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

Abstract

The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of life-history segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved — essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.

Identification of multiple genetically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) in a small coastal watershed

“…Polymerase chain reaction (PCR) was used to amplify 21 neutral microsatellites following published thermocycling protocols. These included 10 microsatellites that are standardized range-wide (Moran et al 2013) and an additional 11 microsatellites (Nelson and Beacham 1998;Naish and Park 2002;Williamson et al 2002). The standardized microsatellite panel was developed for rangewide genetic stock identification (GSI) of Chinook salmon and included genotypes from populations throughout North America (Seeb et al 2007;Moran et al 2013).…”

“…Siletz River fall-run Chinook salmon were grouped with the North Oregon Coast reporting unit in that study, as they were in several other genetic studies (Narum et al 2008;Moran et al 2013). Our analysis also placed SIFA in the North Oregon Coast reporting unit (bootstrap 83%; Fig.…”

“…The extent and scale of intraspecific genetic diversity is therefore a crucial consideration from both conservation and management perspectives (Manel et al 2010;Funk et al 2012). Chinook salmon populations are characterized by hierarchical genetic structure (Seeb et al 2007;Moran et al 2013) with evidence of isolation across their range in the north Pacific (> 10,000 km), within larger river systems (> 1000 km), and regionally among watersheds (< 1000 km). Finer-scale structure in Chinook salmon within smaller coastal watersheds (e.g., the Siletz River <120 km) has been relatively unstudied.…”

“…In Chinook salmon, much of this variation manifests as run-timing Becotypes^which are characterized by mean date of freshwater entry and reproductive status (Waples et al 2004;Moran et al 2013). The 'fall-run', which enter freshwater as reproductively mature adults in late summer and fall, is regionally dominant in the southern extreme of the species range in North America.…”

“…Previous studies that examined salmon populations from the Siletz River using data from neutral genetic variation included only samples from the fall-run, and were part of large-scale efforts to characterize genetic structure in the species and provide methods for identification of fish of unknown origin (Seeb et al 2007;Moran et al 2013;Clemento et al 2014). We studied salmon of different life-history types and used data from three types of molecular marker to: i) identify patterns of neutral genetic variation within the watershed, ii) evaluate whether temporal patterns of life-history variation are correlated with variation at genetic markers known to be associated with run-timing, and iii) determine phylogeographic patterns within the river and compare them to other coastal basins in the North Oregon Coast region.…”