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.