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

Abstract

The last two decades have witnessed rapid developments and increasing interest in use of (1) genetic methods to estimate effective population size (Ne) and (2) close-kin mark-recapture (CKMR) methods to estimate abundance based on the incidence of close relatives. Whereas Ne-estimation methods have been applied to a wide range of taxa, all CKMR applications to date have been for aquatic species. These two fields of inquiry have developed largely independently, and this is unfortunate because deepest insights can be gained by joint evaluation of eco-evolutionary processes. In this synthesis, we outline factors (life-history traits; experimental design; stochasticity; ancillary information) that should be considered in identifying good candidate species and determining sampling/analytical regimes that can produce meaningful estimates. We show that the Ne/N ratio and the probability of a close-kin match both depend on a vector of parental weights that specify relative probabilities that different individuals will produce offspring. Although age-specific vital rates are central to both methodologies, for CKMR they are nuisance parameters that can bias abundance estimates unless properly accounted for, whereas they represent the signals of genetic drift that Ne estimation methods depend on. The most robust implementations of CKMR incorporate information from both parent-offspring pairs and siblings into a single, overarching framework, within which all demographic parameters can be jointly estimated in a way that allows coherent statements about uncertainty. Coordinating Ne and CKMR estimation methods using the same or overlapping datasets would facilitate joint evaluation of both the ecological and evolutionary consequences of abundance.

Genomic databanks and targeted assays help characterise domestic mosquito incursions

“…This knowledge can be useful for building predictive models of pest incursion risk as it can help estimate propagule pressure (Camac, Baumgartner, Hester, Subasinghe, & Collins, 2021), though these estimates will reflect effective rather than census population sizes of incursions. The findings at Tennant Creek pose some additional questions for studies seeking to investigate new invasions using close kin dyad methodologies (Jasper, Hoffmann, & Schmidt, 2021; Waples & Feutry, 2021). While close kin dyad methods have shown promise for investigating invasions of ∼100 generations age (Schmidt et al, 2021), close kin methods should be applied cautiously to invasions that are very new or that are sourced from a small genetic pool.…”

Population abundance in arctic grayling using genetics and close‐kin mark‐recapture

“…This ratio reflects the proportion of the population that represents the genetic diversity within the population (Hedrick, 2005). The ratio of N e /N c can be used to evaluate factors that impact N e (see also Kovach et al, 2020;Waples & Feutry, 2021), where N e allows for assessment of extinction risk (Hedrick, 2005). Our estimate of N e / N c (0.41-0.42) is considerably higher than that obtained for a relict Arctic Grayling population in the southern edge of the species distribution (0.133; Kovach et al, 2020) and is also higher than the median estimate across taxa (0.14, Palstra & Ruzzante, 2008) indicating little concern for genetic diversity within the Lubbock River population.…”

“…Age at maturity and adult lifespan has been shown to vary across a narrow geographic range in Alaska Arctic Grayling (Clark, 1992). Temporally replicated sampling is further needed for the assessment of the potential incidence of skip breeding and its influence on genetic and census estimates (Waples & Feutry, 2021) and of trends in population abundance.…”

Navigating the temporal continuum of effective population size

“…Even though the census population sizes generally correlate with effective population sizes, there is a substantial variation between species and a discrepancy between the several orders of magnitude variation in census population sizes and the much narrower range of Ne estimated from genetic variation (Ellegren & Galtier, 2016). An interesting recent development is the introduction of the close-kin mark-recapture (CKMR) approach that estimates census size using the frequency of parent-offspring pairs identified with genomic methods (Bravington et al, 2016;Ruzzante et al, 2019;Waples & Feutry, 2021). The same data can be used to assess Ne, establishing a direct link between Nc and Ne estimates, which led, for example, to the discovery that the Ne/Nc ratio in southern bluefin tuna is orders of magnitude larger than previously thought (Waples et al, 2018).…”