Domestication relaxed selective constraints on the yak mitochondrial genome
Open accessAbstract
Wild yaks roaming in the high-altitude Qinghai-Tibetan plateau have to maintain high metabolic efficiency. However, domestic yaks do not require such high efficiency because of their limited activity. Hence, domestication may have caused the relaxation of selective constraints on the yak mitochondrial genome because mitochondrial mutations are extremely sensitive to energy-related selective pressures. We have tested this hypothesis by analyzing the mitochondrial genomes of 51 domestic yaks and 21 wild yaks. The results show that the ratio of nonsynonymous/synonymous substitutions in mitochondrial protein-coding genes is significantly higher in domestic yak lineages than those of wild yaks. This genetic difference suggests that the relaxation of selective constraints following the domestication in addition to bottlenecks has allowed faster accumulation of nonsilent substitutions in the yak mitochondrial genome, despite its short domestication history.
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A build-up of deleterious alleles is documented across domesticated species when compared to their wild counterparts.
“A build-up of deleterious alleles is documented across domesticated species when compared to their wild counterparts.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [131]
A higher frequency of non-synonymous substitutions in domesticated yaks compared to the wild yaks has been reported.
“A higher frequency of non-synonymous substitutions in domesticated yaks compared to the wild yaks has also been reported [131].”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [131]
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“Previous studies have observed faster accumulation of non-silent mutations following domestication in some animals, including dog, pig, yak and chicken, which is believed to be a consequence of a decrease in Ne associated with domestication and relaxation of purifying selection on mitochondrial genes in some domestica…”
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“Its inhospitable environment, characterized by severe coldness, severe hypoxia and strong ultraviolet radiation (Su and Wang, 1992; Bickler and Buck, 2007; Cheviron and Brumfield, 2012), has profound effects on animal survival and thus, it is regarded as a global biodiversity hotspot and a natural laboratory for long-…”
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“Recent population-level studies have found increased dN/dS or ratio of nonsynonymous to synonymous diversity (pN/pS) in a number of domesticated lineages compared with their wild relatives (Wang et al. 2011; Hughes 2013).”
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“When likelihood scores between the two models were compared, if the likelihood score of the multi-omega model was higher than that of the single omega model, then the opsin gene had evolved in an unbalanced (non-neutral) manner (Wang et al., 2011).”
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“…were compared with a modern reference collection of charcoal from ~20 common trees and shrubs from the northeastern Tibetan Plateau, assisted by published descriptions of wood anatomy (e.g., Jansen et al. 2000; Suzuki and Noshiro 1988; Zhang and Baas 1992) and online resources (e.g., Wheeler 2011).”
BackgroundSelf-domestication and language evolution
Thomas, J. (2014) · ERA · Cited by 14 · see citing works
The complete mitochondrial genome sequence of the Datong yak ( Bos grunniens )
Wu, X., Chu, M., Liang, C., Ding, X., Guo, X., Bao, P., & Yan, P. (2014) · Mitochondrial DNA Part A · doi:10.3109/19401736.2014.898292 · Cited by 13 · see citing works
“The structural organization of mitogenome is identical to that observed in most other vertebrates (Cheng et al., 2011; Gu et al., 2007; Wang et al., 2011).”
The complete sequence of mitochondrial genome of polled yak ( Bos grunniens )
Chu, M., Wu, X., Liang, C., Pei, J., Ding, X., Guo, X., Bao, P., & Yan, P. (2014) · Mitochondrial DNA Part A · doi:10.3109/19401736.2014.974175 · Cited by 12 · see citing works
“The structural organization of mitogenome is identical to that observed in most other vertebrates (Broughton et al., 2001; Gu et al., 2007; Tu et al., 2014; Wang et al., 2011).”
BackgroundInsights into the Divergence of Chinese Ips Bark Beetles during Evolutionary Adaptation
Du, H., Fang, J., Shi, X., Yu, C., Deng, M., Zhang, S., Liu, F., Zhang, Z., Han, F., & Kong, X. (2022) · Biology · doi:10.3390/biology11030384 · Cited by 11 · see citing works
“Similar results have been found in high-altitude species such as Tibetan wild yak [85], Tibetan human [86], and schizothoracine fish [87].”
ResultEvolution of mitochondrial DNA and its relation to basal metabolic rate
Feng, P., Zhao, H., & Lü, X. (2014) · Mitochondrial DNA · doi:10.3109/19401736.2013.873895 · Cited by 10 · see citing works
“is encoded by the other strand of mtDNA with very different codon usage bias (Hasegawa et al., 1998; Wang et al., 2011), we excluded this gene in our analysis.”
