The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers

The review considers the current problems of molecular phylogenetics based on mitochondrial and chromosomal DNA sequences. The emphasis is placed on mtDNA markers, which are widely employed in reconstructing molecular evolution, but often without a critical analysis of the physiological and biochemical features of mitochondria that affect the adequacy and reliability of the results. In addition to the factors that make mtDNA-based phylogenies difficult to interpret (unrecognized hybridization and introgression events, ancestral polymorphism, and nuclear paralogs of mtDNA sequences), attention is paid to the nonneutrality and unequal mutation rates of mtDNA genes and their fragments, violations of uniparental inheritance of mitochondria, recombination events, natural heteroplasmy, and mtDNA haplotypic diversity. These factors may influence the congruence of phylogenetic inferences and trees constructed for the same organisms with different mtDNA markers or with mitochondrial and nuclear markers. The review supports the viewpoint that mitochondrial genes and their fragments fail to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa. The influence of external conditions on the metabolism and physiology of mitochondria cannot be taken into account in full nor modeled well enough for phylogenetic applications. It is assumed that mtDNA is valuable as a phylogenetic marker primarily because its complete sequence may be analyzed to identify the apomorphic and synmorphic properties of a taxon and to search for informative nuclear paralogs of mtDNA for phylogeographical studies and estimations of relative evolution times.