Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha

Abstract

The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed “the four H’s”: habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.

Stray Rates of Natural‐Origin Chinook Salmon and Steelhead in the Upper Columbia River Watershed

“…For example, in cases of large‐scale reintroduction, such as above Chief Joseph and Grand Coulee dams (Johnson et al. ), high stray rates may be desirable in order to achieve colonization of large areas. Furthermore, managers should consider whether estimates of donor stray rate targets for natural‐origin fish are realistic for application to hatchery‐origin fish, which are cultured under dramatically different conditions.…”

Unlocking the potential of ancient fish DNA in the genomic era

“…In some cases, temporal sampling can be used to replace key assumptions that underlie a model with empirical information. Reconstruction of genetic diversity of >3,000-year-old Chinook salmon (O. tshawytscha) in the Columbia River basin identified the loss of genetic variation prior to human arrival (Johnson, Kemp, & Thorgaard, 2018). Using a similar approach, 1,500-year-old Atlantic cod (Gadus morhua) samples from Iceland were used to reconstruct population abundance trends, identifying higher levels of genetic diversity in the historic population (Olafsdottir, Westfall, Edvardsson, & Palsson, 2014) (Arndt et al, 2003;Grier et al, 2013;Speller, Yang, & Hayden, 2005).…”

To remain or leave: Dispersal variation and its genetic consequences in benthic freshwater invertebrates

“…Due to the constraints imposed by flow and displacement, river habitats may particularly promote population divergence of inhabitants that lack mobility in general, or at critical periods in their life history. Indeed, this scenario of constraint may fundamentally explain the numerous subspecies, strains, and lineages of salmonids whose spawned eggs are retained in specific stretches of particular rivers in the Pacific coast of North America (e.g., Johnson, Kemp, & Thorgaard, 2018;Penaluna et al, 2016). Additional factors may also influence rates of evolution in lotic environments.…”