Repeat annotation
We generated a de novo repeat library of the genome with RepeatModeler – 1.0.11 (Smit, Hubley, & Green,) on scaffolds >100 kbp. This library was combined with all avian and ancestral consensus repeats from Dfam_Consensus-20181026 (Storer, Hubley, Rosen, Wheeler, & Smit, 2021), RepBase-20181026 (Jurka et al., 2005) and the repeat annotation of the Cory’s shearwater (Calonectris borealis ) (Feng et al., 2020), which represents the most closely related sequenced genome. Redundancies among libraries were removed with the script ReannTE_MergeFasta.pl (https://github.com/4ureliek/ReannTE). We then ran RepeatMasker 4.0.7 (Smit et al.,) using the combined library as a reference, with the following parameters: -xsmall -e ncbi -s -gccalc -no_is -gff.