Full-sib reconstruction in haplodiploid populations

Abstract

Estimating colony numbers of invading Bombus terrestris in Japan is the most urgent task for eradicating the alien invasive species. Nests of bumble bees are hardly found in nature. A prospective alternative is estimating the number of nests with polymorphic genetic data of individuals foraging in the field. Full-sib reconstruction from such genetic data is NP-hard in a strict sense, but several heuristic methods have been proposed. Among them, likelihood methods have been often applied for reconstructing full-sibs in nature, but they require relatively large sample sizes for obtaining accuracy in allele frequencies. Alternative methods calculate genetic distances between paired individuals and cluster them into family groups, but there are also pros and cons for applying these methods against real data. We proposed another heuristic pairing and clustering method, Shared Loci Correspondence Analysis (SLCA), for reconstructing full-sib families of haplodipoid populations. In SLCA, genetic similarities among individuals are numbers of loci shared by the paired individuals. The similarity scores are sorted by the correspondence analysis for clustering them into full-sib families. SLCA could be applicable to quite small samples and succeeded to correctly estimate the number of bumble bee nests in the field. We also improved estimation accuracy of SLCA by blunting the similarity index among individuals. The modified SLCA performed almost perfectly against challenging problems when numbers of loci and alleles were equal or greater than eight. Future direction of improving SLCA is discussed.

Combining Harvest and Genetics to Estimate Reproduction in Wolves

“…We also found that sibship frequency‐based estimates of the effective number of breeders were consistent across sample years and had overlapping confidence intervals with estimates based on linkage disequilibrium, another commonly employed single‐sample N b estimator. The value of estimating counts of parents and family groups through sibship reconstruction has been demonstrated in other systems, such as monitoring abundance of social bee colonies by identifying sisters among foraging workers and estimating the number of female sea turtles (green [ Chelonia mydas ] and Kemp's ridley [ Lepidochelys kempii ] sea turtles) laying multiple clutches per season at the same nesting site (Toquenaga and Kokuvo ; Frey et al , ; Geib et al ). Fisheries and aquaculture systems have used similar methods to shed light on genetic variability between age stages, assess stocking strategies, and reconstruct putative parental genotypes among externally fertilized species (Liu and Ely , Li et al , Meraner et al , Hasanat et al ).…”

Mating frequency estimation and its importance for colony abundance analyses in eusocial pollinators: A case study of Bombus impatiens

“…For social insects, population size estimates derived from numbers of individuals counted in the wild misrepresents key population-level processes, because the colony is the reproductive unit. Thus, accurate estimates of colony numbers are crucial for species of conservation concerns, as they are used for the identi cation of drivers of species declines (e.g., correlating population status with land use history) (Maebe et al 2015), for the monitoring and eradication of invasive species (Toquenaga and Kokuvo 2010), and the development of plans for conservation actions and priorities (Hansen and Jensen 2005, Lepais et al 2010, McGrady et al 2021). Many social pollinator species are in decline, which underscores the importance of accurate estimations of colony abundance for these species (Powney et al 2019).…”