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Zoological Research 2022年第4期43卷 666-670页

作者： christian roos Roberto Portela Miguez Dietmar Zinner Tilo Nadler Van Ngoc Thinh Gene Bank of Primates German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Natural History Museum London SW7 BDUK Cognitive Ethology Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Leibniz Science Campus Primate Cognition Goettingen 37077Germany Department of Primate Cognition Georg-August-UniversityGoettingen 37083Germany Three Monkeys Wildlife Conservancy Cuc Phuong CommuneNho Quan DistrictNinh Binh ProvinceVietnam World Wide Fund for Nature(WWF)Vietnam Nam Tu Liem DistrictHanoiVietnam

DEAR EDITOR,Many historical descriptions of new species have included vague or inaccurate information about the type locality.This can lead to confusion in the study of the species and their geographic distributions,thereby hindering conservation efforts.One such example is the southern white-cheeked gibbon(Nomascus siki(Delacour,1951)).The type locality is given as Thua Luu in central Vietnam,which is located within the range of another crested gibbon species(N.annamensis)and more than 200 km south of the known range of N.siki.To investigate the problematic type locality of N.siki,we sequenced the mitochondrial genome of the holotype and compared its cytochrome b gene sequence to those of other georeferenced crested gibbon samples.

关键词： thereby hinder locality

Initiation of the Primate Genome Project

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Zoological Research 2022年第2期43卷 147-149页

作者： Dong-Dong Wu Xiao-Guang Qi Li Yu Ming Li Zhi-Jin Liu Anne DYoder christian roos Takashi Hayakawa Jeffrey Rogers Tomas Marques-Bonet Bing Su Yong-Gang Yao Ya-Ping Zhang Guojie Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China National Resource Center for Non-Human Primates Kunming Primate Research Centerand National Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China Kunming Natural History Museum of Zoology Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Shaanxi Key Laboratory for Animal Conservation College of Life SciencesNorthwest UniversityXi’anShaanxi 710069China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Biology Duke UniversityDurhamNC 27708USA Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGöttingen 37077Germany Faculty of Environmental Earth Science Hokkaido UniversitySapporoHokkaido 060-0810Japan Japan Monkey Centre InuyamaAichi 484-0081Japan Human Genome Sequencing Center Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX 77030USA Institute of Evolutionary Biology(UPF-CSIC) PRBBDr.Aiguader 88Barcelona 08003Spain Catalan Institution of Research and Advanced Studies(ICREA) Passeig de Lluis Companys23Barcelona 08010Spain CNAG-CRG Centre for Genomic Regulation(CRG)Barcelona Institute of Science and Technology(BIST)Baldiri i Reixac 4Barcelona 08028Spain Institut Catalade Paleontologia Miquel Crusafont Universitat Autonoma de BarcelonaEdifici ICTA-ICPc/Columnes s/nCerdanyola del VallèsBarcelona 08193Spain Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese

A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.

关键词： Genome evolution condition.

Mitogenomes of historical type specimens unravel the taxonomy of sportive lemurs(Lepilemur spp.)in Northwest Madagascar

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Zoological Research 2021年第4期42卷 428-432页

作者： christian roos Roberto Portela Miguez Richard Sabin Edward E.Louis Jr Michael Hofreiter Dietmar Zinner Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Natural History Museum London SW7 BDUK Center for Conservation and Research Omaha’s Henry Doorly Zoo and AquariumOmahaNebraska 68107USA Institute for Biochemistry and Biology University of PotsdamPotsdam 14476Germany Cognitive Ethology Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Leibniz Science Campus Primate Cognition Goettingen 37077Germany Department of Primate Cognition Georg-August-UniversityGoettingen 37083Germany

