The genus Oncorhynchus encompasses ten species (and 28 subspecies) of Pacific salmon and Pacific trout (anadromous and freshwater resident) species of the Pacific north Pacific basin, western United States, Canada and Mexico. All ten species (and 28 subspecies) in this group include representatives that are threatened, endangered, sensitive, or species of special concern in portions of their native ranges. To examine the relationships of species and subspecies within Oncorhynchus I sequenced a 1317 bp section of the ND4 mtDNA region. I included six sub-species of O. clarki (cutthroat trout) as well as O. gilae gilae (Gila trout) and O. g. apache (Apache trout). Our results indicated that Salvelinus was the sister group to Oncorhynchus and as expected O. clarki was the sister clade to the O. mykiss clade (including O. g. gilae and O. g. apache). Within the cutthroat clade ( O. clarki), the coastal form O. c. clarki was basal, and the Rio Grande cutthroat (O. c. virginalis) most derived. Divergence dating based on a fossil calibration molecular dock showed the oldest clade (mean node age) was O. masu ssp., which diverged sometime around 7.6 MYA, this overlapped with the divergence (6.3 MYA) of the Pacific salmon clades ((O. gorbuscha + O. nerka ) and (O. tshawytscha + O. kisutch)). The Pacific trout clade ((O. mykiss + O. gilae ssp.) + (O. clarki ssp.) diverged from the Pacific salmon around 6.3 MYA, with most of the diversification within the O. clarki clade occurring in the last 1 MY.

The DAβ region of the Major Histocompatibility Complex (MHC) including exon 1, intron 1 and exon 2 β1 domain) was sequenced in 10 species/subspecies of inland trout, including O. clarki ssp., O. gilae ssp., and O. chrysogaster with a total of 54 new DAβ1 alleles described. The β1 domain was highly polymorphic and was rich in recombination events, which produced trans-specific evolution patterns using the β1 domain. Recombination also occurred in the 3' end of intron 1 which may be responsible for generating new allelic diversity. The length of intron 1 can varied in length between species ranging from 450 bp (Onclcl-DAB1*0301 and Onclle-DAB1*0401) to 626 bp (Onclle-DAB1*0201). Phylogenetic analysis of the inland trout using intron 1 (O. clarki ssp., and O. gilae ssp.) showed that there are two different lineages including a lineage containing alleles from older O. clarki ssp. ( O. c. clarki, O. c. lewisi, O. c. henshawi) as well as alleles from O. gilae ssp., however alleles from more derived species ( O. c. pleuriticus, O. c. utah, O. c. stomias, O. c. virginalis) were absent but occurred in a second lineage. Although reticulate evolution was common, some physiochemical properties of sites within the β1 domain were conserved, especially hydrophobic sites. Amino acid sites that were highly polymorphic (ω > 1) and predicted to be under selection using codeml, were located within 3 sites of these hydrophobic sites.

Analysis of the six Crepidostomum farionis microsatellite loci revealed that the number of alleles and allelic richness per population varied from 2 to 6. A comparison of each locus among populations showed that Rito de las Vacas (VAC) and Doctor creek (DOC) had the fewest number of alleles (2 or 3), and Santa Barbara river (SBM) and Alamitos Creek (ALA) had the greatest. When averaged across loci these trends held, with VAC having the fewest number of alleles and SBM having the greatest. The 12 O. c. virginalis microsatellite loci were higher, overall, in number of alleles and allelic richness. The AMOVA results indicated that most (90%) of the variation in C. farionis was within populations, with an overall multilocus microsatellite F_ST of 0.095. Very little of the variation was among drainages or populations. The AMOVA results for the DAβ1 locus again showed that the highest percent of variation (62%) was within populations with a higher proportion of variation among populations (29%) than among drainages (9%). Pairwise population F_ST values for C. farionis were low and varied from 0.016 (VAC-Rito de la Perchas [PER]) to 0.212 (PER-Rito del La Casa [CAS]) with most pairwise comparisons significant after Bonferroni adjustment. Oncorhynchus c. virginalis pairwise population F_ST values were higher ranging from 0.049 (ALA-SBM) to 0.482 (DOC-ALA). The relationship between F_ST/(1-FST) and geographic distance was significant (R² = 0.305, P = 0.022) for C. farionis but not O. c. virginalis (R² = 0.163, P = 0.146). These results indicate that gene flow of C. farionis is not limited by the movement of O. c. virginalis alone, but has other opportunities including movement through the often sympatric and widely distributed S. trutta (brown trout) which outcompetes O. c. virginalis and keeps the distribution O. c. virginalis limited to isolated headwaters.