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Morphological and molecular analyses of a Philine kinglipini outbreak in summer of 2022 in Jiaozhou Bay,China

Journal of Oceanology and Limnology 2024年第3期42卷 831-848页

作者： Zelin DUAN Yanan YU Jing WANG Junlong ZHANG Nansheng CHEN CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdao 266071China Laboratory of Marine Ecology and Environmental Science Laoshan LaboratoryQingdao 266237China Center for Ocean Mega-Science Chinese Academy of SciencesQingdao 266071China Laboratory of Marine Organism Taxonomy and Phylogeny Qingdao Key Laboratory of Marine Biodiversity and ConservationInstitute of OceanologyChinese Academy of SciencesQingdao 266071China Marine Biological Museum Chinese Academy of SciencesQingdao 266071China Department of Molecular Biology and Biochemistry Simon Fraser UniversityBurnabyBritish ColumbiaV5A 1S6Canada

A sudden and unprecedented outbreak of molluscan Philine kinglipini occurred in summer 2022 in Jiaozhou Bay,Shandong,China,causing substantial damage to local mariculture industry of the Manila clam Ruditapes philippinarum.Although P.kinglipini has been found in many coastal regions of China,the molecular research of P.kinglipini has not been extensively studied,making it difficult to accurately identify and track P.kinglipini samples in field using molecular methods.Samples were collected during the outbreak and their morphological features and molecular sequences were analyzed.Results show that the causative species of the outbreak was P.kinglipini.The mitochondrial genome(mt DNA)of P.kinglipini was constructed for the first time,based on which phylogenetic analysis of the mt DNAs of P.kinglipini and related species in the order Cephalaspidea was carried out.As revealed by metabarcoding analysis of 18S rDNA V4,the seasonal change of P.kinglipini and closely related Philine species was striking with peaks between April and August.Therefore,metabarcoding analysis is applicable tool for monitoring the bloom development of P.kinglipini and related species.This study generated for the first time essential molecular marker sequences and mtDNA of P.kinglipini,which provided a reference for future characterization and monitoring of its outbreaks and for phylogenetic analysis of Philine species.

关键词： marine species outbreaks metabarcoding analysis mitochondrial genome Philine kinglipini phylogenetics spatial-temporal dynamics

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First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae(Coleoptera:Tenebrionoidea)

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Insect Science 2022年第4期29卷 1226-1238页

作者： Chuan Wu Yong Zhou Tian Tian Ting-Jing Li Bin Chen Chongqing Key Laboratory of Vector Insects Institute of Entomology and Molecular BiologyChongqing Normal UniversityChongqingChina

Despite worldwide distribution and rich diversity,the knowledge of mitochondrial genome(mtgenome)characteristics within the family Tenebrionidae(Coleoptera)is still very limited,and phylogenetics remain unresolved for the family.In this study,the mtgenomes for 12 species are newly sequenced and annotated.Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae.Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome,and AT bias,length variation,and codon usage are consistent with other reported beetle mtgenomes.Some intergenic overlap and gap sequences may contain phylogenetically informative information,whereas neither the conserved nor repeat sequences in the control region do.The subfamilies Lagriinae,Pimeliinae,Stenochiinae,and Alleculinae are found to be monophyletic,and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study.Furthermore,Lagriinae is sister to the rest of the subfamilies.At the tribal level,the tribes Lagriini in the subfamily Lagrrinae;Strongyliini in Stenochiinae;Cteniopodini in Alleculinae;and Triboliini,Opatrini,and Amarygmini in Tenebrioninae are monophyletic;while Diaperini in Diaperinae,and Tenebrionini in Tenebrioninae are polyphyletic.

关键词： Alleculinac characteristics Colcopiera mtgenome phylogenetics Tenebrionidac

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Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus

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Animal Models and Experimental Medicine 2022年第5期5卷 410-417页

作者： Xi Yu Gong Cheng Tsinghua-Peking Center for Life Sciences School of MedicineTsinghua UniversityBeijingChina Institute of Infectious Diseases Shenzhen Bay LaboratoryShenzhenChina Institute of Pathogenic Organisms Shenzhen Center for Disease Control and PreventionShenzhenChina School of Life Sciences Tsinghua UniversityBeijingChina

Dengue virus(DENV)is one of the most important arboviral pathogens in the tropics and subtropics,and nearly one-third of the world's population is at risk of infection.The transmission of DENV involves a sylvatic cycle between nonhuman primates(NHP)and Aedes genus mosquitoes,and an endemic cycle between human hosts and predominantly Aedes aegypti.DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes(DENV-1-4).Phylogenetic analyses of DENV have revealed its origin,epidemiology,and the drivers that determine its molecular evolution in nature.This review discusses how phyloge-netic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.

