Supplementary Table 4. Likelihood (ln) scores for gene trees and AU test P values comparing gene tree topologies estimated with
RAxML against the concatenation topology (from Fig. 3, pruned to only include taxa in the subset), calculated under homogeneous
(RAxML) and non-homogeneous (nhPhyML) optimization. The nhPhyML model used unlimited base equilibrium frequencies.
Values in bold highlight cases in which the concatenation topology resulted in either better or non-significantly worse likelihood
scores.
Marker
16S
EHHADH
GCS1
GPR61
IRBP
KIAA
MYH6
PLAGL2
RAG1
RH
RIPK4
RNF213
SLC10A3
SIDKEY
UBE3A
UBE3A-like
ZN503
ZN536
*P ≤ 0.05
**P ≤ 0.01
Gene tree
-14864.72
-8936.46
-12262.50
-8302.04
-8321.28
-6132.85
-6618.56
-5078.39
-13538.95
-7166.99
-6147.82
-8037.27
-7008.45
-8663.05
-6653.75
-4980.31
-8451.09
-10140.27
Homogeneous model (RAxML)
Total evidence tree
AU test – P value
-14869.64
0.0001**
-9147.42
0.0002**
-12713.50
0.0000**
-8549.23
0.0040**
-8585.61
0.0060**
-6536.42
0.0080**
-6991.80
0.0000**
-5372.97
0.0020**
-13967.43
0.0310*
-7440.59
0.0010**
-6434.12
0.0260*
0.0570
-8311.86
-7287.24
0.0030**
-8992.74
0.0230*
-6921.39
0.0020**
-5304.45
0.0000**
-8823.15
0.0001**
-10610.81
0.0180*
Non-homogeneous model (nhPhyML)
Gene tree
Total evidence tree
AU test – P value
-15021.10
-15829.28
0.0000**
-9067.83
0.3790
-9059.33
-12956.40
-13025.29
0.0360*
-8529.00
0.0010**
-8456.60
-8586.84
0.1050
-8559.22
-6852.32
0.4110
-6846.32
-6956.23
-7506.98
0.0000**
-5828.11
0.0030**
-5729.62
-14292.88
-14389.86
0.0001**
-7845.15
-7858.83
0.3800
-6251.58
-6468.04
0.0000**
-8496.57
0.0360*
-8452.17
-7665.74
0.0000**
-7534.02
-8866.67
0.1270
-8839.72
-6923.85
-7129.33
0.0000**
-5572.22
-5699.94
0.0010**
-9162.30
-9263.49
0.0290*
-11086.74
0.0720
-11053.38
1