Table 2.

PSGs from the Single-Branch Foreground Analyses^a

Foreground Branch	Ensembl ID	Gene Symbol	Adjusted P Value (P < 0.05)	Foreground ω	Biochemical Pathway or Gene Function Information
Aglaeactis castelnaudii	11922	JPH1	0	7.53	Part of structural foundation and cross-talk across cell membrane in skeletal muscle
Amazilia amazilia	02317	MDH1	0.017	2.37	Glucose metabolism, Krebs cycle
Amazilia viridicauda	01501	DNAJA1	0.012	281.75	Heat shock protein cochaperone; regulation of apoptosis in response to cellular stress
Amazilia viridicauda	08371	NOB1	0.003	139.67	rRNA processing in the nucleus and cytosol
Chaetocercus mulsant	00167	CACTIN	0.017	34.35	Regulation of innate immune response
Chaetocercus mulsant	18304	COX1	0	1.00021	Respiratory electron transport, oxidative phosphorylation
Chaetocercus mulsant	18150	FEM1A	0	619.67	Substrate recognition; anti-inflammatory signaling
Chaetocercus mulsant	13770	NDUFB4	0.038	108.64	Respiratory electron transport, oxidative phosphorylation
Coeligena violifer	05988	ATG9A	0.007	17.95	Related to autophagy
Coeligena violifer	06887	NDUFB10	0.008	5.91	Respiratory electron transport, oxidative phosphorylation
Colibri coruscans	05988	ATG9A	0.008	22.73	Related to autophagy
Colibri coruscans	13977	CLPB	0	8.61	Longevity regulating pathway; diverse cellular activities
Patagona gigas peruviana	18302	ND1	0	15.53	Respiratory electron transport, oxidative phosphorylation
Phaethornis malaris	11919	ATP6V1D	0.018	1.34	Respiratory electron transport, oxidative phosphorylation; insulin receptor recycling; innate immune system
Phaethornis malaris	11555	MLF1	0.016	13.71	Transcriptional misregulation in cancer
Phlogophilus harterti	08535	MFGE8	0.036	1.13	Metabolism of proteins; promotes phagocytosis of apoptotic cells; immune function
Phlogophilus harterti	06887	NDUFB10	0.003	780.9	Respiratory electron transport, oxidative phosphorylation
Phlogophilus harterti	08539	SDHA	0.04	1.09	Respiratory electron transport, oxidative phosphorylation; Krebs cycle

^aEnsembl IDs begin with prefix ENSTGUP000000. The associated foreground branch omega (ω) values are shown for two site classes. For these site classes, the foreground branches are both evolving under positive selection (ω > 1), but the background branches are either evolving neutrally (ω = 1) or under purifying selection (ω < 1). Genes with foreground ω values just above one should be interpreted with caution, as they may represent positive selection or relaxed purifying selection. Pathway or gene function information was compiled from the Panther and Genecards databases.