Comparative genomics of widespread and narrow-range white-bellied rats in the <i>Niviventer niviventer</i> species complex sheds light on invasive rodent success

Xin-Lai Wu; Dan-Ping Mu; Qi-Sen Yang; Yu Zhang; Yu-Chun Li; Anderson Feijó; Ji-Long Cheng; Zhi-Xin Wen; Liang Lu; Lin Xia; Zhi-Jun Zhou; Yan-Hua Qu; De-Yan Ge

doi:10.24272/j.issn.2095-8137.2022.519

Volume 44 Issue 6

Nov. 2023

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Article Navigation > Zoological Research > 2023 > 44(6): 1052-1063

Xin-Lai Wu, Dan-Ping Mu, Qi-Sen Yang, Yu Zhang, Yu-Chun Li, Anderson Feijó, Ji-Long Cheng, Zhi-Xin Wen, Liang Lu, Lin Xia, Zhi-Jun Zhou, Yan-Hua Qu, De-Yan Ge. Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success. Zoological Research, 2023, 44(6): 1052-1063. doi: 10.24272/j.issn.2095-8137.2022.519

Citation:

Xin-Lai Wu, Dan-Ping Mu, Qi-Sen Yang, Yu Zhang, Yu-Chun Li, Anderson Feijó, Ji-Long Cheng, Zhi-Xin Wen, Liang Lu, Lin Xia, Zhi-Jun Zhou, Yan-Hua Qu, De-Yan Ge. Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success. Zoological Research, 2023, 44(6): 1052-1063. doi: 10.24272/j.issn.2095-8137.2022.519

Citation:

Xin-Lai Wu, Dan-Ping Mu, Qi-Sen Yang, Yu Zhang, Yu-Chun Li, Anderson Feijó, Ji-Long Cheng, Zhi-Xin Wen, Liang Lu, Lin Xia, Zhi-Jun Zhou, Yan-Hua Qu, De-Yan Ge. Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success. Zoological Research, 2023, 44(6): 1052-1063. doi: 10.24272/j.issn.2095-8137.2022.519

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Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success

doi: 10.24272/j.issn.2095-8137.2022.519

Xin-Lai Wu^{1, 2, 6},
Dan-Ping Mu^{2, 3},
Qi-Sen Yang²,
Yu Zhang²,
Yu-Chun Li⁴,
Anderson Feijó²,
Ji-Long Cheng²,
Zhi-Xin Wen²,
Liang Lu⁵,
Lin Xia²,
Zhi-Jun Zhou^{1, 6
,
,},
Yan-Hua Qu^{2
,
,},
De-Yan Ge^{2
,
,}

1.
Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
2.
Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing 100101, China
3.
Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China
4.
Marine College, Shandong University, Weihai, Shandong 264209, China
5.
State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
6.
Hebei Basic Science Center for Biotic Interaction, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China

Permission for field surveys was granted by the Science and Technology Department of Sichuan Province in the Second Tibetan Plateau Scientific Expedition and Research Program from 2019−2023.
The original genomic sequencing reads can be downloaded from the NCBI (PRJNA1026848), China National Center for Bioinformation (PRJCA020058), and Science Data Bank databases (DOI: 10.57760/sciencedb.j00139.00066).
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
D.Y.G. and X.L.W. designed the research. D.Y.G., X.L.W., Z.X.W., A.F., J.L.C., L.X., Q.S.Y., Y.C.L., L.L., and D.P.M. participated in sample collection. X.L.W. and D.Y.G. performed data collection and analyses. X.L.W., D.Y.G., Z.J.Z., Y.Z., and Y.H.Q. wrote the paper. All authors read and approved the final version of the manuscript.

Funds: This work was supported by the Guangdong Provincial Key R&D Program (2022B1111040001), the Second Tibetan Plateau Scientific Expedition and Research Program (2019QZKK0402/2019QZKK0501), and National Natural Science Foundation of China (32170426)

More Information

Corresponding author: E-mail: zhijunzhou@hbu.edu.cn; quyh@ioz.ac.cn; gedy@ioz.ac.cn
Received Date: 2023-03-24
Accepted Date: 2023-03-27

Published Online: 2023-09-13

Publish Date: 2023-11-18

Abstract

Abstract

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima’s D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the “genomic islands of speciation”, we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.
- Niviventer niviventer species complex,
- Widespread species,
- Narrow-range species,
- Speciation,
- Genomic islands of differentiation,
- Phylogenomics

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References(79)

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