The adaptation of organisms to the environment is a fundamental issue in the study of evolutionary biology. However, there is a controversial scientific question that can species living in the same area differentiate into new species during evolution (sympatric speciation). Although some evidence shows speciation occurring in this way, little is known about the gene expression evolution and the characteristics of population genetics as species diverge.  

In order to explore the above mentioned issues, a research team led by Prof. HE Shunping from Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences (CAS), cooperating with Prof. ZHAO Kai from Northwest Institute of Plateau Biology of CAS, studied the genetic and expression variations in two sympatric schizothoracine fishes in a Tibetan Plateau glacier lake. The finding was published in Geneome Biology and Evolution.

Glacier Lake Langcuo, located on the northern of the Yarlung Zangbo River, is at an altitude about 4,300 m. Two sister species of naked carp, Gymnocypris chui and Gymnocypris scleracanthus, are endemic fish that are sympatrically distributed in Lake Langcuo in Tibet.  

In this study, the researchers compared the transcriptomes of different tissues and found that the expression patterns of intraspecific and interspecific organs are different. Through phylogenetic analyses, they found that the two closely related taxa formed a monophyletic complex. Ordination analysis separated samples by organ rather than by species.

Population structure analysis displayed two distinctly divergent clusters of G. chui and G. scleracanthus populations. By contrast, G. scleracanthus population genetic diversity is higher than that of G. chui. Considerable sites of the two populations were differentiated with a coefficient of F_ST = 0.25-0.50, implying that a small proportion of loci nevertheless exhibited deep divergence in two comparisons.  

Further evolutionary selection pressure and functional enrichment analysis revealed biological differences between the two populations. Differentially expressed genes and positive selection genes were mainly concentrated in pathways related to metabolism, nutrition, and morphological development.

Researchers speculated that there was food competition between G. chui and G. scleracanthus in a small plateau glacial lake, and finally they occupied different ecological niches (feeding differences).