Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

Kexin Li, Liuyang Wang, Binyamin A. Knisbacher, Qinqin Xu, Erez Y. Levanon, Huihua Wang, Milana Frenkel-Morgenstern, Satabdi Tagore, Xiaodong Fang, Lily Bazak, Ilana Buchumenski, Yang Zhao, Matěj Lövy, Xiangfeng Li, Lijuan Han, Zeev Frenkel, Avigdor Beiles, Yi Bin Cao, Zhen Long Wang, Eviatar Nevo

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk-basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological-genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk-basalt divergence driving sympatric speciation.

Original languageEnglish
Pages (from-to)7584-7589
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number27
StatePublished - 5 Jul 2016

Bibliographical note

Funding Information:
We thank Huabin Zhao and Wei Hong for their contribution of genome sequence; and Shay Zur for his photo of the sampling site. The following foundations supported this work: the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2016-IAR), the Ancell-Teicher Research Foundation for Genetics and Molecular Evolution, the National Natural Science Foundation of China (Grants 31371209 and 31372193), the foundation of Henan Educational Committee (Grant 13A180717), and the Czech Science Foundation (Project 14-31670P).


  • DNA editing
  • Ecological adaptive speciation
  • MicroRNA regulation
  • Natural selection
  • Nonoptimal codon usage


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