Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead

Abstract

Effective population size (N e) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate N e directly. Consequently, genetic methods to estimate N e have been developed. Two N e estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (N b) when sample sizes were near or greater than the true N b and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of N b. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating N b in steelhead populations in the region.

Loss of genetic variability in the captive stocks of tambaqui,Colossoma macropomum(Cuvier, 1818), at breeding centres in Brazil, and their divergence from wild populations

“…The effective population sizes estimated for most of the stocks analysed in the present study were much lower than the numbers (50–100) estimated to be the minimum necessary to avoid inbreeding depression and establish programs of genetic improvement (Frankham, Bradshaw, & Brook, ; Tave, ). Effective population size is considered to be one of the most important parameters for the evaluation of the viability of populations (Ackerman et al., ). Most of the captive stocks analysed during the present study appear to be too small to avoid inbreeding depression, or for the establishment of programs of genetic improvement.…”

Purging putative siblings from population genetic data sets: a cautionary view

“…It can be shown (Ackerman et al . ) that eqn yields the same estimate of N e as the parentage‐analysis‐without‐parents approach of Waples & Waples (), which calculates inbreeding N e based on the vector of numbers of offspring produced by each parent. Simple rearrangement of eqn produces the expected frequencies of sibships:…”

Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly

“…The increasing availability of genomic information continues to transform the way we study natural populations. It is now possible to accurately and efficiently measure a wide range of important parameters that directly influence the fitness and survival of wild populations such as effective population size (Gilbert & Whitlock, ; Palstra & Fraser, ), effective number of breeders (Ackerman et al., ), extra pair paternity (Firth, Hadfield, Santure, Slate, & Sheldon, ; Griffith, Owens, & Thuman, ), heterozygosity (Fountain et al., ; Saccheri et al., ), inbreeding depression (Huisman, Kruuk, Ellis, Clutton‐Brock, & Pemberton, ) and reproductive success (Coltman et al., ). Another key ecological parameter is dispersal, the ecological and evolutionary causes and consequences of which have been studied for decades.…”