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Science. 2019 Jun 21;364(6446). pii: eaav6202. doi: 10.1126/science.aav6202.

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

Author information

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
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. wwang@mail.kiz.ac.cn rheller@bio.ku.dk guojie.zhang@bio.ku.dk.
27
Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
28
Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark. wwang@mail.kiz.ac.cn rheller@bio.ku.dk guojie.zhang@bio.ku.dk.
29
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China. wwang@mail.kiz.ac.cn rheller@bio.ku.dk guojie.zhang@bio.ku.dk.
#
Contributed equally

Abstract

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

PMID:
31221828
DOI:
10.1126/science.aav6202

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