Extrapair paternity and genetic diversity: the white-throated dipper Cinclus cinclus

Passerine bird species vary considerably in the frequency of extrapair paternity, but the factors causing this variation are not well understood. There is some comparative evidence that extrapair paternity is associated with the population level of genetic diversity, but there is no consensus of how genetic diversity should be measured and compared across species or populations. Here we report a low frequency of extrapair paternity (2% extrapair offspring) in a Norwegian population of the white-throated dipper Cinclus cinclus, which shows strong signs of reduced genetic diversity. We encountered difficulties in constructing a robust parentage analysis system for the species, largely due to consistently low polymorphism levels in 100 heterologous microsatellite markers. Furthermore, single-nucleotide polymorphisms (SNPs) were almost absent in intron sequences in 10 nuclear genes (> 5 kb) that are much more polymorphic in other species. Hence, our results seem consistent with the genetic diversity hypothesis that predicts a low frequency of extrapair paternity in species with low genetic diversity. Heterologous microsatellite markers are generally unsuitable for interspecific comparisons of genetic diversity as they show strong phylogenetic dependency in polymorphism levels. We suggest that SNP rates at homologous nuclear introns, like those presented here, can provide a useful method for obtaining unbiased estimates of genome-wide genetic diversity across populations and species.