Genome evolution of blind subterranean mole rats: Adaptive peripatric versus sympatric speciation

Kexin Li, Shangzhe Zhang, Xiaoying Song, Alexandra Weyrich, Yinjia Wang, Xi Liu, Na Wan, Jianquan Liu, Matěj Lovy, Haihong Cui, Vladimir Frenkel, Avi Titievsky, Julia Panov, Leonid Brodsky, Eviatar Nevo

Research output: Contribution to journalArticlepeer-review

Abstract

Speciation mechanisms remain controversial. Two speciation models occur in Israeli subterranean mole rats, genus Spalax: a regional speciation cline southward of four peripatric climatic chromosomal species and a local, geologic-edaphic, genic, and sympatric speciation. Here we highlight their genome evolution. The five species were separated into five genetic clusters by single nucleotide polymorphisms, copy number variations (CNVs), repeatome, and methylome in sympatry. The regional interspecific divergence correspond to Pleistocene climatic cycles. Climate warmings caused chromosomal speciation. Triple effective population size, Ne, declines match glacial cold cycles. Adaptive genes evolved under positive selection to underground stresses and to divergent climates, involving interspecies reproductive isolation. Genomic islands evolved mainly due to adaptive evolution involving ancient polymorphisms. Repeatome, including both CNV and LINE1 repetitive elements, separated the five species. Methylation in sympatry identified geologically chalk-basalt species that differentially affect thermoregulation, hypoxia, DNA repair, P53, and other pathways. Genome adaptive evolution highlights climatic and geologic-edaphic stress evolution and the two speciation models, peripatric and sympatric.

Original languageEnglish
Pages (from-to)32499-32508
Number of pages10
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number51
DOIs
StatePublished - 22 Dec 2020
Externally publishedYes

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS. We thank Xu Zhang for the Perl scripts, Dorina Meneghini for bioinformatics support, and Jörns Fickel for scientific discussions. This project was supported by the National Natural Science Foundation of China (32071487), Lanzhou University’s “Double First-Class” Guided Project Team Building-Funding-Research Startup Fee (K.L.), the Chang Jiang Scholars Program, the International Collaboration 111 Programme (BP0719040), and the Ancell–Teicher Research Foundation for Genetic and Molecular Evolution.

Funding Information:
We thank Xu Zhang for the Perl scripts, Dorina Meneghini for bioinformatics support, and J?rns Fickel for scientific discussions. This project was supported by the National Natural Science Foundation of China (32071487), Lanzhou University's "Double First-Class" Guided Project Team Building-Funding-Research Startup Fee (K.L.), the Chang Jiang Scholars Program, the International Collaboration 111 Programme (BP0719040), and the Ancell-Teicher Research Foundation for Genetic and Molecular Evolution.

Publisher Copyright:
© 2020 National Academy of Sciences. All rights reserved.

Keywords

  • Genomic sequencing
  • Methylation
  • Repeatome
  • Speciation models
  • Subterranean rodents

ASJC Scopus subject areas

  • General

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