title: Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax.
abstract: 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.
authors.affiliation: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; Institute of Evolution, University of Haifa, Haifa 3498838, Israel; nevo@research.haifa.ac.il likexin323@gmail.com sky109@zjnu.edu.cn wzl@zzu.edu.cn.
authors.forename: Kexin
authors.initials: K
authors.lastname: Li
authors.affiliation: Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27708;
authors.forename: Liuyang
authors.initials: L
authors.lastname: Wang
authors.forename: Binyamin A
authors.initials: BA
authors.lastname: Knisbacher
authors.affiliation: The People's Hospital of Qinghai Province, Xining 810007, China;
authors.forename: Qinqin
authors.initials: Q
authors.lastname: Xu
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel;
authors.forename: Erez Y
authors.initials: EY
authors.lastname: Levanon
authors.affiliation: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
authors.forename: Huihua
authors.initials: H
authors.lastname: Wang
authors.affiliation: Faculty of Medicine, Bar-Ilan University, Safed 13195, Israel;
authors.forename: Milana
authors.initials: M
authors.lastname: Frenkel-Morgenstern
authors.affiliation: Faculty of Medicine, Bar-Ilan University, Safed 13195, Israel;
authors.forename: Satabdi
authors.initials: S
authors.lastname: Tagore
authors.affiliation: Beijing Genomics Institute, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel;
authors.forename: Lily
authors.initials: L
authors.lastname: Bazak
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel;
authors.forename: Ilana
authors.initials: I
authors.lastname: Buchumenski
authors.affiliation: Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Zoology, Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic;
authors.forename: Matěj
authors.initials: M
authors.lastname: Lövy
authors.affiliation: University of Chinese Academy of Sciences, Beijing 100049, China;
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Li
authors.affiliation: Beijing Genomics Institute, BGI-Shenzhen, Shenzhen 518083, China;
authors.forename: Lijuan
authors.initials: L
authors.lastname: Han
authors.affiliation: Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
authors.forename: Zeev
authors.initials: Z
authors.lastname: Frenkel
authors.affiliation: Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
authors.forename: Avigdor
authors.initials: A
authors.lastname: Beiles
authors.affiliation: College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang 321004, China; nevo@research.haifa.ac.il likexin323@gmail.com sky109@zjnu.edu.cn wzl@zzu.edu.cn.
authors.forename: Yi Bin
authors.initials: YB
authors.lastname: Cao
authors.affiliation: School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China nevo@research.haifa.ac.il likexin323@gmail.com sky109@zjnu.edu.cn wzl@zzu.edu.cn.
authors.forename: Zhen Long
authors.initials: ZL
authors.lastname: Wang
authors.affiliation: Institute of Evolution, University of Haifa, Haifa 3498838, Israel; nevo@research.haifa.ac.il likexin323@gmail.com sky109@zjnu.edu.cn wzl@zzu.edu.cn.
authors.forename: Eviatar
authors.initials: E
authors.lastname: Nevo
mesh_terms: D000818:Animals; D002119:Calcium Carbonate; D017753:Ecosystem; D005260:Female; D051456:Gene Flow; D049810:Genetic Speciation; D008297:Male; D035683:MicroRNAs / Q000378:metabolism*; D017640:Silicates; D012987:Soil; D046308:Spalax / Q000235:genetics* / Q000378:metabolism; D061350:Sympatry; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D017640:Silicates; D012987:Soil; C060346:basalt; D002119:Calcium Carbonate
keywords: DNA editing; ecological adaptive speciation; microRNA regulation; natural selection; nonoptimal codon usage