Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (<i>Pteropus alecto</i>)

Haopeng He; Hechuan Yang; Randy Foo; Wharton Chan; Feng Zhu; Yunsong Liu; Xuming Zhou; Liang Ma; Lin-Fa Wang; Weiwei Zhai

doi:10.1016/j.jgg.2023.05.002

Volume 50 Issue 8

Aug. 2023

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Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto)

doi: 10.1016/j.jgg.2023.05.002

a Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
b University of Chinese Academy of Sciences, Beijing 100049, China;
c Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
d Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore;
e Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
f Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

Funds:

This work is supported in part by the National Natural Science Foundation of China (32293190, 32293192) and National Key R&D Program of China (2019YFA0709501). M.L. is supported in part by the National Natural Science Foundation of China (11971459). W.Z. is supported in part by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB17), the National Natural Science Foundation of China (31970566), and National Key R&D Program of China (2018YFC1406902 and 2018YFC0910400). The Duke-NUS team was supported in part by a grant from the Singapore National Research Foundation (NRFCRP10-2012-05).

Received Date: 2023-02-21
Revised Date: 2023-05-03
Accepted Date: 2023-05-03
Publish Date: 2023-05-12

Abstract

Abstract

As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the microevolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.
- Bats,
- The black flying fox,
- Microevolution,
- Population fluctuations,
- Toba eruption

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