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兽类学报 2021年第5期41卷 581-590页

作者：魏辅文黄广平樊惠中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

揭示濒危兽类的演化历史、濒危机制及适应性演化策略,是保护生物学关注的重大科学问题。近十几年来,高通量测序技术的不断发展以及多学科交叉融合,为揭示濒危物种的演化历史、遗传结构、适应性演化及其与肠道微生物的协同演化的分子机... 详细信息

揭示濒危兽类的演化历史、濒危机制及适应性演化策略,是保护生物学关注的重大科学问题。近十几年来,高通量测序技术的不断发展以及多学科交叉融合,为揭示濒危物种的演化历史、遗传结构、适应性演化及其与肠道微生物的协同演化的分子机制提供了重要的技术支撑,由此产生了保护基因组学和保护宏基因组学两个分支学科,为野生动物尤其是濒危动物的保护生物学研究提供了新的方向与思路。本文综述了我国在保护基因组学和保护宏基因组学领域取得的重要进展,并展望未来的发展趋势,以期进一步推动我国濒危兽类保护生物学的发展。

关键词：保护基因组学保护宏基因组学濒危兽类适应性演化肠道微生物

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Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome

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ENVIRONMENT INTERNATIONAL 2021年 155卷 106703页

作者： Zhu, Dong Lu, Lu Zhang, Zejun Qi, Dunwu Zhang, Mingchun O'Connor, Patrick wei, fuwen Zhu, Yong-Guan Chinese Acad Sci Res Ctr Ecoenvironm Sci State Key Lab Urban & Reg Ecol Beijing 100085 Peoples R China China West Normal Univ Coll Life Sci Key Lab Southwest China Wildlife Resources Conser Nanchong 637002 Peoples R China Chengdu Res Base Giant Panda Breeding Chengdu 611081 Sichuan Peoples R China China Conservat & Res Ctr Giant Panda Dujiangyan 611830 Peoples R China China West Normal Univ Coll Environm Sci & Engn Nanchong 637009 Peoples R China Univ Adelaide Ctr Global Food & Resources Adelaide SA 5005 Australia Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Chinese Acad Sci Inst Urban Environm Key Lab Urban Environm & Hlth 1799 Jimei Rd Xiamen 361021 Fujian Peoples R China

The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to subadult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.

关键词： Fungi Protist Antibiotic resistance genes Network analysis Multitrophic communities Neutral model

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Implications of flood disturbance for conservation and management of giant panda habitat in human-modified landscapes

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BIOLOGICAL CONSERVATION 2019年 232卷 35-42页

作者： Ameca, Eric, I Dai, Qiang Nie, Yonggang Gu, Xiaodong wei, fuwen Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol 1 Beichen West Rd Beijing 100101 Peoples R China Univ Veracruz Fac Biol Circuito Gonzalo Aguirre Beltran S-N Xalapa 91090 Veracruz Mexico Chinese Acad Sci Chengdu Inst Biol Meilingshiguan Food Unit Chengdu 610000 Sichuan Peoples R China Sichuan Stn Wildlife Survey & Management Chengdu 610082 Sichuan Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

As certain extreme weather events are becoming frequent and intense, conservationists must identify areas across species' ranges recurrently affected, especially with regard to threatened species. Focusing on the giant panda (Ailuropoda melanoleuca) and historical flood frequency distribution, we determined overlaps between panda distribution affected by floods and nature reserves. We also examined the correspondence between areas subject to high flood exposure densities, areas with high panda habitat use, and areas that exhibit high human density. Of the 67 reserves established for giant panda conservation 7 included areas with the highest flood exposure densities while having a mean exposure ranging between 20 and 75%. In Sichuan province up to 32% of areas of high habitat use were subject to low flood density, and 10% overlapped with areas subject to high flood density. We also found that 40% of the total area with high human density was subject to a high flood density. Our findings indicate that high frequency of flooding is affecting areas of nature reserves where people are rather than areas which pandas are using more intensively. In areas occupied by pandas, strategies should remain focus on mitigating habitat degradation and fragmentation caused by human activities that can also reduce habitat resilience to floods. Management aimed at reducing vulnerability and enhancing resilience in flood-prone areas is warranted if we are to prevent negative indirect impacts on panda habitat driven by human responses to increasingly frequent and intense extreme weather events in the coming decades.

