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.