Inbreeding
In a small population random mating can result in a higher level of inbreeding. To assess the level of inbreeding, we used PLINK to calculate the number and length (> 100 Kb) of ROHs through the autosomal genome for each black-faced and royal spoonbill individual.
We also calculated the genomic inbreeding coefficient,F ROH, which measures the proportion of ROHs in the autosomal genome(M. C. Keller et al., 2011). To calculateF ROH, we divided the total length of ROH by the effective autosomal genome size (the length of non-N bases of the non-sex chromosomes).
In theory, a species with a higher inbreeding rate is expected to have a lower linkage disequilibrium (LD) decay rate(Slatkin, 2008). Therefore we also used PopLDdecay v. 3.40(Zhang, Dong, Xu, He, & Yang, 2019) to calculate the decay of LD, r 2, for the two spoonbill species. To calculate the pair-wiser 2 between two SNPs, the maximum distance between them was set to 150 Kb.