A brief yet severe recent bottleneck for the black-faced spoonbill
To test whether the black-faced spoonbill experienced a recent bottleneck event, we compared the maximum composite likelihood of a recent bottleneck model and a constant population size model based on 215,722 unlinked autosomal SNPs using Fastsimcoal2 (Excoffier, Dupanloup, Huerta-Sánchez, Sousa, & Foll, 2013). The results significantly supported the recent bottleneck model (maximum estimated likelihood= -230,635.54, AIC= 421,681.07, AIC weight= 1.0) instead of a constant population model (maximum estimated likelihood= -232,073.84; AIC= 464,149.07, Δ AIC= 2,868.6, AIC weight= 0.0). The presumed bottleneck event was estimated to be very recent and brief (Fig. 2B), starting approximately six generations ago (95% CI: 4-12 generations ago) and ending about three generations ago (95% credible interval, CI: 2-4 generations ago). Because most black-faced spoonbill individuals (9 of 12 samples) sequenced in this study were victims of a botulism event in 2002, and assuming a generation time of 10 years (Yeung et al., 2006), our results suggest that the recent bottleneck event occurred around the 1940s.