Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

Kathleen G. O'Malley,Allen J. Dill,Ryon Kurth,Michael A. Banks,Dave P. Jacobson

doi:10.1111/eva.12095

Kathleen G. O'Malley, Allen J. Dill + Show 3 more

Open Access

https://doi.org/10.1111/eva.12095

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Abstract

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.

Highlights

A major effort in conservation biology is directed toward defining units within species that are sufficiently differentiated to require discrete management (Frankham 2010)
We found evidence for two genetically distinct migratory runs of Chinook salmon in the Feather River based on variation at two candidate markers for run timing; the circadian clock gene OtsClock1b and Ots515NWFSC, a microsatellite marker linked to a quantitative trait loci for spawning time and body weight in rainbow trout (O. mykiss) (O’Malley et al 2007)
We found no evidence for significant differentiation between the fall and spring migratory groups of Chinook salmon based on data from the nine presumably neutral microsatellite loci (Table 3a)

Summary

Introduction

A major effort in conservation biology is directed toward defining units within species that are sufficiently differentiated to require discrete management (Frankham 2010). Identifying such conservation units (CUs) is an essential first step so that managers and policy makers know the boundaries of the populations that they are trying to conserve (Funk et al 2012). The two most frequently discussed conservation units are evolutionary significant units (ESUs) and management units (MUs). Management units are typically defined as demographically independent populations whose population dynamics (e.g., population growth rate) depend largely on local birth and death rates rather than on immigration (Moritz 1994). As population structure is typically assessed by estimating divergence in the allele frequencies at neutral genetic markers (i.e., microsatellite loci), this class of genetic markers is routinely used to delineate both ESUs (Small et al 1998) and MUs (Palsbøll et al 2006)

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