Estimates of Genetic Introgression, Gene Tree Reticulation, Taxon Divergence, and Sustainability of DNA Barcoding Based on Genetic Molecular Markers

Abstract—The evidence for the possible impact of gene introgression on species evolution, the evolutionary fate of taxa, including reticulations in phylogenetic trees, and the consistency of the latest molecular genetic data with the main modern paradigm, Neo-Darwinism, have been considered in many studies. This study includes a comparative analysis and assessments of validity of the use of molecular markers for species identification, including an approach proposed by one of the authors for the description of biological diversity in the framework of the global DNA barcoding program. The identification of hybrids and the prevalence of genetic introgression are discussed. There are four main issues in the overview presented. (1) A combination of nDNA and mtDNA markers best suits for the hybrid identification and estimates of genetic introgression or gene flow. (2) The available facts for both nDNA and mtDNA diversity make introgression among many animal and plant taxa obvious, although, even for the wide hybrid zones of Mytilus ex. group edulis, for example, introgression may be quite restricted or asymmetric for a significant part of the area, thus holding at least the “source” taxon (taxa) intact. (3) If we accept that sexually reproducing species in marine and terrestrial areas are introgressed, as is evident for many cases, then we should recognize that the orthodox BSC, which postulates a complete lack of gene flow among species, is inadequate due to the fact that many zoological or taxonomic species have currently not yet reached the stage of biological species. However, they will eventually become definitive biological species in future. This conclusion is supported by the genetic distance, which increases with taxa rank, and by the lowest diversity at the intraspecies level as for single mtDNA genes, for complete mitogenomes, and for nDNA genes. (4) A recent study of fish-taxon divergence by means of the vast BOLD (www.boldsystem.org) database showed that the gene trees for taxa up to the family level are basically monophyletic, and interspecies reticulations are rare for most gene trees. The available data allow us to conclude that molecular evolution and, in particular, genetic divergence in the taxon hierarchy are generally in good agreement with BSC and Neo-Darwinism, forming the theoretical basis for the success of DNA barcoding in the animal world, as well as its applicability for other organisms.