Table 1.
LUCA and pre-LUCA clans’ ancestral amino acid frequencies are divided by post-LUCA clan’s ancestral amino acid frequencies to produce measures of relative usage
| Amino acid | LUCA usage | LUCA usage SE | Pre-LUCA usage | Pre-LUCA usage SE |
|---|---|---|---|---|
| V | 1.12 | 0.0241 | 1.04 | 0.0205 |
| G | 1.11 | 0.0283 | 1.09 | 0.0241 |
| I | 1.1 | 0.0325 | 1.07 | 0.0351 |
| M | 1.08 | 0.0386 | 1.1 | 0.0383 |
| A | 1.07 | 0.0317 | 1.03 | 0.0297 |
| T | 1.07 | 0.0369 | 1.05 | 0.0362 |
| H | 1.04 | 0.0416 | 1.17 | 0.0486 |
| E | 1.03 | 0.0357 | 0.911 | 0.0357 |
| C | 1.01 | 0.0722 | 1.03 | 0.0844 |
| P | 1.01 | 0.0282 | 1.04 | 0.0255 |
| K | 0.974 | 0.038 | 0.901 | 0.0334 |
| S | 0.972 | 0.0265 | 1.02 | 0.0239 |
| D | 0.968 | 0.027 | 0.988 | 0.0363 |
| L | 0.942 | 0.0256 | 0.962 | 0.032 |
| N | 0.934 | 0.0374 | 0.996 | 0.0432 |
| R | 0.916 | 0.0265 | 0.915 | 0.0271 |
| F | 0.895 | 0.032 | 1.02 | 0.0394 |
| Y | 0.858 | 0.0341 | 0.982 | 0.0309 |
| Q | 0.827 | 0.031 | 0.847 | 0.0304 |
| W | 0.649 | 0.0476 | 0.865 | 0.0526 |
The SE of the amino acid usages were calculated using an approximation derived from a Taylor expansion of the ratio (51). For each of the 20 ancestral amino acid frequencies, the SE of the weighted means across all the clans within the LUCA and pre-LUCA phylostrata (weighted by the maximum number of ancestral sites across all Pfams in a given clan) were calculated using the weighted_se() function in the diagis R package (52). See Materials and Methods for more detail.