Accurate information on name-bearing types,including corresponding type localities,is essential for proper taxonomy.However,such geographic information is often missing or unreliable.The localities of type specimens collected 100–200 years ago can be difficult to trace due to changes in local names or simple inaccuracies.Such a case can be found for the gray-backed sportive lemur(Lepilemur dorsalis),with its type locality imprecisely fixed as Northwest Madagascar.In recent years,eight species have been newly described for the Inter-River-Systems(IRSs)of this region,however the designation of L.dorsalis remains controversial due to a lack of a precise type locality.Here,we sequenced the complete mitochondrial genomes(mitogenomes)of type specimens of L.dorsalis and L.grandidieri,which is currently recognized as a synonym of L.dorsalis and compared their sequences with those of samples of known provenance from different IRSs.Results showed that the two type specimens of L.dorsalis and L.grandidieri had identical mitogenome sequences and clustered closely with samples collected in IRS V,indicating that the type locality could be fixed to IRS V.Consequently,L.dorsalis occurs in IRS V,and L.grandidieri and L.mittermeieri are junior synonyms of L.dorsalis.This finding demonstrates the value of type specimens for clarifying phylogeographic and taxonomic questions and clarifies the taxonomy of sportive lemurs in Northwest Madagascar.

关键词： precise identical finding

Reconstructing the phytogeny of new world monkeys(platyrrhini):evidence from multiple non-coding loci

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Current Zoology 2019年第5期65卷 579-588页

作者： Xiaoping WANG Burton K.LIM Nelson TING Jingyang HU Yunpeng LIANG christian roos Li YU State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan UniversityKunmingChina School of Life Sciences Yunnan UniversityKunmingChina epartm ent of Natural History Royal Ontario MuseumTorontoONCanada Department of Anthropology and Institute of Ecology and Evolution University of OregonEugeneOregonUSA State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina Kunming College of Life Science University of Chinese Academy of SciencesKunmingChina Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchKellnerwegGottingenGermany

Among mammalian phylogenies,those characterized by rapid radiations are particularly problematic.The New World monkeys(NWMs,Platyrrhini)comprise 3 families and 7 subfamilies,which radiated within a relatively short time period.Accordingly,their phylogenetic relationships are still largely disputed.In the present study,56 nuclear non-coding loci,including 33 introns(INs)and 23 intergenic regions(IGs),from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies.Of the 56 loci,43 have not been used in previous NWM phylogenetics.We applied concatenation and coalescence tree-inference methods,and a recently proposed question-specific approach to address NWM phylogeny.Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets.However,a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods,albeit with varying degrees of statistical support.In detail,our results indicated the sister-group relationships between the families Atelidae and Pitheciidae,and between the subfamilies Aotinae and Callithrichinae among Cebidae.Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches.However,the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling.Overall,our work has important implications for phylogenetic studies dealing with rapid radiations.

关键词： coalescence concatenation non-coding nuclear genes primates phylogenetics

Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples

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Zoological Research 2021年第3期42卷 280-286页

作者： Ming Zhang Peng Cao Qing-Yan Dai Yong-Qiang Wang Xiao-Tian Feng Hong-Ru Wang Hong Wu Albert Min-Shan Ko Xiao-Wei Mao Yi-Chen Liu Li Yu christian roos Tilo Nadler Wen Xiao E.Andrew Bennett Qiao-Mei Fu Key Laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China CAS Center for Excellence in Life and Paleoenvironment Beijing 100044China University of Chinese Academy of Sciences Beijing 100049China Institute of Cultural Relics and Archaeology in Xinjiang UrumqiXinjiang 830011China State Key Laboratory for Conservation and Utilization of Bioresource in Yunnan Yunnan UniversityKunmingYunnan 650091China Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGottingen 37077Germany Wildlife Consultant Cuc Phuong CommuneNho QuanNinh Binh 430000Vietnam Institute of Eastern-Himalaya Biodiversity Research Dali UniversityDaliYunnan 671003China

DNA studies of endangered or extinct species often rely on ancient or degraded remains.The majority of ancient DNA(aDNA)extraction protocols focus on skeletal elements,with skin and hair samples rarely explored.Similar to that found in bones and teeth,DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes.Thus,the development of effective DNA extraction methods is required for these materials.Here,we compared the performance of two DNA extraction protocols(commercial and custom laboratory aDNA methods)on hair and skin samples from decades-old museum specimens to Iron Age archaeological material.We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation,skin yielded more endogenous DNA than hair of the samples and protocols tested.While both methods recovered DNA from ancient soft tissue,the laboratory method performed better overall in terms of DNA yield and quality,which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.

