Comparable genomic diversity between the black-faced spoonbill and royal spoonbill
We re-sequenced the genomes of 11 black-faced spoonbill individuals, nine of which were from Tainan County, Taiwan, the wintering ground of more than 50% of the species’ world population (Chesser, Yeung, Yao, Tian, & Li, 2010) and two from the Deep Bay Wetland, Hong Kong (Fig. 1A; Table S4). We also used the draft genome of the black-faced spoonbill as the reference to re-sequence the whole genomes of nine wild royal spoonbill individuals from Australia (Table S4). The genomic diversities of the two spoonbill species are comparable: the nucleotide diversity (π ) and mean individual heterozygosity of the black-faced spoonbill are 1.11× 10-3 and 1.09× 10-3, respectively. The comparable figures are 1.06× 10-3 and 1.05× 10-3 in the royal spoonbill (Table S5). The genome-wide heterozygosities of both spoonbill species are relatively low (Table S6) compared with those of most of the 32 avian species (Lai et al., 2019; Li et al., 2014) in the “Least Concern“ category in the IUCN Red List (mean± S.D.= 2.50± 1.07× 10-3), but twice that of the critically endangered crested ibis (Nipponia nippon (S. Li et al., 2014); = 0.43× 10-3), and close to that of seven vulnerable species(S. Li et al., 2014) (1.18± 0.85× 10-3). Our results suggest that the genetic diversity of black-faced spoonbills is still comparable to those of the un-threatened royal spoonbill and other vulnerable but not endangered avian species. The genome-wide genetic distance (D xy) between the two spoonbills was estimated to be 0.0020. This is consistent with the short mitochondrial DNA distance (the Tamura-Nei distance= 0.015) observed between these two sister species (Chesser et al., 2010).