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PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation

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MICROBIOME 2023年第1期11卷 221-221页

作者： Huang, Guangping Shi, Wenyu Wang, Le Qu, Qingyue Zuo, Zhenqiang Wang, Jinfeng Zhao, Fangqing wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Chinese Acad Sci Inst Microbiol Microbial Resource & Big Data Ctr Beijing Peoples R China Chinese Acad Sci Beijing Inst Life Sci Lab Computat Genom Beijing 100101 Peoples R China Jiangxi Agr Univ Coll Forestry Nanchang 330045 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

BackgroundThe gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool *** pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance *** study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife.6KUVWwvzFXHebBwiyZoAvnVideo AbstractConclusionsOur study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife.6KUVWwvzFXHebBwiyZoAvnVideo Abstract

关键词： Wild mammal Gut microbiome Giant panda Diversity Adaptive evolution Conservation

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造礁石珊瑚演化发育生物学研究进展

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中国科学:生命科学 2024年第5期54卷 805-818页

作者：张志伟周文良张晶晶胡怡思魏辅文南方海洋科学与工程广东省实验室(广州) 海洋生物演化与保护生物学研究中心广州大学生命科学学院江西农业大学林学院

造礁石珊瑚是海洋中的关键动物类群.在漫长的演化过程中,造礁石珊瑚获得与虫黄藻细胞内共生、生物矿化造礁等重要功能性状,是珊瑚礁生态系统的框架生物,在维持生态系统生物多样性及生态调节功能等方面发挥关键作用.同时,以造礁石珊瑚为... 详细信息

造礁石珊瑚是海洋中的关键动物类群.在漫长的演化过程中,造礁石珊瑚获得与虫黄藻细胞内共生、生物矿化造礁等重要功能性状,是珊瑚礁生态系统的框架生物,在维持生态系统生物多样性及生态调节功能等方面发挥关键作用.同时,以造礁石珊瑚为代表的刺胞动物是双侧动物最近缘的分支,在系统发育演化上占据非常关键的地位,其胚层、体轴以及多种功能细胞的发育调控等相关研究结果,对探讨双侧动物相应性状的演化起源具有极其重要的指导意义.本文梳理造礁石珊瑚在演化发育生物学领域的研究进展,重点关注其重要细胞类群、胚层和体轴、繁殖策略及其细胞内共生和生物矿化等关键性状的演化起源和发育调控机制等.同时,本文提出几个未来造礁石珊瑚演化发育研究值得重点关注的方向,包括关键功能性状的分子基础、生殖细胞发育和性别决定、干细胞与再生能力等.

关键词：造礁石珊瑚演化发育生物学繁殖策略细胞内共生生物矿化

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Habitat connectivity drives panda recovery

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CURRENT BIOLOGY 2024年第17期34卷 3894-3904.e3页

作者： Wang, Meng Wang, Guiming Huang, Guangping Kouba, Andy Swaisgood, Ronald R. Zhou, Wenliang Hu, Yibo Nie, Yonggang wei, fuwen Jiangxi Agr Univ Coll Forestry Jiangxi Prov Key Lab Conservat Biol Nanchang 330045 Peoples R China Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Mississippi State Univ Dept Wildlife Fisheries & Aquaculture Starkville MS 39762 USA Conservat Sci & Wildlife Hlth San Diego Zoo Wildlife Alliance Escondido CA 92027 USA Ctr Evolut & Conservat Biol Southern Marine Sci & Engn Guangdong Lab Guangzhou Guangzhou 511458 Peoples R China

