopsis subgenus Windwardia （Florin） Samylina, Phoenicopsis neimengguensis sp.nov., is recognized from the Middle Jurassic Zhaogou Formation in the Shiguai Basin, a Jurassic coal-bearing sedime...A new species of Phoenicopsis subgenus Windwardia （Florin） Samylina, Phoenicopsis neimengguensis sp.nov., is recognized from the Middle Jurassic Zhaogou Formation in the Shiguai Basin, a Jurassic coal-bearing sedimentary basin in Inner Mongolia, China. Linear leaves are in bundles of six to eight and are attached on a short shoot. The leaf is amphistomatic with one or two irregular rows of longitudinally oriented stomata in each intercostal zone on the upper epidermis and three or four （occasionally six） rows of stomata in each intercostal zone on the lower epidermis. Each stomata is surrounded by four to six subsidiary cells with unevenly developed papillae. The anticlinal walls of epidermal cells are straight. Cuticular thickenings or papillae are present on the outer surface of the periclinal walls. This is the first time that Phoenicopsis subgenus Windwardia （Florin） Samylina is recognized from the Middle Jurassic of Inner Mongolia, China. The occurrence of the new species is noteworthy because it extends the geological and geographic distribution of Phoenicopsis subg. Windwardia in China and Eurasia. The discovery is significant as it increases our knowledge of Phoenicopsis subg. Windwardia by providing new data on morphological and epidermal features.展开更多
According to the Chinese Pharmacopoeia,the Chinese medicinal material(Asari Radix et Rhizoma)Xixin is derived from the species Asarum heterotropoides var.mandshuricum,A.sieboldii,and A.sieboldii var.seoulense.However,...According to the Chinese Pharmacopoeia,the Chinese medicinal material(Asari Radix et Rhizoma)Xixin is derived from the species Asarum heterotropoides var.mandshuricum,A.sieboldii,and A.sieboldii var.seoulense.However,many species of the genus Asarum are labeled as"Xixin","Tu-Xixin",or"Nan-Xixin"for sale in producing areas.To distinguish Chinese Asarum species and to ensure their safety and efficacy,we examined the microscopic characteristics of subg.Asarum plants in China(including subg.Asarum plants in the classification system of Flora Reipublicae Popularis Sinicae and the later published Asarum yunnanense)using a hand microtome and a microscopic digital imaging system based on our previous research.Microscopic features of the blades,petioles,and roots of A.yunnanense were investigated for the first time.Moreover,we compared nine species and one variety of the subg.Asarum(i.e.,A.yunnanense,A.caudigerellum,A.himalaicum,A.pulchellum,A.debile,A.caulescens,A.renicordatum,A.caudigerum,A.caudigerum var.cardiophyllum and A.geophilum)in China based on microscopic characteristics of the blades.Several parameters,such as morphological characteristics and distribution of hairs on both upper and lower leaf epidermises;morphological characteristics of hair cells;anticlinal walls of lower epidermal cells;size relationship between outer periclinal walls and cavity outlines of oil cells on lower leaf epidermis;presence or absence of the irregular cells containing red to brown substances among mesophyll cells;and the diameter of the largest vessels in midribs of the blades,were used for discrimination among species.To the best of our knowledge,we provided the first identification key for the 10 taxa based on blade microscopic characteristics that could be used to distinguish these taxa.Based on the key,23 commercial samples collected from seven provinces of China were authenticated as whole dried herbs of A.himalaicum,A.caudigerellum,A.caudigerum,A.pulchellum and A.caulescens.These findings indicated that microscopic approach and related techniques were convenient and feasible and could be used for the authentication of crude drugs from Chinese subg.Asarum species.展开更多
Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.Ho...Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.However,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied.In the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes.Gene content,gene order,and GC content were highly similar in these plastomes.The inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and S.rosmarinus).In Salvia,sequence divergence was higher in non-coding regions than in coding regions.We found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research.This study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia subg.Glutinaria.The newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.展开更多
基金supported by the Key Science & Technology Project of Gansu Province (22ZD6NA007)the National Key Research and Development Program of China (2021YFD2200202)Computing support was provided by the Supercomputing Center of Lanzhou University
文摘The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylogeny-based trait evolution.However,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear discordant.Here,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent“phylogenetic discordance”between different morphological traits and probable species phylogeny in the Allium subg.Cyathophora.Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the KS distribution.However,GTD was high across the genomes of subg.Cyathophora:~27%e38.9%of the SCG trees were in conflict with the species tree.Plasmid and nuclear incongruence was also present.Our coalescent simulations indicated that such GTD was mainly a product of ILS.Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg.Cyathophora phylogeny may have caused the character transition,as well as the anomalous cpDNA tree.Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.
