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.