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Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Zoological Research 2021年第4期42卷 450-460页

作者： Lin Zeng He-Qun Liu Xiao-Long Tu Chang-Mian ji Xiao Gou Ali Esmailizadeh Sheng Wang Ming-Shan Wang Ming-Cheng Wang Xiao-Long Li Hadi Charati Adeniyi CAdeola Rahamon Akinyele Moshood Adedokun Olatunbosun Oladipo Sunday Charles Olaogun Oscar jSanke Mangbon Godwin F Sheila Cecily Ommeh Bernard Agwanda j.cqueline kasiiti lichoti jian-Lin Han Hong-Kun Zheng Chang-Fa Wang Ya-Ping Zhang Laurent A.F.Frantz Dong-Dong Wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China College of Animal Science and Technology Yunnan Agricultural UniversityKunmingYunnan 650201China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKermanPB 76169-133Iran Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Sino-Africa joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Institute of Three-River-Source National Park Chinese Academy of SciencesXiningQinghai 810008China School of Biological and Chemical Sciences Queen Mary University of LondonLondon E14NSUK Department of Genetics Albert Einstein College of MedicineBronxNew YorkNY 10461USA Annoroad Gene Tech.(Beijing)Co. Ltd.Beijing 100176China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Federal College of Animal Health and Production Technology Moor-PlantationIbadan 234102Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Institute For Biotechnology Research jomo Kenyatta University of Agriculture and Technology Nairobi 62000-00200Kenya Department of Zoology National Museums of KenyaNairobi 40658-00100Kenya State Department of Livestock Ministry of AgricultureLivestockFisheries and IrrigationN

Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan ***,the kiang,a closely related equid species,also inhabits this *** reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan ***,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has *** assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in *** Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high *** addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan *** findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

关键词： Kiang Donkey High altitude Adaptation Selection

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维普期刊数据库

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A cryptic mitochondrial DNA link between North European and West African dogs

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journal of Genetics and Genomics 2017年第3期44卷 163-170页

作者： Adeniyi C.Adeola Sheila C.Ommeh jiao-jiao Song S.Charles Olaogun Oscar j.Sanke Ting-Ting Yin Guo-Dong Wang Shi-Fang Wu Zhong-Yin Zhou j.cqueline K.lichoti Bernard R.Agwanda Philip M.Dawuda Robert W.Murphy Min-Sheng Peng Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University Kunming 650091 China

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA（mt DNA） D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups（matrilines; clades）： A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf（Canis lupus lupaster）. The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1（but not the entire haplogroup D） coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.

关键词： Dog Mitochondrial DNA Africa Haplogroup D Late-glacial dispersal Hybridization

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维普期刊数据库

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Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

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Zoological Research 2020年第1期41卷 51-60页

作者： Xi-Yao Ma Tiao Ning Adeniyi CAdeola jie Li Ali Esmailizadeh j.cqueline Klichoti Bernard RAgwanda jainagul Isakova Almaz AAldashev Shi-Fang Wu He-Qun Liu Najmudinov Tojiddin Abdulloevich Manilova Elena Afanasevna Khudoidodov Behruz Ibrohimovich Rahamon Akinyele Moshood Adedokun Sunday Charles Olaogun Oscar jSanke Godwin FMangbon Xi Chen Wei-Kang Yang Zhe Wang Min-Sheng Peng Sheila COmmeh Yan Li Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunmingYunnan 650091China Agriculture College Kunming UniversityKunmingYunnan 650214China Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province Kunming UniversityKunmingYunnan 650214China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Sino-Africa joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKerman PB 76169-133Iran State Department of Livestock Ministry of Agriculture Livestock and FisheriesNairobi 00100Kenya Department of Zoology National Museums of KenyaNairobi 00100Kenya Institute of Molecular Biology and Medicine Bishkek 720040Kyrgyzstan E.N.Pavlovsky Institute of Zoology and Parasitology Academy of Sciences of Republic of TajikistanDushanbe 734025Tajikistan Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Research Center for Ecology and Environment of Central Asia Chinese Academy of SciencesUrumqiXinjiang 830011China Key Laboratory of Biogeography and Bioresource in Arid Land Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiang 830011China Department of Physiology Hebei Medical UniversityShijiazhuangHebei 050017China Hebei Key Laboratory of Animal Science Hebei Medical UniversityShijiazhuangHebei 050017China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Animal Biotechnology Group Institute of Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairob

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in ***,domestication histories of these two lineages remain *** therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,*** Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype *** contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype *** the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication *** from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of ***,the migration routes inferred from diversity decay suggested different expansion across China between the two ***,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.

关键词： Donkey lineage Domestication history Population Expansion

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