Long-term historical demography
To infer the historical demography of the black-faced spoonbill, we applied SMC ++(Terhorst et al., 2017) which employs a coalescent-based method utilizing information on the site frequency spectrum and linkage disequilibrium of a set of diploid genomes to infer the historical demographic dynamics of the population concerned. To enhance base calling accuracy, we used the VCF containing diploid genotypes generated from all individuals (N=9) with coverage greater than 15 for the SMC ++ analysis. We used the command –CV to perform cross-validation which yielded model parameters for calculating the effective population size through time. The generation time of the black-faced spoonbill was set to ten, and the mutation rate was set to 3.6× 10-8 per site per generation(Axelsson, Smith, Sundström, Berlin, & Ellegren, 2004). We also used SMC ++ to infer the historical demography of the royal spoonbill based on diploid genotypes with coverage greater than 15 (N=7).