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.