Genetic substructure and admixture as important factors in linkage disequilibrium‐based estimation of effective number of breeders in recovering wildlife populations

Abstract

The number of effective breeders (N b) and effective population size (N e) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium‐based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993–2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on N b and N e, by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for N e were larger than N b and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of N b and N e. Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on N b and N e.

A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data

“…We begin with admixture, which can be pervasive in natural populations ( Hudjashov et al. 2017 ; Kopatz et al. 2017 ; Browning et al.…”

Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia

“…The degree of genetic differentiation observed among the Gobi and Himalayan populations is larger than the average Fst between distinctive subpopulations in northwestern Europe (0.051) [88]. Interestingly, the genetic differentiation between the southern (clade 1) and northern (clade 3a) subpopulations of Scandinavian brown bears has decreased from F ST = 0.051 to F ST = 0.014 during 20 years [89], because of an annual population increase of 4.5% and increased gene flow between these subpopulations [77, 90]. In contrast, a population genetic study [64] found a high pairwise F ST (0.23) between brown bear populations in the South Selkirk Mountains in North America, which has been isolated for several decades from the neighboring populations across a 5-km wide valley filled containing a town and rural farms.…”

American black bear population fragmentation detected with pedigrees in the transborder Canada–United States region

“…Nonetheless, there are promising techniques using linkage disequilibrium to estimate effective population size (N e ). In recent examples, simulations demonstrated relatively accurate detection of early fragmentation into smaller units (England et al 2010), and the re-establishment of connectivity in a recovering system (Kopatz et al 2017). This method may not be well-suited to our study area because the populations of bears on each side of our studied fractures are rather large (see above).…”