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Genome-Wide Characterization of the Hyaluronidase Gene Family and Their Potential Roles in Viviparous Black Rockfish(Sebastes schlegeli)

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Journal of Ocean University of China 2024年第2期23卷 487-498页

作者： LIU Zhiying NIU Jingning ZHAO Xi LIU Huaxiang LI Zibin HE Yan QI Jie MOE Key Laboratory of marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China Key Laboratory of Tropical Aquatic Germplasm of Hainan Province Sanya Oceanographic InstituteOcean University of ChinaSanya 572025China

Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction *** from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be *** the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and *** spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other *** adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site *** results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other *** positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in ***,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression *** results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.

关键词： adaptation of viviparous black rockfish(Sebastes schlegelii) hyaluronidase selective pressure analysis

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A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation

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marine life Science & Technology 2024年第1期6卷 168-181页

作者： Jiwen Liu Da-Wei Li Xinxin He Ronghua Liu Haojin Cheng Chenglong Su Mengna Chen Yonghong Wang Zhongsheng Zhao Hanyue Xu Zhangyu Cheng Zicheng Wang Nikolai Pedentchouk David J.Lea-Smith Jonathan D.Todd Xiaoshou Liu Meixun Zhao Xiao-Hua Zhang Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life SciencesOcean University of ChinaQingdao 266003China Laboratory for marine Ecology and Environmental Science Laoshan LaboratoryQingdao 266237China institute of evolution and marine biodiversity Ocean University of ChinaQingdao 266003China Key Laboratory of marine Chemistry Theory and Technology Ministry of EducationOcean University of ChinaQingdao 266100China Key Lab of Submarine Geosciences and Prospecting Techniques Ministry of Education/College of Marine GeosciencesOcean University of ChinaQingdao 266100China Key Laboratory of Physical Oceanography Ministry of Education/Research Vessel CentreOcean University of ChinaQingdao 266100China School of Environmental sciences University of East AngliaNorwich NR47TJUK School of Biological sciences University of East AngliaNorwich NR47TJUK

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor ***,the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is ***,analyses of carbon isotope composition in a~750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition,with anomalous ^(14)C ages likely caused by seismically driven mass transport and the funneling effect of trench *** community composition and diverse enzyme activities in the upper~27 cm differed from those at lower depths,probably due to sudden sediment deposition and differences in redox condition and organic matter *** lower depths,microbial population numbers,and composition remained relatively constant,except at some discrete depths with altered enzyme activity and microbial phyla abundance,possibly due to additional sudden sedimentation events of different *** is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth’s deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic *** depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.

关键词： Hadal subseafloor Deep water sediment Mariana Trench Radiocarbon Microbial community Redox potential

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Characterization of Nutrients,Heavy Metals,Petroleum and Their Impact on Phytoplankton in Laizhou Bay:Implications for Environmental Management and Monitoring

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Journal of Ocean University of China 2024年第3期23卷 822-834页

作者： WANG Kai ZHAO Linlin ZHU Yugui YANG Liqiang WANG Yunfeng HONG Xuguang college of marine life Science Ocean University of ChinaQingdao 266003China First institute of Oceanography Ministry of Natural ResourcesQingdao 266061China college of Fisheries Ocean University of ChinaQingdao 266003China institute of Oceanology Chinese Academy of SciencesQingdao 266071China Southern marine Science and Engineering Guangdong Laboratory Guangzhou 511458China

The Laizhou Bay(LB)represents a substantial ecological area that is vulnerable to human activities and confronts diverse environmental *** study provides a comprehensive characterization of nutrients,petroleum,heavy metals,and phytoplankton community structure across seven distinct areas in *** results indicate relatively high concentrations of NO_(2)-N,SiO_(4)-Si,and NO_(3)-N in the Southwest Laizhou Bay(SWLB)and Huanghe River Estuary(HRE).In contrast,the East Laizhou bay(ELB)and the North of Huanghe River Estuary(NHRE)exhibit the highest concentrations of heavy metals(As,Cr and Hg).The areas with high phytoplankton density and community diversity are mainly located in the *** adjusting for basic environmental factors,phytoplankton density and Margalef richness index D are significantly associated with nutrients(NO_(3)-N,NO_(2)-N,NH_(4)-N,SiO_(4)-Si),and heavy metal(Cr)*** highlight that,in addition to Xiaoqinghe River,nutrients brought by the Mihe River in the SWLB and heavy metal(Cr)pollution in the ELB resulting from industrial and mining activities along the coast significantly influence phytoplankton growth and community ***,it is recommended that more monitoring and management efforts be focused on these regions in the future.

