Convergent genomic signatures of high altitude adaptation among domestic mammals

Wu, Dong‐Dong; Yang, Cuiping; Wang, Mingshan; Dong, Kunzhe; Yan, Dawei; Hao, Ziqian; Fan, Songqing; Chu, Shuzhou; Shen, Qingwu; Jiang, Liping; Li, Yán; Zeng, Lin; Liu, He-Qun; Xie, Hailian; Ma, You-Zhi; Kong, Xiaoyan; Yang, Shuli; Dong, Xinxing; Koshkoiyeh, Ali Esmailizadeh; Irwin, David M.; Xiao, Xiao; Li, Ming; Yang, Dong; Wang, Wen; Shi, Peng; Li, Haipeng; Ma, Yue; Gou, Xin; Chen, Yongbin; Zhang, Yaping

doi:10.1101/743955

Cited by 12 publications

(14 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, various within‐ and between‐species analyses of altitude adaptation have also shown that in most cases different genetic architectures and physiological mechanisms underlie these adaptations (IV). A comprehensive study comparing populations living at the Tibetan plateau and from the lowlands of different species (humans and domestic mammals, including sheep, goats and cattle) found few genetic variants (3–45 sites out of 182K SNPs) under convergent evolution across all species (Wu et al ). The authors suggest that evolution acts on genes involved in similar functional pathways within a network rather than on single genes.…”

Section: Genetic Background Of High‐altitude Adaptationmentioning

confidence: 99%

“…However, there are some common genes with signals of positive selection across species, which suggests convergent evolution at the molecular level, e.g. EPAS1 , JAZF1 , DKK2 and SPON1 show signatures of adaptation in cattle, sheep and goat populations of the Tibetan plateau (Wu et al ). EPAS1 (or HIF2A ) is probably the most prominent hypoxia‐related gene that shows signatures of adaptation in multiple species.…”

Section: Genetic Background Of High‐altitude Adaptationmentioning

confidence: 99%

See 1 more Smart Citation

Selection signatures for high‐altitude adaptation in ruminants

Friedrich

Wiener

2020

Animal Genetics

View full text Add to dashboard Cite

Summary High‐altitude areas are important socio‐economical habitats with ruminants serving as a major source of food and commodities for humans. Living at high altitude, however, is extremely challenging, predominantly due to the exposure to hypoxic conditions, but also because of cold temperatures and limited feed for livestock. To survive in high‐altitude environments over the long term, ruminants have evolved adaptation strategies, e.g. physiological and morphological modifications, which allow them to cope with these harsh conditions. Identification of such selection signatures in ruminants may contribute to more informed breeding decisions, and thus improved productivity. Moreover, studying the genetic background of altitude adaptation in ruminants provides insights into a common molecular basis across species and thus a better understanding of the physiological basis of this adaptation. In this paper, we review the major effects of high altitude on the mammalian body and highlight some of the most important short‐term (coping) and genetically evolved (adaptation) physiological modifications. We then discuss the genetic architecture of altitude adaptation and target genes that show evidence of being under selection based on recent studies in various species, with a focus on ruminants. The yak is presented as an interesting native species that has adapted to the high‐altitude regions of Tibet. Finally, we conclude with implications and challenges of selection signature studies on altitude adaptation in general. We found that the number of studies on genetic mechanisms that enable altitude adaptation in ruminants is growing, with a strong focus on identifying selection signatures, and hypothesise that the investigation of genetic data from multiple species and regions will contribute greatly to the understanding of the genetic basis of altitude adaptation.

show abstract

Section: Genetic Background Of High‐altitude Adaptationmentioning

confidence: 99%

Section: Genetic Background Of High‐altitude Adaptationmentioning

confidence: 99%

Selection signatures for high‐altitude adaptation in ruminants

Friedrich

Wiener

2020

Animal Genetics

View full text Add to dashboard Cite

show abstract

“…ZFAND2A is predicted to be a target gene of the HIF1A transcription factor using known transcription factor binding site motifs from the TRANSFAC database (Matys et al 2006;Rouillard et al 2016). Moreover, ZFAND2A was recently reported to undergo positive selection and exhibit significantly down-regulated expression in the Tibetan pig (Wu et al 2019). Meanwhile, activation of GPER1 by 17β-estradiol (E2) and the specific agonist G-1 will trigger a GPER1-EGFR-MAPK1-FOS signaling pathway, leading to the increased expression level of VEGF through upregulation of HIF1A (Francesco et al 2014;Xiang et al 2018).…”

Section: Population-stratified Svs and Candidate Adaptive Genesmentioning

confidence: 99%

Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

Cheng

Wang

et al. 2020

Preprint

View full text Add to dashboard Cite

Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. To investigate the role of SVs in high-altitude adaptation (HAA), we here generated a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using the nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% were sequence-resolved for the first time. We systemically assessed the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 189 genomes, we identified 90 Tibetan-Han stratified SVs and 124 candidate adaptive genes. Besides, we discovered 15 adaptive introgressed SV candidates and provided evidence for a deletion of 335 base pairs at 1p36.32. Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future HAA studies.

show abstract

“…A central question is whether the convergence in phenotype reflects similar underlying molecular events. Most empirical and theoretical work to address this question has focused on unicellular organisms, mammals, model plants, and crops ( Zhang, 2006 ; Li et al., 2010 ; Lin et al., 2012 ; Tenaillon et al., 2012 ; Zhen et al., 2012 ; Lenser and Theißen, 2013 ; Stern, 2013 ; Storz, 2016 ; Woodhouse and Hufford, 2019 ; Wu et al., 2020a , 2020b ; Zhang et al., 2020 ). Recently, the availability of genomic data has enabled the expansion of molecular convergence analyses to non-model organisms.…”

Section: Introductionmentioning

confidence: 99%

Genomic Convergence in the Adaptation to Extreme Environments

Wang

Guo

et al. 2020

Plant Communications

View full text Add to dashboard Cite

Convergent evolution is especially common in plants that have independently adapted to the same extreme environments (i.e., extremophile plants). The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants. In this review, we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments. Despite being well studied by candidate gene approaches, convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes. By contrast, genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments. Examples include the convergence of biological pathways and changes in gene expression, gene copy number, amino acid usage, and GC content. Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes. In several cases, multiple types of convergence events have been found to co-occur. However, empirical and theoretical studies of this higher level convergent evolution are still limited. In conclusion, both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments.

show abstract

Convergent genomic signatures of high altitude adaptation among domestic mammals

Cited by 12 publications

References 71 publications

Selection signatures for high‐altitude adaptation in ruminants

Selection signatures for high‐altitude adaptation in ruminants

Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

Genomic Convergence in the Adaptation to Extreme Environments

Contact Info

Product

Resources

About