Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and f...Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.展开更多
This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships an...This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships and taxonomy within Batrachospermaceae,we integrated molecular and morphological data,and explored the phylogeny,character evolution,and ancestral geographical origin and provided a theoretical support for the classification and geographic origination of Batrachospermaceae.Our findings reveal distinct relationships within the phylogenetic tree.Notably,10 genera(Sirodotia,Batrachospermum,Tuomeya,Volatus,Lympha,Nothocladus,Torularia,Sheathia,Nocturama,and Petrohua)are closely associated in the rbcL phylogenetic tree.Additionally,four genera(Kumanoa,Hoefkenia,Notohesperus,and Virescentia)exhibit high support ratios,indicating their close interrelations.Other genera,including Paludicola,Visia,Acarposporophycos,Macrosporophycos,Visioidea,Balliopsis,and Psilosiphon,exhibit clustering traits.Furthermore,the multigene sequences provide a robust support for Montagnia that forms a monophyletic group.Ancestral reconstruction of morphological characters identifies nine primitive character states,including whorl,fascicle length,cortical cells,secondary fascicles,the shape of carpogonical branch,spermatangia,carposporophyte,carpogonium and trichogyne,with Visia likely representing ancestral traits in Batrachospermaceae.Furthermore,geographical origin maps suggest a potential common ancestral of Batrachospermaceae origin in the American continent.Additional to conventional analyses,including evolutionary and ancestral reconstruction investigations into key morphological characters,we attempt to reconstruct the biogeography within the Batrachospermaceae,thus contributing to a nuanced understanding of its origin.展开更多
Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a...Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.展开更多
Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides ...Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides a natural laboratory for examining these relationships among sympatric species.Here,we investigated the dietary composition and gut microbiota of six passerine species inhabiting the QTP,comprising two endemic residents(White-rumped Snowfinch Onychostruthus taczanowskii and Ground Tit Pseudopodoces humilis),two nonendemic residents(Rock Sparrow Petronia petronia and Eurasian Tree Sparrow Passer montanus),and two nonendemic migratory species(Twite Linaria flavirostris and Black Redstart Phoenicurus ochruros),using highthroughput 18S and 16S rRNA sequencing.Our results revealed that dietary composition—dominated by Archaeplastida,Metazoa,Fungi,and the SAR supergroup—exhibited no significant interspecific variation,reflecting a high degree of trophic niche overlap.Although the overall diet was similar across species,the relative abundances of certain dietary components independently influenced specific microbial taxa.In particular,dietary Archaeplastida and Fungi showed phylogeny-independent positive correlations with 16 and 3 microbial genera,respectively,revealing fine-scale diet-microbiota associations.Evidence of phylosymbiosis was detected,as closely related species harbored more similar microbial communities driven by species-specific microbial biomarkers.Notably,our results suggested deterministic processes played a stronger role in endemic species,whereas stochastic community assembly dominated in non-endemic species,indicating distinct assembly mechanisms shaped by biogeographic history.Overall,this study reveals that while dietary similarity promotes convergent trophic niches among sympatric passerines,host phylogeny exerts a stronger influence on gut microbiota composition and assembly.These findings underline the synergistic roles of diet-microbiota interactions and phylosymbiosis dynamics as key adaptive strategies that enable birds to cope with the extreme environments of the QTP.展开更多
Non-coding RNAs(ncRNAs)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and development.Several novel tra...Non-coding RNAs(ncRNAs)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and development.Several novel transcripts have been identified via high-throughput sequencing.However,identifying ncRNAs among the transcripts of novel species using alignment-based features is difficult.Thus,developing a fast and accurate method based on alignment-free features to identify ncRNAs among novel transcripts is necessary.In this study,we proposed a new approach,namely,coding potential prediction based on alignment-free features(CPAF),to identify ncRNAs among a large number of candidates.CPAF used four types of features:Fickett score;Hexamer score;composition,transition,and distribution features;and modified k-mer.From the results,CPAF performed better than previous state-of-the-art methods in predicting ncRNA transcripts,with particular reference to small ncRNAs.Finally,we applied CPAF to identify ncRNAs in Pacific oyster transcripts.Our approach identified more ncRNAs than other previously used methods.展开更多
