Table 1 Human, chimpanzee and gorilla Log-likelihoods (rounded to closest integer) of the MLEs for three rooted trees under the nonstationary (NONSTA), stationary (STA) and reversible (REV) models. If NONSTA or STA places the root correctly, the corresponding log likelihood appears in bold.
From: Rooting a phylogenetic tree with nonreversible substitution models
gene | root placement | NONSTA | STA | REV |
|---|---|---|---|---|
human | -1320 | -1324 | -1324 | |
ATP6 | chimp | -1318 | -1323 | -1324 |
gorilla | -1318 | -1322 | -1324 | |
human | -384 | -389 | -392 | |
ATP8 | chimp | -384 | -389 | -392 |
gorilla | -384 | -389 | -392 | |
human | -2842 | -2876 | -2877 | |
COX1 | chimp | -2846 | -2874 | -2876 |
gorilla | -2834 | -2875 | -2876 | |
human | -1285 | -1293 | -1295 | |
COX2 | chimp | -1286 | -1294 | -1295 |
gorilla | -1281 | -1292 | -1295 | |
human | -1477 | -1493 | -1496 | |
COX3 | chimp | -1476 | -1493 | -1496 |
gorilla | -1472 | -1493 | -1496 | |
human | -2205 | -2236 | -2236 | |
CYTB | chimp | -2208 | -2235 | -2236 |
gorilla | -2203 | -2235 | -2236 | |
human | -1787 | -1804 | -1805 | |
ND1 | chimp | -1783 | -1804 | -1805 |
gorilla | -1776 | -1802 | -1805 | |
human | -1949 | -1974 | -1975 | |
ND2 | chimp | -1950 | -1974 | -1975 |
gorilla | -1941 | -1974 | -1975 | |
human | -663 | -679 | -680 | |
ND3 | chimp | -666 | -679 | -680 |
gorilla | -665 | -679 | -680 | |
human | -2593 | -2612 | -2613 | |
ND4 | chimp | -2589 | -2612 | -2613 |
gorilla | -2579 | -2612 | -2613 | |
human | -519 | -525 | -525.8 | |
ND4L | chimp | -523 | -525 | -525.8 |
gorilla | -520 | -526 | -525.8 | |
human | -3600 | -3624 | -3629 | |
ND5 | chimp | -3611 | -3628 | -3629 |
gorilla | -3583 | -3628 | -3629 | |
human | -913 | -917 | -918 | |
ND6 | chimp | -912 | -917 | -918 |
gorilla | -913 | -917 | -918 |