Table 1 Cumulative P-values for testing prior tree hypothesis T₁ on retrotransposon counts¹⁸ amended from^16. Additional P-values can be calculated at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/.

Multi-directional searches: markers are equally identifiable for the three trees				One-directional searches: markers for the third tree are unidentifiable
Insertion count	P value^a	Insertion count	P value^a	Insertion count	P_B value^b	Insertion count	P_B value^b
[1 0 0]	0.3333	[5 1 0]	0.0178	[1 0 X]	0.5000	[5 1 X]	0.1094
[1 1 0]	0.5556	[5 2 0]	0.0453	[1 1 X]	0.7500	[5 2 X]	0.2266
[2 0 0]	0.1111	[6 0 0]	0.0014	[2 0 X]	0.2500	[6 0 X]	0.0156
[2 1 0]	0.2593	[6 1 0]	0.0069	[2 1 X]	0.5000	[6 1 X]	0.0625
[2 2 0]	0.4074	[6 2 0]	0.0197	[2 2 X]	0.6875	[6 2 X]	0.1445
[3 0 0]	0.0370	[7 0 0]	0.0005	[3 0 X]	0.1250	[7 0 X]	0.0078
[3 1 0]	0.1111	[7 1 0]	0.0026	[3 1 X]	0.3125	[7 1 X]	0.0352
[3 2 0]	0.2099	[7 2 0]	0.0083	[3 2 X]	0.5000	[7 2 X]	0.0898
[4 0 0]	0.0123	[8 0 0]	0.0002	[4 0 X]	0.0625	[8 0 X]	0.0039
[4 1 0]	0.0453	[8 1 0]	0.0010	[4 1 X]	0.1875	[8 1 X]	0.0195
[4 2 0]	0.1001	[8 2 0]	0.0034	[4 2 X]	0.3438	[8 2 X]	0.0547
[5 0 0]	0.0041	[9 0 0]	0.00005	[5 0 X]	0.0313	[9 0 X]	0.0020

^aFor cases when all markers are observable (P); ^bRevised values to accommodate the single reference genome bias (P_B), excluding markers supporting T₃.

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