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

Abstract

Knowing how many individuals there are in a population is a fundamental problem in the management and conservation of freshwater and marine fish. We compare abundance estimates (census size, Nc) in seven brook trout Salvelinus fontinalis populations using standard mark–recapture (MR) and the close‐kin mark–recapture (CKMR) method. Our purpose is to validate CKMR as a method for estimating population size. Close‐kin mark–recapture is based on the principle that an individual's genotype can be considered a “recapture” of the genotypes of each of its parents. Assuming offspring and parents are sampled independently, the number of parent–offspring pairs (POPs) genetically identified in these samples can be used to estimate abundance. We genotyped (33 microsatellites) and aged c. 2,400 brook trout individuals collected over 5 consecutive years (2014–2018). We provide an alternative interpretation of CKMR in terms of the Lincoln–Petersen estimator in which the parents are considered as tagging the offspring rather than the offspring “recapturing” the parents. Despite various sources of uncertainty, we find close agreement between standard MR abundance estimates obtained through double‐pass electrofishing and CKMR estimates, which require information on age‐specific fecundity, and population‐ and age‐specific survival rates. Population sizes (trueN^) are estimated to range between 300 and 6,000 adult individuals. Our study constitutes the first in situ validation of CKMR and establishes it as a useful method for estimating population size in aquatic systems where assumptions of random sampling and thorough mixing of individuals can be met.

Effective number of white shark (Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand

“…For instance, quantifying changes in Nb over time provides high power to detect declines in Nb (Luikart et al, 2020 ) and has helped to identify factors relevant to shaping populations (i.e., management interventions, demographic parameters) with successful outcomes reported for populations of commercially important bony fishes. Examples include salmon (Bacles et al., 2018; Perrier et al., 2016), trout (Ruzzante et al., 2019; Whiteley et al., 2013; Wood et al., 2014), snapper (Jones et al., 2019), and tuna (Waples et al., 2018). In these examples, both Nb and Ne were used to investigate demographic (i.e., variance in reproductive success under commercial harvest conditions) and environmental (i.e., stream productivity, competition, habitat quality, year‐of‐the‐young development) effects on long‐term population viability, with significant implications for management and conservation.…”

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

“…True POPs share on average half their genes and are likely to be confused only with full siblings, which can be distinguished based on experimental design, or because POPs must share at least one allele at each locus. Therefore, robust parentage assignments can generally be made using relatively modest numbers of loci (Rawding et al 2014; Bravington et al 2016a; Ruzzante et al 2019). In contrast, reliably distinguishing HSPs from unrelated or more distantly-related individuals (e.g., cousins) is challenging and generally requires at least 10 3 SNPs.…”

“…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).…”

Beyond hybridization: the genetic impacts of nonreproductive ecological interactions of salmon aquaculture on wild populations

“…Finally, molecular approaches to mark-recapture abundance estimation (i.e. CKMR, Bravington et al 2016) also offer the potential to quantify changes in population size over time and have been used in marine and freshwater fish species (Bravington et al 2016, Waples et al 2018, Ruzzante et al 2019. Such approaches could be used to quantify population trends in effective size in the absence of assessment data and monitor for ecological and non-reproductive genetic interactions in future.…”