Abstract
Abstract We present practical lessons learned from applying the recent close-kin mark–recapture (CKMR) abundance estimation method to thornback ray (Raja clavata). For CKMR, related individuals are identified from their genotypes and their number and pattern is used for abundance estimation. We genotyped over 7000 individuals collected in the Bay of Biscay using Single Nucleotide Polymorphism (SNP) markers finding 99 parent–offspring pairs. The estimated number of adult thornback rays in the central Bay of Biscay was around 135000 (CV 0.19) in 2013. In total, four lessons were drawn: (i) CKMR helps identifying metapopulation structure, which if ignored might affect abundance estimates and/or time trends. There was strong evidence for two distinct local populations of thornback ray with no demographic connectivity. (ii) Demographic sample composition can affect precision and needs to include a range of birth years, which turned out to be difficult for thornback ray. (iii) Reasonable age information for potential offspring is essential. (iv) The sex of potential parents is needed and might be identified from sex-related SNPs. Reliable abundance estimation by CKMR appears feasible for a wide range of species provided that: sampling adequately covers potential local population structure, has appropriate demographic composition, and the age of potential offspring is reasonably well-known.
Highlights
Reliable abundance estimates are essential for terrestrial wildlife management and the sustainable exploitation of marine living resources
Using the exclusion rate (WPSEX), 99 parent–offspring pairs (POPs) were identified among the 6555 individuals; two offspring had both parents in the sample
As expected, using only Single Nucleotide Polymorphism (SNP) with minor allele frequency (MAF) > 0.3 decreased the number of missed POPs more rapidly with increasing number of SNPs compared to using all SNPs (MAF > 0.1; Figure 2a), but at the same time slowed down the reduction of false positive POPs as the number of SNPs increased (Figure 2b)
Summary
Reliable abundance estimates are essential for terrestrial wildlife management and the sustainable exploitation of marine living resources. The recently introduced close-kin mark–recapture (CKMR) method for absolute abundance estimation leads to a change in paradigm (Bravington et al, 2016b). Instead of surveying large areas of land or sea for counting individuals, a number of individuals are sampled, genotyped, and compared pairwise to look for specific types of kin, for example parent–offspring pairs (POPs). The rest is classical mark–recapture abundance estimation with the only difference that individuals are not physically marked, released, and recaptured, but rather mature individuals are “recaptured” either directly via sampling themselves and their offspring (Bravington et al, 2016b) or indirectly by sampling at least two offspring (Hillary et al, 2018).
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