Globally, the majority of habitat loss is irreversible, and most species will never recover their former ranges. We have learned a great deal about what leads to population decline and extinction, but less about recovery. The recently downlisted giant panda provides a unique opportunity to understand the mechanisms of species recovery. In our study, we estimate giant panda suitable habitats, population density, and gene flow across landscapes to fully investigate the direct and indirect ecological mechanisms underlying bold conservation strategies. We found that the Giant Panda National Survey has modestly but systematically underestimated population size. China's effort to mitigate anthropogenic disturbances was associated with increased panda population density through improving habitat quality and reducing habitat fragmentation. Enhanced landscape connectivity reduced inbreeding via gene flow but indirectly increased inbreeding temporarily due to high local panda density. Although the panda's recovery has been geographically uneven, we provide evidence for improving connectivity and gene flow resulting from conservation efforts. If these processes can be sustained and improved, the panda's path to recovery will be less encumbered by loss of genetic diversity, fostering hope that the present rate of recovery will not be stalled. Findings from this study will not only help guide future giant panda conservation management but also provide a model for how a more mechanistic examination of the genetic processes underlying species recovery can foster the development of more effective strategies for endangered species recovery.

关键词： effective population size gene flow genetic diversity giant panda habitat patches landscape connectivity population density species recovery

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TAS2R20 variants confer dietary adaptation to high-quercitrin bamboo leaves in Qinling giant pandas

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ECOLOGY AND EVOLUTION 2020年第12期10卷 5913-5921页

作者： Hu Xiangxu Wang Guan Shan Lei Sun, Shuyan Hu Yibo wei fuwen Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Boston Childrens Hosp Dept Lab Med Boston MA USA Harvard Med Sch Boston MA 02115 USA Nanjing Normal Univ Coll Life Sci Jiangsu Key Lab Biodivers & Biotechnol Nanjing Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China

Sensitivity to bitter tastes provides animals with an important means of interacting with their environment and thus, influences their dietary preferences. Genetic variants encoding functionally distinct receptor types contribute to variation in bitter taste sensitivity. Our previous study showed that two nonsynonymous sites, A52V and Q296H, in the TAS2R20 gene are directionally selected in giant pandas from the Qinling Mountains, which are speculated to be the causative base-pair changes of Qinling pandas for the higher preference for bamboo leaves in comparison with other pandas. Here, we used functional expression in engineered cells to identify agonists of pTAS2R20 (i.e., giant panda's TAS2R20) and interrogated the differences in perception in the in vitro responses of pTAS2R20 variants to the agonists. Our results show that pTAS2R20 is specifically activated by quercitrin and that pTAS2R20 variants exhibit differences in the sensitivity of their response to the agonist. Compared with pTAS2R20 in pandas from other areas, the receptor variant with A52V and Q296H, which is most commonly found in Qinling pandas, confers a significantly decreased sensitivity to quercitrin. We subsequently quantified the quercitrin content of the leaves of bamboo distributed in the Qinling Mountains, which was found to be significantly higher than that of the leaves of bamboo from panda habitats in other areas. Our results suggest that the decreased sensitivity to quercitrin in Qinling pandas results in higher-quercitrin-containing bamboo leaves to be tasting less bitter to them and thus, influences their dietary preference. This study illustrates the genetic adaptation of Qinling pandas to their environments and provides a fine example of the functional effects of directional selection in the giant panda.

关键词： bamboo leaves bitter taste receptor dietary adaptation giant panda quercitrin

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Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown- and- white coat color in giant pandas

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2024年第11期121卷 e2317430121页

作者： Guan, Dengfeng Sun, Shuyan Song, Lingyun Zhao, Pengpeng Nie, Yonggang Huang, Xin Zhou, Wenliang Yan, Li Lei, Yinghu Hu, Yibo wei, fuwen Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Jiangxi Agr Univ Jiangxi Prov Key Lab Conservat Biol Nanchang 330045 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Shaanxi Louguantai Rescue & Breeding Ctr Rare Wild Xian 710402 Peoples R China Southern Marine Sci & Engn Guangdong Lab Guangzhou Ctr Evolut & Conservat Biol Guangzhou 511458 Peoples R China

