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Genomic insights into marine environment adaptation and conservation of the threatened olive ridley turtle ( Lepidochelys olivacea)

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ISCIENCE 2025年第2期28卷 111776页

作者： Yang, Lin Chen, Yiting Wang, Shaofeng Zhang, Chenglong Huang, Xin Du, Xin Zhou, Wenliang wei, fuwen Southern Marine Sci & Engn Guangdong Lab Guangzhou Ctr Evolut & Conservat Biol Guangzhou Peoples R China Jiangxi Agr Univ Coll Forestry Jiangxi Key Lab Conservat Biol Nanchang 330045 Jiangxi Peoples R China Hong Kong Univ Sci & Technol Dept Ocean Sci Hong Kong Peoples R China Guangdong Huidong Sea Turtle Natl Nat Reserve Huizhou Peoples R China Marine Protected Area Adm Sansha City Hainan Peoples R China Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China

Sea turtles are marine flagship species and most of them are currently in a threatened state. Long-term surviving in the ocean has driven significant morphological and physiological changes for this group, which makes them an ideal model for studying adaptive evolution of marine environments. Herein, we present a chromosome-scale genome of Lepidochelys olivacea with a genome size of 2.22 Gb and a contig N50 of 97.3 Mb. Comparative genomic analyses uncovered a suite of adaptive changes in genes related to olfaction, vision, virus defense, and longevity, which may help explain the genetic underpinnings of its marine environment adaptation. We also observed that the genome-wide heterozygosity of L. olivacea was low (6.45e-4), consistent with its prolonged population decline. Overall, our study provides valuable genetic resources for understanding evolutionary adaptations to aquatic environment and for the conservation of this threatened species.

关键词： Evolutionary biology Genomics Nature conservation

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Toward a predictable cask theory of species extinction assessment in the Anthropocene

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FRONTIERS IN ECOLOGY AND THE ENVIRONMENT 2024年第3期22卷 e2714页

作者： Chen, Youhua Dai, Qiang Zhou, Jin Tang, Danni Li, De-Zhu wei, fuwen Zhan, Xiangjiang Chinese Acad Sci Chengdu Inst Biol Chengdu Peoples R China Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Germplasm Bank Wild Species Kunming Inst Bot Kunming Peoples R China Jiangxi Agr Univ Coll Forestry Prov Key Lab Conservat Biol Nanchang Peoples R China

Predicting species extinction is challenging in the context of climate change. The International Union for Conservation of Nature (IUCN) Red List of Threatened Species assesses species extinction risk by accounting for population size and global range of taxa, but this approach neglects the importance of genetic variability. Here, we propose a life strategy index (LSI) for predicting the extinction risks of species under climate change. The LSI is composed of three fundamental and independent components: namely, evolutionary potential, ecological potential, and colonization potential. The LSI constitutes a so-called "cask" theory of species extinction, which predicts that extinction likelihood is determined by the relative deficiency of any of the three components. The indicative variables used to construct the proposed LSI make the index applicable to assessments of (and predictions for) the extinction risk of different taxa in the face of climate change, which can inform management and conservation of imperiled species in a more scientific and precise manner.

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The genome of African manatee Trichechus senegalensis reveals secondary adaptation to the aquatic environment

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ISCIENCE 2024年第7期27卷 110394页

作者： Huang, Xin Dong, Guixin Fan, Huizhong Zhou, Wenliang Huang, Guangping Guan, Dengfeng Zhang, Delu wei, fuwen Ctr Evolut & Conservat Biol Southern Marine Sci & Engn Guangdong Lab Guangzhou Guangzhou 511458 Peoples R China Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Guangdong Chimelong Grp Co Ltd Guangzhou 511400 Peoples R China Jiangxi Agr Univ Coll Forestry Jiangxi Prov Key Lab Conservat Biol Nanchang 330045 Peoples R China Chimelong Ocean Kingdom Zhuhai 519000 Peoples R China

