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
The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fr...The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.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
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
Leaf litter plays an essential role in the functioning of forest ecosystems.They are a source of organic matter,act as a protective layer in forest soils,and provide a nurturing habitat for micro-and macro-organisms.T...Leaf litter plays an essential role in the functioning of forest ecosystems.They are a source of organic matter,act as a protective layer in forest soils,and provide a nurturing habitat for micro-and macro-organisms.Through their successional occurrence,litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling.Despite their importance in terrestrial ecosystems,host tree species and phylogenies'effect on saprobic fungal dominance and diversity are poorly understood.The present study aims to elucidate saprobic leaf-litter fungal taxonomy,phylogeny and diversity in six phylogenetically related host species in Thailand,using morphological characters and multi locus phylogeny.The host species are Dipterocarpus alatus(DA)(Dipterocarpaceae),Nayariophyton zizyphifolium(NZ)and Microcos paniculata(MP)(Malvaceae),Afzelia xylocarpa(AZ),Dalbergia cana(DC),and Dalbergia cultrata(DCul)(Fabaceae),located in Doi Tung,Chiang Rai Province,Thailand.The selected host species are mostly native to the East Asian region.We hypothesized that tree host phylogeny significantly influences the diversity of fungal communities,and that each community is unique across phylogenetically distantly related hosts.The study revealed one family,two new genera,15 new species,13 new host records,and 11 new geographical records with two new combinations of fungi which are treated in detail.Additional taxa identified,mostly to the genus level,were considered for the statistical analysis.In cases where different taxa within the same genus were found but could not be identified to species,they were treated as distinct taxa(e.g.,sp.1 and sp.2).The statistical analysis was performed to estimate the diversity and relative abundance of each taxon visualized in heatmaps and cluster analysis.The study evidenced multiple levels of diversity and host-preference existing within leaf litter fungi.The reported taxa belonged to the Dothideomycetes and Sordariomycetes,25 families and 31 genera.Most of the saprobic fungi exhibited host-exclusivity,meaning they were observed and recorded exclusively on specific host species and not on others.This resulted in a lower occurrence and overlap of fungi among the other host species.Therefore,the saprobic fungi indicated specialization on particular hosts,and the term"specialists"referred to the saprobic fungal taxa that are adapted to thrive on specific host species,rather than generalists that can inhabit multiple host species.Host family level harboured a higher number of unique saprobic taxa than host species level,as evidenced by the statistical analysis.Moreover,the saprobic fungal communities were influenced by seasonal effects during the collecting period.A core group of fungi could be identified as"generalists"observed in all the host species.The study highlights the diversity of saprobes dwelling in the leaf litter of forest ecosystems and reveals their high degree of host species-specificity.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
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
Yunnan Province is located in southwestern China,at the core and intersection of the“Himalaya”,“Indo-Burma”and“Mountains of Southwest China”biodiversity hotspots.It is the most biodiverse province in China,actin...Yunnan Province is located in southwestern China,at the core and intersection of the“Himalaya”,“Indo-Burma”and“Mountains of Southwest China”biodiversity hotspots.It is the most biodiverse province in China,acting as a major center for the origin and diversification of numerous species,and of which lignicolous freshwater fungi are one of the rich bioresources.As a part of our ongoing studies on freshwater fungi in Yunnan Province China,we collected lignicolous freshwater ascomycetes from Yunnan plateau lakes,combining morphological characteristics and multi-gene phylogenetic analysis(including,ITS,LSU,SSU,tef1-α,tub2 and rpb2)to identify the species and reveal their phylogenetic placement.A total of 293 freshwater ascomycetes were collected,and through rigorous analysis,126 species were identified,spanning three classes,24 orders,39 families,and 70 genera.Most of these fungi belong to Dothideomycetes and Sordariomycetes,with a few of Eurotiomycetes.Based on morphological and phylogenetic analyses,we introduce two new genera,Neomoromyces and Rostraeuseptisporum,and 40 new species,viz.,Apiospora fuxianhuensis,A.lacustris,Atractospora hydei,Chaetopsina hydei,C.septata,Chloridium hydei,Ch.yunnanense,Dematiosporium hydei,D.muriforme,Dictyocheirospora yunnanensis,Distoseptispora dujuanhuensis,Di.hongheensis,Di.jingdongensis,Halobyssothecium hydei,Hongkongmyces