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Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
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
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“The improved continuity of our long-read assembly is evident by having a much higher contig and scaffold N50 values and lower contig and scaffold counts over the previously reported short-read assemblies for the muskox and other ruminant genomes assembled from short reads65.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [65]
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Metadata
- Authors
- Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., Wang, Y., Zhao, Y., Zhang, C., Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., da Fonseca, R. R., Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Y., Duan, S., Gao, Y., Zhang, Y. E., Chen, C., Hvilsom, C., Epps, C. W., Chemnick, L. G., Dong, Y., Mirarab, S., Siegismund, H. R., Ryder, O. A., Gilbert, M. T. P., Lewin, H. A., Zhang, G., Heller, R., & Wang, W.
- Affiliations
- Northwestern Polytechnical University (CN)
- Northwest A&F University (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Museum für Naturkunde (DE)
- Lanzhou University (CN)
- Kunming Institute of Zoology (CN)
- China National GeneBank (CN)
- Kashi University (CN)
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
- Nowbio Biotechnology Company, Kunming 650201, China.
- Chinese Academy of Sciences (CN)
- Copenhagen Zoo (DK)
- Oregon State University (US)
- San Diego Zoo Institute for Conservation Research (US)
- Yunnan Agricultural University (CN)
- University of California San Diego (US)
- University of Copenhagen (DK)
- University of California, Davis (US)
- Corresponding author
- Chen, Lei
- Qiu, Qiang
- Jiang, Yu
- Wang, Kun
- Lin, Zeshan
- Li, Zhipeng
- Zhang, Guojie
- Heller, Rasmus
- Wang, Wen
- ORCID
- Chen, Lei
- Qiu, Qiang
- Jiang, Yu
- Wang, Kun
- Lin, Zeshan
- Li, Zhipeng
- Bibi, Faysal
- Yang, Yongzhi
- Liu, Guichun
- Li, Qiye
- Fu, Weiwei
- Pan, Xiangyu
- Liu, Chang
- Yang, Jie
- Zhang, Chenzhou
- Yin, Yuan
- Wang, Yu
- Zhao, Yue
- Zhang, Chen
- Wang, Zhongkai
- Qin, Yanli
- Liu, Wei
- Wang, Bao
- Ren, Yandong
- Zhang, Ru
- Zeng, Yan
- da Fonseca, Rute R.
- Wei, Bin
- Li, Ran
- Wan, Wenting
- Zhao, Ruoping
- Zhu, Wenbo
- Wang, Yutao
- Duan, Shengchang
- Gao, Yun
- Zhang, Yong E.
- Chen, Chunyan
- Hvilsom, Christina
- Epps, Clinton W.
- Dong, Yang
- Mirarab, Siavash
- Siegismund, Hans Redlef
- Ryder, Oliver A.
- Gilbert, M. Thomas P.
- Lewin, Harris A.
- Zhang, Guojie
- Heller, Rasmus
- Wang, Wen
- Venue
- Science
- Published
- 2019-06-21
- Volume
- 364
- Issue
- 6446
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2953226067
- Cited by
- 441
- References
- 193
- Citations by year
- 2026: 34 · 2025: 64 · 2024: 87 · 2023: 55 · 2022: 82 · 2021: 61 · 2020: 41 · 2019: 15
- FWCI
- 17.36
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Lanzhou University Institutional Repository (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- National Natural Science Foundation of China (31501984, 31822052)
- Fundamental Research Funds for the Central Universities (3102019JC007)
- National Program for Support of Top-notch Young Professionals
- Lundbeck Fellowship (R190-2014-2827)
- Carlsberg Foundation (CF16-0663)
- 1000 Talent Project of Shaanxi Province
- Strategic Priority Research Program of CAS (XDB13000000)
- Talents Team Construction Fund of Northwestern Polytechnical University
- Villum Foundation Young Investigator (VKR023447)
- Central Public-interest Scientific Institution Basal Research Fund (Y2019GH13)
- Villum Investigator Grant
- Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (DNRF96)
- Natural science foundation from Jilin province (20170101158JC)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- ruminants, ruminant evolution, incomplete lineage sorting, population bottleneck, human migration out of Africa, horn evolution, cancer genes, deer, reindeer, Arctic adaptation, genomic selection
- MeSH terms
- Animals, Phylogeny, Ruminants, Genome, Sequence Analysis, DNA, Evolution, Molecular
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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