Table 2.

Shimodaira-Hasegawa test for incongruence among tree topologies for different segments of the core genome alignment

Segment	1	2	3	4	5	6	7	8	9
1	–	10,378	17,700	26,494	11,041	12,955	15,541	8745	12,441
2	7100	–	1908	11,511	4635	4823	5961	5295	8089
3	13,765	5472	–	13,087	10,540	15,234	10,690	10,714	10,508
4	14,493	11,159	7432	–	6411	9415	8898	12,331	13,047
5	13,057	8894	12,004	16,317	–	14,431	10,825	12,648	11,782
6	8979	7055	8418	5340	8223	–	2023	9517	8523
7	15,661	10,081	10,433	6309	11,983	4014	–	13,848	15,287
8	3819	3428	4378	8328	5980	3416	3095	–	3069
9	6474	4660	6312	9181	3951	4865	4985	2889	–

For the sequence data of each segment (rows), the differences in log-likelihood scores between the original tree topology and each other tree topology (columns) are given.

P-values for the differences are all lower than 0.001