hydei,Kirschsteiniothelia hydei,Mytilinidion hydei,Neomoromyces hydei,Obliquifusoideum hydei,Ophioceras yunnanense,Plagiascoma hydei,Pseudodactylaria lacustris,Pseudostanjehughesia hydei,Rostraeuseptisporum hydei,Sporidesmiella dujuanhuensis,S.guttulata,S.hongheensis,S.hydei,S.lacustris,Sporidesmium dianchiense,Sp.distoseptatum,Sp.dujuanhuense,Sp.hongheense,Sp.lacustris,Sp.kunmingense,Sp.yangzonghaiense,Sp.yilonghuense,Thysanorea hydei,Tetraploa verrucosa,Xylolentia hydei.Detailed morphological descriptions and illustrations of these species are provided,along with a discussion of their phylogenetic relationships and distinctive morphological characters.Furthermore,five new combinations are introduced,viz.,Pseudodactylaria flammulicornuta(≡Dodactylaria flammulicornuta),P.palmae(≡Do.palmae),P.tunicata(≡Do.tunicata),P.uliginicola(≡Do.uliginicola)and Pseudostanjehughesia verrucosa(≡Ceratosporium verrucosum).Based on molecular sequence data and morphological characteristics,Dictyocheirospora aquadulcis and Dic.lithocarpi have been synonymized with Dic.heptaspora,Dic.alangii synonymized with Dic.appendiculata;Dictyosporium lakefuxianense synonymized with Pseudodictyosporium wauense,Distoseptispora nanchangensis synonymized with Distoseptispora aquatica,Chaetopsina beijingensis synonymized with Ch.fulva.Ten new geographical records are reported in China and 10 species are first reported from freshwater habitats,and 6 species are newly reported both from China and from freshwater habitats.This study fills a gap in the research on fungal diversity in Yunnan Province,and improves our understanding of their ecological roles in freshwater ecosystems.Phylogenetic analysis provides a reliable molecular framework for the classification of lignicolous freshwater fungi,supporting the reassessment of fungal taxonomy and ensuring a more objective and evolutionarily natural classification of species.This work is dedicated to Professor Kevin D.Hyde on his 70th birthday,in recognition of his lifetime contributions to mycology and his extensive research and training of students.His wide-ranging work on freshwater fungi is highlighted in this paper.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
Diatrypaceae is among the most species-rich families within Xylariales,exhibiting a global distribution,a broad host range,and diverse ecological lifestyles.However,its taxonomy remains problematic due to overlapping ...Diatrypaceae is among the most species-rich families within Xylariales,exhibiting a global distribution,a broad host range,and diverse ecological lifestyles.However,its taxonomy remains problematic due to overlapping morphological traits,insufficient diagnostic features in historical classifications,and the frequent absence of type specimens and corresponding multilocus sequence data in GenBank.These limitations have resulted in poorly resolved generic boundaries and hinder accurate identification and natural classification within the family.In this study,we undertook an integrative taxonomic revision of Diatrypaceae by examining 17 herbarium specimens loaned from major international collections(B,BPI,BRIP,E,G,K,NY,PC,PDD,S),supplemented by redrawn illustrations from original descriptions where type material was unavailable.Additionally,approximately 150 fresh collections from China,Italy,and Thailand were investigated through single spore isolation and morphological examination.Molecular data were generated for multi-gene phylogenetic analysis based on combined ITS,tub2,LSU,and rpb2 sequences.Phylogenetic reconstruction using Maximum likelihood and Bayesian inference supports the recognition of 183 species within 34 genera,including the introduction of ten novel genera:Allantoideospora,Alloperoneutypa,Brunneosepta,Fusiformiascus,Guttuliascospora,Imitatirotula,Lineariascus,Retiticulatihypha,Sessiliascus,and Trichromostroma.The study also describes 29 novel species,23 previously known species,and proposes 56 new combinations,all of which are illustrated and compared with morphological data and phylogenetically related taxa.Until further investigation using molecular data is proven,several morphologically characterized genera(Dothideovalsa,Echinomyces,Endoxylina,Leptoperidia,and Rostronitschkia)were placed within Diatrypaceae.This comprehensive morphomolecular framework significantly refines the taxonomy of Diatrypaceae and provides a foundation for future systematic and ecological studies in this complex family.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
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
[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 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
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
Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red rive...Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.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 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
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 grants from the Agriculture Seed Improvement Projects of Shandong Province(Nos.2022LZGCQY010,2021ZLGX03,and 2021TSGC 1240)the China Agriculture Research System Project(No.CARS-49)。
