Oncorhynchus at the southern extent of their range: a study of mtDNA control–region sequence with special reference to an undescribed subspecies of O. mykiss from Mexico

Abstract

Nucleotide sequences from the right-domain of salmonid mitochondrial DNA (mtDNA) control region flanking the phenylalanine tRNA gene (tRNAPhe) were determined for 5 species and 14 subspecies of Oncorhynchus at the southern extent of their range. In all but one population, the right domain contained two 72 bp tandem repeats located between the tRNAPhe gene and the conserved sequence block CSB-3. At the species level we found 46–83% homology between these two repeats. The repeat closest to tRNAPhe contained 43% of the phylogenetically informative sites. The largest number of transversions (N=6) were found outside of both repeat sequences. Phylogenetic inference based on mtDNA right-domain sequence was congruent with other analyses at the species level, but gave variable results in association drawn at the subspecific level. The right-domain contained three highly conserved sequences corresponding to the mtDNA transcription factor, and the heavy- and light-strand promoters. In four O. mykiss from Rio Yaqui, Mexico, the repeat containing the heavy-strand promoter (HSP) was deleted. The mtDNA HSP is responsible for transcription of the 16S and 12S rRNAs, 12 of the 13 protein-coding genes, and most of the tRNA genes. Rio Yagui trout showed no heteroplasmy or tissue specificity for this deletion. This HSP deletion suggests the possibility of a primitive transcriptional promoter with bidirectional capacity in this species, similar to that reported in avian and amphibian mtDNA. These data expand our understanding of genetic diversity in Oncorhynchus at the southern extent of their range with a knowledge of the evolutionary mechanisms that may have led to that diversity.