Population sampling and whole genome resequencing
In addition to the sample used for reference genome sequencing, we also re-sequenced eleven black-faced spoonbills whose tissue was collected from individuals that had been rescued or had accidentally died in Tainan County, Taiwan (N=) and the Deep Bay Wetland, Hong Kong (N=2), as well as tissue samples of royal spoonbills from Australia (N=9).
We used a protocol from Gemmel and Akiyam (2006) to extract gross DNA from these tissue samples for resequencing. A whole genome re-sequencing library with insert size 50 bp was constructed for each individual. Our sequencing data was generated using an Illumina HiSeq 4000 platform (BGI).