The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain...The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain the diversification of taxa from the Indian subcontinent into Southeast Asia,two principal hypotheses have been proposed:the“Biotic-ferry”and“Step-stone”models.The subfamily Perittopinae,a lineage of semi-aquatic bugs comprising a single genus and 20 extant species,provides an ideal system for testing these hypotheses due to its disjunct distribution spanning the Indian subcontinent and Southeast Asia.This study conducted a comprehensive taxonomic analysis of the entire subfamily,incorporating newly defined morphological characters and multilocus phylogenetic analyses to reconstruct evolutionary relationships and historical biogeography.Morphological and phylogenetic evidence confirmed the monophyly of Perittopinae and supported the establishment of three new genera-Indoperittopus gen.nov.,Pachyperittopus gen.nov.,and Falciperittopus gen.nov.-in addition to four new species and four new combinations.Biogeographic reconstructions indicated a southern Indian origin,with initial diversification potentially occurring during the mid-Paleocene,coinciding with the major phases of the India-Eurasia collision.Subsequent range expansion over marine barriers facilitated colonization of the northern Sunda Shelf,consistent with the“Step-stone”dispersal mechanism.Later northward expansion from the southern Sunda Shelf during the early Miocene triggered further diversification of the genus Perittopus within the Indo-China Peninsula.These findings advance understanding of Perittopinae systematics,phylogeny,and historical biogeography,identifying the northward drift of the Indian plate and its eventual collision with Eurasia as catalysts of diversification within this semi-aquatic lineage.展开更多
Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic ...Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages,leading to the recognition of nine tribes:Hypodaphnideae,Cryptocaryeae,Cassytheae,Neocinnamomeae,Caryodaphnopsideae,Mezilaureae,Perseeae,Laureae,and Cinnamomeae,with Mezilaureae validated here.Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity.Taxonomic studies have focused mainly on the most diverse regions,e.g.,tropical Asia,tropical America,and Africa(Madagascar),with six new genera described and five reinstated since the last major overview of the family.The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic.Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages,with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events.Phylogeographic studies,predominantly from East Asia,have shown patterns of in situ survival and demographic stability or expansion during the Quaternary.Nevertheless,many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae.A multifaceted approach integrating genomic studies,field work,morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.展开更多
The black coral genus Bathypathes Brook,1889 represents a relatively diverse and ecologically important assemblage comprising the deep-sea hard substrate communities.Recent phylogenetic investigations have revealed th...The black coral genus Bathypathes Brook,1889 represents a relatively diverse and ecologically important assemblage comprising the deep-sea hard substrate communities.Recent phylogenetic investigations have revealed the polyphyletic nature of Bathypathes,urging further morphological analysis to understand its systematics.By combing morphological and molecular data,we describe Bathypathes multifurcata sp.nov.and report B.pseudoalternata Molodtsova,Opresko&Wagner,2022based on the specimens collected from the tropical western Pacific.The phylogenetic topology reconstructed using nuclear ITS1-5.8S-ITS2 and three mitochondrial fragments suggests the separation of Bathypathes into four groups.Our analysis of morphological characters,particularly the colony branch and pinnule patterns also roughly classify Bathypathes into four morphological groups A–D.Group A is characterized by the unbranched colony and the subopposite arrangement of pinnules.In contrast to Group A,Groups B–D have the alternately arranged pinnules.Among these,Group C exhibits a distinctly long unpinnulated stem compared to Groups B and D.Group B has unbranched colony,relatively short unpinnulated stem,and spines on pinnules have blunt apex.Within Group D,large colonies(higher than 40 cm)have one or a few branches,small colonies(less than 40 cm)are unbranched,and spines on pinnules have acute apex.Further data particularly those species without sequences are necessary to verify the classification of these groups.展开更多
Subgenus Melanocrommyum is the second largest subgenus of Allium,with a wide distribution ranging from the Canary Islands to northwestern India.This study investigates the phylogeny,biogeographic patterns,and morpholo...Subgenus Melanocrommyum is the second largest subgenus of Allium,with a wide distribution ranging from the Canary Islands to northwestern India.This study investigates the phylogeny,biogeographic patterns,and morphological character evolution of the subgenus using 117 accessions representing 107taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum.Although the subgenus is monophyletic,significant incongruence exists between morphological and molecular data.Our plastome-based phylogenetic analysis identified five distinct lineages(A-E),corresponding to the geographic distributions of the species.However,plastome lineages(A-E)and ITS clusters(A-G)were incongruent.Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene.Our finding that Melanocrommyum plastomes have lost inf A and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification.We also found that narrow leaves and fasciculate to semiglobose inflorescences may represent ancestral traits within the subgenus.This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum,suggesting recent diversification influenced by tectonic events and climate change,while highlighting the complexity of molecular and morphological data integration.展开更多