Sirenians exhibit unique aquatic adaptations, showcasing both convergent adaptive features shared with cetaceans and unique characteristics such as cold sensitivity and dense bones. Here, we report a chromosomelevel genome of the African manatee ( Trichechus senegalensis ) with high continuity, completeness, and accuracy. We found that genes associated with osteopetrosis have undergone positive selection ( CSF1R and LRRK1 ) or pseudogenized ( FAM111A and IGSF23 ) in the African manatee, potentially contributing to the dense bone formation. The loss of KCNK18 may have increased their sensitivity to cold water temperatures. Moreover, we identified convergent evolutionary signatures in 392 genes among fully aquatic mammals, primarily enriched in skin or skeletal system development and circadian rhythm, which contributed to the transition from terrestrial to fully aquatic lifestyles. The African manatee currently possesses a small effective population size and low genome-wide heterozygosity. Overall, our study provides genetic resources for understanding the evolutionary characteristics and conservation efforts of this species.

关键词： African manatee genome Convergent evolutionary aquatic mammals Currently low genome small effective population

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Adaptive evolution of traits for parasitism and pathogen transmission potential in bat flies

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National Science Review 2025年第3期12卷 46-59页

作者： Guangping Huang Xing Liu Xin Huang Chuang Gao Zhilin Wang Junxia Li Xiaocui wei Wen-Hua Yu Yi Wu Ying Liu Jiang Feng Yang Li fuwen wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Jiangxi Provincial Key Laboratory of Conservation Biology College of Forestry Jiangxi Agricultural University University of Chinese Academy of Sciences Key Laboratory of Conservation and Application in Biodiversity of South China School of Life Sciences Guangzhou University Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University

Deciphering the mechanisms underlying the transmission and spillover of zoonoses from reservoir hosts is essential in preventing future global pandemics. Bat flies—obligate blood-feeding ectoparasites of bats—are known carriers of diverse viruses. Here, we conducted a de novo assembly of a chromosome-level genome for the bat fly species Phthiridium sp. Comparative genomic analysis unveiled genes associated with specialized traits, such as the loss of eyes and wings, as well as elongated legs, which have adapted to parasitism on the dense fur of bats. Utilizing small RNA sequencing, we identified a spectrum of known and previously unclassified viruses in bat flies. Notably, experimental evidence indicated that bat flies can also feed on mammalian hosts other than bats, suggesting the potential for the spillover of bat-borne ***, we demonstrated the role of the bat fly's RNA interference pathway in influencing the diversity and evolution of viruses. In summary, this study not only presents a new genome catalog to unveil the evolutionary mechanisms underpinning bat fly parasitism, but also provides a novel research system that can be used to investigate the mechanisms of cross-species transmission of bat-borne viruses and the co-evolution of bats and viruses.

关键词： bat fly bat host–pathogen interactions ectoparasites adaptive evolution virus–host dynamics antiviral RNA interference

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A new era for evolutionary developmental biology in non-model organisms

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Science China(Life Sciences) 2020年第8期63卷 1251-1253页

作者： fuwen wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China University of Chinese Academy of Sciences Beijing 100049China

Since the publication of The Origin of Species by Charles Darwin,evolutionary biology has developed into a key discipline of biology and experienced several important expansions contributed by the sequential integrati... 详细信息

关键词： Crick evolutionary Species

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Toward the generation of pure coral genomes with experimental and bioinformatic improvements

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The Innovation 2024年第4期5卷 30-32页

作者： Yisi Hu Zhiwei Zhang Shuyan Sun Youfang Sun Hui Huang Wenliang Zhou fuwen wei Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)Guangzhou 511458China Jiangxi Provincial Key Laboratory of Conservation Biology College of ForestryJiangxi Agricultural UniversityNanchang 330029China Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China

Stony corals,the primary architects of coral reef ecosystems,are largely underrepresented in omics studies despite their *** presence of endosymbiotic Symbiodiniaceae algae complicates the extraction of pure coral DNA,posing a challenge for genomic ***,we devised a comprehensive methodological framework that incorporates various experimental treatments to achieve 99%purity in coral DNA extraction and a robust bioinformatics pipeline to guarantee the assembly of high-quality,contamination-free coral *** of our framework using Acropora millepora samples demonstrated its efficacy and superiority in obtaining high-quality pure coral genomes using easily accessible adult *** integrated framework serves as a critical foundation for largescale genome-enabled research on stony corals,providing insight into coral evolution and conservation.

