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

TLDR: Empirical evidence of the usefulness of different molecular-based methods to estimate the effective population size (N(e) for conservation purposes in endangered livestock populations is reported, and their use in livestock conservation programs should be carried out with caution.

Abstract: Empirical evidence of the usefulness of different molecular-based methods to estimate the ef- fective population size (Ne) for conservation purposes in endangered livestock populations is reported. The black-coated Asturcon pony pedigree (1,981 individu- als) was available. Additionally, a total of 267 Asturcon individuals born in 1998, 2002, and 2008 were typed for 15 microsatellites. These yearly cohorts (co- hort1998, 2002, 2008) included almost all individuals kept for reproduction at the end of the corresponding foaling season. The genealogical realized N N e () was estimat- ed for each cohort by using the individual increase in inbreeding. Molecular N e was computed by using 1) linkage disequilibrium (N e(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 N e 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 N e(D) were highly biased upward, with the maximum N e(D) value obtained for cohort 2002 (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), esti- mates 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 cohort 2008). 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 meth- ods were strongly affected by a weak drift signal, par- ticularly when samplings were not spaced a sufficient number of generations or a sufficient time apart. The use of molecular-based estimates of N e is not straight- forward, and their use in livestock conservation pro- grams 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.