Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

Abstract

Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

“…; Petrou et al . ). Only embryos expressing no paternal (coho salmon) alleles were retained for RAD sequencing; the family with the largest number of haploid offspring was selected for use in this study.…”

Is isolation by adaptation driving genetic divergence among proximate Dolly Varden char populations?

“…Here, we argue that selection for alternative life histories is the most plausible explanation for the observed differences. The Alaska Peninsula is a zone of secondary contact for other species isolated to the north and south during the last glacial maximum (e.g., chum salmon, Petrou et al 2013). Dolly Varden occur as two subspecies in Alaska, northern form S. m. malma, and southern form S. m. lordi (Mecklenburg et al 2002).…”

“…The origins of populations in different glacial refuges blend with ecological processes over a range of broad and local scales to create the observed contemporary population structure (Churikov and Gharrett ; Castric and Bernatchez ; Petrou et al. ). Adaptation occurs through selection of successful traits within a locally reproducing population, isolated from other populations by geography or homing behavior (Ricker ; Taylor ; Quinn ; Fraser et al.…”

“…An ongoing balance between reproductive isolation resulting from homing to natal breeding areas and gene flow among populations caused by successful reproduction of individuals that stray (reproduce in a nonnatal site) maintains varying levels of structuring broadly observed as isolation by distance (Olsen et al 2011;Templin et al 2011;Moran et al 2012) . The origins of populations in different glacial refuges blend with ecological processes over a range of broad and local scales to create the observed contemporary population structure (Churikov and Gharrett 2002;Castric and Bernatchez 2003;Petrou et al 2013). Adaptation occurs through selection of successful traits within a locally reproducing population, isolated from other populations by geography or homing behavior (Ricker 1972;Taylor 1991;Quinn 2005;Fraser et al 2011).…”

Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams

“…: +1 517 353 3288; email: scribne3@msu.edu ecological diversity across populations of many species throughout North America and Europe (Roman & Darling, 2007;Dlugosch & Parker, 2008;Keller & Taylor, 2008), including anadromous Salmonidae (Thomas et al, 1986;Labelle, 1992;Nielsen, 1999). Analyses of recently deglaciated habitats and of species and populations that have colonized them have led to important findings regarding the relative importance of extinction, recolonization and secondary contact (Bernatchez & Wilson, 1998;Rowe et al, 2004;Crispo & Hendry, 2005), that contrast classical population genetic predictions for equilibrium populations (Comps et al, 2001;Petrou et al, 2013). Findings from studies of natural colonization events and of time-dependent ecological and successional changes in habitat (Milner & York, 2001) that affect population demography and concomitantly population levels of genetic variability (Crawford & Whitney, 2010) have important implications for conservation and restoration strategies for threatened or declining populations, including Pacific salmon (genus Oncorhynchus Suckley 1861).…”