Brucellosis is a zoonosis that causes economic losses worldwide,as well as human morbidity and poverty.It is caused by Brucella spp.,which are animal pathogens~([1]).Among the 13 identified species,Brucella melitensis...Brucellosis is a zoonosis that causes economic losses worldwide,as well as human morbidity and poverty.It is caused by Brucella spp.,which are animal pathogens~([1]).Among the 13 identified species,Brucella melitensis is the most common and is frequently isolated from both humans and livestock~([2]).展开更多
The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogen...The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogeny of this family, especially within Acer. The analyses were performed in separate and combined sequence data sets, with the Sapindaceae and Hippocastanaceae being selected as outgroups. It was indicated that the Aceraceae was monophyletic and D. sinensis was basal to the rest of the family but the two genera of it might be not monophyletic because Dipteronia dyerana was nested within Acer. The result inferred from the combined data showed greater resolution within Acer than that from the two separate data sets. The monophyly of most sections in Xu's system (1996) were supported with high bootstrap values, and some relationships between (or among) sections were also inferred, such as sect. Palmata and sect. Microcarpa; sect. Platanoidea, sect. Lithocarpa and sect. Macrophylla; sect. Integrifolia, sect. Trifoliata and sect. Pentaphylla; and sect. Acer, sect. Goniocarpa and sect. Saccharina (sensu Ogata). However, the sectional status and circumscriptions of some of the above-mentioned sections should be further adjusted. It seemed that the Xu's delimitations of sect. Rubra and sect. Saccharodendran should be revaluated.展开更多
The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as ...The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as sample taxa. The sequence constitutions and variations were analyzed and the molecular phylogenetic trees were reconstructed based on the combined sequence data （795bp length in total） of 12S rDNA and 16S rDNA, using the grasshopper Pyrgomorpha conica of Pyrgomorphidae as the outgroup. The results showed that the rates of the two kinds of transitions are obviously much higher than that of the four kinds of Wansversions in these combined 12S＋16S rDNA sequence data. The saturation ofnucleotide substitutions happened in 12S and 16S rDNA sequence data. The molecular phylogenetic trees indicated that Oedipodinae is a monophyletic group and this subfamily is a natural one, but Catantopinae and Acridinae are non-monophyletic. Oedipodnae is a relatively primitive group within the Acrididae, whereas the Oxyinae may have diverged later than Oedipodinae, but earlier than most other species of Acridide.展开更多
Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote heal...Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote health, but their functional properties are yet poody dascdbed. As indicated by the 16S rRNA gene sequences of ileal micrebiota in nursing piglets （at the age of 21 and 28 d） and 28-day-old weaned piglets （weaned at 21 d of age）, the microbiota were mainly comprised of gram-positive bacteria. There were 40 operational taxonomic units （OTUs） （from 171 clones） in the ileum of nursing piglets aged 21 d, 61 OTUs （from 194 clones） in the ileum of nursing piglets aged 28 d, and 56 OTUs （from 171 clones） in the ileum of weaned piglets aged 28 d. The flea of nursing piglets aged 21 d were dominantly occupied by Lactobacilli （87.7%） as well as Streptococ cus （ 3.5 % ）. Lactobacillus amy/ovorus （41.5 % ）, Lactobaci/lus sp. （ 19.3 % ）, Lactobaci/lus reuteri （ 12.3 % ）, Lactobacillus salivarius （ 9.4 % ） and L. mucosae （4.7%） were the predominant species among Lactobacil/L Similar results were obtained in the nursing piglets at 28 d of age ex- cept that Lactobaci/li decreased to 71.1% and Streptococcus increased to 21.1% significantly. Lactobacillus （52.0%） and Streptococcus （26.3%） were the two major groups in the ileum of weaned piglets aged 28 d. Lactobacillus amylovorus （31.6%） and Lactobaci/lus reuteri （ 16.4% ） was the two most important species in Lactobacillus. Therefore, Lactobacilli were predominant in the ileum of nursing and weaned piglets, and they had the highest diversity, followed by Streptococcus. The diversity of ileal microbiota was not different remarkably between the nursing piglets and the weaned piglets, but the composition changed significantly. These findings are helpful to understand ileal bacterial ecophysiology and further develop nutritional regimes to prevent or counteract complications during the weaning transition.展开更多
The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fi...The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fishes. Sister groups A (S. hollandi) and B-E (S. sinensis + S. denticulatus + S. yunnanensis + S. polylepis) represent the first phyletic branching within the genus Spinibarbus. The phyletic division of second sister groups B (S. sinensis) and C-E (S. denticulatus + S. yunnanensis + S. polylepis) is supposed to be resulted from the upheaval of Yunnan-Guizhou Plateau and the subsequent drainages' division. The phyletic division of third sister groups C (S. denticulatus) and D^E (S. yunnanensis + S. polylepis) is supposed to be resulted from the environmental differentiation between Yunnan-Guizhou Plateau and the lowlands of middle and lower Pearl and Yuanjiang Rivers.展开更多
