iScience (Oct 2020)
An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species
- Peijun Zhang,
- Yong Zhao,
- Chang Li,
- Mingli Lin,
- Lijun Dong,
- Rui Zhang,
- Mingzhong Liu,
- Kuan Li,
- He Zhang,
- Xiaochuan Liu,
- Yaolei Zhang,
- Yuan Yuan,
- Huan Liu,
- Inge Seim,
- Shuai Sun,
- Xiao Du,
- Yue Chang,
- Feida Li,
- Shanshan Liu,
- Simon Ming-Yuen Lee,
- Kun Wang,
- Ding Wang,
- Xianyan Wang,
- Michael R. McGowen,
- Thomas A. Jefferson,
- Morten Tange Olsen,
- Josefin Stiller,
- Guojie Zhang,
- Xun Xu,
- Huanming Yang,
- Guangyi Fan,
- Xin Liu,
- Songhai Li
Affiliations
- Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Yong Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Chang Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
- Mingli Lin
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Lijun Dong
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Rui Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Mingzhong Liu
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- Kuan Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
- He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Xiaochuan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby 2800, Denmark
- Yuan Yuan
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
- Huan Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Australia
- Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Yue Chang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Feida Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
- Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- Xianyan Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian 361005, China
- Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington DC 20560, USA
- Thomas A. Jefferson
- Clymene Enterprises, Yerba Valley Way, Lakeside, CA 92040, USA
- Morten Tange Olsen
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen 1353, Denmark
- Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; Corresponding author
- Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Fuyang, BGI-Shenzhen, Fuyang, Anhui 236009, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guandong 518083, China; Corresponding author
- Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore; Corresponding author
- Journal volume & issue
-
Vol. 23,
no. 10
p. 101640
Abstract
Summary: The Indo-Pacific humpback dolphin (Sousa chinensis) is a small inshore species of odontocete cetacean listed as Vulnerable on the IUCN Red List. Here, we report on the evolution of S. chinensis chromosomes from its cetruminant ancestor and elucidate the evolutionary history and population genetics of two neighboring S. chinensis populations. We found that breakpoints in ancestral chromosomes leading to S. chinensis could have affected the function of genes related to kidney filtration, body development, and immunity. Resequencing of individuals from two neighboring populations in the northwestern South China Sea, Leizhou Bay and Sanniang Bay, revealed genetic differentiation, low diversity, and small contemporary effective population sizes. Demographic analyses showed a marked decrease in the population size of the two investigated populations over the last ~4,000 years, possibly related to climatic oscillations. This study implies a high risk of extinction and strong conservation requirement for the Indo-Pacific humpback dolphin.
