Table 5 Robustness of inferences about long-term shifts in the intensity of selection pressure at the origin of the human–chimpanzee clade (H5)
Model CModel D
GeneAnalysispSHIFTωBGωFGLRTpSHIFTωBGωFGLRT
NR2C1Original0.360.252.06P = 0.00040.350.262.13P = 0.0004
MG940.370.251.02P = 0.00150.360.271.04P = 0.0017
Gene treeMatchMatchMatchN.A.MatchMatchMatchN.A.
Bootstrap[0.17–0.57][0.11–0.42][0.31–8.32]N.A.[0.18–0.47][0.18–0.41][0.4–9.41]N.A.
NR1D1Original0.0020126.89P = 0.00320.060.814.88P = 0.0465
MG940.0020162.68P = 0.00570.070.744.19P = 0.0511
Gene treeMatchMatchMatchN.A.MatchMatchMatchN.A.
Bootstrap[0–8e-3][0–2.12]a[8.84–99]N.A.[0.02–0.13][0.38–1.43][0–22.31]N.A.
PGROriginal0.300.542.57P = 0.00360.300.542.57P = 0.0036
MG940.300.592.70P = 0.00490.300.602.68P = 0.0049
Gene tree0.310.542.54P = 0.00110.310.542.54P = 0.0038
Bootstrap[0.18–0.5][0.22–0.7][0.65–5.11]N.A.[0.22–0.42][0.41–0.68][0.77–8.37]N.A.
NR2E3Original0.220.413.39P = 0.00490.220.413.39P = 0.0022
MG940.210.453.97P = 0.00510.210.453.94P = 0.0015
Gene tree*********N.A.*********N.A.
Bootstrap[0.13–0.36][0.26–0.71][0.36–99]N.A.[0.11–0.34][0.27–0.69][0.6–13.98]N.A.
ESRRBOriginal0.270.120.61P = 0.00710.270.120.61P = 0.0071
MG940.260.170.80P = 0.00810.260.170.80P = 0.0081
Gene tree0.270.120.61P = 0.00760.270.130.61P = 0.0076
Bootstrap[0.15–0.84]a[0–0.21]a[0.07–1.92]N.A.[0.1–0.40][0.06–0.22][0.07–1.84]N.A.
  • Robustness and bootstrapping analyses were carried out for genes having at least one q-value of <0.05. For analyses under the gene tree, a match designation indicates that the gene tree was identical to the organismal tree. Analyses that were impossible because the gene tree topology prevented specification of H5 are indicated by ***.

  • a Bimodal distribution.