关键词： Huanghe River Estuary Laizhou Bay nutrients heavy metals phytoplankton biodiversity

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Bird specimen number linked with species trait and climate niche breadth

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Avian Research 2024年第1期15卷 108-115页

作者： Xiaoyu Duan Xiongwei Huang Jingya Zhang Shuo Lv Gang Song Yanping Wang Gang Feng Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau&Inner Mongolia Key Laboratory of Grassland Ecology School of Ecology and EnvironmentInner Mongolia UniversityHohhot010020China Key Laboratory of marine Biotechnology of Fujian Province Institute of OceanologyCollege of Marine SciencesFujian Agriculture and Forestry UniversityFuzhou350002China Key Laboratory of Zoological Systematics and evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China Laboratory of Island Biogeography and Conservation Biology College of Life SciencesNanjing Normal UniversityNanjing210023China

Biological specimens are fundamental for taxonomy and flora/fauna *** importantly,they also play crucial roles in recording environmental impacts on morphology and behavior,which is vital for biodiversity research and ***,there are few systematic studies on the patterns and drivers of bird specimen number at regional *** study is the first attempt to examine the relationships between bird specimen number and species traits as well as climate niche breadth in China,aiming to answer two questions:1)how do species’temperature niche breadth and precipitation niche breadth influence specimen number?2)which trait is most associated with bird specimen number?The associations between bird specimen number and explanatory variables were examined using ordinary least squares,generalized linear models,phylogenetic generalized linear mixed models,and multiple *** results showed that Muscicapidae was the family with the highest specimen number,and Passeriformes was the order with the highest specimen *** specimen number significantly increased with larger temperature niche breadth and precipitation niche *** number was also positively associated with geographic range size,habitat specificity,hunting vulnerability and clutch size,but negatively associated with body *** findings suggest that future bird specimen collection should pay more attention to birds with limited ecological niches,large body sizes,and small clutch *** research enhances the use of bird specimen data to study and preserve biodiversity.

关键词： biodiversity conservation Biological specimens Bird traits Scientific collection Specimen number Temperature and precipitation

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Improving landscape connectivity through habitat restoration:application for Asian elephant conservation in Xishuangbanna Prefecture,China

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Integrative Zoology 2024年第2期19卷 319-335页

作者： Bin WAN Wenwen LI Peng LIU Nian YANG Shang CHEN Xianming GUO Bin WANG Li ZHANG Key Laboratory for biodiversity Science and Ecological Engineering Ministry of EducationCollege of Life SciencesBeijing Normal UniversityBeijingChina Research Center for Coastal Zone Science and marine Development Strategy First Institute of OceanographyMinistry of Natural ResourcesQingdaoChina School of Biological sciences The University of Hong KongPokfulamHong KongChina Research institute of Xishuangbanna National Nature Reserve JinghongChina Xishuangbanna Asian Elephant Conservation and Management Center JinghongChina

Habitat restoration is an effective method for improving landscape connectivity,which can reduce habitat *** landscape connectivity could promote connections between habitat,which is extremely essential to preserve gene flow and population *** study proposes a methodological framework to analyze landscape connectivity for Asian elephant habitat conservation,aiming to provide practical options for reducing habitat fragmentation and improving habitat *** approach involved combining a species distribution model using MaxEnt and landscape functional connectivity models using graph theory to assess the impact on connectivity improvement via farmland/plantation restoration as *** results showed that:(1)there were 119 suitable habitat patches of Asian elephant covering a total area of 1952.41 km^(2).(2)The connectivity between habitats improved significantly after vegetation restoration and the gain first decreased and then increased with the increase of dispersal distance.(3)The first few new habitat patches that were identified played an important role in improving connectivity,and the variation rate of connectivity gradually leveled off as the number of new habitats increased.(4)Prioritization of the 25 best new habitat patches increased connectivity from 0.54%to 5.59%as the dispersal distance increased and mainly was located between two Asian elephant distribution regions and two *** of new habitat patches was effective for improving or restoring *** findings can be used as guidance for improving the studied fragmented Asian elephant habitats,and they can also be used as a reference for the habitat restoration of other endangered species heavily affected by habitat fragmentation.

