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Table 2 Gene sets of ancestral forms and counts of various events in parsimonious scenarios depending on the gain penalty.

From: Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Gain penalty (g) Number of genes (COGs)
  .1 .2 .3 .4 .5 .6 .7 .8 .9 1 1.25 1.5 2 3 5 7 10
LUCA – genome tree 84 98 109 132 212 214 266 285 310 572 623 733 956 1211 1525 1664 1725
LUCA – rRNA tree 84 112 151 195 271 240 304 293 319 643 645 682 894 1123 1407 1564 1668
Archaeal Ancestor genome tree 390 391 427 521 663 660 732 727 750 977 982 1046 1178 1295 1508 1619 1673
Archaeal Ancestor rRNA tree 390 431 511 599 709 672 740 729 755 922 922 958 1086 1209 1417 1544 1636
Bacterial ancestor genome tree 169 193 243 283 397 415 476 506 532 773 841 986 1259 1582 1879 2028 2091
Bacterial ancestor rRNA tree 169 267 355 525 613 585 653 646 672 925 928 961 1162 1380 1653 1807 1933
HGT genome tree 13241 13001 12315 11464 9462 9312 8733 8365 8315 5495 5136 4238 2646 1295 368 97 13
HGT rRNA tree 15145 14161 12949 11074 9133 9007 8416 8158 8146 5040 4961 4253 2654 1529 546 224 51
Loss genome tree 0 45 220 512 1506 1595 1989 2259 2301 5121 5562 6872 9944 13695 17535 19230 19947
Loss rRNA tree 0 172 478 1135 2100 2175 2567 2763 2773 5879 5977 6997 10137 13301 17489 19539 21050
Total events genome tree 16407 16212 15701 15142 14134 14073 13878 13790 13782 13782 13864 14276 15756 18156 21069 22493 23126
Total events rRNA tree 18311 17499 16593 15375 14399 14348 14149 14087 14085 14085 14104 14416 15957 17996 21201 22929 24267
Single scenarios genome tree 3166 3091 3163 3075 2496 3150 3166 3159 3166 1613 3150 2958 2246 2600 2907 3048 3122
Single scenarios rRNA tree 3166 3139 3164 3147 2494 3144 3166 3152 3166 1806 3108 2894 2399 2587 2982 3081 3154