Title

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

Authors

Lei Chen, Northwestern Polytechnical University
Qiang Qiu, Northwestern Polytechnical University
Yu Jiang, Northwest A&F University
Kun Wang, Northwestern Polytechnical University
Zeshan Lin, Northwestern Polytechnical University
Zhipeng Li, Chinese Academy of Agricultural Sciences
Faysal Bibi, Museum für Naturkunde
Yongzhi Yang, Lanzhou University
Jinhuan Wang, Kunming Institute of Zoology Chinese Academy of Sciences
Wenhui Nie, Kunming Institute of Zoology Chinese Academy of Sciences
Weiting Su, Kunming Institute of Zoology Chinese Academy of Sciences
Guichun Liu, Northwestern Polytechnical University
Qiye Li, China National Genebank
Weiwei Fu, Northwest A&F University
Xiangyu Pan, Northwest A&F University
Chang Liu, Northwestern Polytechnical University
Jie Yang, Northwestern Polytechnical University
Chenzhou Zhang, Northwestern Polytechnical University
Yuan Yin, Northwestern Polytechnical University
Yu Wang, Northwest A&F University
Yue Zhao, Northwest A&F University
Chen Zhang, Northwestern Polytechnical University
Zhongkai Wang, Northwestern Polytechnical University
Yanli Qin, Northwestern Polytechnical University
Wei Liu, Kunming Institute of Zoology Chinese Academy of Sciences
Bao Wang, Kunming Institute of Zoology Chinese Academy of Sciences
Yandong Ren, Kunming Institute of Zoology Chinese Academy of Sciences
Ru Zhang, Northwestern Polytechnical University
Yan Zeng, Kunming Institute of Zoology Chinese Academy of Sciences
Rute R. Da Fonseca, Københavns Universitet
Bin Wei, Northwest A&F University
Ran Li, Northwest A&F University
Wenting Wan, Northwestern Polytechnical University

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.

Publication Title

Science

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