Genomic Differentiation During Speciation In The Blind Mole Rat(Spalax)

Speciation is the basis of biodiversity.Ecological speciation refers to the process of speciation in which different groups of ancestral species diverged from each other due to ecological diversity.There are two speciation patterns including radiative speciation and bifurcating divergence.How the blind mole rat Spalax in Israel evolved to different species due to climatic and edaphic selection is not clear till now.Here we compared and contrasted the population genomes of the five species,and showed the genome architechture during speciation,population demography,split pattern,and genes helping the population adaptate to local environment.And the main results are listed below:1.Whole-genome resequencing was performed on 52 individuals distributed in 5 different regions in Israel,mapping to reference genome,and whole-genome data of 41 individuals were obtained after filtering of closely related individials.All the neighbor joining trees,principal component analysis and structure analysis showed the individuals from the same species clustered together but separated from other species;Trees reconstructed based on SNPs from coding and non-coding regions were the same.2.All five species of Spalax were evolved in bifurcating divergence.S.carmeli split from S.golani through bifurcating divergence about 1.3Mya,and followed by another bifurcating speciation of S.galili from S.golani 0.48 Mya.In 180 kya,S.judaei split from S.carmeli by bifurcation.3.S.golani showed the highest genetic diversity,followed by S.carmeli and S.galili,S.judaei showed the lowest genetic diversity,which was consistent with the generation time of these species.S.galili and S.judaei showed the largest genetic divergence and the parapatric species,S.galili?chalk and S.galili?basalt showed the lowest differentiation.4.D-statistics and Treemix analysis showed S.galili?chalk and S.galili?basalt had limited gene flow;however,the gene flow among other populations was restricted.IBD analysis showed S.golani and S.galili were genetically closer while S.judaei and S.carmeli were close to each other.F3-test showed us none of the species were hybridized from other two species.5.Spalax speciation was related to climate oscillation during Pleistocene.Triple population declines were consistent with three glacial periods like LGM?Saalian and Eburonian.Two population expansions were detected: one was between 0.3-1.3 Mya,during which S.galili speciated from S.golani;the other was between 0.1-0.2 Mya,during which S.judaei split from S.carmeli.6.Each species used the same putatively selected genes(PSGs)to adapt to the same stresses suggesting that they reflected adaptations to burrow life underground like hypoxia and hypercapnia.BCL7 B and Tusc2 were found to be selected possibly because of cancer resistance.F8 was selected in S.galili and S.golani,probably because the aggression between individuals were stronger than that in the other two populations of S.carmeli and S.judaei.Hspa14 was also selected in S.judaei species,which distributed in the hot,dry southern Negev desert.Several reproductive isolation genes were found in each species.