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Yang MA, Korsnack K. Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom. Biol Methods Protoc 2024; 9:bpae013. [PMID: 38463936 PMCID: PMC10924719 DOI: 10.1093/biomethods/bpae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/27/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.
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Affiliation(s)
- Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, United States
| | - Kylie Korsnack
- Teaching and Scholarship Hub, University of Richmond, Richmond, VA 23173, United States
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2
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Wang H, Yang MA, Wangdue S, Lu H, Chen H, Li L, Dong G, Tsring T, Yuan H, He W, Ding M, Wu X, Li S, Tashi N, Yang T, Yang F, Tong Y, Chen Z, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang Z, Gao Y, Zhang M, Wang X, Zhang C, Yuan K, Ko AMS, Aldenderfer M, Gao X, Xu S, Fu Q. Human genetic history on the Tibetan Plateau in the past 5100 years. Sci Adv 2023; 9:eadd5582. [PMID: 36930720 PMCID: PMC10022901 DOI: 10.1126/sciadv.add5582] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Using genome-wide data of 89 ancient individuals dated to 5100 to 100 years before the present (B.P.) from 29 sites across the Tibetan Plateau, we found plateau-specific ancestry across plateau populations, with substantial genetic structure indicating high differentiation before 2500 B.P. Northeastern plateau populations rapidly showed admixture associated with millet farmers by 4700 B.P. in the Gonghe Basin. High genetic similarity on the southern and southwestern plateau showed population expansion along the Yarlung Tsangpo River since 3400 years ago. Central and southeastern plateau populations revealed extensive genetic admixture within the plateau historically, with substantial ancestry related to that found in southern and southwestern plateau populations. Over the past ~700 years, substantial gene flow from lowland East Asia further shaped the genetic landscape of present-day plateau populations. The high-altitude adaptive EPAS1 allele was found in plateau populations as early as in a 5100-year-old individual and showed a sharp increase over the past 2800 years.
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Affiliation(s)
- Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Melinda A. Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Hongliang Lu
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Haibing Yuan
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Shuai Li
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Feng Yang
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Yuanhong He
- School of Archaeology and Museology, Sichuan University, Chengdu 610064, China
- Center for Archaeological Science, Sichuan University, Chengdu 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zhaoxia Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi’an 710069, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, Merced, CA 95343, USA
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Qi Zhi Institute, Shanghai 200232, China
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3
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Kumar V, Bennett EA, Zhao D, Liang Y, Tang Y, Ren M, Dai Q, Feng X, Cao P, Yang R, Liu F, Ping W, Zhang M, Ding M, Yang MA, Amridin B, Muttaliu H, Wang J, Fu Q. Genetic continuity of Bronze Age ancestry with increased Steppe-related ancestry in Late Iron Age Uzbekistan. Mol Biol Evol 2021; 38:4908-4917. [PMID: 34320653 PMCID: PMC8557446 DOI: 10.1093/molbev/msab216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of the Bactria–Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events that impacted the demography and population structure of this region, we generated 27 genome-wide single-nucleotide polymorphism capture data sets of Late Iron Age individuals around the Historical Kushan time period (∼2100–1500 BP) from three sites in South Uzbekistan. Overall, Bronze Age ancestry persists into the Iron Age in Uzbekistan, with no major replacements of populations with Steppe-related ancestry. However, these individuals suggest diverse ancestries related to Iranian farmers, Anatolian farmers, and Steppe herders, with a small amount of West European Hunter Gatherer, East Asian, and South Asian Hunter Gatherer ancestry as well. Genetic affinity toward the Late Bronze Age Steppe herders and a higher Steppe-related ancestry than that found in BMAC populations suggest an increased mobility and interaction of individuals from the Northern Steppe in a Southward direction. In addition, a decrease of Iranian and an increase of Anatolian farmer-like ancestry in Uzbekistan Iron Age individuals were observed compared with the BMAC populations from Uzbekistan. Thus, despite continuity from the Bronze Age, increased admixture played a major role in the shift from the Bronze to the Iron Age in southern Uzbekistan. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting more widespread admixture among local populations.