BackgroundInfluentialmtDNA sequence, phylogeny and evolution of laboratory mice
Zheng, J., Chen, Y., Deng, F., Huang, R., Petersen, F., Ibrahim, S. M., & Yu, X. (2014) · Mitochondrion · doi:10.1016/j.mito.2014.07.006 · Cited by 9 · see citing works
The complete mitochondrial genome of Sunan yak (Bos grunniens) and a phylogenetic study
Zhou, X., Wu, X., Liang, C., Guo, X., Chu, M., Wang, H., Pei, J., Bao, P., Ding, X., & Yan, P. (2019) · Mitochondrial DNA Part B · doi:10.1080/23802359.2018.1546149 · Cited by 8 · see citing works
Hwang, H.-S., Cho, B., Cho, J., Park, B., & Kim, T. W. (2022) · Journal of Marine Science and Engineering · doi:10.3390/jmse10030400 · Cited by 8 · see citing works
Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks
Kang, Y., Guo, S., Wang, X., Cao, M., Pei, J., Li, R., Bao, P., Wang, J., Lamao, J., Gongbao, D., et al. (2022) · Animals · doi:10.3390/ani12192682 · Cited by 8 · see citing works
“[4] defined a third maternal branch that only included wild yaks and further observed the effects of relaxed selection among domesticated yaks as a consequence of domestication.”
BackgroundComplex Evolutionary Patterns Revealed by Mitochondrial Genomes of the Domestic Horse
Ning, T., Li, J., Lin, K., Xiao, H., Wylie, S. J., Hua, S., Li, H., & Zhang, Y.-P. (2014) · Current Molecular Medicine · doi:10.2174/1566524014666141203100940 · Cited by 7 · see citing works
“These suggest that domestication have caused the relaxation of selective constraints on their mitochondrial genomes [36, 37].”
BackgroundCharacterization of the complete mitochondrial genome sequence of Gannan yak ( Bos grunniens )
Wu, X., Ding, X., Chu, M., Guo, X., Bao, P., Liang, C., & Yan, P. (2014) · Mitochondrial DNA Part A · doi:10.3109/19401736.2014.926530 · Cited by 6 · see citing works
“The structural organization of mitogenome is identical to that observed in most other vertebrates (Broughton et al., 2001; Gu et al., 2007; Tu et al., 2014; Wang et al., 2011).”
BackgroundDong, C., Duan, X., Laghari, M. Y., Zhang, M., Ma, X., Chen, B., Li, X., & Xu, P. (2020) · Marine Biotechnology · doi:10.1007/s10126-020-09946-7 · Cited by 6 · see citing works
Ni, P., Bhuiyan, A. A., Chen, J., Li, J., Zhang, C., Zhao, S., Du, X., Li, H., Yu, H., Liu, X., et al. (2018) · Genetica · doi:10.1007/s10709-018-0018-y · Cited by 6 · see citing works
王, 绪., 汪, 登., 何, 舜., & 周, 传. (2011) · Scientia Sinica Vitae · doi:10.1360/052010-41 · Cited by 6 · see citing works
Prehistoric Colonization and Demographic History of Modern Humans on the Tibetan Plateau
Qi, X., Cui, C., Ouzhuluobu, Wu, T., & Su, B. (2014) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0025527 · Cited by 6 · see citing works
Shi, T., Dimitrov, I., Yinling, Z., Tax, F. E., Yi, J., Gou, X., & Li, J. (2015) · Plant Molecular Biology · doi:10.1007/s11103-015-0366-2 · Cited by 5 · see citing works
Analysis of the Complete Mitochondrial Genome of Pteronura brasiliensis and Lontra canadensis
Wei, Q., Wang, X., Dong, Y., Shang, Y., Sun, G., Wu, X., Zhao, C., Sha, W., Yang, G., & Zhang, H. (2023) · Animals · doi:10.3390/ani13203165 · Cited by 5 · see citing works
“Studies on the mitochondrial genome of domesticated animals, such as dogs, cattle, and yaks had shown relaxed selection patterns when compared with their wild relatives under the adaptation to domesticated environments [16–18].”
BackgroundCao, Z., Wang, S., Qi, M., Zhang, J., Liu, R., Ren, X., Wu, Q., Cui, Z., & Dong, H. (2023) · Microbial Pathogenesis · doi:10.1016/j.micpath.2023.106470 · Cited by 5 · see citing works
Zheng, H.-X., Yan, S. L., Zhang, M., Gu, Z., Wang, J., & Li, J. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae175 · Cited by 5 · see citing works
“Previous studies have revealed that mutations in mtDNA are shaped by natural selection in modern humans and other species (Elson et al. 2004; Ruiz-Pesini et al. 2004; Ingman and Gyllensten 2007; Shen et al. 2009; Wang et al. 2011; Liu et al. 2012; Kang et al. 2013, 2016; Zheng et al. 2017).”
