Abstract
The review is devoted to the recent problems of molecular phylogenetics based on the mitochondrial and chromosomal DNA sequences. The main subjects of the paper are the most widely used mtDNA markers though their application is not well enough (of critically considered) supported from the point of physiology and biochemistry of these organelles. Besides some well known aspects embarrassing the mt-markers phylogeny interpretations (hybridization and introgression events, ancestral polymorphism and nuclear paralogs of mtDNA) the attention is concentrated on non-neutrality and disproportional mutability of mt-genes and their fragments, on uniparental inheritance violations, recombinational events and heteroplasmy. These factors may influence the congruence of phylogenetic inferences and trees based on different mt-markers and when they compared with nuclear markers. Many authors suppose that the sequence comparisons of mt-genes and their fragments alone are not adequate to the studies of evolution. The notion is put forward that the influence of external conditions on metabolism and physiology of mitochondria could not be fully taken into account and modelled to be applied for phylogenetic tasks. The values of mt-markers could be revealed by the comparison of the whole mtDNA sequences of different taxa and searching the informative syn- and apomorphic properties and nuclear paralogs.
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