关键词： dengue virus(DENV) evolution flavivirus phylogenetics

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Molecular Phylogeny, Species Delimitation and Taxonomic Revision of the Australian Spider Wasp Genus Heterodontonyx Haupt, 1935 (Hymenoptera: Pompilidae)

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Advances in Entomology 2024年第2期12卷 105-128页

作者： Mahin Sadat Chavoshi Jolfaei Juanita Rodriguez Australian National Insect Collection CSIRO Canberra Australia Research School of Biology Australian National University Canberra Australia

Heterodontonyx (Pompilidae: Pepsinae) is an understudied genus with Australasiandistribution and most species are endemic to Australia. There have recently been sometaxonomic changes involving the genera Heterodontonyx and Cryptocheilus based on molecular and morphological evidence, however, phylogenetic relationships within Heterodontonyx, species delimitation and formal revision have not been conducted. Here, we construct a Maximum Likelihood phylogeny estimate of Heterodontonyx based on ITS1, 5.8S, ITS2 region of 30 samples representing seven Heterodontonyx morphospecies. bPTP species delimitation approach was employed and ultimately the taxonomic revision of the genus was carried out. Phylogenetic analyses strongly support the monophyly of Heterodontonyx and the species delimitation method recognizes eight species among which one new species is identified.

关键词： Pompilidae Taxonomy Australian Pomplids phylogenetics

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Complete mitochondrial genome of the leaf muntjac(Muntiacus putaoensis) and phylogenetics of the genus Muntiacus

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Zoological Research 2017年第5期38卷 310-316页

作者： Guo-Gang Li Ming-Xia Zhang Kyaw Swa Kyaw-Win Maung Rui-Chang Quan Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Yezin Nay Pyi Taw 05282 Myanmar Center for Integrative Conservation Xishuangbanna Tropical Botanical Garden Chinese Academy of Sciences Mengla Yunnan 666303China Hponkan Razi Wildlife Sanctuary Offices Putao Kachin 01051 Myanmar Forest Research Institute Forest Department Ministry of Environmental Conservation and Forestry Yezin Nay Pyi Taw 05282 Myanmar

The leaf muntjac （Muntiacus putaoensis） is an endemic deer species found in the east trans- Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported. Most mitochondrial genes, except for ND6 and eight tRNAs, were encoded on the heavy strand. The overall base composition of the heavy strand was 33.1% A, 29.3% T, 24.2% C, and 13.4% G, with a strong AT bias of 62.4%. There were seven regions of gene overlap totaling 95 bp and 11 intergenic spacer regions totaling 74 bp. Phylogenetic analyses （ML and BI） among the Muntiacus genus based on the sequenced of mitogenome and ND4L-ND4 supported M. putaoensis as a member of Muntiacus, most closely related to M. vuquangensis. However, when analyses based on cyt b included two more muntjacs, M. truongsonensis was most closely related to M. putaoensis rather than M. vuquangensis, and together with M. rooseveltorum, likely forming a M. rooseveltorum complex of the species. This study will help in the exploration of the evolutionary history and taxonomic status of the leaf muntjac, as well as its protection as a genetic resource.