Brown- and - white giant pandas (hereafter brown pandas) are distinct coat color mutants found exclusively in the Qinling Mountains, Shaanxi, China. However, its genetic mechanism has remained unclear since their discovery in 1985. Here, we identified the genetic basis for this coat color variation using a combination of field ecological data, population genomic data, and a CRISPR-Cas9 knockout mouse model. We de novo assembled a long- read - based giant panda genome and resequenced the genomes of 35 giant pandas, including two brown pandas and two family trios associated with a brown panda. We identified a homozygous 25 - bp deletion in the first exon of Bace2, a gene encoding amyloid precursor protein cleaving enzyme, as the most likely genetic basis for brown- and - white coat color. This deletion was further validated using PCR and Sanger sequencing of another 192 black giant pandas and CRISPR-Cas9 edited knockout mice. Our investigation revealed that this mutation reduced the number and size of melanosomes of the hairs in knockout mice and possibly in the brown panda, further leading to the hypopigmentation. These findings provide unique insights into the genetic basis of coat color variation in wild animals. Significance Coat color variation is one of the most diverse traits in wild animals. The giant pandas can have a color photo because of the occurrence of brown pandas. However, the genetic basis of the brown- and - white coat color has remained elusive in the past about four decades. We identified a homozygous 25 - bp deletion in the first exon of Bace2 as the most likely genetic basis for brown- and - white coat color variation in giant pandas. Our study provides unique insights into the genetic basis of coat color variation in wild animals and will guide scientific breeding of the rare brown pandas.

关键词： coat color variation brown giant panda population genomics Bace2 melanosome

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Spatial patterns and conservation of genetic and phylogenetic diversity of wildlife in China

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SCIENCE ADVANCES 2021年第4期7卷 000-000页

作者： Hu, Yibo Fan, Huizhong Chen, Youhua Chang, Jiang Zhan, Xiangjiang Wu, Hua Zhang, Baowei Wang, Meng Zhang, Wenyan Yang, Lin Hou, Xian Shen, Xing Pan, Tao Wu, wei Li, Jun Hu, Haihua wei, fuwen Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming Yunnan Peoples R China Chinese Acad Sci Chengdu Inst Biol Chengdu Peoples R China Chinese Res Inst Environm Sci State Key Lab Environm Criteria & Risk Assessment Beijing Peoples R China Cent China Normal Univ Sch Life Sci Inst Evolut & Ecol Wuhan Peoples R China Anhui Univ Sch Life Sci Hefei Peoples R China Chinese Acad Sci Inst Bot State Key Lab Systemat & Evolutionary Bot Beijing Peoples R China Southern Marine Sci & Engn Guangdong Lab Guangzho Guangzhou Guangdong Peoples R China

Genetic diversity and phylogenetic diversity reflect the evolutionary potential and history of species, respectively. However, the levels and spatial patterns of genetic and phylogenetic diversity of wildlife at the regional scale have largely remained unclear. Here, we performed meta-analyses of genetic diversity in Chinese terrestrial vertebrates based on three genetic markers and investigated their phylogenetic diversity based on a dated phylogenetic tree of 2461 species. We detected strong positive spatial correlations among mitochondrial DNA-based genetic diversity, phylogenetic diversity, and species richness. Moreover, the terrestrial vertebrates harbored higher genetic and phylogenetic diversity in South China and Southwest China than in other regions. Last, climatic factors (precipitation and temperature) had significant positive effects while altitude and human population density had significant negative impacts on levels of mitochondrial DNA-based genetic diversity in most cases. Our findings will help guide national-level genetic diversity conservation plans and a post-2020 biodiversity conservation framework.