关键词： Asian elephant connectivity habitat restoration habitat suitability landscape graphs

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Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area

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marine life Science & Technology 2024年第2期6卷 349-362页

作者： Zhixin Zhang Jinxin Zhou Jorge García Molinos Stefano Mammola Ákos Bede‑Fazekas Xiao Feng Daisuke Kitazawa Jorge Assis Tianlong Qiu Qiang Lin CAS Key Laboratory of Tropical marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Guangdong Provincial Key Laboratory of Applied marine Biology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China marine biodiversity and Ecological evolution Research Center South China Sea Institute of OceanologyGuangzhou 510301China Global Ocean and Climate Research Center South China Sea Institute of OceanologyGuangzhou 510301China institute of Industrial Science The University of Tokyo5-1-5 KashiwanohaKashiwaChiba 277-8574Japan Arctic Research Center Hokkaido UniversitySapporoHokkaido 001-0021Japan Finnish Museum of Natural History University of HelsinkiHelsinkiFinland Molecular Ecology Group(MEG) Water Research Institute(IRSA)National Research Council of Italy(CNR)28922 Verbania PallanzaItaly National biodiversity Future Center(NBFC) PalermoItaly institute of Ecology and Botany HUN-REN Centre for Ecological ResearchVácrátótHungary Department of Environmental and Landscape Geography ELTE Eötvös Loránd UniversityBudapestHungary Department of Biology University of North CarolinaChapel HillNC 27599USA Centre of marine sciences University of AlgarveCampus de GambelasFaroPortugal CAS Key Laboratory of Experimental marine Biology Institute of OceanologyChinese Academy of SciencesQingdao 266071China University of Chinese Academy of sciences Beijing 100049China

Correlative species distribution models(SDMs)are important tools to estimate species’geographic distribution across space and time,but their reliability heavily relies on the availability and quality of occurrence *** can be biased when occurrences do not fully represent the environmental requirement of a *** tested to what extent species’physiological knowledge might influence SDM *** on the Japanese sea cucumber Apostichopus japonicus within the coastal ocean of East Asia,we compiled a comprehensive dataset of occurrence *** then explored the importance of incorporating physiological knowledge into SDMs by calibrating two types of correlative SDMs:a naïve model that solely depends on environmental correlates,and a physiologically informed model that further incorporates physiological information as *** further tested the models’sensitivity to calibration area choices by fitting them with different buffered areas around known *** with naïve models,the physiologically informed models successfully captured the negative influence of high temperature on *** and were less sensitive to the choice of calibration *** naïve models resulted in more optimistic prediction of the changes of potential distributions under climate change(i.e.,larger range expansion and less contraction)than the physiologically informed *** findings highlight benefits from incorporating physiological information into correlative SDMs,namely mitigating the uncertainties associated with the choice of calibration *** these promising features,we encourage future SDM studies to consider species physi-ological information where available.

关键词： Bayesian approach Climate change Habitat suitability Physiological knowledge Species distribution model

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Endogenous retrovirus activation: potential for immunology and clinical applications

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National Science Review 2024年第4期11卷 21-23页

作者： Jundan Yu Peishan Qiu Jingwen Ai Bo Liu Guan-Zhu Han Fan Zhu Wenhong Zhang Jie Cui Department of Infectious Diseases Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response National Medical Center for Infectious Diseases Huashan Hospital Shanghai Medical College Fudan University CAS Key Laboratory of Molecular Virology &Immunology Shanghai Institute of Immunity and Infection Chinese Academy of Sciences University of Chinese Academy of sciences Shanghai Huashen institute of Microbes and Infections college of life sciences Nanjing Normal University State Key Laboratory of Virology and Department of Medical Microbiology School of Basic Medical SciencesWuhan University The institute of Infection and Health Research Fudan University Key Laboratory of Medical Molecular Virology(MOE/MOH) Shanghai Medical CollegeFudan University Laboratory for marine Biology and Biotechnology Qingdao Marine Science and Technology Center

Endogenous retroviruses (ERVs), the remnants of ancient retrovirus infections, constitute approximately 8% of the human genome and play important roles in human evolution, development,and diseases. Multiple drugs, such as DNA methyltransferase inhibitors and lysine-specific histone demethylase 1inhibitors, reactivate ERVs, induce viral mimicry and trigger innate immune responses to enhance tumor immunogenicity.