关键词： Muntiacus Muntiacus putaoensis Mitogenome phylogenetics

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Postcranial disparity of galeaspids and the evolution of swimming speeds in stem-gnathostomes

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National Science Review 2023年第7期10卷 81-90页

作者： Zhikun Gai Xianghong Lin Xianren Shan Humberto G.Ferrón Philip C.J.Donoghue Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences University of Chinese Academy of Sciences Bristol Palaeobiology Group School of Earth Sciences University of Bristol Instituto Cavanilles de Biodiversidad i Biología Evolutiva Universitat de València

Galeaspids are extinct jawless relatives of living jawed vertebrates whose contribution to understanding the evolutionary assembly of the gnathostome bodyplan has been limited by absence of postcranial remains.Here,we describe Foxaspis novemura gen.et sp.nov.,based on complete articulated remains from a newly discovered Konservat-Lagerstatte in the Early Devonian(Pragian,～410 Ma) of Guangxi,South China.F,novemura had a broad,circular dorso-ventrally compressed headshield,slender trunk and strongly asymmetrical hypochordal tail fin comprised of nine ray-like scale-covered digitations.This tail morphology contrasts with the symmetrical hypochordal tail fin of Tujiaaspis vividus,evidencing disparity in galeaspid postcranial anatomy.Analysis of swimming speed reveals galeaspids as moderately fast swimmers,capable of achieving greater cruising swimming speeds than their more derived jawless and jawed relatives.Our analyses reject the hypothesis of a driven trend towards increasingly active food acquisition which has been invoked to characterize early vertebrate evolution.

关键词： Galeaspida jawed vertebrates evolution functional morphology phylogenetics modelling

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HIV-1 Transmission among Injecting Drug Users is Principally Derived from Local Circulating Strains in Guangxi, China

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Biomedical and Environmental Sciences 2023年第5期36卷 418-430页

作者： CEN Ping LIANG Hua Yue YANG Yuan ZHANG Fei YANG Shi Xiong MO Ju Cong FENG Yi HUANG Jie Gang NING Chuan Yi HUANG Chun Yuan YANG Yao LIANG Na LIANG Bing Yu YE Li LIANG Hao Guangxi Key Laboratory of AIDS Prevention and Treatment School of Public HealthGuangxi Medical UniversityNanning 530021GuangxiChina Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry Life Science InstituteGuangxi Medical UniversityNanning 530021GuangxiChina Nanning Center for Disease Control and Prevention Nanning 530023GuangxiChina State Key Laboratory of Infectious Disease Prevention and Control(SKLID) Chinese Center for Disease Control and Prevention(China CDC)Collaborative Center for Diagnosis and Treatment of Infectious DiseaseBeijing 102206China

Objective The mode of human immunodeficiency virus(HIV) transmission via injection drug use(IDU)still exists, and the recent shift in IDU-related transmission of HIV infection is largely unknown. The purpose of this study was to analyze the spatiotemporal sources and dynamics of HIV-1 transmission through IDU in Guangxi.Methods We performed a molecular epidemiological investigation of infections across Guangxi from2009 to 2019. Phylogenetic and Bayesian time-geographic analyses of HIV-1 sequences were performed to confirm the characteristics of transmission between IDUs in combination with epidemiological data.Results Among the 535 subjects, CRF08_BC(57.4%), CRF01_AE(28.4%), and CRF07_BC(10.7%) were the top 3 HIV strains;72.6% of infections were linked to other provinces in the transmission network;93.6% of sequence-transmitted strains were locally endemic, with the rest coming from other provinces,predominantly Guangdong and Yunnan;92.1% of the HIV transmission among people who inject drugs tended to be transmitted between HIV-positive IDUs.Conclusion HIV recombinants were high diversity, and circulating local strains were the transmission sources among IDUs in Guangxi. However, there were still cases of IDUs linked to other provinces.Coverage of traditional prevention strategies should be expanded, and inter-provincial collaboration between Guangxi, Yunnan, and Guangdong provinces should be strengthened.

关键词： HIV-1 Injection drug use Transmission Strain source phylogenetics

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Origin and evolution of green plants in the light of key evolutionary events

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Journal of Integrative Plant Biology 2022年第2期64卷 516-535页

作者： Zhenhua Zhang Xiaoya Ma Yannan Liu Lingxiao Yang Xuan Shi Hao Wang Runjie Diao Bojian Zhong College of Life Sciences Nanjing Normal UniversityNanjing210023 China

Green plants(Viridiplantae)are ancient photosynthetic organisms that thrive both in aquatic and terrestrial ecosystems,greatly contributing to the changes in global climates and ecosystems.Significant progress has been made toward understanding the origin and evolution of green plants,and plant biologists have arrived at the consensus that green plants first originated in marine deep-water environments and later colonized fresh water and dry land.The origin of green plants,colonization of land by plants and rapid radiation of angiosperms are three key evolutionary events during the long history of green plants.However,the comprehensive understanding of evolutionary features and molecular innovations that enabled green plants to adapt to complex and changeable environments are still limited.Here,we review current knowledge of phylogenetic relationships and divergence times of green plants,and discuss key morphological innovations and distinct drivers in the evolution of green plants.Ultimately,we highlight fundamental questions to advance our understanding of the phenotypic novelty,environmental adaptation,and domestication of green plants.

