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Some limitations in the use of the mitochondrial DNA cytb gene as a molecular marker for phylogenetic and population-genetic studies by the example of the Apodemus genus

A. Lapinski,M. Pavlenko,L. Solovenchuk,V. Gorbachev

Published 2016 in Russian Journal of Genetics: Applied Research

ABSTRACT

The interpretation of a signal produced by the mtDNA cytb gene as a molecular marker in phylogenetic and population-genetic research can be complicated by the cumulative influence of parallel mutations, i.e., by the entropy of nucleotide sequences that impede differentiation among the effects of the hybridization, natural polymorphisms, and artifacts imposed by pseudo-genes. We analyzed possible limitations in the use of the mtDNA cytb gene as a molecular marker by the example of the Apodemus genus. For this purpose, the entropy of nucleotide sequences was calculated and the probable tracts of gene conversion were sought in samples of various Apodemus species from Tibet, Korea, the southern part of the Russian Primorye, and Western Europe. Many haplotypes were identified as containing tracts of gene conversion. A high level of nucleotide sequence variability was found in species from the Tibetian Plateau, particularly, in A. draco, presumably due to the influence exercised by the low-effective size of populations on the rate of point mutation accumulation and also the role of cytochrome b in the adaptation to unfavorable environment. The effects of hypervariability in the cytb nucleotide sequences of some samplings resulting in the entropy growth, imitating gene conversion when compared to other species of the genus were analyzed. Furthermore, the examples of possible pseudo-gene interference among the published cytb sequences are provided. It is suggested that the strategy in the use of the mtDNA cytb gene in population genetics and phylogenetics should be adapted to the degree of gene variability. The emphasis is placed on the necessity of close control over sequencing data at all stages of their analysis.

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