Usefulness of molecular-based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcón pony

Empirical evidence of the usefulness of different molecular-based methods to estimate the effective population size (Ne) for conservation purposes in endangered livestock populations is reported. The black-coated Asturcón pony pedigree (1,981 individuals) was available. Additionally, a total of 267 Asturcón individuals born in 1998, 2002, and 2008 were typed for 15 microsatellites. These yearly cohorts (cohort₁₉₉₈, ₂₀₀₂, ₂₀₀₈) included almost all individuals kept for reproduction at the end of the corresponding foaling season. The genealogical realized Ne Formula was estimated for each cohort by using the individual increase in inbreeding. Molecular Ne was computed by using 1) linkage disequilibrium [Ne₍D₎], 2) a temporal method based on F-statistics [Ne₍T₎], 3) an unbiased temporal method [Ne₍JR₎], and 4) a Bayesian temporal method [Ne₍B₎]. Estimates of Formula increased from cohort₁₉₉₈ (18.8 ± 5.1) to cohort₂₀₀₈ (24.9 ± 5.2), illustrating the history of the population and its breeding policy of avoiding matings between close relatives. The estimates of Ne₍D₎ were highly biased upward, with the maximum Ne₍D₎ value obtained for cohort₂₀₀₂ (137.0). The estimates of Ne₍T₎, Ne₍JR₎, and Ne₍B₎ showed similar performance. However, Ne₍JR₎ estimates were very consistent across cohorts, varying from 14.9 to 15.5 after correcting for the effect of overlapping generations. When the drift signal was not strong (pair cohort₁₉₉₈-cohort₂₀₀₂), estimates of Ne₍T₎ and Ne₍B₎ were not realistic. Estimates of Ne₍B₎ tended to be biased downward (being 9.0 or below for the sampling pairs including cohort₂₀₀₈). Results of Ne₍D₎ are more likely to be estimates of the effective number of breeders producing the sample, rather than the effective size for a generation. The temporal methods were strongly affected by a weak drift signal, particularly when samplings were not spaced a sufficient number of generations or a sufficient time apart. The use of molecular-based estimates of Ne is not straightforward, and their use in livestock conservation programs should be carried out with caution. Sampling strategies (including sampling sizes, sampling periods, and the age structure of the sampled individuals) must be carefully planned to ensure that robust estimates of Ne are obtained.