Assessing performance of single-sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed

Abstract

Estimating effective population size (Ne) using linkage disequilibrium (LD) information (Ne(LD)) has the operational advantage of using a single sample. However, Ne(LD) estimates assume discrete generations and its performance are constrained by demographic issues. However, such concerns have received little empirical attention so far. The pedigree of the endangered Gochu Asturcelta pig breed includes individuals classified into discrete filial generations and individuals with generations overlap. Up to 780 individuals were typed with a set of 17 microsatellites. Performance of Ne(LD) was compared with Ne estimates obtained using genealogical information, molecular coancestry (Ne(M)) and a temporal (two-sample) method (Ne(JR)). Molecular-based estimates of Ne exceeded those obtained using pedigree data. Estimates of Ne(LD) for filial generations F3 and F4 (17.0 and 17.3, respectively) were lower and steadier than those obtained using yearly or biannual samplings. Ne(LD) estimated for samples including generations overlap could only be compared with those obtained for the discrete filial generations when sampling span approached a generation interval and demographic correction for bias was applied. Single-sample Ne(M) estimates were lower than their Ne(LD) counterparts. Ne(M) estimates are likely to partially reflect the number of founders rather than population size. In any case, estimates of LD and molecular coancestry tend to covary and, therefore, Ne(M) and Ne(LD) can hardly be considered independent. Demographically adjusted estimates of Ne(JR) and Ne(LD) took comparable values when: (1) the two samples used for the former were separated by one equivalent to discrete generations in the pedigree and (2) sampling span used for the latter approached a generation interval. Overall, the empirical evidence given in this study suggested that the advantage of using single-sample methods to obtain molecular-based estimates of Ne is not clear in operational terms. Estimates of Ne obtained using methods based in molecular information should be interpreted with caution.