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Affiliation(s)
- Vikas Kumar
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Dongyue Zhao
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Yun Liang
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Yunpeng Tang
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Meng Ren
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Qinyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA, 23173, USA
| | - Berdimurodov Amridin
- Institute of Archaeology, Academy of Sciences of Uzbekistan, Samarkand, Uzbekistan
| | - Hasanov Muttaliu
- Institute of Archaeology, Academy of Sciences of Uzbekistan, Samarkand, Uzbekistan
| | - Jianxin Wang
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.,Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Wang T, Wang W, Xie G, Li Z, Fan X, Yang Q, Wu X, Cao P, Liu Y, Yang R, Liu F, Dai Q, Feng X, Wu X, Qin L, Li F, Ping W, Zhang L, Zhang M, Liu Y, Chen X, Zhang D, Zhou Z, Wu Y, Shafiey H, Gao X, Curnoe D, Mao X, Bennett EA, Ji X, Yang MA, Fu Q. Human population history at the crossroads of East and Southeast Asia since 11,000 years ago. Cell 2021; 184:3829-3841.e21. [PMID: 34171307 DOI: 10.1016/j.cell.2021.05.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/17/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022]
Abstract
Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.
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Affiliation(s)
- Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Northwest University, Xi'an 710069, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Guangmao Xie
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China; College of History, Culture and Tourism, Guangxi Normal University, Guilin 541001, China
| | - Zhen Li
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Xuechun Fan
- International Research Center for Austronesian Archaeology, Pingtan 350000, China; Fujian Museum, Fuzhou 350001, China
| | - Qingping Yang
- Guangxi Institute of Cultural Relic Protection and Archaeology, Nanning 530022, China
| | - Xichao Wu
- Fujian Longyan Museum, Longyan 364000, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Ling Qin
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Fajun Li
- Department of Anthropology, School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yalin Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoshan Chen
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Dongju Zhang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhenyu Zhou
- Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China
| | - Yun Wu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Archaeological Institute for Yangtze Civilization, Wuhan University, Wuhan 430072, China
| | - Hassan Shafiey
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Darren Curnoe
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW, 2010, Australia
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xueping Ji
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; Yunnan Key Laboratory of Earth System Science, Yunnan University, Kunming 650500, China.
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Department of Biology, University of Richmond, Richmond, VA 23173, USA.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; Shanghai Qi Zhi Institute, Shanghai 200232, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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5
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Zhang M, Sun G, Ren L, Yuan H, Dong G, Zhang L, Liu F, Cao P, Ko AMS, Yang MA, Hu S, Wang GD, Fu Q. Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs. Mol Biol Evol 2021; 37:1462-1469. [PMID: 31913480 DOI: 10.1093/molbev/msz311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Relics and Archaeology, Hangzhou, China
| | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education, Department of Archaeology, Sichuan University, Chengdu, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA
| | - Songmei Hu
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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6
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Zhang D, Xia H, Chen F, Li B, Slon V, Cheng T, Yang R, Jacobs Z, Dai Q, Massilani D, Shen X, Wang J, Feng X, Cao P, Yang MA, Yao J, Yang J, Madsen DB, Han Y, Ping W, Liu F, Perreault C, Chen X, Meyer M, Kelso J, Pääbo S, Fu Q. Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau. Science 2020; 370:584-587. [DOI: 10.1126/science.abb6320] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Dongju Zhang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Frontier Center for Eco-environment and Climate Change in Pan-third Pole Regions, Lanzhou University, Lanzhou 730000, China
| | - Huan Xia
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fahu Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Ting Cheng
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Diyendo Massilani
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Xuke Shen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian Wang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- School of Earth Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, VA 23173, USA
| | - Juanting Yao
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jishuai Yang
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - David B. Madsen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
- Department of Anthropology, University of Nevada–Reno, Reno, NV 89557, USA
| | - Yuanyuan Han
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Wanjing Ping
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Feng Liu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Charles Perreault
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoshan Chen
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
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7
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Abstract
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.
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Affiliation(s)
- Elisabeth de Boer
- Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Aileen Kawagoe
- Department of Social Studies, New International School of Japan, Tokyo, Japan
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8
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Ding M, Wang T, Ko AMS, Chen H, Wang H, Dong G, Lu H, He W, Wangdue S, Yuan H, He Y, Cai L, Chen Z, Hou G, Zhang D, Zhang Z, Cao P, Dai Q, Feng X, Zhang M, Wang H, Yang MA, Fu Q. Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans. Proc Biol Sci 2020; 287:20192968. [PMID: 32183622 DOI: 10.1098/rspb.2019.2968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.
