An elevated level of genetic drift in the black-faced spoonbill
A bottleneck event could intensify the effect of genetic drift, resulting in an increased rate of extinction and therefore a deficiency of low-frequency alleles as well as an over-abundance of medium frequency alleles (Tajima, 1989; Gattepaille, Jakobsson, & Blum, 2013; Maruyama & Fuerst, 1985). To measure the strength of genetic drift in the black-faced spoonbill, we calculated the folded site frequency spectrum (SFS) of unlinked SNPs of the autosomal chromosomes for the two spoonbill species. The folded SFS of the two spoonbill species were bimodal distributions (Fig. 3C) with a tall peak for singletons (minor SNPs carried by only one haplotype) and a lower peak for medium-frequency SNPs. However, the frequency of singletons in the black-faced spoonbill (21.9%; 47,227 of 215,722 SNPs) was significantly lower than that in the royal spoonbill (30.7%;χ 2= 24.82, p = 0.000). In theory, genome-wide Tajima’s D values would be higher with fewer low-frequency SNPs (Tajima, 1989) (e.g. singletons), as was the case in the black-faced spoonbill (mean Tajima’s D = 0.24± 0.98, the number of total SNPs, n = 4,522,032) compared with the royal spoonbill (mean Tajima’s D = 0.05± 0.99, n = 4,437,044;t = 296.51, p < 0.001; Fig. 3D). The lower singleton frequency and higher Tajima’s D values suggest that the black-faced spoonbill has been subjected to stronger genetic drift caused by the recent population bottleneck.