关键词： Conservation

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Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards

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GENOME BIOLOGY 2025年第1期26卷 1-24页

作者： Yang, Lin Jin, Hong Yang, Qien Poyarkov, Andrey Korablev, Miroslav Rozhnov, Viatcheslav Shao, Junjie Fu, Qiaomei Hernandez-Blanco, Jose Antonio Zhan, Xiangjiang Yu, Li Alexandrov, Dmitry Dai, Qingyan Munkhtsog, Bariushaa Du, Xin Munkhtsog, Bayaraa Ma, Liqing Chen, Wanlin Malykh, Sergei Jin, Yipeng He, Shunfu Zhang, Tongzuo Wu, Guosheng Shi, Yonghong wei, fuwen Hu, Yibo Chinese Acad Sci Inst Zool CAS Key Lab Anim Ecol & Conservat Biol Beijing Peoples R China Jiangxi Agr Univ Coll Forestry Jiangxi Key Lab Conservat Biol Nanchang Jiangxi Peoples R China Southern Marine Sci & Engn Ctr Evolut & Conservat Biol Guangdong Lab Guangzhou Peoples R China Chinese Acad Sci Northwest Inst Plateau Biol Key Lab Adaptat & Evolut Plateau Biota Xining Qinghai Peoples R China Russian Acad Sci AN Severtsov Inst Ecol & Evolut Moscow Russia Univ Chinese Acad Sci Beijing Peoples R China Chinese Acad Sci Inst Vertebrate Paleontol & Paleoanthropol Key Lab Vertebrate Evolut & Human Origins Beijing Peoples R China Yunnan Univ State Key Lab Conservat & Utilizat Bioresource Kunming 650091 Yunnan Peoples R China Irbis Mongolia Ctr Ulaanbaatar Mongolia Mongolian Acad Sci Inst Biol Ulaanbaatar Mongolia Qinghai Univ Qinghai Acad Anim Sci & Vet Med Qinghai Prov Key Lab Pathogen Diag Anim Dis Xining 810016 Qinghai Peoples R China Qinghai Univ Green Techn Res Prevent & Control Xining Qinghai Peoples R China China Agr Univ Coll Vet Med Clin Dept Beijing Peoples R China Xining Wildlife Zoo Xining Qinghai Peoples R China Golmud Forestry & Grassland Stn Qinghai Prov Haixi 816000 Peoples R China

BackgroundLong-term persistence of species with low genetic diversity is the focus of widespread attention in conservation biology. The snow leopard, Panthera uncia, is a big cat from high-alpine regions of Asia. However, its subspecies taxonomy, evolutionary history, evolutionary potential, and survival strategy remain unclear, which greatly hampers their *** sequence a high-quality chromosome-level genome of the snow leopard and the genomes of 52 wild snow leopards. Population genomics reveal the existence of two large genetic lineages in global snow leopards, the northern and southern lineages, supported by the biogeography. The Last Glacial Maximum drove the divergence of two lineages. Microclimate differences and large rivers between the western and central Himalayas likely maintain the differentiation of two lineages. EPAS1 is positively selected in the southern lineage with almost fixed amino acid substitutions and shows an increased allele frequency with elevation. Compared to the southern lineage, the northern lineage exhibits a lower level of genomic diversity and higher levels of inbreeding and genetic load, consistent with its recent population decline. We find that snow leopards have extremely low genomic diversity and higher inbreeding than other Carnivora species;however, strong deleterious mutations have been effectively purged in snow leopards by historical population bottlenecks and inbreeding, which may be a vital genetic mechanism for their population survival and *** findings reveal the survival strategy of a species with low genetic diversity and highlight the importance of unveiling both genetic diversity and genetic burden for the conservation of threatened species.

关键词： Snow leopards Population genomics Genetic structure Genomic diversity Deleterious variants EPAS1

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The endangered red panda in Himalayas: Potential distribution and ecological habitat associates

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GLOBAL ECOLOGY AND CONSERVATION 2020年 21卷

作者： Thapa, Arjun Hu, Yibo Aryal, Prakash Chandra Singh, Paras Bikram Shah, Karan Bahadur wei, fuwen Chinese Acad Sci Inst Zool Lab Anim Ecol & Conservat Biol 1-5 Beichenxi Rd Beijing 100101 Peoples R China Chinese Acad Sci Ctr Excellence Anim Evolut & Genet Kunming 650223 Yunnan Peoples R China GoldenGate Int Collage Kathmandu 4059 Nepal Natl Trust Nat Conservat POB 3712 Khumaltar Lalitpur Nepal Himalayan Nat Trishakti Marg Kathmandu 10918 Nepal