[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homol...[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homologous sequences between them and 11 relative species of Artemia from GenBank were compared;the molecular phylogenetic tree was constructed by Mega Microsoft using Artemiopsis stefanssoni as outgroup.[Result] Artemia persimilis was the primal group in genus Artemia;Artemia franciscana and Artemia monica were the evolved groups;Artemia urmiana,Artemia sinica and other Artemia species from China shared a close genetic relationship.[Conclusion] Based on the 16S rDNA sequence of them,the phylogenetic relationships of these bisexual Artemia species were A.persimilis→A.urmiana,A.sinica and A.tibetiana→A.tunisiana→A.monica→A.Franciscan.展开更多
The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which ...The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which eleven were ingroups representing ten of the eleven families, were selected to produce a phylogenetic inference of nepomorphan superfamilial or familial relationships via parsimony and Bayesian techniques. Our results supported the monophylies of Nepomorpha, Naucoroidea （Aphelocheiridae ＋ Naucoridae）, Nepoidea （Belostomatidae ＋ Nepidae）, Ochteroidea （Ochteridae ＋ Gelastocoridae） and Pieoidea （Pleidae ＋ Helotrephidae）; the most basal lineage of Ochteroidea; Notonectoidea contained Notonectidae only and formed a new sister relationship with （Pleoidea ＋ Naucoroidea）; and the sister relationship of （Nepoidea ＋ Corixoidea）. The Hox genes are suitable molecular markers to resolve phylogenetic relationships at superfamily or family levels in Heteroptera.展开更多
The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 b...The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 bp, with ITS1 (285-290 bp) slightly longer than ITS2 (205-211 bp). Of the 669 aligned positions, 109 sites (56 in ITS1, 52 in ITS2, and one in 5.8S region) were phylogenetically informative. Only one most parsimonious tree of 252 steps was obtained in PAUP analysis when gaps were treated as the fifth state. The traditional division of Chloranthus on the basis of habit seems to be quite unnatural. Evidence from the sequence of ITS region, just as that from cytology and anatomy, strongly suggested the separation of the genus into two groups according to the characteristics of androecial organs: one contains C. angustifolius, C. nervosus, C. japonicus and C. fortunei, and the other comprises the remaining species.展开更多
文摘Composition Vector Tree(CVTree) is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It has been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplast genomes, mitochondrial genomes, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16 S r RNA sequences, we showed that CVTree software is an efficient and effective tool for studying phylogeny and taxonomy based on genome sequences. The code of CVTree software can be available at https://github.com/ghzuo/cvtree.
基金Supported by the National Natural Science Foundation of China(No.32170204)。
文摘This study presents a comprehensive phylogenetic analysis on Batrachospermaceae based on key taxonomic identifiers(rbcL,psaA,psbA,and COI-5P)from some genera.To systematically explore the phylogenetic relationships and taxonomy within Batrachospermaceae,we integrated molecular and morphological data,and explored the phylogeny,character evolution,and ancestral geographical origin and provided a theoretical support for the classification and geographic origination of Batrachospermaceae.Our findings reveal distinct relationships within the phylogenetic tree.Notably,10 genera(Sirodotia,Batrachospermum,Tuomeya,Volatus,Lympha,Nothocladus,Torularia,Sheathia,Nocturama,and Petrohua)are closely associated in the rbcL phylogenetic tree.Additionally,four genera(Kumanoa,Hoefkenia,Notohesperus,and Virescentia)exhibit high support ratios,indicating their close interrelations.Other genera,including Paludicola,Visia,Acarposporophycos,Macrosporophycos,Visioidea,Balliopsis,and Psilosiphon,exhibit clustering traits.Furthermore,the multigene sequences provide a robust support for Montagnia that forms a monophyletic group.Ancestral reconstruction of morphological characters identifies nine primitive character states,including whorl,fascicle length,cortical cells,secondary fascicles,the shape of carpogonical branch,spermatangia,carposporophyte,carpogonium and trichogyne,with Visia likely representing ancestral traits in Batrachospermaceae.Furthermore,geographical origin maps suggest a potential common ancestral of Batrachospermaceae origin in the American continent.Additional to conventional analyses,including evolutionary and ancestral reconstruction investigations into key morphological characters,we attempt to reconstruct the biogeography within the Batrachospermaceae,thus contributing to a nuanced understanding of its origin.
基金funded by the Shenzhen Science and Technology Program(Grant No.JCYJ20241202130723030)the National Natural Science Foundation of China(Grant No.32170238)+2 种基金the Guangdong Pearl River Talent Program(Grant No.2021QN02N792)the Shenzhen Fundamental Research Program(Grant No.JCYJ20220818103212025)the Chinese Academy of Agricultural Sciences Elite Youth Program(110243160001007)to Z.W.