关键词： Ailuropoda melanoleuca Extreme weather events Flood disturbance Habitat use Human density Nature reserves

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Seasonal competition between sympatric species for a key resource: Implications for conservation management

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BIOLOGICAL CONSERVATION 2019年 234卷 1-6页

作者： Nie, Yonggang Zhou, Wenhang Gao, Kai Swaisgood, Ronald R. wei, fuwen Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Chinese Acad Sci CAS Ctr Excellence Anim Evolut & Genet Kunming 650223 Yunnan Peoples R China Beijing Normal Univ Sch Life Sci Beijing 100875 Peoples R China San Diego Zoo Inst Conservat Res San Diego CA 92027 USA

Competition often occurs between two or more sympatric species that use similar ecological niches. During competition, a superior species may exclude the competitor from parts of its fundamental niche or make it go extinct. Determining the potential competition between two sympatric species including an endangered one has important implications for conservation management. We evaluated potential food competition between the wild boar and the giant panda in a key national nature reserve established primarily for the giant panda protection. We monitored foraging plots for 9 years, conducted food macronutrient analysis, and combined our analysis with long-term population monitoring results for two species. The wild boar population increased dramatically in the past 18 years, benefiting from conservation policies of the Chinese government, whereas the giant panda population decreased. We found evidence for competition for bamboo shoots, an important seasonally limiting resource. The wild boar had a higher utilization rate at foraging plots than giant panda, which also avoided plots used by wild boar. This study indicates key seasonal food competition may exist between wild boar and giant panda. This competition for a key food resource may have negative impacts on giant panda populations, particularly under the substantial increase of the wild boar, yet this possibility has not figured prominently in conservation planning and policy for panda reserves. We suggest long-term monitoring of this competitive relationship across reserves to determine when and where management intervention is needed. And, we might need more flexible policies instead of the current "one size fits all" one.

关键词： Conservation policy Endangered species Food competition Giant panda Sympatric species Wild boar

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Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution

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GENOME BIOLOGY 2019年第1期20卷 1页

作者： Fan, Huizhong Wu, Qi wei, fuwen Yang, Fengtang Ng, Bae Ling Hu, Yibo 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 Wellcome Sanger Inst Wellcome Genome Campus Cambridge England

Background Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. Results Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. Conclusions We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.

关键词： Giant panda Chromosome-level genome Chromosome evolution Evolutionary breakpoint region Carnivora

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中国生物多样性保护取得的主要成绩、面临的挑战与对策建议

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中国科学院院刊 2021年第4期36卷 375-383页

作者：魏辅文平晓鸽胡义波聂永刚曾岩黄广平中国科学院动物研究所北京100101

经过近30年的发展,我国基本实现了生物多样性的全方位系统保护。目前,生物多样性保护已上升为国家战略,被纳入国家的顶层设计,相关法规制度逐步完善,科学研究取得重大突破。通过实施生物多样性保护和生态修复重大工程,建立自然保护地体... 详细信息