文摘The Chamidae are widely distributed in the tropical to temperate seas,with>70 known species.Currently,their classification relies mainly on traditional morphological methods and identification primarily on small fragment genes,such as COI.The intrafamily phylogenetic relationships are ambiguous,lacking support from reliable molecular data.In this study,the mitochondrial genomes of eight species of Chamidae were sequenced for the first time and then annotated.Their structures and compositional characteristics were analyzed.The mitochondrial gene order in this family differed significantly.Concurrently,the evolutionary position and phylogenetic relationship among Chamidae species were explored,and the Veneroida phylogenetic tree was recreated.Maximum Likelihood and Bayesian Inference analyses supported the monophyly of Chamidae.Additionally,the divergence time within Chamidae was estimated based on mitochondrial DNA sequences,with the most ancient divergence estimated to occur during the early Cretaceous period,128 MYA.This phylogeny is significant for understanding the diversity and taxonomic status of Chamidae.
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 grants from Chiang Mai University and the National Research Center of Thailand(No.42A650198)grateful to the Chiang Mai University Presidential Scholarship 2020+3 种基金the National Research Council of Thailand(NRCT)grant‘Total fungal diversity in a given forest area with implications towards species numbers,chemical diversity and biotechnology’(Grant Number N42A650547)Thailand Science and Innovation(TSRI)and National Science and Innovation Fund(NSRF)Fundamental fund grant(Grant No.662A1616047),entitled‘Biodiversity,ecology,and applications of plant litter-inhabiting fungi for waste degradation’for partially funding this researchMartin van de Bult,Narong Apichai and the Doi Tung Development Project for allowing sample collection(Permission Number 7700/17142)with the title‘The diversity of saprobic fungi on selected hosts in northern Thailand’funded by the Distinguished Scientist Fellowship Program(DSFP),King Saud University,Kingdom of Saudi Arabia.
文摘Leaf litter plays an essential role in the functioning of forest ecosystems.They are a source of organic matter,act as a protective layer in forest soils,and provide a nurturing habitat for micro-and macro-organisms.Through their successional occurrence,litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling.Despite their importance in terrestrial ecosystems,host tree species and phylogenies'effect on saprobic fungal dominance and diversity are poorly understood.The present study aims to elucidate saprobic leaf-litter fungal taxonomy,phylogeny and diversity in six phylogenetically related host species in Thailand,using morphological characters and multi locus phylogeny.The host species are Dipterocarpus alatus(DA)(Dipterocarpaceae),Nayariophyton zizyphifolium(NZ)and Microcos paniculata(MP)(Malvaceae),Afzelia xylocarpa(AZ),Dalbergia cana(DC),and Dalbergia cultrata(DCul)(Fabaceae),located in Doi Tung,Chiang Rai Province,Thailand.The selected host species are mostly native to the East Asian region.We hypothesized that tree host phylogeny significantly influences the diversity of fungal communities,and that each community is unique across phylogenetically distantly related hosts.The study revealed one family,two new genera,15 new species,13 new host records,and 11 new geographical records with two new combinations of fungi which are treated in detail.Additional taxa identified,mostly to the genus level,were considered for the statistical analysis.In cases where different taxa within the same genus were found but could not be identified to species,they were treated as distinct taxa(e.g.,sp.1 and sp.2).The statistical analysis was performed to estimate the diversity and relative abundance of each taxon visualized in heatmaps and cluster analysis.The study evidenced multiple levels of diversity and host-preference existing within leaf litter fungi.The reported taxa belonged to the Dothideomycetes and Sordariomycetes,25 families and 31 genera.Most of the saprobic fungi exhibited host-exclusivity,meaning they were observed and recorded exclusively on specific host species and not on others.This resulted in a lower occurrence and overlap of fungi among the other host species.Therefore,the saprobic fungi indicated specialization on particular hosts,and the term"specialists"referred to the saprobic fungal taxa that are adapted to thrive on specific host species,rather than generalists that can inhabit multiple host species.Host family level harboured a higher number of unique saprobic taxa than host species level,as evidenced by the statistical analysis.Moreover,the saprobic fungal communities were influenced by seasonal effects during the collecting period.A core group of fungi could be identified as"generalists"observed in all the host species.The study highlights the diversity of saprobes dwelling in the leaf litter of forest ecosystems and reveals their high degree of host species-specificity.