关键词： endogenous ancient primarily

Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei(Blyth, 1847) and description of a new species

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Zoological Research 2020年第6期41卷 656-669页

作者： christian roos Kristofer MHelgen Roberto Portela Miguez Naw May Lay Thant Ngwe Lwin Aung Ko Lin Aung Lin Khin Mar Yi Paing Soe Zin Mar Hein Margaret Nyein Nyein Myint Tanvir Ahmed Dilip Chetry Melina Urh EGrace Veatch Neil Duncan Pepijn Kamminga Marcus AHChua Lu Yao christian Matauschek Dirk Meyer Zhi-Jin Liu Ming Li Tilo Nadler Peng-Fei Fan Le Khac Quyet Michael Hofreiter Dietmar Zinner Frank Momberg Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Gene Bank of Primates German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Chances for Nature(CfN) Goettingen 37073Germany Australian Museum Research Institute Australian MuseumSydneyNew South Wales 2010Australia Natural History Museum London SW7 BDUK Wildlife Conservation Society(WCS)-Myanmar Program Yangon 11041Myanmar Fauna&Flora International(FFI)-Myanmar Programme Yangon 11201Myanmar Popa Mountain Park Nature and Wildlife Conservation DivisionForest DepartmentPopa 05242Myanmar World Wide Fund for Nature(WWF)-Myanmar Yangon 11191Myanmar Department of Zoology Jagannath UniversityDhaka 1100Bangladesh Primate Research and Conservation Division AaranyakGuwahatiAssam 781028India Department of Anthropology Emory UniversityAtlantaGA 30322USA Department of Anthropology Yale UniversityNew HavenCT 06511USA Department of Mammalogy American Museum of Natural HistoryNew YorkNY 10024USA Naturalis Biodiversity Center Leiden 2333 CRThe Netherlands Lee Kong Chian Natural History Museum National University of SingaporeSingapore 117377Singapore Department of Environmental Science and Policy George Mason UniversityFairfaxVA 22030USA 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 SciencesKunmingYunnan 650223China Cuc Phuong Commune Nho Quan DistrictNinh Binh ProvinceVietnam School of Life Sciences Sun Yat-Sen UniversityGuangzhouGuangdong 510275China Center for Biodiversity Conservation and Endangered Species Ho-Chi-Minh CityVietnam Institute for Biochemistry and Biology University of PotsdamPotsdam 14476Germany Cognitive Ethology Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Leibniz Science Campus Primate Cognition Goettingen 37077Germany De

Trachypithecus,which currently contains 20 species divided into four groups,is the most speciose and geographically dispersed genus among Asian colobines.Despite several morphological and molecular studies,however,its evolutionary history and phylogeography remain poorly understood.Phayre’s langur(Trachypithecus phayrei) is one of the most widespread members of the genus,but details on its actual distribution and intraspecific taxonomy are limited and controversial.Thus,to elucidate the evolutionary history of Trachypithecus and to clarify the intraspecific taxonomy and distribution of T.phayrei,we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens,including two holotypes.Phylogenetic analyses revealed a robustly supported phylogeny of Trachypithecus,suggesting that the T.pileatus group branched first,followed by the T.francoisi group,and the T.cristatus and T.obscurus groups most recently.The four species groups diverged from each other 4.5-3.1 million years ago(Ma),while speciation events within these groups occurred much more recently(1.6-0.3 Ma).Within T.phayrei,we found three clades that diverged 1.0-0.9 Ma,indicating the existence of three rather than two taxa.Following the phylogenetic species concept and based on genetic,morphological,and ecological differences,we elevate the T.phayrei subspecies to species level,describe a new species from central Myanmar,and refine the distribution of the three taxa.Overall,our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of T.phayrei but the entire Trachypithecus genus as well.