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Affiliation(s)
- Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,University of Chinese Academy of Sciences, 100049, People's Republic of China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China
| | - Hui Wang
- Fudan Archaeological Science Institute, Fudan University, Shanghai 200433, People's Republic of China.,Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou 730030, People's Republic of China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Hongliang Lu
- Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuanhong He
- Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Linhai Cai
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, People's Republic of China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Guangliang Hou
- Department of Life and Geography, Qinghai Normal University, Xining 810000, People's Republic of China
| | - Dongju Zhang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhaoxia Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,Department of Biology, University of Richmond, Richmond, VA, USA
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,University of Chinese Academy of Sciences, 100049, People's Republic of China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
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9
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Min-Shan Ko A, Zhang Y, Yang MA, Hu Y, Cao P, Feng X, Zhang L, Wei F, Fu Q. Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage. Curr Biol 2019; 28:R693-R694. [PMID: 29920259 DOI: 10.1016/j.cub.2018.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Present-day giant pandas (Ailuropoda melanoleuca) are estimated to have diverged from their closest relatives, all other bears, ∼20 million years ago, based on molecular data [1]. With fewer than 2,500 individuals living today [2], it is unclear how well genetic data from extant and historical giant pandas [3] reflect the past [3]. To date, there has been no complete mitochondrial DNA (mtDNA) sequenced from an ancient giant panda. Here, we use ancient DNA capture techniques [4] to sequence the complete mitochondrial genome of a ∼22,000-year-old giant panda specimen (radiocarbon date of 21,910-21,495 cal BP with ± 2σ at 95.4% probability; Lab.no Beta-473743) from the Cizhutuo Cave, in Leye County, Guangxi Province, China (Figure 1A). Its date and location in Guangxi, where no wild giant pandas live today, as well as the difficulty of DNA preservation in a hot and humid region, place it as a unique specimen to learn about ancient giant pandas from the last glacial maximum. We find that the mtDNA lineage of the Cizhutuo panda coalesced with present-day pandas ∼183 thousand years ago (kya, 95% HPD, 227-144 kya), earlier than the time to the most recent common ancestor (TMRCA) of mtDNA lineages shared by present-day pandas (∼72 kya, 95% HPD, 94-55 kya, Supplemental Information). Furthermore, the Cizhutuo panda possessed 18 non-synonymous mutations across six mitochondrial genes. Our results show that the Cizhutuo mtDNA lineage underwent a distinct history from that of present-day populations.
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Affiliation(s)
- Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; University of Chinese Academy of Sciences, 100049, China
| | - Yingqi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Yibo Hu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Fuwen Wei
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; University of Chinese Academy of Sciences, 100049, China; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China; University of Chinese Academy of Sciences, 100049, China.
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10
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Wang GD, Zhang M, Wang X, Yang MA, Cao P, Liu F, Lu H, Feng X, Skoglund P, Wang L, Fu Q, Zhang YP. Genomic Approaches Reveal an Endemic Subpopulation of Gray Wolves in Southern China. iScience 2019; 20:110-118. [PMID: 31563851 PMCID: PMC6817678 DOI: 10.1016/j.isci.2019.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/21/2019] [Accepted: 09/05/2019] [Indexed: 12/30/2022] Open
Abstract
Although gray wolves (Canis lupus) are one of the most widely distributed terrestrial mammals, their origins in China are not well understood. We sequenced six specimens from wolf skins, showing that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau and Northern China, suggesting that SC gray wolves may form a distinct subpopulation. Of SC gray wolves, one wolf from Zhejiang carries a genetic component from a canid and had gene flow from a population related to or further diverged from wolves than the dhole. This may indicate that interspecific gene flow likely played an important role in shaping the speciation patterns and population structure in the genus Canis. Our study is the first to survey museum gray wolves' genomes from Southern China, highlighting how sequencing the paleogenome from museum specimens can help us to study extinct species.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Heng Lu
- Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | | | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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11
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Wang X, Zhou BW, Yang MA, Yin TT, Chen FL, Ommeh SC, Esmailizadeh A, Turner MM, Poyarkov AD, Savolainen P, Wang GD, Fu Q, Zhang YP. Canine transmissible venereal tumor genome reveals ancient introgression from coyotes to pre-contact dogs in North America. Cell Res 2019; 29:592-595. [PMID: 31160719 DOI: 10.1038/s41422-019-0183-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 05/15/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Bo-Wen Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Chinese Academy of Sciences, 100044, Beijing, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Fang-Liang Chen
- Kunming Police Dog Base of the Ministry of Public Security, Kunming, 650204, Yunnan, China
| | - Sheila C Ommeh
- Animal Biotechnology Group, Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 00200, Kenya
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Melissa M Turner
- Department of Forestry and Environmental Resources, Fisheries, Wildlife, and Conservation Biology Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andrei D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Leninskiy Prospect, 33, Moscow, Russia, 119071
| | - Peter Savolainen
- Department of Gene Technology, KTH-Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Chinese Academy of Sciences, 100044, Beijing, China. .,Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, 100044, Beijing, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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12
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Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, Rahbek C, Kroonen G, Peyrot M, McColl H, Vasilyev SV, Veselovskaya E, Gerasimova M, Pavlova EY, Chasnyk VG, Nikolskiy PA, Gromov AV, Khartanovich VI, Moiseyev V, Grebenyuk PS, Fedorchenko AY, Lebedintsev AI, Slobodin SB, Malyarchuk BA, Martiniano R, Meldgaard M, Arppe L, Palo JU, Sundell T, Mannermaa K, Putkonen M, Alexandersen V, Primeau C, Baimukhanov N, Malhi RS, Sjögren KG, Kristiansen K, Wessman A, Sajantila A, Lahr MM, Durbin R, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E. The population history of northeastern Siberia since the Pleistocene. Nature 2019; 570:182-188. [PMID: 31168093 DOI: 10.1038/s41586-019-1279-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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Affiliation(s)
- Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Vladimir V Pitulko
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia.