文摘Deep relationships in the angiosperm tree of life remain highly controversial.To address this,we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius,confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data.To dissect this classic cyto-nuclear conflict,we developed the‘PhyloForensics’framework,a novel diagnostic approach to systematically identify sources of phylogenetic instability.This framework revealed that signal heterogeneity(topological entropy variance)and information content(the proportion of informative sites)are the primary drivers of gene-tree conflict.Empirically validating this,we show that removing a small subset of“loudly conflicted”genes resolves deep-level incongruence,yielding a single,highly-supported topology previously obscured by noise.Finally,complementing this sequence-based resolution,we demonstrate that mitogenome architecture provides powerful phylogenetic signals,revealing predictable,mitogenome-wide evolutionary patterns,such as a significant negative correlation between branch length and both GC content and RNA editing sites.By integrating a validated conflict-resolution framework with architectural genomics,our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.
基金supported by the National Key Research and Development Program of China(2024YFC2310303)the National Natural Science Foundation of China(NSFC,No.32471572)awarded to D.L.+1 种基金NSFC(No.32171490)awarded to Y.W.Hebei Natural Science Foundation(HNSF,C2021204059)awarded to Y.S。
文摘Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments.The Qinghai-Tibet Plateau(QTP),characterized by harsh conditions,provides a natural laboratory for examining these relationships among sympatric species.Here,we investigated the dietary composition and gut microbiota of six passerine species inhabiting the QTP,comprising two endemic residents(White-rumped Snowfinch Onychostruthus taczanowskii and Ground Tit Pseudopodoces humilis),two nonendemic residents(Rock Sparrow Petronia petronia and Eurasian Tree Sparrow Passer montanus),and two nonendemic migratory species(Twite Linaria flavirostris and Black Redstart Phoenicurus ochruros),using highthroughput 18S and 16S rRNA sequencing.Our results revealed that dietary composition—dominated by Archaeplastida,Metazoa,Fungi,and the SAR supergroup—exhibited no significant interspecific variation,reflecting a high degree of trophic niche overlap.Although the overall diet was similar across species,the relative abundances of certain dietary components independently influenced specific microbial taxa.In particular,dietary Archaeplastida and Fungi showed phylogeny-independent positive correlations with 16 and 3 microbial genera,respectively,revealing fine-scale diet-microbiota associations.Evidence of phylosymbiosis was detected,as closely related species harbored more similar microbial communities driven by species-specific microbial biomarkers.Notably,our results suggested deterministic processes played a stronger role in endemic species,whereas stochastic community assembly dominated in non-endemic species,indicating distinct assembly mechanisms shaped by biogeographic history.Overall,this study reveals that while dietary similarity promotes convergent trophic niches among sympatric passerines,host phylogeny exerts a stronger influence on gut microbiota composition and assembly.These findings underline the synergistic roles of diet-microbiota interactions and phylosymbiosis dynamics as key adaptive strategies that enable birds to cope with the extreme environments of the QTP.
基金supported by the National Natural Science Foundation of China(No.11701546).
文摘Non-coding RNAs(ncRNAs)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and development.Several novel transcripts have been identified via high-throughput sequencing.However,identifying ncRNAs among the transcripts of novel species using alignment-based features is difficult.Thus,developing a fast and accurate method based on alignment-free features to identify ncRNAs among novel transcripts is necessary.In this study,we proposed a new approach,namely,coding potential prediction based on alignment-free features(CPAF),to identify ncRNAs among a large number of candidates.CPAF used four types of features:Fickett score;Hexamer score;composition,transition,and distribution features;and modified k-mer.From the results,CPAF performed better than previous state-of-the-art methods in predicting ncRNA transcripts,with particular reference to small ncRNAs.Finally,we applied CPAF to identify ncRNAs in Pacific oyster transcripts.Our approach identified more ncRNAs than other previously used methods.
基金supported by the Natural Science Foundation of Tianjin,China(24JCYBJC01910)National Natural Science Foundation of China(32322012,32470467)。
文摘The collision of the Indian and Eurasian plates during the Eocene represents a major tectonic shift that significantly altered biotic dynamics and promoted species diversification across the Oriental region.To explain the diversification of taxa from the Indian subcontinent into Southeast Asia,two principal hypotheses have been proposed:the“Biotic-ferry”and“Step-stone”models.The subfamily Perittopinae,a lineage of semi-aquatic bugs comprising a single genus and 20 extant species,provides an ideal system for testing these hypotheses due to its disjunct distribution spanning the Indian subcontinent and Southeast Asia.This study conducted a comprehensive taxonomic analysis of the entire subfamily,incorporating newly defined morphological characters and multilocus phylogenetic analyses to reconstruct evolutionary relationships and historical biogeography.Morphological and phylogenetic evidence confirmed the monophyly of Perittopinae and supported the establishment of three new genera-Indoperittopus gen.nov.,Pachyperittopus gen.nov.,and Falciperittopus gen.nov.-in addition to four new species and four new combinations.Biogeographic reconstructions indicated a southern Indian origin,with initial diversification potentially occurring during the mid-Paleocene,coinciding with the major phases of the India-Eurasia collision.Subsequent range expansion over marine barriers facilitated colonization of the northern Sunda Shelf,consistent with the“Step-stone”dispersal mechanism.Later northward expansion from the southern Sunda Shelf during the early Miocene triggered further diversification of the genus Perittopus within the Indo-China Peninsula.These findings advance understanding of Perittopinae systematics,phylogeny,and historical biogeography,identifying the northward drift of the Indian plate and its eventual collision with Eurasia as catalysts of diversification within this semi-aquatic lineage.