经过近30年的发展,我国基本实现了生物多样性的全方位系统保护。目前,生物多样性保护已上升为国家战略,被纳入国家的顶层设计,相关法规制度逐步完善,科学研究取得重大突破。通过实施生物多样性保护和生态修复重大工程,建立自然保护地体系,划定生态保护红线等措施,我国重要生态系统和珍稀濒危物种得到了有效保护,社会参与和公众意识得到明显提升。此外,通过缔结多项生物多样性相关的国际公约和协定,以及倡议成立"一带一路"绿色发展国际联盟等举措,我国完成了从重要参与者向积极贡献者的履约角色转变。然而,我国生物多样性保护也存在一些有待解决和加强的问题,如:资金投入机制单一,数据整合程度不够,对海洋等生态系统的保护投入不足,以及追求数量目标而忽视生态系统结构和完整性等。未来,应转变保护策略,强化顶层设计;加强公约间协同增效,将生物多样性保护与国土空间规划和环境污染治理等相结合;从追求数量目标转为提升质量,加大海洋生物多样性保护,以及野生动物遗传资源库和野外台站建设力度,加强外来入侵生物和野生动物疫源疫病研究;搭建大数据平台,推动生物多样性信息共享和深度挖掘,为全球生态文明建设贡献中国智慧和中国方案。

关键词：生物多样性公约生态文明野生动植物自然保护地体系协同增效海洋保护

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Predictive Control Method of Reaming up in the Raise Boring Process Using Kernel Based Extreme Learning Machine

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PROCESSES 2023年第1期11卷 277-277页

作者： Jing, Guoye Yan, wei Hu, fuwen Univ Sci & Technol Beijing Sch Civil & Resources Engn Beijing 100083 Peoples R China China Coal Res Inst Mine Construct Branch Beijing 100013 Peoples R China North China Univ Technol Sch Mech & Mat Engn Beijing 100144 Peoples R China

Raise boring is an important method to construct the underground shafts of mines and other underground infrastructures, by drilling down the pilot hole and then reaming up to the desired diameter. Seriously different from the drilling operations of the mechanical parts in mechanized mass production, it is very difficult to obtain a good consistency in the construction environments of each raise or shaft, to be more exact, every construction process is highly customized. The underground bottom-up reaming process is impossible to be observed directly, and the rock breaking effect is very difficult to be measured in real-time, due to the rock debris freely falling under the excavated shaft. The optimal configurations of the operational parameters in the drilling and working pressures, torque, rotation speed and penetration speed, mainly depend on the accumulation of construction experience or empirical models. To this end, we presented a machine learning method, based on the extreme learning machine, to determine in real-time, the relationships between the working performance and the operational parameters, and the physical-mechanical properties of excavated geologic zones, aiming at a higher production or excavation rate, safer operation and minimum ground disturbance. This research brings out new possibilities to revolutionize the process planning paradigm of the raise boring method that traditionally depends on experience or subject matter expertise.

关键词： underground construction raise boring method extreme learning machine predictive control

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Seasonal and reproductive variation in chemical constituents of scent signals in wild giant pandas

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Science China(Life Sciences) 2019年第5期62卷 648-660页

作者： Wenliang Zhou Yonggang Nie Yibo Hu Ronald R.Swaisgood Yaohua Zhang Dingzhen Liu fuwen wei Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Institute for Conservation Research San Diego Zoo Global State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture Institute of Zoology Chinese Academy of Sciences University of Chinese Academy of Sciences

Seasonally reproducing animals show many behavioral and physiological changes during the mating period, including increased signaling for intrasexual competition and mate attraction. We collected 102 anogenital gland secretions(AGS) from marking trees in Foping Nature Reserve, and used gas chromatography mass spectrometry to analyze these chemical composition. Of these marks, all but one were from males, confirmed with DNA analysis. We found that several chemical constituents, especially volatile compounds, were present only during the mating season and that the relative abundance of many compounds changed as a function of breeding season, whereas nonvolatile compounds were lower in the mating season. This seasonal variation in chemical composition of AGS most likely plays an important role in governing giant panda reproduction, including mate location, attraction, and male-male competition. The chemical properties of many of these putative chemosignals—such as volatility and longevity—are suggestive of these roles, and undoubtedly contribute to successful reproduction for this species with a characteristically sophisticated chemical communication system. We also found a number of important differences between the chemical constituents of AGS from wild pandas and those found in previous studies with captive pandas, suggesting that inappropriate chemosignal composition may contribute to poor reproductive success in captive breeding programs.

