Positive Selection Analysis
We evaluated the selective constraints of genes that could be associated with pelagic lifestyle. For this purpose, we performed the analysis with HyPhy 2.5 (Kosakovsky Pond, Frost, & Muse, 2005), using Procellariiformes data (1:1 MSAs). Prior to the analysis, non-reliable positions across all 1:1 orthologs MSAs were filtered with ZORRO (Wu, Chatterji, & Eisen, 2012) (default options; MSA with average quality < 5 were filtered). We used the aBSREL method (Smith et al., 2015) to test for positive selection, and the RELAX method (Wertheim, Murrell, Smith, Pond, & Scheffler, 2015) to test for relaxed/intensified selection. We also performed a Gene ontology (GO) enrichment analysis of the candidate genes using the GOstats (Falcon & Gentleman, 2007) R package against the background GOs of 1:1 orthologs.