Effective Population Size and Sibship Reconstruction: An Evaluation of Power Using Known Populations of Snake River Hatchery Steelhead

Effective population size (N_e) is arguably the most important metric in conservation biology. N_e affects population viability, genetic drift, and natural selection and accounts for a population’s abundance and demography. In most natural populations, it is difficult to collect adequate data to calculate N_e directly. As a result, genetic methods have been developed and implemented. One genetic method is reconstruction of sibling relationships using genotype data. In this study, we evaluated the ability to reconstruct known sibling relationships among six hatchery steelhead populations using the program COLONY and 95 single nucleotide polymorphisms (SNPs). Further, we determined our ability to estimate the true effective number of breeders (N_b) for the six populations. We evaluated > 2,500,000 pairwise sibling relationships. COLONY was able to accurately identify > 95% of the true full sibling relationships. Moreover, COLONY had a < 0.3% false positive rate among unrelated relationships. Despite our poor ability to accurately reconstruct half sibling relationships, COLONY was able to accurately estimate the true N_b for each of the six hatchery populations. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating N_b in steelhead populations in the region.