Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: a closer look at the highly fragmented inland species.

Abstract The genus Oncorhynchus includes Pacific salmon and trout (anadromous and land-locked) species of the western United States and Mexico. All species and subspecies in this group are threatened, endangered, sensitive, or species of conservation concern in portions of their native ranges. To examine the relationships of the species within Oncorhynchus we sequenced a 768 bp fragment of the protein-encoding ND4 mtDNA region. We included all six recognized subspecies of O . clarki (cutthroat trout), O . gilae gilae (Gila trout) and O . g . apache (Apache trout). Gene trees from likelihood and Bayesian phylogenetic analyses revealed that Salvelinus was the sister group to Oncorhynchus , and as expected based on previous studies, O . clarki was sister to a clade that consisted of O . mykiss plus O . g . gilae and O . g . apache . Within the cutthroat clade ( O . clarki ), the coastal form O . c . clarki was basal with the Rio Grande cutthroat ( O . c . virginalis ) most derived. Divergence dating based on a fossil calibration molecular clock showed the oldest clade (mean node age) was O . masou ssp., which diverged roughly 7.6 MYA. Highest probability density intervals for divergence of O. masou overlapped with divergence (6.3 MYA) of 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.