Genetic Diversity and Population Structure of Spring Chinook Salmon from the Upper Willamette River, Oregon

Abstract

Effective management of Pacific salmon requires an accurate understanding of both population genetic diversity and structure. Spring Chinook Salmon Oncorhynchus tshawytscha from the upper Willamette River (UWR), Oregon, are listed as threatened under the U.S. Endangered Species Act, and although this evolutionarily significant unit is recognized to be distinct from other Columbia River stocks, genetic relationships among its constituent hatchery and wild populations remain obscure. We used genotypic data from 13 microsatellite loci to test whether hatchery populations of UWR spring Chinook Salmon are most similar to wild populations within the same subbasin, or whether hatchery populations from different subbasins are more similar to each other than to local wild populations. We also tested for differences between the genetic diversities of hatchery and wild populations, as measured through heterozygosity and allelic richness. Our results suggest that populations are weakly structured among subbasins and, in all cases, hatchery populations are genetically most similar to local wild populations. We also found heterozygosity to be higher (P = 0.009) in hatchery populations (median, 81.5%) than in wild populations (median, 75.2%), but observed no significant difference with respect to allelic richness (P = 0.406). We conclude that hatchery-origin UWR spring Chinook Salmon represent genetically appropriate founder populations for ongoing reintroduction programs and recommend that the conservation and recovery of this stock proceed through management actions developed specifically for each subbasin. We further recommend that current restrictions on hatchery stock transfers among UWR subbasins be continued to preserve extant population genetic structure.

Received January 8, 2014; accepted April 29, 2014

ACKNOWLEDGMENTS

The authors thank the many field biologists, particularly Suzette Savoie and Kip Carlson, who collected fin tissue, scale, and otolith samples from countless salmon carcasses. Hatchery managers Brett Boyd, Dan Peck, Greg Grenbemer, Kurt Kremers, and Dan Straw facilitated sample collections of hatchery fish. Ewann Berntson and Richard Carmichael graciously provided spring Chinook Salmon tissue samples from Catherine Creek Hatchery. We appreciate the technical assistance provided by members of Oregon State University's Marine Fisheries Genetics and Ecological and Conservation Genetics laboratories, including Michael Banks, Kathleen O’Malley, David Jacobsen, Jen Britt, Jonathan Minch, and Amelia Whitcomb. This work was funded by the U.S. Army Corps of Engineers (Task Order W9127N-11-2-0002-0004) and administrative assistance was provided by David Leonhardt. Comments from three anonymous reviewers greatly improved a previous version of the manuscript. The views expressed here are those of the authors and do not necessarily reflect the policies and positions of the Oregon Department of Fish and Wildlife.