Genetic‐Based Estimates of Adult Chinook Salmon Spawner Abundance from Carcass Surveys and Juvenile Out‐Migrant Traps

Abstract

Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmon Oncorhynchus spp. listed under the Federal Endangered Species Act. We investigated genetic approaches to estimate the 2009 spawner abundance for a population of Columbia River Chinook Salmon Oncorhynchus tshawytscha via genetic mark–recapture and rarefaction curves. The marks were the genotyped carcasses collected from the spawning area during the first sampling event. The second sampling event consisted of a collection of juveniles from a downstream migrant trap located below the spawning area. The parents that assigned to the juveniles through parentage analysis were considered the recaptures, which was a subset of the genotypes captured in the second sample. Using the Petersen estimator, the genetic mark–recapture spawner abundance estimates based on the binomial and hypergeometric models were 910 and 945 Chinook Salmon, respectively. These results were in agreement with independently derived spawner abundance estimates based on redd counts, area‐under‐the‐curve methods, and carcass tagging based on the Jolly–Seber model. Using a rarefaction curve approach, which required only the juvenile offspring sample, our estimate of successful breeders was 781 fish. Our genetic‐based approaches provide new alternatives to estimate adult Pacific salmon abundance in challenging environmental conditions or for populations with poor or unknown estimates of precision.

Use of genotyping by sequencing data to develop a high‐throughput and multifunctional SNP panel for conservation applications in Pacific lamprey

“…Enumeration of spawners is also difficult for small populations of anadromous fishes that spawn in 'flashy' watersheds (i.e. with higher flow rates and more rapid changes in water level) where carcasses do not persist (Rawding et al 2014). In two cases where we knew the true numbers of adults that produced a collection of larvae/juveniles, the 95% CIs of the N b estimates contained the true values.…”

Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance

“…Introduced in Bravington, Skaug, and Anderson (2016, but see also Skaug, 2001;and Rawding, Sharpe, & Blankenship, 2014), the CKMR method is based on the principle that an individual's genotype can be considered a "recapture" of the genotypes of each of its parents and analyses the number and pattern of parent-offspring pairs (POPs) in a mark-recapture (MR) framework.…”

Close-kin methods to estimate census size and effective population size

“…The two kinship categories that have been used to date with close-kin mark-recapture (CKMR) are parent-offspring pairs (POPs) and siblings. Successful application of CKMR methods to a number of fish species (Rawding et al 2014; Bravington et al 2016a; Hillary et al 2018; Bradford et al 2018; Ruzzante et al 2019; Bravington et al 2019), together with refinements in statistical methodology (Bravington et al 2016b; Skaug 2017; Conn et al 2020), have generated a great deal of interest in using this approach more broadly to study marine, freshwater, and terrestrial taxa (e.g., Stewart et al 2018; Oleksiak and Rajora 2020). The basic principles of CKMR have also been used to place an upper bound on the pre-Columbian human population size in the Caribbean (Fernandes et al 2020).…”