基金supported by National Natural Science Foundation of China(41172009)Specialized Research Fund for the Doctoral Program of Higher Education(20100061110034)+2 种基金China Geological Survey Grant(1212011120149)Project‘‘111"of ChinaFundamental Scientific Research Fund of Jilin University(2013)
文摘A new species of Phoenicopsis subgenus Windwardia （Florin） Samylina, Phoenicopsis neimengguensis sp.nov., is recognized from the Middle Jurassic Zhaogou Formation in the Shiguai Basin, a Jurassic coal-bearing sedimentary basin in Inner Mongolia, China. Linear leaves are in bundles of six to eight and are attached on a short shoot. The leaf is amphistomatic with one or two irregular rows of longitudinally oriented stomata in each intercostal zone on the upper epidermis and three or four （occasionally six） rows of stomata in each intercostal zone on the lower epidermis. Each stomata is surrounded by four to six subsidiary cells with unevenly developed papillae. The anticlinal walls of epidermal cells are straight. Cuticular thickenings or papillae are present on the outer surface of the periclinal walls. This is the first time that Phoenicopsis subgenus Windwardia （Florin） Samylina is recognized from the Middle Jurassic of Inner Mongolia, China. The occurrence of the new species is noteworthy because it extends the geological and geographic distribution of Phoenicopsis subg. Windwardia in China and Eurasia. The discovery is significant as it increases our knowledge of Phoenicopsis subg. Windwardia by providing new data on morphological and epidermal features.
文摘According to the Chinese Pharmacopoeia,the Chinese medicinal material(Asari Radix et Rhizoma)Xixin is derived from the species Asarum heterotropoides var.mandshuricum,A.sieboldii,and A.sieboldii var.seoulense.However,many species of the genus Asarum are labeled as"Xixin","Tu-Xixin",or"Nan-Xixin"for sale in producing areas.To distinguish Chinese Asarum species and to ensure their safety and efficacy,we examined the microscopic characteristics of subg.Asarum plants in China(including subg.Asarum plants in the classification system of Flora Reipublicae Popularis Sinicae and the later published Asarum yunnanense)using a hand microtome and a microscopic digital imaging system based on our previous research.Microscopic features of the blades,petioles,and roots of A.yunnanense were investigated for the first time.Moreover,we compared nine species and one variety of the subg.Asarum(i.e.,A.yunnanense,A.caudigerellum,A.himalaicum,A.pulchellum,A.debile,A.caulescens,A.renicordatum,A.caudigerum,A.caudigerum var.cardiophyllum and A.geophilum)in China based on microscopic characteristics of the blades.Several parameters,such as morphological characteristics and distribution of hairs on both upper and lower leaf epidermises;morphological characteristics of hair cells;anticlinal walls of lower epidermal cells;size relationship between outer periclinal walls and cavity outlines of oil cells on lower leaf epidermis;presence or absence of the irregular cells containing red to brown substances among mesophyll cells;and the diameter of the largest vessels in midribs of the blades,were used for discrimination among species.To the best of our knowledge,we provided the first identification key for the 10 taxa based on blade microscopic characteristics that could be used to distinguish these taxa.Based on the key,23 commercial samples collected from seven provinces of China were authenticated as whole dried herbs of A.himalaicum,A.caudigerellum,A.caudigerum,A.pulchellum and A.caulescens.These findings indicated that microscopic approach and related techniques were convenient and feasible and could be used for the authentication of crude drugs from Chinese subg.Asarum species.
基金supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(Grant No:2017eLSFGBOWSe02)。
文摘Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.However,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied.In the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes.Gene content,gene order,and GC content were highly similar in these plastomes.The inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and S.rosmarinus).In Salvia,sequence divergence was higher in non-coding regions than in coding regions.We found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research.This study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia subg.Glutinaria.The newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.
