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

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

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

ISSN: 2730-7182