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Three articles and a perspective in this week’s issue of Science present the Ruminant Genome Project’s (RGP) initial findings, which range from explaining how deer antlers exploit cancer-associated signaling pathways to regenerate, to informing reindeer genetic adaptations that have helped these animals thrive in the frigid Arctic. The work provides an unprecedented look into the genomics, evolution and adaptation of ruminants, a group of highly successful and diverse mammals with significant agricultural, conservational and biomedical importance, and one that includes many well-known domestic and wild taxa, such as cows, goats, reindeer and giraffes. Faysal Bibi, a paleontologist at the Museum für Naturkunde Berlin, was a coauthor of one of the articles.

Despite the fact that ruminant taxa can be found in most places on the planet, the evolutionary origin and diversification of ruminants as well as the genetics underlying their unique traits remain relatively unknown. To better resolve ruminant genetics, Lei Chen of Northwestern Polytechnical University, Xi’an, China, and colleagues assembled the genomes of 44 ruminant species across all six ruminant families – a dataset encompassing more than 40 trillion base pairs. Chen et al. then used these, as well as other ruminant genomes, to create a time-calibrated phylogenetic tree of the group, which was able to resolve the evolutionary history of many ruminant genera. Interestingly, the results revealed large declines in ruminant populations nearly 100,000 years ago, reductions that coincide with the migration of humans out of Africa and may be evidence of early humans' impact on various ruminant species, the authors say.

Faysal Bibi, a paleontologist at the Museum für Naturkunde Berlin, was a coauthor of one of the articles. He provided information from the fossil record for the age-calibration of the ruminant phylogeny, and contributed to the evolutionary interpretations of the data. “I was shocked to see the extent of the population declines in almost all the sequenced species,” he says. “We already knew that many large herbivores succumbed to late Pleistocene extinctions, but this data shows that many surviving species also came close to being wiped out at some point in the last 100,000 years,” Bibi adds.

Were these extinctions and population declines caused by humans? “We have yet to find good evidence that shows the last 100,000 years was any different in terms of climate than previous Ice Ages. This leaves the human factor, but building a solid case is not so easy,” says Bibi, “More work is needed to be sure.”

This work was undertaken by a consortium of >20 universities or institutes mainly led by Northwestern Polytechnical University of China, University of Copenhagen, Northwest Agriculture and Forestry University, and Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences et al.

Article:

"Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits," by L. Chen; Q. Qiu; K. Wang; Z. Lin; G. Liu; C. Liu; J. Yang; C. Zhang; Y. Yin; C. Zhang; Z. Wang; Y. Qin; R. Zhang; W. Wan; W. Zhu; W. Wang at Northwestern Polytechnical University in Xi’an, China; Y. Jiang; W. Fu; X. Pan; Y. Wang; Y. Zhao; B. Wei; R. Li at Northwest A&F University in Yangling, China; Z. Li at Chinese Academy of Agricultural Sciences in Changchun, China; F. Bibi at Leibniz Institute for Evolution and Biodiversity Science in Berlin, Germany; Y. Yang at Lanzhou University in Lanzhou, China; J. Wang; W. Nie; W. Su; G. Liu; W. Liu; B. Wang; Y. Ren; Y. Zeng; W. Wan; R. Zhao; Y.E. Zhang; C. Chen; G. Zhang; W. Wang at Chinese Academy of Sciences in Kunming, China; Q. Li; G. Zhang at BGI-Shenzhen in Shenzhen, China; R.R. da Fonseca; H.R. Siegismund; M.T.P. Gilbert; G. Zhang; R. Heller at University of Copenhagen in Copenhagen, Denmark; Y. Wang at Kashgar University in Kashgar, China; S. Duan; Y. Gao at Nowbio Biotechnology Company in Kunming, China; Y.E. Zhang; C. Chen at University of Chinese Academy of Sciences in Beijing, China; C. Hvilsom at Copenhagen Zoo in Frederiksberg, Denmark; C.W. Epps at Oregon State University in Corvallis, OR; L.G. Chemnick; O.A. Ryder at San Diego Zoo Institute for Conservation Research in Escondido, CA; Y. Dong at Yunnan Research Institute for Local Plateau Agriculture and Industry in Kunming, China; Y. Dong at Yunnan Agricultural University in Kunming, China; S. Mirarab; O.A. Ryder at University of California, San Diego in La Jolla, CA; M.T.P. Gilbert at Norwegian University of Science and Technology in Trondheim, Norway; H.A. Lewin at University of California, Davis in Davis, CA.

Contact: Wen Wang at wwang@mail.kiz.ac.cn, Rasmus Heller at rheller@bio.ku.dk, Guojie Zhang at guojie.zhang@bio.ku.dk

DOI Information: Reporters wishing to link to this paper's abstract on sciencemag.org can use the following URL:https://science.sciencemag.org/cgi/doi/10.1126/science.aav6202

Note: A summary of this paper will be published in print by the journal Science on Friday, 21 June. A full-text version of this paper will be published online when the embargo lifts at https://www.sciencemag.org.