Genomics and morphometrics reveal the adaptive evolution of pikas

Rui-Xiang Tang; Jiao Wang; Yi-Fei Li; Cheng-Ran Zhou; Guan-Liang Meng; Feng-Jun Li; Yue Lan; Megan Price; Lars Podsiadlowski; Yan Yu; Xu-Ming Wang; Yin-Xun Liu; Bi-Song Yue; Shan-Lin Liu; Zhen-Xin Fan; Shao-Ying Liu

doi:10.24272/j.issn.2095-8137.2022.072

Volume 43 Issue 5

Sep. 2022

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Rui-Xiang Tang, Jiao Wang, Yi-Fei Li, Cheng-Ran Zhou, Guan-Liang Meng, Feng-Jun Li, Yue Lan, Megan Price, Lars Podsiadlowski, Yan Yu, Xu-Ming Wang, Yin-Xun Liu, Bi-Song Yue, Shan-Lin Liu, Zhen-Xin Fan, Shao-Ying Liu. Genomics and morphometrics reveal the adaptive evolution of pikas. Zoological Research, 2022, 43(5): 813-826. doi: 10.24272/j.issn.2095-8137.2022.072

Citation:

Rui-Xiang Tang, Jiao Wang, Yi-Fei Li, Cheng-Ran Zhou, Guan-Liang Meng, Feng-Jun Li, Yue Lan, Megan Price, Lars Podsiadlowski, Yan Yu, Xu-Ming Wang, Yin-Xun Liu, Bi-Song Yue, Shan-Lin Liu, Zhen-Xin Fan, Shao-Ying Liu. Genomics and morphometrics reveal the adaptive evolution of pikas. Zoological Research, 2022, 43(5): 813-826. doi: 10.24272/j.issn.2095-8137.2022.072

Citation:

Rui-Xiang Tang, Jiao Wang, Yi-Fei Li, Cheng-Ran Zhou, Guan-Liang Meng, Feng-Jun Li, Yue Lan, Megan Price, Lars Podsiadlowski, Yan Yu, Xu-Ming Wang, Yin-Xun Liu, Bi-Song Yue, Shan-Lin Liu, Zhen-Xin Fan, Shao-Ying Liu. Genomics and morphometrics reveal the adaptive evolution of pikas. Zoological Research, 2022, 43(5): 813-826. doi: 10.24272/j.issn.2095-8137.2022.072

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Genomics and morphometrics reveal the adaptive evolution of pikas

doi: 10.24272/j.issn.2095-8137.2022.072

Rui-Xiang Tang^{1, 2, #},
Jiao Wang^{1, #},
Yi-Fei Li^{3, #},
Cheng-Ran Zhou^{1, 4, #},
Guan-Liang Meng⁵,
Feng-Jun Li¹,
Yue Lan¹,
Megan Price¹,
Lars Podsiadlowski⁵,
Yan Yu¹,
Xu-Ming Wang²,
Yin-Xun Liu^{1, 2},
Bi-Song Yue¹,
Shan-Lin Liu⁶,
Zhen-Xin Fan^{1, 7
,
,},
Shao-Ying Liu^{2
,
,}

1.
Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
2.
Sichuan Academy of Forestry, Chengdu, Sichuan 610081, China
3.
Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
4.
BGI-Shenzhen, Shenzhen, Guangdong 518083, China
5.
Zoological Research Museum Alexander Koenig, Bonn D-53113, Germany
6.
Department of Entomology, China Agriculture University, Beijing 100193, China
7.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China

#Authors contributed equally to this work

Funds: This work was supported by the National Natural Science Foundation of China (31470110, 31970399) and China National GeneBank (CNGB)

More Information

Corresponding author: E-mail: zxfan@scu.edu.cn; shaoyliu@163.com
Received Date: 2022-06-16
Accepted Date: 2022-08-18

Published Online: 2022-08-22

Publish Date: 2022-09-18

Abstract

Abstract

Pikas (Lagomorpha: Ochotonidae) are small mouse-like lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang (Tibet) Plateau (QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81 specimens, representing 27 putative pika species. The genome-wide tree based on 4 090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa, Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other pikas. Consistently, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearing-related genes. Analysis of shared amino acid substitutions and positively selected genes (PSGs) in Alienauroa and Ochotona identified two genes, i.e., mitochondrial function-related TSFM (p.Q155E) and low-light visual sensitivity-related PROM1 (p.H419Y). Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments (e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.
- Pikas,
- Genomics,
- Morphometrics,
- Adaptive evolution,
- Sensory and energy functions

#Authors contributed equally to this work

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References(86)

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