关键词： Colobinae Integrative zoology Mitochondrial genome Museum specimens New species

Global view on virus infection in non-human primates and implications for public health and wildlife conservation

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Zoological Research 2021年第5期42卷 626-632页

作者： Zhi-Jin Liu Xue-Kun Qian Min-Heng Hong Jia-Li Zhang Da-Yong Li Tian-Han Wang Zuo-Min Yang Li-Ye Zhang Zi-Ming Wang Hua-Jian NieKe-Yue Fan Xiong-Fei Zhang Meng-Meng Chen Wei-Lai Sha christian roos Ming Li College of Life Sciences Capital Normal UniversityBeijing 100048China College of Life Sciences Hebei UniversityBaodingHebei 071002China CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China College of Life Sciences China West Normal UniversityNanchongSichuan 637009China College of Life Sciences Qufu Normal UniversityQufuShandong 273100China Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Gene Bank of Primates German Primate CenterLeibniz Institute for Primate ResearchGoettingen 37077Germany Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Viruses can be transmitted from animals to humans(and vice versa)and across animal species.As such,host-virus interactions and transmission have attracted considerable attention.Non-human primates(NHPs),our closest evolutionary relatives,are susceptible to human viruses and certain pathogens are known to circulate between humans and NHPs.Here,we generated global statistics on virus infections in NHPs(VI-NHPs)based on a literature search and public data mining.In total,140 NHP species from 12 families are reported to be infected by 186 DNA and RNA virus species,68.8%of which are also found in humans,indicating high potential for crossing species boundaries.

关键词： species. primates attention

景观基因组学揭示猕猴面对未来气候变化的风险

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景观基因组学揭示猕猴面对未来气候变化的风险

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea(Spix,1823)resolves a taxonomic conundrum

第十六届全国野生动物生态与资源保护学术研讨会

作者：吴芮封祁纪伟李文博汪玲沈颖刘佳文滕扬 christian roos 李明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中国科学院大学生命科学学院中国科学院动物进化与遗传前沿交叉卓越创新中心

气候变化如何影响生物多样性是保护生物学中的一个热门话题。自二十世纪以来,全球生物群落一直受到人类活动和人为气候变暖的影响。对非人灵长类物种来说,气候变化威胁到约55%的物种,是加速非人灵长类动物数量减少的主要原因之一。了解... 详细信息

气候变化如何影响生物多样性是保护生物学中的一个热门话题。自二十世纪以来,全球生物群落一直受到人类活动和人为气候变暖的影响。对非人灵长类物种来说,气候变化威胁到约55%的物种,是加速非人灵长类动物数量减少的主要原因之一。了解野生动物如何响应气候变化,综合评估气候变化下物种的适应潜力和迁移能力对有针对性地保护野生动物非常重要。猕猴(Macaca mulatta)是分布广泛且适应多种气候类型的非人灵长类动物。该物种在迁移、扩散和定殖到亚洲的过程中非常成功,展示了其对气候和环境变化非凡的适应能力。本研究以猕猴为对象,通过其在气候变化下的生态和遗传适应的分析,探讨和阐明未来气候变化将如何影响猕猴的分布,以及未来哪些种群在气候变化下会显示较高的脆弱性。本研究通过物种分布模型预测猕猴当前和未来的种群地理分布;筛选全基因组范围的单核苷酸多态性位点,使用基因型环境关联和选择特征分析共同鉴定了在猕猴适应广泛的气候条件方面发挥重要作用的遗传变异和候选基因;基于梯度森林模型预测未来情境中猕猴各个种群的基因组脆弱性。结果表明,全球变暖将对全球猕猴造成很大影响,温度的季节性(temperature seasonality, BIO4)对猕猴适宜栖息地的影响最大,未来中国中部和北部、印度北部猕猴生态脆弱性较高,猕猴会向更高海拔的青藏高原区域扩散。Cabin1和Aadac基因的等位基因频率具有沿BIO4变量梯度发生变化的模式,这些基因可能对猕猴的能量供应和储存能力有影响,其适应性变异可能对猕猴响应寒冷或炎热的气候环境有正向的作用。河南太行种群具有最高的基因组脆弱性,和较高的生态脆弱性。同时该种群具有较高的近亲繁殖水平和较低的杂合率,其遗传负荷的情况与小种群中遗传负荷情况相符,因此该种群在未来迫切地需要更多的遗传监测和相应的保护策略。该研究强调了结合生态和基因组数据来预测种群对未来变化脆弱性的重要性,是衡量气候变化对濒危物种影响和提供有针对性保护策略的有效工具。

