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

Abstract

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.

Keywords: Atlantic salmon; Lincoln‐Petersen; abundance estimation; census size; close‐kin mark–recapture; mating success; mature male parr; population size; reproductive success; sampling bias.

FIGURE 1

Sampling locations for adult (autumn 2018) and juvenile (summer 2019) salmon in River Vigda. Juveniles were sampled at ten electrofishing stations (St. 2–St. 12), and adults were sampled throughout the anadromous part of the river, divided into five zones (Zone 1–Zone 5). PIT‐tagged adults were registered by permanently installed antenna at the river entrance

FIGURE 2

Abundance estimates for salmon in River Vigda in the 2018 breeding season. Conventional estimates are counts in spawning surveys, with corrected estimates taking into account that not all adults had entered the river at the time surveys were carried out. Close‐kin mark–recapture (CKMR) estimates are based on either scales sampled during spawning surveys (Survey) or on the registration of PIT‐tagged adults that entered the river (PIT). CKMR Survey estimates are corrected for size‐biased sampling (CKMR Survey corrected size). CKMR PIT estimates are corrected for sea‐age‐biased sampling, as only 1 SW adults were part of this sample

FIGURE 3

Presence of 54 PIT‐tagged 1 SW salmon in River Vigda in autumn 2018. Black dots indicate the date of registration at the river entrance in upstream and downstream direction, with gray lines indicating the duration of presence in the river. Duration is unknown for individuals for which no registration of leaving was made. The dotted vertical line represents when the spawning survey was conducted

FIGURE 4

Number of juveniles collected at ten sampling stations (gray bars) in River Vigda and that were assigned to parents in genetic analysis (black bars)

FIGURE A1

(A) Total length [mm] of salmon classified into three size categories (<3 kg, 3–7 kg, >7 kg) in 66 salmon caught during spawning surveys. (B) Variation in total length [mm] among salmon of different sea age in 66 salmon caught during spawning surveys. Dotted lines indicate the size limits (660 and 880 mm) for the estimation of body weight categories

FIGURE A2

Distribution of the number of offspring assigned to males (A) and females (B) sampled during spawning surveys in River Vigda in autumn 2018