Considering sampling bias in close-kin mark-recapture (CKMR) abundance estimates of Atlantic salmon

Genetic methods for the estimation of population size can be powerful
alternatives to conventional methods. Close-kin mark-recapture (CKMR) is
based on the principles of conventional mark-recapture, but instead of
being physically marked, individuals are marked through their close kin.
The aim of this study was to evaluate the potential of CKMR for the
estimation of spawner abundance in Atlantic salmon and how age, sex,
spatial, and temporal sampling bias may affect CKMR estimates. Spawner
abundance in a wild population was estimated from genetic samples of
adults returning in 2018 and of their potential offspring collected in
2019. Adult samples were obtained in two ways. First, adults were sampled
and released alive in the breeding habitat during spawning surveys.
Second, genetic samples were collected from out-migrating smolts PIT
tagged in 2017 and registered when returning as adults in 2018. CKMR
estimates based on adult samples collected during spawning surveys were
somewhat higher than conventional counts. Uncertainty was small
(CV<0.15), due to the detection of a high number of
parent-offspring-pairs. Sampling of adults was age- and size-biased and
correction for those biases resulted in moderate changes in the CKMR
estimate. Juvenile dispersal was limited, but spatially balanced sampling
of adults rendered CKMR estimates robust to spatially biased sampling of
juveniles. CKMR estimates based on returning PIT tagged adults were
approximately twice as high as estimates based on samples collected during
spawning surveys. We suggest that estimates based on PIT tagged fish
reflect the total abundance of adults entering the river, while estimates
based on samples collected during spawning surveys reflect the abundance
of adults present in the breeding habitat at the time of spawning. Our
study showed that CKMR can be used to estimate spawner abundance in
Atlantic salmon, with a moderate sampling effort, but a carefully designed
sampling regime is required.