Nomenclature of Mitochondrial DNA Haplotypes for Oncorhynchus mykiss

Abstract

Congruence of genetic data is critical for comparative and collaborative studies on natural fish populations. A comprehensive list of reported mitochrondrial DNA haplotypes for Oncorhynchus mykiss generated using the S-Phe/P2 primer set is presented as a resource for future investigations of this species.

Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

“…The most common haplotype, 1K, accounted for approximately 45% of recovered sequences and was found roughly equally in inland and coastal localities. Mitochondrial haplotypes described in this study were designated according to previously established nomenclature developed to identify control region haplotypes (Nielsen et al 1994, Graziano et al 2005). Our sequence evaluation extended beyond the region used in the original nomenclature assignment and identified additional genetic variation which subdivided previously designated mtDNA haplotypes into haplotype subtypes.…”

“…Haplotype labels correspond to those in Table 1. Haplotype names are based on the existing nomenclature (Graziano et al 2005). Distinct haplotypes defined by variation outside the named sequences are denoted by a letter following the haplotype.…”

Disruption of historical patterns of isolation by distance in coastal steelhead

“…However, the Frag1 ? Frag2 alignment, which covered nucleotide sites 1021-1109 (Graziano et al 2005), cannot distinguish several known haplotypes described by Graziano et al (2005), which are defined by these and nine additional variable nucleotide sites in the full P2/S-Phe region. In addition, we observed four new haplotypes, two in historical specimens and two in modern individuals (Pearse and Garza 2008).…”

“…However, due to degradation of DNA in the historical samples, amplification of the full P2/S-Phe region target was unsuccessful. We therefore designed primers (Table 2) to amplify two smaller, overlapping fragments that together cover 139 bp of the P2/S-Phe region, and include all but two of the sites known to be variable in O. mykiss (Graziano et al 2005). We verified that all primer combinations amplify the same gene region by sequencing products from a single modern individual with all possible forward and reverse primer combinations and compiling the resulting sequences with complete P2/S-Phe sequences from other modern individuals to ensure correct alignment.…”

“…Thus, these sequences were excluded from further consideration in the present analysis. Graziano et al (2005) standardized the nomenclature for 29 mtDNA control region haplotypes previously observed in O. mykiss based on the P2/S-Phe region. However, the Frag1 ?…”