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 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the National Natural Science Foundation of China(Project ID:32060005,U2002203)National Science and Technology Fundamental Resources Investigation Program of China(2021FY100900)+4 种基金the Yunnan Fundamental Research Project(202201AW070001)High-Level Talents Program of Yunnan Province(YNQR-QNRC-2020-113)Foundation of Yunnan Province Science and Technology Department(202305AM070003)Second Tibetan Plateau Scientific Expedition and Research Program(Grant No.2024QZKK02010303)Distinguished Scientist Fellowship Programme(DSFP)of King Saud University.
文摘Yunnan Province is located in southwestern China,at the core and intersection of the“Himalaya”,“Indo-Burma”and“Mountains of Southwest China”biodiversity hotspots.It is the most biodiverse province in China,acting as a major center for the origin and diversification of numerous species,and of which lignicolous freshwater fungi are one of the rich bioresources.As a part of our ongoing studies on freshwater fungi in Yunnan Province China,we collected lignicolous freshwater ascomycetes from Yunnan plateau lakes,combining morphological characteristics and multi-gene phylogenetic analysis(including,ITS,LSU,SSU,tef1-α,tub2 and rpb2)to identify the species and reveal their phylogenetic placement.A total of 293 freshwater ascomycetes were collected,and through rigorous analysis,126 species were identified,spanning three classes,24 orders,39 families,and 70 genera.Most of these fungi belong to Dothideomycetes and Sordariomycetes,with a few of Eurotiomycetes.Based on morphological and phylogenetic analyses,we introduce two new genera,Neomoromyces and Rostraeuseptisporum,and 40 new species,viz.,Apiospora fuxianhuensis,A.lacustris,Atractospora hydei,Chaetopsina hydei,C.septata,Chloridium hydei,Ch.yunnanense,Dematiosporium hydei,D.muriforme,Dictyocheirospora yunnanensis,Distoseptispora dujuanhuensis,Di.hongheensis,Di.jingdongensis,Halobyssothecium hydei,Hongkongmyces hydei,Kirschsteiniothelia hydei,Mytilinidion hydei,Neomoromyces hydei,Obliquifusoideum hydei,Ophioceras yunnanense,Plagiascoma hydei,Pseudodactylaria lacustris,Pseudostanjehughesia hydei,Rostraeuseptisporum hydei,Sporidesmiella dujuanhuensis,S.guttulata,S.hongheensis,S.hydei,S.lacustris,Sporidesmium dianchiense,Sp.distoseptatum,Sp.dujuanhuense,Sp.hongheense,Sp.lacustris,Sp.kunmingense,Sp.yangzonghaiense,Sp.yilonghuense,Thysanorea hydei,Tetraploa verrucosa,Xylolentia hydei.Detailed morphological descriptions and illustrations of these species are provided,along with a discussion of their phylogenetic relationships and distinctive morphological characters.Furthermore,five new combinations are introduced,viz.,Pseudodactylaria flammulicornuta(≡Dodactylaria flammulicornuta),P.palmae(≡Do.palmae),P.tunicata(≡Do.tunicata),P.uliginicola(≡Do.uliginicola)and Pseudostanjehughesia verrucosa(≡Ceratosporium verrucosum).Based on molecular sequence data and morphological characteristics,Dictyocheirospora aquadulcis and Dic.lithocarpi have been synonymized with Dic.heptaspora,Dic.alangii synonymized with Dic.appendiculata;Dictyosporium lakefuxianense synonymized with Pseudodictyosporium wauense,Distoseptispora nanchangensis synonymized with Distoseptispora aquatica,Chaetopsina beijingensis synonymized with Ch.fulva.Ten new geographical records are reported in China and 10 species are first reported from freshwater habitats,and 6 species are newly reported both from China and from freshwater habitats.This study fills a gap in the research on fungal diversity in Yunnan Province,and improves our understanding of their ecological roles in freshwater ecosystems.Phylogenetic analysis provides a reliable molecular framework for the classification of lignicolous freshwater fungi,supporting the reassessment of fungal taxonomy and ensuring a more objective and evolutionarily natural classification of species.This work is dedicated to Professor Kevin D.Hyde on his 70th birthday,in recognition of his lifetime contributions to mycology and his extensive research and training of students.His wide-ranging work on freshwater fungi is highlighted in this paper.