The red panda Ailurus fulgens, an endangered herbivorous member of the order Carnivora that is endemic to the eastern Himalayan broadleaf and coniferous forests, is surviving under threats induced by human activity and climate change. The distribution range of the red panda in Nepal represents an understudied remnant population at the edge of its western biogeographic distribution range. To build a potentially suitable habitat, we used red panda occurrence and the least correlated bioclimatic variables in MaxEnt modeling. In addition, habitat variables were recorded in transects and quadrat plots to identify ecologically important variables for the red panda habitat. Currently, 14.23% (21,680 km(2)) of Nepal is a climatically suitable habitat for the red panda. The mean temperature of the warmest quarter, annual temperature range, mean temperature of the coldest quarter and precipitation of the coldest quarter are the major contributing variables in the model, with an area under the ROC curve (AUC) of 0.94. Climatic, geographic, and habitat group variables have considerable contributions, while disturbance has a low contribution. Multiple factor analysis identified mixed broadleaf forest, East Himalayan oak-laurel forest, canopy cover >20%, ground substrate use, bamboo cover >20%, tree stump presence, fallen logs of small trees and habitat without grazing as having high contributions in the qualitative groups. Similarly, the elevation, distance from settlements and roads, distance to water sources, annual temperature range, mean diurnal range and annual precipitation were important variables in the quantitative groups. The results will help guide conservation managers in implementing effective habitat management programs for the red panda. (C) 2020 The Authors. Published by Elsevier B.V.

关键词： Himalayas Habitat feature Multiple factor analysis Red panda

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中国濒危兽类保护遗传学研究进展与展望

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兽类学报 2021年第5期41卷 571-580页

作者：魏辅文马天笑胡义波中国科学院动物研究所动物生态与保护生物学院重点实验室

我国是全球生物多样性大国,拥有包括大熊猫、金丝猴、华南虎、麋鹿、白鱀豚等特有物种和旗舰物种在内的丰富兽类资源。近几十年来,土地利用模式转变、盗猎、环境污染、气候变化等因素使许多兽类物种面临生存威胁,导致物种遗传多样性丧... 详细信息

我国是全球生物多样性大国,拥有包括大熊猫、金丝猴、华南虎、麋鹿、白鱀豚等特有物种和旗舰物种在内的丰富兽类资源。近几十年来,土地利用模式转变、盗猎、环境污染、气候变化等因素使许多兽类物种面临生存威胁,导致物种遗传多样性丧失。而遗传多样性是生物多样性的基本组成部分,决定了物种和种群能否长期生存。保护遗传学作为保护生物学的一大分支学科,旨在通过遗传学分析探明种群遗传变异和物种濒危的遗传学机制。近40年来,随着研究手段和技术的不断发展,我国兽类保护遗传学在遗传多样性和近交水平评估、景观遗传学、生态遗传学和圈养种群遗传管理等方面都取得了重要成果。然而,未来人类社会发展可能为濒危兽类带来的威胁依然存在,高通量测序等新技术的进一步发展则能够帮助我们更加深入地了解濒危物种和种群遗传适应与濒危机制,从而实现对濒危兽类的有效管理与保护。

关键词：保护遗传学濒危兽类非损伤性遗传取样法遗传多样性景观遗传学

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Structural variation provides novel insights into dog domestication

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National Science Review 2019年第1期6卷 123页

作者： fuwen wei CAS Key Lab of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of Sciences

The article ‘Structural variation during dog domestication:insights from grey wolf and dhole genomes’ by Wang et al. presented the first and comprehensive study of the evolutionary dynamics of structural variation of dogs based on three assembled Canine genomes [1].Structural variations (SVs) play a prominent role during the domestication of animals in phenotypic evolution, disease susceptibility and environmental adaptation. As the first animal to be domesticated, the dog is of great interest and significance to

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