Table 1.
Top Scoring Gene Families at Branch-Site and Site Tests for Positive Selection.
| Test Used | Gene Family | Branch | Δln L | P-value | FDR | dS | ω (proportion) | Drosophila melanogaster Gene Name | Function Annotated in Flybase and Uniprot | Duplicates in Ants | Uniprot ID | References |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Branch-site test | 150 | 6 | 16.1 | 1.4e-8 | 2.2e-6 | 0.93 | 281 (4.2%) | Tequila | Serine-type endopeptidase activity; long-term memory; aging | – | O45029 | Didelot et al. (2006), Chen et al. (2012), and Remolina et al. (2012) |
| 11650a | 5 | 12.1 | 8.4e-7 | 7.9e-5 | 0.059 | 299 (2.5%) | CG17321 | Unknow | – | Q9VJ40 | – | |
| 453 | 6 | 11.4 | 1.9e-6 | 1.5e-4 | 0.29 | 44 (2.2%) | Guanine nucleotide exchange factor in mesoderm | Ral GTPase binding; imaginal disc-derived wing vein specification | – | A1ZBA1 | Blanke and Jackle (2006) | |
| 361 | 1 | 10.9 | 3.0e-6 | 2.3e-4 | 0.090 | 1.2 (6.9%) | Megator | Spindle assembly | – | A1Z8P9 | Qi et al. (2004) | |
| 5623 | 1 | 10.6 | 4.0e-6 | 3.0e-4 | 0.13 | 24 (4.6%) | Methylthioribose-1-phosphate isomerase | Catalyzes interconversion of methylthioribose-1-phosphate into methylthioribulose-1-phosphate; wing disc development | – | Q9V9X4 | Bronstein et al. (2010) | |
| 1050 | 6 | 10.1 | 6.7e-6 | 4.7e-4 | 0.49 | 45 (3%) | Dis3 | Regulation of gene expression; nuclear RNA surveillance; neurogenesis | – | Q8MSY2 | Kuan et al. (2009), Kiss and Andrulis (2010), Neumuller et al. (2011) | |
| 793 | 4 | 9.6 | 1.2e-5 | 7.6e-4 | 0.085 | ∞ (0.6%) | Embargoed | Protein binding; protein transporter activity; protein export from nucleus; multicellular organismal development; centriole replication | – | Q9TVM2 | Collier et al. (2000); Roth et al. (2003) | |
| 8639 | 6 | 9.5 | 1.4e-5 | 8.3e-4 | 0.26 | ∞ (11%) | ATP synthase, subunit b, mitochondria | Hydrogen-exporting ATPase activity, phosphorylative mechanism; phagocytosis, engulfment | – | Q94516 | Stroschein-Stevenson et al. (2005) | |
| 3983 | 4 | 8.9 | 2.4e-5 | 0.0014 | 0.036 | ∞ (0.5%) | Lysyl oxidase-like 2 | Protein-lysine 6-oxidase activity | – | Q8IH65 | Molnar et al. (2003), Molnar et al. (2005) | |
| 2208 | 6 | 8.7 | 3.0e-5 | 0.0016 | 0.49 | ∞ (1.2%) | Cytochrome P450 reductase | NADPH-hemoprotein reductase activity; oxidation-reduction process; putative function in olfactory clearance | – | Q27597 | Hovemann et al. (1997) | |
| Site test | 3245 | – | 10.6 | 4.2e-6 | 0.0041 | – | 2.4 (2.1%) | CG6752 | Unknown | Yes | Q9VFC4, Q8SZS1 | – |
| 6214 | – | 8.3 | 4.6e-5 | 0.038 | – | 8.3 (0.9%) | CG42343 | Unknown | No | B7Z153, Q9VRI6 | – | |
| 6649 | – | 8.0 | 6.6e-5 | 0.045 | – | 4.9 (4.7%) | CG7845 | Muscle cell homeostasis | No | Q7K4B2 | Kucherenko et al. (2011) | |
| 5707 | – | 7.9 | 7.2e-5 | 0.045 | – | 3.4 (2.1%) | Mitochondrial ribosomal protein L37 | Structural constituent of ribosome; translation | No | Q9VGW9, Q3YNF4, Q3YNF5 | Kim, Morrow, et al. (2010) | |
| 2372 | – | 7.8 | 7.6e-5 | 0.045 | – | 3.2 (1.9%) | Mitochondrial trifunctional protein α subunit | Long-chain-3-hydroxyacyl-CoA dehydrogenase activity; long-chain-enoyl-CoA hydratase activity; response to starvation; determination of adult lifespan; fatty acid beta-oxidation; wound healing | No | Q8IPE8, Q9V397 | Kishita, Tsuda, Aigaki (2012) | |
| 8490 | – | 7.4 | 1.2e-4 | 0.062 | – | 6.2 (2.0%) | Phosphatidylinositol synthase | CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity; phototransduction | No | Q8IR29, Q8SX37 | Wang and Montell (2006) | |
| 3891 | – | 6.8 | 2.2e-4 | 0.11 | – | 9.4 (0.3%) | CG1607 | Potential amino acid transmembrane transporter activity | No | Q9V9Y0, Q95T33 | – | |
| 2074 | – | 6.5 | 3.1e-4 | 0.14 | – | 4.2 (4.0%) | CG9715 | Unknown | Yes | Q9VVA9, Q960D5 | – | |
| 1584 | – | 6.3 | 4.0e-4 | 0.17 | – | 2.3 (2.7%) | Unextended | Potential role in cellular ion homeostasis | No | A8Y516 | – | |
| 1053 | – | 6.2 | 4.2e-4 | 0.17 | – | 9.1 (0.2%) | Coat protein (coatomer) β | Biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Required for limiting lipid storage in lipid droplets. Involved in innate immune response | No | P45437 | Bard et al. (2006), Beller et al. (2008), Cronin et al. (2009) |
Note.–Gene families are ranked based on their log-likelihood ratios (Δln L). Results of the branch-site test were filtered to keep only internal ant branches of the phylogenetic tree (branches 1 to #6) and with a dS on the tested branch below 1. Results of both tests were filtered to keep families with a good support for the detection of sites evolving under positive selection (BEB posterior probability > 0.9). Manual inspection of the best hits confirmed that the signal of positive selection seemed genuine for all cases, except for family 12370 in the branch-site test results, which was removed from the list.
aExample used in figure 2.