关键词：生态脆弱性基因组脆弱性物种分布模型基因环境关联分析种群基因组学

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Zoological Research 2021年第6期42卷 761-771页

作者： Jean P.Boubli Mareike C.Janiak Leila M.Porter Stella de la Torre Liliana Cortes-Ortiz Maria N.Fda Silva Anthony B.Rylands Stephen Nash Fabricio Bertuol Hazel Byrne Felipe E.Silva Fabio Rohe Dorien de Vries Robin M.D.Beck Irune Ruiz-Gartzia Lukas F.K.Kuderna Tomas Marques-Bonet Tomas Hrbek Izeni P.Farias Anneke Hvan Heteren christian roos School of Science Engineering&EnvironmentUniversity of SalfordSalford M54WTUK Instituto Nacional de Pesquisas da Amazonia ManausAmazonas 69060-001Brazil Department of Anthropology Northern Illinois UniversityDeKalbIL 60115-2828USA College of Biological and Environmental Sciences Universidad San Francisco de QuitoQuito 170901Ecuador Department of Ecology and Evolutionary Biology University of MichiganAnn ArborMI 48109USA Re:wild AustinTX 78767USA Laboratorio de Evolução e Genética Animal Universidade Federal do AmazonasManausAmazonas 69080-900Brazil Department of Anthropology University of UtahSalt Lake CityUT 84112USA Research Group on Primate Biology and Conservation MamirauaInstitute for Sustainable DevelopmentTeféAmazonas 69553-225Brazil Experimental and Health Sciences Department(DCEXS) Institut de Biologia EvolutivaUniversitat Pompeu Fabra-CSICBarcelona 08002Spain Department of Biology Trinity UniversitySan AntonioTX 78212USA Bavarian State Collection of Zoology Zoologische Staatssammlung MünchenStaatliche Naturkundliche Sammlungen Bayerns81247 MunichGermany GeoBio-Center Ludwig-Maximilians-Universitat München80333 MunichGermany Department Biologie II Ludwig-Maximilians-Universitat München82152 MunichGermany Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate Research37077 GottingenGermany

The pygmy marmoset,the smallest of the anthropoid primates,has a broad distribution in Western Amazonia.Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimoes-Amazonas rivers.However,reconciling this new biological evidence with current taxonomy,i.e.,two subspecies,Cebuella pygmaea pygmaea(Spix,1823)and Cebuella pygmaea niveiventris(Lönnberg,1940),was problematic given the uncertainty as to whether Spix’s pygmy marmoset(Cebuella pygmaea pygmaea)was collected north or south of the Napo and Solimoes-Amazonas rivers,making it unclear to which of the two newly revealed species the name pygmaea would apply.Here,we present the first molecular data from Spix’s type specimen of Cebuella pygmaea,as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality(Tabatinga)on both sides of the river.With these data,we can confirm the correct names of the two species identified,i.e.,C.pygmaea for animals north of the Napo and Solimoes-Amazonas rivers and C.niveiventris for animals south of these two rivers.Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to reevaluate the geographical distribution for the two Cebuella species.We dated the split of these two species to 2.54 million years ago.We discuss additional,more recent,subdivisions within each lineage,as well as potential contact zones between the two species in the headwaters of these rivers.

关键词： Historic DNA DNA taxonomy Pygmy marmoset Cebuella pygmaea C.niveiventris Amazon Type specimen

黔金丝猴(Rhinopithecus brelichi)的杂交起源演化历史

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黔金丝猴(Rhinopithecus brelichi)的杂交起源演化历史