基金supported by the National Natural Science Foundation of China(31970222,31770569,31500454,31500165,32260060,32270217,32260056,31970223,32400180)the Science and Technology Basic Resources Investigation Program of China(2017FY100100,2017FY100102)+7 种基金Biodiversity Conservation Program of Chinese Academy of Sciences(ZSSD-013)National Key Research and Development Program of China(2022YFC2601200,2023YFF0805800)Yunnan Fundamental Research Projects(202201AS070055,202301AU070224)the 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy of Sciences(XTBG-1450101)Australian Research Council grant(DP130104314)RSNZ Marsden grant(11-UOO-043)Xingdian Talent Support Program(XDRC-QNRC-2022-0323)Shandong Provincial Natural Science Foundation(ZR2022QC214).
文摘Over the past two decades,our understanding of Lauraceae,a large family of woody plants,has undergone significant advances in phylogeny,taxonomy,and biogeography.Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages,leading to the recognition of nine tribes:Hypodaphnideae,Cryptocaryeae,Cassytheae,Neocinnamomeae,Caryodaphnopsideae,Mezilaureae,Perseeae,Laureae,and Cinnamomeae,with Mezilaureae validated here.Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity.Taxonomic studies have focused mainly on the most diverse regions,e.g.,tropical Asia,tropical America,and Africa(Madagascar),with six new genera described and five reinstated since the last major overview of the family.The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic.Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages,with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events.Phylogeographic studies,predominantly from East Asia,have shown patterns of in situ survival and demographic stability or expansion during the Quaternary.Nevertheless,many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae.A multifaceted approach integrating genomic studies,field work,morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.
基金Supported by the National Natural Science Foundation of China(Nos.41930533,42176128)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB42000000)+1 种基金the Senior User Project of R/V Kexue(No.KEXUE2020GZ02)the Science and Technology Program of Nanji Islands National Marine Nature Reserve Administration(No.JJZB-PYCG-2021112901)。
文摘The black coral genus Bathypathes Brook,1889 represents a relatively diverse and ecologically important assemblage comprising the deep-sea hard substrate communities.Recent phylogenetic investigations have revealed the polyphyletic nature of Bathypathes,urging further morphological analysis to understand its systematics.By combing morphological and molecular data,we describe Bathypathes multifurcata sp.nov.and report B.pseudoalternata Molodtsova,Opresko&Wagner,2022based on the specimens collected from the tropical western Pacific.The phylogenetic topology reconstructed using nuclear ITS1-5.8S-ITS2 and three mitochondrial fragments suggests the separation of Bathypathes into four groups.Our analysis of morphological characters,particularly the colony branch and pinnule patterns also roughly classify Bathypathes into four morphological groups A–D.Group A is characterized by the unbranched colony and the subopposite arrangement of pinnules.In contrast to Group A,Groups B–D have the alternately arranged pinnules.Among these,Group C exhibits a distinctly long unpinnulated stem compared to Groups B and D.Group B has unbranched colony,relatively short unpinnulated stem,and spines on pinnules have blunt apex.Within Group D,large colonies(higher than 40 cm)have one or a few branches,small colonies(less than 40 cm)are unbranched,and spines on pinnules have acute apex.Further data particularly those species without sequences are necessary to verify the classification of these groups.
基金supported by grants from the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)the state research project‘Taxonomic Revision of Polymorphic Plant Families of the Flora of Uzbekistan’(FZ20200929321)+3 种基金the State Programs for 2021-2025‘Grid mapping of the flora of Uzbekistan’and the‘Digital Nature.Development of a digital platform for the flora of Central Uzbekistan’,implemented by the Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan for the period 2025-2029National Natural Science Foundation of China(32322006)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149)the R&D Program of Yunnan Province(202103AF140005).
