Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals.
Studies of genetic adaptation, a central focus of evolutionary biology, most often focus on the host's genome and only rarely on its co-evolved microbiome. The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for the survival of human and other mammalian species. Yaks (Bos grunniens) and Tibetan sheep (T-sheep) (Ovis aries) have adaptations for living in this harsh high-altitude environment, where nomadic Tibetan people keep them primarily for food and livelihood [1]. Adaptive evolution affects energy-metabolism-related genes in a way that helps these ruminants live at high altitude [2, 3]. Herein, we report convergent evolution of rumen microbiomes for energy harvesting persistence in two typical high-altitude ruminants, yaks and T-sheep. Both ruminants yield significantly lower levels of methane and higher yields of volatile fatty acids (VFAs) than their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries). Ultra-deep metagenomic sequencing reveals significant enrichment in VFA-yielding pathways of rumen microbial genes in high-altitude ruminants, whereas methanogenesis pathways show enrichment in the cattle metagenome. Analyses of RNA transcriptomes reveal significant upregulation in 36 genes associated with VFA transport and absorption in the ruminal epithelium of high-altitude ruminants. Our study provides novel insights into the contributions of microbiomes to adaptive evolution in mammals and sheds light on the biological control of greenhouse gas emissions from livestock enteric fermentation.
State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
Zhigang
Z
Zhang
State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.
Dongming
D
Xu
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China.
Li
L
Wang
State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
Junjun
J
Hao
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
Jinfeng
J
Wang
State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
Xin
X
Zhou
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China.
Weiwei
W
Wang
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China.
Qiang
Q
Qiu
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China.
Xiaodan
X
Huang
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China.
Jianwei
J
Zhou
State Key Laboratory of Grassland Agro-ecosystems and International Center for Tibetan Plateau Ecosystem Management of the School of Life Science, Lanzhou University, Lanzhou 730000, Gansu, China. Electronic address: longrj@lzu.edu.cn.
Ruijun
R
Long
Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: zhfq@biols.ac.cn.
Fangqing
F
Zhao
State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; KIZ-SU Joint Laboratory of Animal Model and Drug Development, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China. Electronic address: ship@mail.kiz.ac.cn.
Peng
P
Shi
D000222:Adaptation, Physiological; D000531:Altitude; D000818:Animals; D005075:Biological Evolution; D002417:Cattle / Q000382:microbiology*; D002681:China; D000069196:Gastrointestinal Microbiome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D034561:Sheep, Domestic / Q000382:microbiology*