| | - Vitor C Sousa
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Constanza de la Fuente
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Human Genetics Department, University of Chicago, Chicago, IL, USA
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | | | - Konstantinos Giampoudakis
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Guus Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Michaël Peyrot
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sergey V Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elizaveta Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
- Russian State University for Humanities (RSUH), Moscow, Russia
| | - Margarita Gerasimova
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elena Y Pavlova
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Polar Geography Department, Arctic & Antarctic Research Institute, St Petersburg, Russia
| | | | - Pavel A Nikolskiy
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Andrei V Gromov
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Valeriy I Khartanovich
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Pavel S Grebenyuk
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
- Northeast State University, Magadan, Russia
| | - Alexander Yu Fedorchenko
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander I Lebedintsev
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Sergey B Slobodin
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Boris A Malyarchuk
- Institute of Biological Problems of the North, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- University of Greenland, Nuuk, Greenland
| | - Laura Arppe
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Tarja Sundell
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Mannermaa
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
| | - Mikko Putkonen
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Verner Alexandersen
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Primeau
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Anna Wessman
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Marta Mirazon Lahr
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Sanger Institute, Cambridge, UK.
- GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.
- The Danish Institute for Advanced Study, The University of Southern Denmark, Odense, Denmark.
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Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, Liu Q, Walters RG, Lin K, Ju J, Korneliussen T, Yang MA, Fu Q, Wang J, Zhou L, Krogh A, Zhang H, Wang W, Chen Z, Cai Z, Yin Y, Yang H, Mao M, Shendure J, Wang J, Albrechtsen A, Jin X, Nielsen R, Xu X. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell 2018; 175:347-359.e14. [DOI: 10.1016/j.cell.2018.08.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/12/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023]
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Yang MA, Fu Q. Insights into Modern Human Prehistory Using Ancient Genomes. Trends Genet 2018; 34:184-196. [DOI: 10.1016/j.tig.2017.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/26/2017] [Accepted: 11/29/2017] [Indexed: 01/05/2023]
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Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse. Curr Biol 2015; 25:2577-83. [PMID: 26412128 DOI: 10.1016/j.cub.2015.08.032] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/06/2015] [Accepted: 08/14/2015] [Indexed: 12/22/2022]
Abstract
Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Melinda A Yang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Matteo Fumagalli
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Gila Kahila Bar-Gal
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel
| | - Anders Albrechtsen
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen 2200N, Denmark
| | - Filipe G Vieira
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Bent Petersen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Andaine Seguin-Orlando
- National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark
| | - Kim Magnussen
- National High-Throughput DNA Sequencing Centre, University of Copenhagen, Copenhagen 1353K, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Belen Lorente-Galdos
- ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain
| | - Sagi Polani
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Koret School of Veterinary Medicine, The Hebrew University, Rehovot 76100, Israel
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | | | | | - Claudia Feh
- Station Biologique de la Tour du Valat, Arles 13200, France
| | - Charles L Greenblatt
- Department of Microbiology and Molecular Genetics, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Natalia I Abramson
- Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia
| | | | - Renate Schafberg
- Martin-Luther-University Halle-Wittenberg, Museum of Domesticated Animals "Julius Kühn", Halle 06108, Germany
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, Saint-Petersburg 199034, Russia; Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk 677980, Russia
| | - Thomas Sicheritz-Ponten
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
| | - Tomas Marques-Bonet
- ICREA at the Institut de Biologia Evolutiva (CSIC-University Pompeu Fabra), Barcelona 08003, Spain; Centro Nacional de Analisis Genomico (CNAG-CRG), Barcelona 08023, Spain
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Molly McCue
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern 3001, Switzerland
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark; Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, 31000 Toulouse, France.
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Yang MA, Malaspinas AS, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Mol Biol Evol 2012; 29:2987-95. [PMID: 22513287 DOI: 10.1093/molbev/mss117] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.
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Affiliation(s)
- Melinda A Yang
- Department of Integrative Biology, University of California, Berkeley.
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