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
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 worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecula...The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.展开更多
Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta ...Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.展开更多
Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations...Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations.Despite recent studies on their biogeographic history,how these species adapted to geographical changes remains unclear.In this study,divergence times and reconstructed ancestral traits were estimated based on phylogenetic analysis of mitochondrial and nuclear DNA sequences,totaling 4048 bp.Results indicated that the divergence between lotic-specialized and generalist species occurred during the middle to late Miocene(95% confidence interval(CI):16-13 million years ago(Ma)),correlating with the long-lasting arid period(14-12 Ma)and uplift of the Wuyi-Nanling mountains(15-11 Ma).Ancestral trait reconstruction revealed notable morphological changes associated with the emergence of lotic-specialized lineages.Specifically,male body size increased from 130 mm to 140 mm,and epibranchial traits shifted from thin to thick structures.Additionally,variation in tongue movability and skin texture were observed among lotic species.Each morphological shift is hypothesized to have an ecological basis,facilitating adaptation to specific environmental conditions.Overall,this study represents the first comprehensive attempt to elucidate the evolution of ancestral traits among divergent species of modern Asian newts,providing a deeper understanding of their adaptive responses to historical geographical and climatic changes.展开更多
The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 specie...The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.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 Ministry of Science and Higher Education of the Russian Federation(No.075-152021-1037,Internal No.15.BRK.21.0001)。
文摘The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
基金Supported by the Research and Development Program of Shandong Province,China(Major Science and Technology Innovation Project)(No.2021CXGC011306)the MNR Key Laboratory of Eco-Environmental Science and Technology,China(No.MEEST-2021-05)+2 种基金the Natural Science Foundation of Shandong Province(No.ZR2020MD002)the Doctoral Science Research Foundation of Yantai University(Nos.SM15B01,SM19B70,SM19B28)the“Double-Hundred Action”of Yantai City(No.2320004-SM20RC02)。
文摘Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.
基金supported by the Japan Science and Technology Agency:Support for Pioneering Research Initiated by the Next Generation presented by the Division of Graduate Studies,Kyoto University(A94231600003)and the Nagao Project。
文摘Pachytriton,and Paramesotriton,are primarily distributed across East Asia,displaying a broad range of environmental adaptations,including generalists inhabiting both lotic and lentic habitats and lotic specializations.Despite recent studies on their biogeographic history,how these species adapted to geographical changes remains unclear.In this study,divergence times and reconstructed ancestral traits were estimated based on phylogenetic analysis of mitochondrial and nuclear DNA sequences,totaling 4048 bp.Results indicated that the divergence between lotic-specialized and generalist species occurred during the middle to late Miocene(95% confidence interval(CI):16-13 million years ago(Ma)),correlating with the long-lasting arid period(14-12 Ma)and uplift of the Wuyi-Nanling mountains(15-11 Ma).Ancestral trait reconstruction revealed notable morphological changes associated with the emergence of lotic-specialized lineages.Specifically,male body size increased from 130 mm to 140 mm,and epibranchial traits shifted from thin to thick structures.Additionally,variation in tongue movability and skin texture were observed among lotic species.Each morphological shift is hypothesized to have an ecological basis,facilitating adaptation to specific environmental conditions.Overall,this study represents the first comprehensive attempt to elucidate the evolution of ancestral traits among divergent species of modern Asian newts,providing a deeper understanding of their adaptive responses to historical geographical and climatic changes.
基金This work was supported by National Natural Science Foundation of China (No. 30570247)the Natural Science Foundation of Shanxi Province (No. 2003-1087)
文摘The phylogenetic relationships of genera in the subfamily Apaturinae were examined using mtDNA sequence data from 1,471 bp of cytochrome oxidase subunit Ⅰ （COI）. The mitochondrial COI gene from a total of 16 species in 11 genera were sequenced to obtain mtDNA data, along with those of 4 species obtained from GenBank, to construct the MP and the NJ trees using Athyma jina, Penthema adelma, Polyura nepenthes, and Charaxes bernardus as outgroups. The transitions at the third codon positions of the COI data set were found saturated, but they were retained for analysis, because they contain the majority of the phylogenetic information. The impacts of equal weight assumptions for all characters in the parsimonious analysis were assessed by potential alternations in clades in response to different transition/transversion weighting schemes. The results indicated four distinct major groups in Apaturinae. Moreover, several well supported and stable clades were found in the Apaturinae. The study also identified undetermined taxon groups whose positions were weakly supported and were subject to changes under different weighting schemes. Within the Apaturinae, the clustering results are approximately identical to the classical morphological classification. The mtDNA data suggest the genus Mimathyma as a monophyletic group. Lelecella limenitoides and Dilipa fenestra have close relationship with very strong support in all phylogenetic trees. It also supports the taxonomic revision of removing several species from Apatura to other genera, namely Mimathyma schrenckii, M. chevana, M. nycteis, Chitoria subcaerulea, C. fasciola, C. pallas, and Helcyra subalba.
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.
