Mitochondrial Genome “Evolution” of Arctic Warbler (Phylloscopus borealis sensu lato) Occurs in Its Nuclear Genome

Abstract—

Sequencing of a partial fragment of the mitochondrial ND5–cytb genes (1553 bp) and its nuclear copies in Phylloscopus borealis sensu lato (s.l.) individuals, belonging to different taxonomic groups from different parts of the range was carried out. The identity of the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms to those in nuclear copies of borealis mtDNA was demonstrated. Differences between the examinandus mitochondrial haplotypes and nuclear copies of borealis mtDNA were low (P = 0.02), and the genetic divergence in borealis–examinandus, borealis–xanthodryas, and examinandus–xanthodryas mtDNA itself considerably exceeded these values (P = 0.035, 0.044, and 0.046, respectively). For the first time, nuclear copy of the mitochondrial haplotype of the easternmost xanthodryas form was found in nuclear genome of one borealis individual from the western part of the breeding range (Komi Republic), and nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were found to be close to the borealis mitochondrial haplotypes from Kytlym (Sverdlovsk oblast) (P = 0.018). Thus, the source of most substitutions in the mitochondrial DNA of the studied forms are mutations that arose in nuclear copies of mitochondrial genes. The origin of examinandus and xanthodryas mitochondrial haplotypes from nuclear copies of borealis mtDNA and close similarity of their nuclear genomes give reason to consider mitogenomes of these forms as haplotype variants of a single species, Ph. borealis s. l. With high degree of probability, it can be argued that the haplotype divergence time of the analyzed forms is considerably lower than 2.5–3 million years, as previously hypothesized by a number of authors, and the “molecular clock,” which does not take into account recombination events between nuclear and mitochondrial genomes, cannot be used in this case.