文摘Subgenus Melanocrommyum is the second largest subgenus of Allium,with a wide distribution ranging from the Canary Islands to northwestern India.This study investigates the phylogeny,biogeographic patterns,and morphological character evolution of the subgenus using 117 accessions representing 107taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum.Although the subgenus is monophyletic,significant incongruence exists between morphological and molecular data.Our plastome-based phylogenetic analysis identified five distinct lineages(A-E),corresponding to the geographic distributions of the species.However,plastome lineages(A-E)and ITS clusters(A-G)were incongruent.Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene.Our finding that Melanocrommyum plastomes have lost inf A and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification.We also found that narrow leaves and fasciculate to semiglobose inflorescences may represent ancestral traits within the subgenus.This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum,suggesting recent diversification influenced by tectonic events and climate change,while highlighting the complexity of molecular and morphological data integration.
基金supported by a Gansu Province Health Industry Scientific Research Plan Project(No.GSWSKY2018-10)The Major Science and Technology Innovation Project of Gansu Provincial Health and Health Industry(GSWSKY2024-7)。
文摘Brucellosis is a zoonosis that causes economic losses worldwide,as well as human morbidity and poverty.It is caused by Brucella spp.,which are animal pathogens~([1]).Among the 13 identified species,Brucella melitensis is the most common and is frequently isolated from both humans and livestock~([2]).
文摘The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trn L-F region were sequenced for 41 species of the Aceraceae, representing both genera Acer and Dipteronia, to reconstruct phylogeny of this family, especially within Acer. The analyses were performed in separate and combined sequence data sets, with the Sapindaceae and Hippocastanaceae being selected as outgroups. It was indicated that the Aceraceae was monophyletic and D. sinensis was basal to the rest of the family but the two genera of it might be not monophyletic because Dipteronia dyerana was nested within Acer. The result inferred from the combined data showed greater resolution within Acer than that from the two separate data sets. The monophyly of most sections in Xu's system (1996) were supported with high bootstrap values, and some relationships between (or among) sections were also inferred, such as sect. Palmata and sect. Microcarpa; sect. Platanoidea, sect. Lithocarpa and sect. Macrophylla; sect. Integrifolia, sect. Trifoliata and sect. Pentaphylla; and sect. Acer, sect. Goniocarpa and sect. Saccharina (sensu Ogata). However, the sectional status and circumscriptions of some of the above-mentioned sections should be further adjusted. It seemed that the Xu's delimitations of sect. Rubra and sect. Saccharodendran should be revaluated.
基金Supported by National Natural Science Foundation of China(30160015)
文摘The phylogenetic relationships among all taxa within the Acrididae （Orthoptera： Acridoidea） were largely unknown until now. In this study, to further investigations, 24 species of Acrididae from China were used as sample taxa. The sequence constitutions and variations were analyzed and the molecular phylogenetic trees were reconstructed based on the combined sequence data （795bp length in total） of 12S rDNA and 16S rDNA, using the grasshopper Pyrgomorpha conica of Pyrgomorphidae as the outgroup. The results showed that the rates of the two kinds of transitions are obviously much higher than that of the four kinds of Wansversions in these combined 12S＋16S rDNA sequence data. The saturation ofnucleotide substitutions happened in 12S and 16S rDNA sequence data. The molecular phylogenetic trees indicated that Oedipodinae is a monophyletic group and this subfamily is a natural one, but Catantopinae and Acridinae are non-monophyletic. Oedipodnae is a relatively primitive group within the Acrididae, whereas the Oxyinae may have diverged later than Oedipodinae, but earlier than most other species of Acridide.
基金Supported by grants from Knowledge Innovation Project of Chinese Academy of Sciences (KSCX2-YW-N-051 and SW-323)NSFC(30901040, 30901041, 30928018, 30828025, 30700581, and 30771558)+2 种基金National Basic Research Program of China(2009CB118800)National 863 project (2008AA10Z316)National Scientific and Technological Supporting Project(2007BAQ01047 and 2006BAD12B07)~~
文摘Weaning of piglets is generally considered as a stressor which changes intestinal ecosystem and leads to clinical implications. Microbiota inhabiting in small intestine （especially ileum） are assumed to promote health, but their functional properties are yet poody dascdbed. As indicated by the 16S rRNA gene sequences of ileal micrebiota in nursing piglets （at the age of 21 and 28 d） and 28-day-old weaned piglets （weaned at 21 d of age）, the microbiota were mainly comprised of gram-positive bacteria. There were 40 operational taxonomic units （OTUs） （from 171 clones） in the ileum of nursing piglets aged 21 d, 61 OTUs （from 194 clones） in the ileum of nursing piglets aged 28 d, and 56 OTUs （from 171 clones） in the ileum of weaned piglets aged 28 d. The flea of nursing piglets aged 21 d were dominantly occupied by Lactobacilli （87.7%） as well as Streptococ cus （ 3.5 % ）. Lactobacillus amy/ovorus （41.5 % ）, Lactobaci/lus sp. （ 19.3 % ）, Lactobaci/lus reuteri （ 12.3 % ）, Lactobacillus salivarius （ 9.4 % ） and L. mucosae （4.7%） were the predominant species among Lactobacil/L Similar results were obtained in the nursing piglets at 28 d of age ex- cept that Lactobaci/li decreased to 71.1% and Streptococcus increased to 21.1% significantly. Lactobacillus （52.0%） and Streptococcus （26.3%） were the two major groups in the ileum of weaned piglets aged 28 d. Lactobacillus amylovorus （31.6%） and Lactobaci/lus reuteri （ 16.4% ） was the two most important species in Lactobacillus. Therefore, Lactobacilli were predominant in the ileum of nursing and weaned piglets, and they had the highest diversity, followed by Streptococcus. The diversity of ileal microbiota was not different remarkably between the nursing piglets and the weaned piglets, but the composition changed significantly. These findings are helpful to understand ileal bacterial ecophysiology and further develop nutritional regimes to prevent or counteract complications during the weaning transition.