关键词： adaptation divergence times green plants key innovations phylogenetics terrestrialization

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phylogenetics and Molecular Divergence of Tilapia Fish (Oreochromis Species) Using Mitochondrial D-Loop and Cytochrome b Regions

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American Journal of Molecular Biology 2018年第1期8卷 39-57页

作者： Ekerette Emmanuel Ekerette Ekei Victor Ikpeme Ogbuagu Ugorji Udensi Michael Ohiokhuaobo Ozoje Owoidihe Monday Etukudo Anthony John Umoyen Samuel Olutunde Durosaro Matthew Wheto Department of Genetics and Biotechnology University of Calabar Calabar Nigeria Department of Animal Breeding and Genetics Federal University of Agriculture Abeokuta Nigeria

Understanding the level of genetic diversity in any population is an important requisite towards strategizing measures for conservation and improvement of stocks. This study focused on the assessment of phylogenetics and molecular divergence of tilapia fish species obtained from two populations (Domita in South-South and Odeda in South-West, Nigeria) using the displacement loop (D-loop) and cytochrome b region of the mitochondrial deoxyribonucleic acid (mtDNA). A total of 28 samples (15 from South-South and 13 from South-West) were used for the genetic analysis. DNA was extracted from the tissue of all the samples using Quik-gDNATM miniPrep kit. The D-loop containing the hypervariable region was sequenced for all samples from the two populations, while cytochrome b (Cyt b) region of mtDNA was only sequenced for samples from South-South population. Chromatograms of the sequences were viewed and edited using Bioedit software. Multiple sequence alignment was carried out using molecular evolutionary genetic analysis (MEGA) software before subsequent genetic analyses. Phylogenetic analysis grouped the samples into two clusters based on population. Also, when the two mitochondrial regions were pooled together, they clustered into two major groups based on mitochondrial regions. Analysis of molecular variance (AMOVA) revealed 37.32% variation within population and 62.68% variation among population with a significant fixation index of 0.627 (p 0.05). The genetic distance inferred between D-loop regions of South-South and South-West populations was 0.243. Maternal lineage analysis revealed that the origin of tilapia fish from both populations could be traced to Oreochromis spirilus and Oreochromis leucostictus based on mitochondrial D-loop region. The findings of this study revealed molecular divergence among the tilapia populations and may serve as pivot information for the genetic improvement of this important species.

关键词： phylogenetics Molecular Divergence Maternal Lineage Tilapia Fish

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An early Cambrian Sidneyia(Arthropoda) resolves the century-long debate of its head organization

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Science China Earth Sciences 2023年第3期66卷 521-527页

作者： Kunsheng DU David L.BRUTON Jie YANG Xiguang ZHANG Research Center of Paleobiology Yuxi Normal UniversityYuxi 653100China Institute of Paleontology Yunnan University(Chenggong)Kunming 650500China Natural History Museum(Geology) University of OsloPostboks 1172 BlindernOslo NO-0318Norway

We report the extraordinarily preserved euarthropod Sidneyia minor sp.***.from the Cambrian Stage 3 Xiaoshiba Lagerst?tte in Yunnan,South China.So far this is the earliest occurrence of the genus.As with other species of Sidneyia,the new taxon shares similar features such as a crescent-shaped head shield with paired lateral notches for stalked eyes,but more significantly and new,is the presence of three pairs of post-antennal appendages beneath the head shield identified by micro-CT methods.We conclude that Sidneyia is a sister group to other members of Vicissicaudata within the diverse radiation of Artiopoda.

关键词： Sidneyia Cephalic organization Euarthropods phylogenetics Evolution Cambrian Stage 3

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