Mitochondrial Variation and Biogeographic History of Chinook Salmon

Abstract

The genetic variation of many species in the Northern Hemisphere has been influenced by climatic changes during the Pleistocene Epoch. Phylogeographic studies can help determine intraspecific relationships and postglacial recolonization routes for many of these species, potentially leading to a more complete understanding of how flora and fauna respond to dramatic climate change. We analyzed the variation in the mitochondrial DNA sequences of Chinook salmon Oncorhynchus tshawytscha from California to the Kamchatka Peninsula, Russia, to gain insight into the role of Pleistocene glaciation in the genetic structuring of this species. The geographic distribution of haplotypes revealed high levels of genetic diversity in the Columbia River drainage. Nested clade analysis suggests northward expansion from this area during the late Pleistocene, a hypothesis that is further supported by evidence of demographic growth and population expansion in the northern portion of the species' range. Estimates of the divergence time between two phylogenetic clades are correlated with interglacial periods of the Pleistocene. The data suggest the absence of Chinook salmon from the current northern part of its distribution until the late Pleistocene, when northward expansion from a southern refugium occurred (during an interglacial period), followed by the recent genetic divergence of these northern populations.

Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography

“…This northern peak in diversity is not consistent with widespread recolonization from the interior Columbia River spring-early-summer-run populations, none of which were particularly diverse themselves (Winans 1989;Narum et al 2010; the current study, but see Beacham et al 2006). The interior basins of the Fraser and Columbia rivers must have shared Chinook salmon migrants at some low level, either through former, perhaps early Pleistocene connections (Martin et al 2010) or via long-distance strays (Ford 1998); however, it is almost certainly not the case that the Fraser Basin and the rest of Cascadia (north to the Stikine River) were extensively recolonized by fish from the upper Columbia, as suggested for most fish species by McPhail and Lindsey (1986). If so, one would expect populations in the Fraser and Thompson rivers (Groups 11 and 12), and in regions further north, to nest within Columbia River populations.…”

Low Variation in a Y‐Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

“…Linked traits could also influence the physiological pathways affecting survival (e.g., growth rate and immune function). High divergence between haplotypes of Y-linked markers and mitochondrial markers was also seen in Rainbow Trout (Brunelli et al 2008, and Chinook Salmon (Martin et al 2010), suggesting fundamentally different evolutionary mechanisms between Y chromosome and autosomal-mitochondrial variations.…”

Salmon Genetics and Management in the Columbia River Basin

“…Mitochondrial DNA is typically inherited from the mother only. This simple inheritance and fast rate of evolution (as much as ten times faster that of nuclear DNA (Castro et al 2010) make it a useful marker for phylogenetic studies (e.g., McVeigh and Davidson 1991, Domanico and Phillips 1995, Martin et al 2010. While mtDNA has been used to examine population-level questions; the maternal inheritance limits the genetic information available from this marker.…”