Data availability statement
No new sequence data were generated during this study. Data for the four case studies are available at NCBI BioProject (https://www.ncbi.nlm.nih.gov/bioproject) under the following accession numbers: Darwin’s finches: PRJNA263122 (Lamichhaney et al. 2015), Anopheles : PRJNA67511 (Fontaine et al. 2015), Drosophila : PRJNA554139 (Mai et al. 2019), Heliconius : PRJEB1749 (Martin et al. 2013). Metazoan genomes are available at NCBI RefSeq (https://www.ncbi.nlm.nih.gov/refseq/; O’Leary et al. 2016); for individual accession numbers see Table S1. Multiple sequence alignments, phylogenetic trees, and other results of this study are available at DataDryad (DOI: 10.5061/dryad.kprr4xhb3).