BackgroundWild yak Bos mutus (Przewalski, 1883)
Jianlin, H. (2014) · Cambridge University Press eBooks · doi:10.1017/cbo9781139568098.014 · Cited by 5 · see citing works
Feng, P., & Zhou, Q. (2017) · Journal of Mammalian Evolution · doi:10.1007/s10914-017-9399-4 · Cited by 5 · see citing works
“Because ND6 is encoded by the light strand of mtDNA with very different codon usage bias (Hasegawa et al. 1998; Wang et al. 2011; Feng et al. 2015), it was excluded in our analysis.”
Pendleton, A. L., Shen, F., Taravella, A. M., Emery, S., Veeramah, K. R., Boyko, A. R., & Kidd, J. M. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/118794 · Cited by 5 · see citing works
Characterization of the complete mitochondrial genome of Tibet Gaoshan Yak (Bos grunniens)
Ren, W., Zhang, Q., Dingkao, R., Huang, C., Wang, X., Zhang, Z., Jiang, H., Guo, X., Yan, P., & Liang, C. (2021) · Mitochondrial DNA Part B · doi:10.1080/23802359.2021.2001389 · Cited by 4 · see citing works
Comparative Analysis of the Umami Taste Receptor Gene Tas1r1 in Mustelidae
Tarusawa, Y., & Matsumura, S. (2020) · ZOOLOGICAL SCIENCE · doi:10.2108/zs190086 · Cited by 3 · see citing works
“The plausibility of models was also examined based on AIC, following Wang et al. (2011).”
MethodExtreme nearly neutral evolution in mitochondrial genomes of laboratory mouse strains
Yonezawa, T., & Hasegawa, M. (2013) · Gene · doi:10.1016/j.gene.2013.08.022 · Cited by 3 · see citing works
Nätt, D. (2011) · DiVA (Linkoping University) · Cited by 3 · see citing works
Li, B., Yang, J., Liu, Y., & Jiang, M. (2023) · Animals · doi:10.3390/ani13182963 · Cited by 2 · see citing works
“Further, the effects of relaxed selection among domestic yaks due to the consequence of domestication was observed [17].”
BackgroundMitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla
Mei, X., Wang, X., Wu, X., Liu, G., Chen, Y., Zhou, S., Shang, Y., Liu, Z., Yang, X., Sha, W., et al. (2024) · Animals · doi:10.3390/ani14101434 · Cited by 2 · see citing works
“Firstly, numerous studies have demonstrated that elevated/decreased ω values cannot be solely attributed to Ne; often, other forces are also at play [11–13].”
BackgroundMolecular evolution of the mitochondrial genome underlies semi-aquatic adaptation in lutrinae
Wei, Q., Wang, X., Dong, Y., Mei, X., Shang, Y., Sun, G., Wu, X., Gao, X., Zhao, C., Sha, W., et al. (2024) · Organisms Diversity & Evolution · doi:10.1007/s13127-024-00650-1 · Cited by 1 · see citing works
“…selection evolutionary pattern has been reported in some domesticated lineages, weakly locomotive molluscs, birds, and mammalian lineage mitogenomes (Björnerfeldt et al., 2006; Hughes, 2013; MacEachern et al., 2009; Shen et al., 2009; Sun et al., 2017; Wang et al., 2011; Zhang et al., 2013).”
Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years
Gilardet, A., Oppenheimer, J., Sinding, M. S., Lord, E., Chacón-Duque, J. C., Oteo‐García, G., Xenikoudakis, G., Kosintsev, P. A., Southon, J. R., Vasiliev, S. K., et al. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf206 · Cited by 1 · see citing works
Evidence of Relaxed Selection in the Mitochondrial Genomes of Phototrophic Paulinella Lineages
Han, S., Lhee, D., Yang, J. H., Bhattacharya, D., & Yoon, H. S. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag052 · Cited by 1 · see citing works
Li, Z.-B., Li, T.-S., Li, M. Y., Li, Z.-D., Wang, J.-L., Li, G.-X., Lv, J.-S., Li, L.-X., Ye, X.-D., & Ling, X.-D. (2026) · Animals · doi:10.3390/ani16142121 · Cited by 1 · see citing works
“During evolution, yaks have progressively adapted to this harsh environment, rendering them an exemplary biological model for investigating the mechanisms underlying high-altitude hypoxia adaptation in mammals [4–6].”
