Table 4.
Summary of All Codeml Results for Shared Pathways, PSGs, and/or Positively Selected Sites for High-Elevation Species >1,500 m (Coeligena coeligena, Adelomyia melanogenys, Chaetocercus mulsant, Amazilia viridicauda, Colibri coruscans, Aglaeactis castelnaudii, Coeligena violifer, Metallura phoebe, and Patagona gigas peruviana)a
| Species | Shared Pathway/Gene Function under Selection | Shared PSG | Unique PSG | Shared Positively Selected Site |
|---|---|---|---|---|
| A. viridicauda | Promotes apoptosis in response to cellular stress mediated by exposure to anisomycin or UV | DNAJA1 | — | |
| Ch. mulsant | Involved in regulation of innate immune response; regulation of lipopolysaccharide-mediated signaling pathway (can induce apoptosis) | CACTIN | — | |
| Negative regulation of inflammatory response | FEM1A | — | ||
| Respiratory electron transport, oxidative phosphorylation | COX1 | — | ||
| High-elevation species >1,500 m | Glutathione metabolism | MGST3 | Ser141 | |
| Respiratory electron transport, oxidative phosphorylation | NDUFS8 | Ser69 | ||
| Pyruvate metabolism, citric acid cycle | PDHB | Val214 | ||
| Glycerophospholipid biosynthesis; metabolism; fatty acid metabolism | HADHB | — | ||
| (Not well characterized) | 15014 | Ser20 | ||
| (Not well characterized) | AAMDC | — | ||
| Assists with protein folding | CCT3 | — | ||
| Cell signaling; cell cycle | CDKN1B | — | ||
| Viral mRNA translation | EEF1B2 | — | ||
| Immune function; viral mRNA translation | EEF2 | — | ||
| Cellular response to hypoxia | EPAS1 | — | ||
| (Not well characterized) | 09734 | — |
From left to right, the table shows the group of species that share pathways, PSGs, and positively selected sites (yes–yes–yes), share pathways and PSGs but not sites (yes–yes–no), and that have different PSGs involved in similar pathways/functions (yes–no–no). For shared sites, we show the reference amino acid (first sequence in alignment) and site position, otherwise a dash is shown if no positively selected sites were identified or shared. Unannotated PSGs are labeled with their Ensembl ID (prefix ENSTGUP000000).