关键词： giant panda chemical communication anogenital gland secretions chemical composition reproduction

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Assessing the Effectiveness of China's Panda Protection System

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CURRENT BIOLOGY 2020年第7期30卷 1280-+页

作者： wei, wei Swaisgood, Ronald R. Pilfold, Nicholas W. Owen, Megan A. Dai, Qiang wei, fuwen Han, Han Yang, Zhisong Yang, Xuyu Gu, Xiaodong Zhang, Jindong Yuan, Shibin Hong, Mingsheng Tang, Junfeng Zhou, Hong He, Ke Zhang, Zejun China West Normal Univ Key Lab Southwest China Wildlife Resources Conser Minist Educ Nanchong 637009 Peoples R China San Diego Zoo Global Inst Conservat Res Escondido CA 92027 USA Chinese Acad Sci Chengdu Inst Biol Chengdu 610041 Peoples R China Chinese Acad Sci Inst Zool Key Lab Anim Ecol & Conservat Biol Beijing 100101 Peoples R China Sichuan Stn Wild Life Survey & Management Chengdu 610082 Peoples R China

Protected areas form the backbone of biodiversity conservation, yet their effectiveness is often not known nor even evaluated [1-3]. China-best known for its record of ecological degradation in the face of rapidly increasing gross domestic product and resource consumption [4]-has in recent years enacted a series of policies and programs to conserve its natural resources. Chief among them is an ambitious protected area system covering 17% of its terrestrial land mass [4,5]. An important early impetus for the establishment of this reserve system was the protection of the giant panda (Ailuropoda melanoleuca) [5-8]. Using data from two previous large-scale surveys [9-10] separated by a decade, and including over 50,000 habitat plots, we examined the panda population and habitat trends inside and outside reserves. Despite ambitious ecocompensation programs in panda habitat outside reserves [11-13], the protection provided by reserves reduced most classes of human disturbance compared to outside reserves, and most disturbances decreased through time more strongly inside than outside reserves. Reserves also contained more and increasing suitable panda than found outside reserves [14,15]. Comparing reserve performance, reserves with increasing older forests and bamboo correlated with increasing panda populations. Together these findings indicate that China's panda reserves have been effective and that they are functioning better over time, conserving more and better habitats and containing more pandas. While China's protected area system still has much room for improvement [4, 5], including to support pandas [16], these findings underscore the progress made in China's nascent environmental movement.

关键词： anthropogenic disturbance conservation policy giant panda habitat protected areas reserve efficacy species conservation wildlife management

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Synteny search identifies carnivore Y chromosome for evolution of male specific genes

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Integrative Zoology 2019年第3期14卷 224-234页

作者： Huizhong FAN Yibo HU Lei SHAN Lijun YU Bing WANG Min LI Qi WU fuwen wei Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingChina

The explosive accumulation of mammalian genomes has provided a valuable resource to characterize the evolution of the Y ***,the Y-chromosome sequence has been characterized in only a small handful of species,with the majority being model ***,identification of Y-linked scaffolds from unordered genome sequences is becoming more ***,we used a syntenic-based approach to generate the scaffolds of the male-specific region of the Y chromosome(MSY)from the genome sequence of 6 male carnivore *** results identified 14,15,9,28,14 and 11 Y-linked scaffolds in polar bears,pacific walruses,red pandas,cheetahs,ferrets and tigers,covering 1.55 Mbp,2.62 Mbp,964 Kb,1.75 Mb,2.17 Mbp and 1.84 Mb MSY,*** the candidate Y-linked scaffolds in 3 selected species(red pandas,polar bears and tigers)were successfully verified using polymerase chain *** re-annotated 8 carnivore MSYs including these 6 Y-linked scaffolds and domestic dog and cat MSY;a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were *** 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts,indicating less purifying selection for MSY *** together,our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genomes and provides a preliminary evolutionary study for carnivore MSY genes.

关键词： carnivore species evolution male-specific region of Y chromosomes sex chromosome synteny

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