Transition Bias and Its Compensation in the Evolutionary Lineage of the Subfamily Murinae (Rodentia): Analysis of Nuclear and Mitochondrial DNA Markers

Abstract

A comparative analysis of the rates of molecular evolution, transition bias, and its evolutionary compensation was carried out on mitochondrial (D-loop, Cytb, COI, 12S RNA) and nuclear (IRBP, Fv) DNA markers in the Murinae subfamily. According to the levels of variability, the markers can be divided into three classes: (1) hypervariable (D-loop), (2) rapidly evolving (Cytb, COI), and (3) conservative (12S RNA, IRBP, Fv). The nature of nucleotide substitutions appears by the levels of variability. With the D-loop, there is a maximum initial bias, which is already partially compensated for during the early stages of speciation, and completely compensated at the stages of species divergence. The pronounced bias within the Cytb and COI genes is only partially compensated, moreover at the genus levels. The 12S RNA, IRBP, and Fv genes with a low level of transition bias do not show evolutionary compensation as such, and the decrease of the ts/tv index in the evolutionary lineage has a technical character and is a consequence of a relative decrease of the difference in the frequencies of transitions and transversions against the background of an absolute increase in the frequencies of substitutions. The positive relationship between the intensity of nucleotide substitutions, the level of transition bias, and the rates of its evolutionary compensation proves that these phenomena have the same primary basis.