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Advances in environmental DNA monitoring:standardization,automation,and emerging technologies in aquatic ecosystems

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Science China(life sciences) 2024年第7期67卷 1368-1384页

作者： Suxiang Lu Honghui Zeng Fan Xiong Meng Yao Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China institute of Ecology College of Urban and Environmental SciencesPeking UniversityBeijing 100871China School of life sciences Peking UniversityBeijing 100871China institute of Deep Sea Science and Engineering Chinese Academy of SciencesSanyaChina Center for Excellence in Animal evolution and Genetics Chinese Academy of SciencesKunmingChina

Environmental DNA(eDNA)monitoring,a rapidly advancing technique for assessing biodiversity and ecosystem health,offers a noninvasive approach for detecting and quantifying species from various environmental *** this review,a comprehensive overview of current eDNA collection and detection technologies is provided,emphasizing the necessity for standardization and automation in aquatic ecological ***,the intricacies of water bodies,from streams to the deep sea,and the associated challenges they pose for eDNA capture and analysis are *** paper delineates three primary eDNA survey methods,namely,bringing back water,bringing back filters,and bringing back data,each with specific advantages and constraints in terms of labor,transport,and data ***,innovations in eDNA sampling equipment,including autonomous drones,subsurface samplers,and in-situ filtration devices,and their applications in monitoring diverse taxa are ***,recent advancements in species-specific detection and eDNA metabarcoding are addressed,highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of *** implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological ***,the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term *** propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring,aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.

关键词： eDNA methodology sampler environment biomonitoring ecogenomic sensors ocean observation instrument

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Conservation genomics of the critically endangered Chinese pangolin

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Science China life sciences 2024年第10期67卷 2051-2061页

作者： Shichao Wei Huizhong Fan Wenliang Zhou Guangping Huang Yan Hua Shibao Wu Xiao Wei Yiting Chen Xinyue Tan Fuwen Wei Jiangxi Province Key Laboratory of Conservation Biology College of ForestryJiangxi Agricultural University Center for evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) institute of Zoology Chinese Academy of Sciences Guangdong Provincial Key Laboratory of Silviculture Protection and UtilizationGuangdong Academy of Forestry School of life Science South China Normal University Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi

The Chinese pangolin(Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters(MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.

关键词： Manis pentadactyla conservation genomics demographic history human activities conservation strategies

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Jurassic integrative stratigraphy,biotas,and paleogeographical evolution of the Qinghai-Tibetan Plateau and its surrounding areas

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Science China Earth sciences 2024年第4期67卷 1195-1228页

作者： Jianguo LI Xin RAO Lin MU Xiaohui CUI Xin LI Hui LUO Peixue LIU Center for Excellence in life and Paleoenvironment Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjing 210008China Nanjing college University of Chinese Academy of SciencesNanjing 211135China

The Qinghai-Tibetan Plateau experienced a unique geological evolution during the Jurassic,driven by the termination of the Palaeotethys and the reduction of the *** Indian Plate separated from the northern margin of Gondwana and drifted northward from the Southern *** that the timing of strata serves as the basis for reconstructing geological history,the present work aimed to develop a new multiple stratigraphic and chronologic framework for the Jurassic strata of the Qinghai-Tibetan Plateau region via a synthesis of the material on lithostratigraphy,palaeontology,iso-radiometric dating,magnetostratigraphy,and other techniques with an emphasis on recent progress and *** new framework included the Jurassic System from the four major subdivisions of the plateau:the Baryan Har,Qiangtang,Lhasa-Gandise,and Southern Xizang(Himalaya).Ultimately,a more complete,refined biostratigraphic sequence was proposed,comprising the most common fossils in the plateau and those that are stratigraphically significant for the Jurassic stratigraphy,including ammonites,bivalves,brachiopods,foraminifera,radiolarians,and dinoflagellate cysts for the marine strata,and pollen and spores,and charophytes for the terrestrial *** biostratigraphic framework was correlated with the Jurassic international standard zonation of the Geological Time Scale 2020 via standard or representative species or genera of *** on this framework,we constructed a lateral correlation of the Jurassic strata between different basins of the *** palaeontologic correlation in the present work shows that the Lhasa-Gandise Block had a closer relationship with the Qiangtang Block than with the Southern Xizang Himalaya during the Jurassic ***,the Lhasa-Gandise Block and Qiangtang Block shared similar marine fauna features of the north marginal East *** contrasts the opinion suggesting that the Yarlung Zangbo Tethys was a small back-arc basin.A c

关键词： Biostratigraphy Chronostratigraphy Correlation Yarlung Zangbo suture Bangong Co-Nujiang suture Tethys

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