文摘The cyprinid genus Spinibarbus consists of 5 species. They form into a monophyly by three synapomorphies. Based on 19 external and skeletal characters, the most parsimonious cladogram is constructed for Spinibarbus fishes. Sister groups A (S. hollandi) and B-E (S. sinensis + S. denticulatus + S. yunnanensis + S. polylepis) represent the first phyletic branching within the genus Spinibarbus. The phyletic division of second sister groups B (S. sinensis) and C-E (S. denticulatus + S. yunnanensis + S. polylepis) is supposed to be resulted from the upheaval of Yunnan-Guizhou Plateau and the subsequent drainages' division. The phyletic division of third sister groups C (S. denticulatus) and D^E (S. yunnanensis + S. polylepis) is supposed to be resulted from the environmental differentiation between Yunnan-Guizhou Plateau and the lowlands of middle and lower Pearl and Yuanjiang Rivers.
基金Supported by National Natural Science Foundation of China(30770263)~~
文摘[Objective] The research aimed at investigating the taxonomic position and phylogenetic relationship of bisexual brine shrimps.[Method] 16S rDNA of three species of bisexual Artemia from China was determined;the homologous sequences between them and 11 relative species of Artemia from GenBank were compared;the molecular phylogenetic tree was constructed by Mega Microsoft using Artemiopsis stefanssoni as outgroup.[Result] Artemia persimilis was the primal group in genus Artemia;Artemia franciscana and Artemia monica were the evolved groups;Artemia urmiana,Artemia sinica and other Artemia species from China shared a close genetic relationship.[Conclusion] Based on the 16S rDNA sequence of them,the phylogenetic relationships of these bisexual Artemia species were A.persimilis→A.urmiana,A.sinica and A.tibetiana→A.tunisiana→A.monica→A.Franciscan.
基金supported by the Natural Science Foundation of China(Nos.30725005,31071959,J0930005)supported by the Ministry of Education of China(No.20100031110026)
文摘The phylogenetic relationships among the Nepomorpha （Hemiptera： Heteroptera） were analyzed based on nuclear protein coding genes-partial sequences of four Hox genes： abd-A, Dfd, Ubx and pb. Fifteen taxa, of which eleven were ingroups representing ten of the eleven families, were selected to produce a phylogenetic inference of nepomorphan superfamilial or familial relationships via parsimony and Bayesian techniques. Our results supported the monophylies of Nepomorpha, Naucoroidea （Aphelocheiridae ＋ Naucoridae）, Nepoidea （Belostomatidae ＋ Nepidae）, Ochteroidea （Ochteridae ＋ Gelastocoridae） and Pieoidea （Pleidae ＋ Helotrephidae）; the most basal lineage of Ochteroidea; Notonectoidea contained Notonectidae only and formed a new sister relationship with （Pleoidea ＋ Naucoroidea）; and the sister relationship of （Nepoidea ＋ Corixoidea）. The Hox genes are suitable molecular markers to resolve phylogenetic relationships at superfamily or family levels in Heteroptera.
文摘The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from ten species of Chloranthus Swartz and two outgroup species of Sarcandra Gardn. were sequenced. The regions ranged in length from 654 to 663 bp, with ITS1 (285-290 bp) slightly longer than ITS2 (205-211 bp). Of the 669 aligned positions, 109 sites (56 in ITS1, 52 in ITS2, and one in 5.8S region) were phylogenetically informative. Only one most parsimonious tree of 252 steps was obtained in PAUP analysis when gaps were treated as the fifth state. The traditional division of Chloranthus on the basis of habit seems to be quite unnatural. Evidence from the sequence of ITS region, just as that from cytology and anatomy, strongly suggested the separation of the genus into two groups according to the characteristics of androecial organs: one contains C. angustifolius, C. nervosus, C. japonicus and C. fortunei, and the other comprises the remaining species.
