Summary of Our Conclusions and of the Analyses Reported in the Paper byHughes et al. (2001) [i]
| Gene family genes | Abbrev in OMIM | Hughes' abbrev (when different) | Phylogenetic analyses H-Fig. 1 | Duplication time estimates H-Fig. 3 | Phylogenetic consistency H-Fig. 4+5 | Total Hughes et al | Our conclusion |
| 16 gene fam | 15 gene fam | 7 gene fam | 42 gene fam | 42 gene fam | |||
| Acetylcholine rec (nicot.) | ACHR | N.A. | * | ||||
| Acetyl-coA carboxylase | ± | ± | |||||
| Actin | ACT | − | − | − | |||
| ACTB-ACTG1 | + | ||||||
| ACTG2 (ACTH)-ACTA2 (ACTSA) | * (+) | ||||||
| ACTA1-ACTC | * (+) | ||||||
| Acyl-coA dehydrogenase | ACAD | − | − | ± | |||
| ADP-ribosylation factor | ARF | − | − | ± | |||
| Anlon exchanger (SLC4A) | SLC4A | AE | − | − | + (◊) | ||
| Aquaporin | AQP | − | − | ± | |||
| Arrestin | ARR | − | − | * | |||
| Brain amilor, sens. Na ch | ACCN | BNAC | + | + | + | ||
| Cyclin-dependent kinase | CDK | − | − | − | ± | ||
| Enolase | ENO | ENOL | − | − | * (+) | ||
| ERBB receptor protein-TK | ERBB | − | − | − | + (◊) | ||
| Even-skipped | EVX | ± | + | ||||
| Frizzled | FZD | ± | + | ||||
| GLI zinc-finger protein | GLI | + | − | − | + (◊) | ||
| Glucagon | GCG | − | − | + | |||
| Glucose transporter (SLC2A) | SLC2A | GLUT | + | + | * (+) | ||
| G protein-coupled receptor | GPR | − | − | ± | |||
| G nucleotide binding prot. | GNB | − | − | * (+) | |||
| Hedgehog | HH | + | + | + | |||
| Hepatocyte nuclear factor | TCF | HNF | ± | ± | |||
| Immunoglobulin-related | IG | + | + | ± | |||
| Inhibin | INHB | N.A. | + | ||||
| Insulin-like GF-BP | IFGBP | IGBP | − | − | + (◊) | ||
| Integrin α | ITGA | INTA | − | − | − | ||
| ITGAv, 5 and 2B | + | ||||||
| ITGA3, 6 and 7 | + | ||||||
| ITGA4 and 9 | + | ||||||
| Integrin β | ITGB | INTB | − | − | − | ||
| ITGB3, 6 and 8 | + | ||||||
| ITGB1, 4 and 7 | + | ||||||
| Intermediate filament | IF | − | − | ± | |||
| Myosin light chain | MYL | ± | + | ||||
| NAB transcriptional regul. | NAB | ± | ± | ||||
| NRAMP (SLC11A) | SLC11A | NRAMP | ± | + | |||
| Nuclear hormone receptor | NHR | − | − | − | |||
| RARA-RARG | + | ||||||
| NR4A1-NR4A2 | + | ||||||
| Tachykinin (neurokinin) | TAC | NKN | − | − | + | ||
| Nitric oxide synthase | NOS | − | − | + (◊) | |||
| Olfactory receptor | OR | N.A. | ± | ||||
| Pancr. polypeptide/NPY | NPY | ± | + | ||||
| Peroxidase | ± | * | |||||
| Proteasome β subunit | PSMB | − | − | * | |||
| RAD52 | RAD52 | − | − | * | |||
| Ras-related | RASR | − | − | ± | |||
| Sodium channel | SCN | − | + | − | + (◊) | ||
| Synaptobrevin | SYB | − | − | * | |||
| Wnt-related | WNT | − | − | ± | |||
| Total supporting | 0+ | 6+ | 0+ | 4+ | 20+ (6 ◊) | ||
| Total inconsistent | 16− | 9− | 7− | 26− | 0− | ||
| Total not informative | 9± | 13± | |||||
| 3 N.A. | 9*(3 of which +) Including actins: 11* (5 of which +) |
[i] In their figures 1, 3, and 4+5.
[ii] +, The analysis supports chromosome duplication vs. individual gene duplication; −, the analysis rejects chromosome duplication; ±, the analysis is not informative. N.A., the family was not analyzed. The last column shows our interpretation for each gene family considering the totality of evidence, including chromosomal localization. (◊) The gene family's phylogeny is not consistent with that of the Hox gene family; however, in all of these cases very few taxa were included. *, The gene family members are located outside of the extended Hox cluster. “(+)” indicates support for duplication concomitantly with large chromosome regions other than those bearing the Hox clusters (i.e., they belong to a different paralogon).