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]).
基金supported by the National Natural Science Foundation of China(Grant No.32350410401)the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou province(Grant No.U1812401).
文摘Diatrypaceae is among the most species-rich families within Xylariales,exhibiting a global distribution,a broad host range,and diverse ecological lifestyles.However,its taxonomy remains problematic due to overlapping morphological traits,insufficient diagnostic features in historical classifications,and the frequent absence of type specimens and corresponding multilocus sequence data in GenBank.These limitations have resulted in poorly resolved generic boundaries and hinder accurate identification and natural classification within the family.In this study,we undertook an integrative taxonomic revision of Diatrypaceae by examining 17 herbarium specimens loaned from major international collections(B,BPI,BRIP,E,G,K,NY,PC,PDD,S),supplemented by redrawn illustrations from original descriptions where type material was unavailable.Additionally,approximately 150 fresh collections from China,Italy,and Thailand were investigated through single spore isolation and morphological examination.Molecular data were generated for multi-gene phylogenetic analysis based on combined ITS,tub2,LSU,and rpb2 sequences.Phylogenetic reconstruction using Maximum likelihood and Bayesian inference supports the recognition of 183 species within 34 genera,including the introduction of ten novel genera:Allantoideospora,Alloperoneutypa,Brunneosepta,Fusiformiascus,Guttuliascospora,Imitatirotula,Lineariascus,Retiticulatihypha,Sessiliascus,and Trichromostroma.The study also describes 29 novel species,23 previously known species,and proposes 56 new combinations,all of which are illustrated and compared with morphological data and phylogenetically related taxa.Until further investigation using molecular data is proven,several morphologically characterized genera(Dothideovalsa,Echinomyces,Endoxylina,Leptoperidia,and Rostronitschkia)were placed within Diatrypaceae.This comprehensive morphomolecular framework significantly refines the taxonomy of Diatrypaceae and provides a foundation for future systematic and ecological studies in this complex family.
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.
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(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.
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 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Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences （1140 bp）of one red river pig （ Potamochoerus porcus ）, one bearded pig （ Sus barbatus ）, and several Eurasian wild boars （ Sus scorfa ） were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups： （1） the relatively primitive animals from Philippine Islands （such as S. cebifrons and S. philippensis ）, Sulawesi and it＇s adjacent islands （S. celebensis）, （2） the Eurasian wild boars （S. scrofa and the mysterious S. salvanius）, and （3） other pigs （such as S. barbatus and S. verrucosus）, which might further diverged as the islands type （such as S. barbatus from Sumatra and Borneo） and the continental type （such as Malay Peninsula wild boar）.
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 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.
