Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits-Reference-Cited by-同舟云学术

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Published:2019-06-21 Issue:6446 Volume:364 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Chen Lei¹^ORCID,Qiu Qiang¹^ORCID,Jiang Yu²^ORCID,Wang Kun¹^ORCID,Lin Zeshan¹^ORCID,Li Zhipeng³^ORCID,Bibi Faysal⁴^ORCID,Yang Yongzhi⁵^ORCID,Wang Jinhuan⁶,Nie Wenhui⁶,Su Weiting⁶,Liu Guichun¹⁷,Li Qiye⁸,Fu Weiwei²^ORCID,Pan Xiangyu²^ORCID,Liu Chang¹^ORCID,Yang Jie¹^ORCID,Zhang Chenzhou¹^ORCID,Yin Yuan¹^ORCID,Wang Yu²^ORCID,Zhao Yue²^ORCID,Zhang Chen¹^ORCID,Wang Zhongkai¹^ORCID,Qin Yanli¹^ORCID,Liu Wei⁷^ORCID,Wang Bao⁷^ORCID,Ren Yandong⁷^ORCID,Zhang Ru¹^ORCID,Zeng Yan⁷^ORCID,da Fonseca Rute R.⁹¹⁰^ORCID,Wei Bin²^ORCID,Li Ran²^ORCID,Wan Wenting¹⁷,Zhao Ruoping⁷,Zhu Wenbo¹^ORCID,Wang Yutao¹¹^ORCID,Duan Shengchang¹²^ORCID,Gao Yun¹²^ORCID,Zhang Yong E.¹³¹⁴¹⁵^ORCID,Chen Chunyan¹³¹⁴,Hvilsom Christina¹⁶^ORCID,Epps Clinton W.¹⁷^ORCID,Chemnick Leona G.¹⁸,Dong Yang¹⁹²⁰^ORCID,Mirarab Siavash²¹^ORCID,Siegismund Hans Redlef⁹,Ryder Oliver A.¹⁸²²^ORCID,Gilbert M. Thomas P.²³²⁴^ORCID,Lewin Harris A.²⁵^ORCID,Zhang Guojie⁷⁸¹⁵²⁶^ORCID,Heller Rasmus⁹^ORCID,Wang Wen¹⁷¹⁵^ORCID

Affiliation:

1. Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China.

2. Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.

3. Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.

4. Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, Germany.

5. State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.

6. Kunming Cell Bank, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

7. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

8. China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.

9. Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.

10. Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

11. College of Life and Geographic Sciences, Kashgar University, Kashgar 844000, China.

12. Nowbio Biotechnology Company, Kunming 650201, China.

13. Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

14. University of Chinese Academy of Sciences, Beijing 100049, China.

15. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.

16. Copenhagen Zoo, Frederiksberg, Denmark.

17. Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA.

18. San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.

19. Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming 650201, China.

20. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.

21. Department of Electrical and Computer Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

22. Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA.

23. EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

24. Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway.

25. Department of Evolution and Ecology and the UC Davis Genome Center, University of California, Davis, CA, 95616, USA.

26. Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.

Abstract

Phylogeny and characteristics of ruminants Ruminants are a diverse group of mammals that includes families containing well-known taxa such as deer, cows, and goats. However, their evolutionary relationships have been contentious, as have the origins of their distinctive digestive systems and headgear, including antlers and horns (see the Perspective by Ker and Yang). To understand the relationships among ruminants, L. Chen et al. sequenced 44 species representing 6 families and performed a phylogenetic analysis. From this analysis, they were able to resolve the phylogeny of many genera and document incomplete lineage sorting among major clades. Interestingly, they found evidence for large population reductions among many taxa starting at approximately 100,000 years ago, coinciding with the migration of humans out of Africa. Examining the bony appendages on the head—the so-called headgear—Wang et al. describe specific evolutionary changes in the ruminants and identify selection on cancer-related genes that may function in antler development in deer. Finally, Lin et al. take a close look at the reindeer genome and identify the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic. Science , this issue p. eaav6202 , p. eaav6335 , p. eaav6312 ; see also p. 1130

Funder

National Natural Science Foundation of China

Fundamental Research Funds for the Central Universities

National Program for Support of Top-notch Young Professionals

Lundbeck Fellowship

Carlsberg Foundation

1000 Talent Project of Shaanxi Province

Strategic Priority Research Program of CAS

Talents Team Construction Fund of Northwestern Polytechnical University

Villum Foundation Young Investigator

Central Public-interest Scientific Institution Basal Research Fund

Villum Investigator Grant