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

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.