关键词： coral guarantee purity

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The metabolic adaptation in wild vertebrates via omics approaches

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Life Metabolism 2022年第3期1卷 234-241页

作者： Xin Du Yisi Hu Guangping Huang fuwen wei Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)GuangzhouGuangdong 511458China

Metabolism is the basis for sustaining life and essential to the adaptive evolution of *** the development of high-throughput sequencing technology,genetic mechanisms of adaptive evolution,including metabolic adaptation,have been extensively resolved by omics approaches,but a deep understanding of genetic and epigenetic metabolic adaptation is still *** metabolic adaptations from genetic and epigenetic perspectives in wild vertebrates is vital to understanding species evolution,especially for the early stages of adaptative ***,we summarize the advances in our understanding of metabolic adaptations via omics approaches in wild vertebrates based on three types of cases:extreme environment,periodically changing environment,and changes of species *** conclude that the understanding of the formation of metabolic adaptations at the genetic level alone can well identify the adaptive genetic variation that has developed during evolution,but cannot resolve the potential impact of metabolic adaptations on the adaptative evolution in the ***,it seems imperative to include epigenomics and metabolomics in the study of adaptation,and that in the future genomic and epigenetic data should be integrated to understand the formation of metabolic adaptation of wild vertebrate organisms.

关键词： adaptative evolution metabolic adaptation comparative genomics multi-omics epigenetics

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Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates

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SCIENCE OF THE TOTAL ENVIRONMENT 2022年第Part2期838卷 156178页

作者： Huang, Guangping Qu, Qingyue Wang, Meng Huang, Mingpan Zhou, Wenliang wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China China Univ Chinese Acad Sci Beijing 100049 Peoples R China Ctr Evolut & Conservat Biol Southern Marine Sci & Engn Guangdong Lab Guangzho Guangzhou 511458 Peoples R China

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to beta-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the

关键词： Microbial diversity Antibiotic resistance Gut microbiome Vertebrate conservation Environment factors Global landscape

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Spatial-temporal population dynamics of the critically endangered Blue-crowned Laughingthrush Pterorhinus courtoisi:a 22-year longitudinal study

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Science China(Life Sciences) 2024年第8期67卷 1769-1771页

作者： Tao Liu Jutao He Chang Xiao Jie Liu Jie Sun Minling Li Yuanhua Hong weiwei Zhang fuwen wei Jiangxi Provincial Key Laboratory of Conservation Biology Jiangxi Agricultural UniversityNanchang 330045China Forestry Bureau of Wuyuan Shangrao 333299China

Dear Editor,Population size is a crucial indicator in evaluating the conservation status of a *** the patterns of population fluctuation and the distribution range of endangered species is important for biodiversity c... 详细信息

关键词： Population crown dynamics

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Gut microbiome as a key monitoring indicator for reintroductions of captive animals

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CONSERVATION BIOLOGY 2024年第1期38卷 e14173-e14173页

作者： Huang, Guangping Qi, Dunwu Yang, Zhisong Hou, Rong Shi, Wenyu Zhao, Fangqing Li, Zitian Yan, Li wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Sichuan Key Lab Conservat Biol Endangered Wildlife Chengdu Res Base Giant Panda Breeding Chengdu Peoples R China Sichuan Acad Giant Panda Chengdu Peoples R China China Agr Univ Coll Biol Sci Beijing Peoples R China Chinese Acad Sci Beijing Inst Life Sci Lab Computat Genom Beijing Peoples R China Jiangxi Agr Univ Coll Forestry Nanchang Peoples R China Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China

Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.

关键词： conservation biology gut microbiome monitoring indicator reintroduction wildlife

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