Characterization of the complete mitochondrial genome of the Xueduo yak (Bos grunniens)
Zhou, X., Wu, X., Ding, X., Liang, C., Guo, X., Chu, M., Wang, H., Pei, J., Bao, P., & Yan, P. (2019) · Mitochondrial DNA Part B · doi:10.1080/23802359.2019.1591210 · Cited by 1 · see citing works
Effect of locomotor preference on the evolution of mitochondrial genes in Bovidae
Shi, L., Wang, X., Yang, X., Lyu, T., Wang, L., Zhou, S., Dong, Y., Wu, X., Shang, Y., & Zhang, H. (2024) · Scientific Reports · doi:10.1038/s41598-024-63937-5 · Cited by 1 · see citing works
“Research has demonstrated that habitat type affects mitochondrial gene evolution 16,17 .”
BackgroundTian, Y., Lin, Y., Ma, Y., Li, J., Sahu, S. K., Fan, J., Lin, C., Li, Z., Shi, M., He, F., et al. (2025) · Biology · doi:10.3390/biology14010030 · Cited by 1 · see citing works
“In addition, relaxed purifying selection under human management could also contribute to the excess accumulation of deleterious mutations, even for large-effect damaging alleles [17,18].”
Golmud Yak’ının (Bos grunniens) Tam Mitogenomu: Sekans, Karakterizasyon ve Filogenetik Analiz
Li, G., Shengmei, C. H. E. N., Yinlu, X. I. E., Weixin, G. U. O., & Ma, Z. (2022) · Kafkas Universitesi Veteriner Fakultesi Dergisi · doi:10.9775/kvfd.2022.27313
Wu, Y., Yao, Y., Dong, M., Xia, T., Li, D., Xie, M., Wu, J., Wen, A., Wang, Q., Zhu, G., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12038031
Xu, D., Li, R., Xu, Y., Guo, W., Chen, S., Li, W., Huang, W., Lei, C., & Ma, Z. (2024) · Russian Journal of Genetics · doi:10.1134/s1022795424700376
“Yak ( Bos grunniens ), known as the “boat of the plateau,” is a vulnerable bovine species endemic to the Qinghai-Tibet Plateau (QTP) with an altitude of 2000–6000 m above sea level [1, 2].”
Derivation of Human Constructs of RealityPreprint
Bednarik, R. G. (2025) · Qeios · doi:10.32388/gbuz3t
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Population structure and domestication history of the Javan banteng ( Bos javanicus javanicus )Preprint
Wang, X., Aninta, S. G., Garcia‐Erill, G., Li, Z., Khan, A., Liu, X., Bertola, L. D., Dharmayanthi, A. B., Yulianto, Y., Yonathan, Y., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.01.646613
“The higher total load in Bali cattle is consistent with a typical domestication syndrome where human husbandry results in relaxed selection pressure, so that deleterious mutations accumulate more readily (Larson and Fuller 2014; Wang et al. 2011).”
Zhang, X., Zhi-bin, H., Zhong-li, P., Wang, H., & Huang, Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.08.675018
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Population structure and domestication history of the Javan banteng
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- Authors
- Wang, Z., Yonezawa, T., Liu, B., Ma, T., Shen, X., Su, J., Guo, S., Hasegawa, M., & Liu, J.
- Affiliations
- Lanzhou University (CN)
- Fudan University (CN)
- Chinese Academy of Sciences (CN)
- Northwest Institute of Plateau Biology (CN)
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-12-14
- Volume
- 28
- Issue
- 5
- Pages
- 1553-1556
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2125852604
- Cited by
- 98
- References
- 23
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 6 · 2023: 4 · 2022: 6 · 2021: 3 · 2020: 8 · 2019: 6 · 2018: 5 · 2017: 9 · 2016: 6 · 2015: 5 · 2014: 15 · 2013: 11
- FWCI
- 2.52
- Type
- journal article
- Language
- en
- Open access
- green
- ir.lzu.edu.cn
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Lanzhou University Institutional Repository (submittedVersion, cc-by-nc)
- Funders
- National Science Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- yak, mitochondrial genome, domestication, relaxed selection, nonsynonymous substitutions, wild yak, population bottleneck, metabolic efficiency, high-altitude adaptation, Tibetan Plateau
- MeSH terms
- Animals, Animals, Domestic, Cattle, Energy Metabolism, Phylogeny, Population Density, Selection, Genetic, Likelihood Functions, Evolution, Molecular, Genome, Mitochondrial
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