Table 1.

Summary of key relationships and support values for phylogenetic analyses of different data coding schemes and taxon composition. Centopomidae includes Lates and Centropomus (Greenwood, 1976; Li et al., 2011). For each analysis the basic characteristics and outcomes are reported.

Data Scheme	Numer of Partitions	Pleuronectiformes Monophyletic?	Bootstrap Support or Posterior Probability For Pleuronectoidei	Sister Group of Pleuronectoidei	Bootstrap Support or Posterior Probability for Sister of Pleuronectoidei	Sister of Psettodes	Bootstrap Support or Posterior Probability for Sister of Psettodes
ML Analysis
1N2N3N	18	No	100	Centropomidae	32	Toxotes jaculatrix	27
1N2N3RY	18	No	98	Centropomidae	73	Toxotes jaculatrix	39
1N2N	18	No	70	Centropomidae	67	Other Carangimorpha, not Pleuronectifomres + Centropomidae excluding Polydactylus sextarius and Eleutheronema rhadinum	21
1N2N3N No Missing Data	18	No	100	Centropomidae	34	Eleutheronema rhadinum	47
1N2N3RY No Missing Data	18	No	99	Centropomidae	81	Pleuronectiformes+Other Carangimorpha excluding Eleutheronema rhadinum	34
1N2N No Missing Data	18	No	92	Centropomidae	87	Other Carangimorpha excluding Toxotes jaculatrix and Eleutheronema rhadinum	16
1N2N3N Rogue Taxa Removed	18	No	100	Centropomidae	29	Polydactylus sextarius + Eleutheronema rhadinum	36
1N2N Rogue Taxa Removed	18	No	82	Centropomidae	75	Other Carangimorpha, not Pleuronectifomres + Centropomidae, excluding Polydactylus sextarius and Eleutheronema rhadinum	42
GTR-CAT Model
1N2N3RY	6	No	0.87	Centropomidae	0.5	Part of four branch polytomy at base of Carangimorpha	0.99
1N2N	6	No	0.94	Polytomy including Centropomidae	-	Part of five branch polytomy at base of Carangimorpha	-
p4 Multiple Composition Vectors
1N2N3N	6	No	59	Centropomidae	54	Eleutheronema rhadinum + Polydactylus sextarius	100
1N2N3RY	6	No	100	Centropomidae	98	Other Carangimorpha excluding Toxotes jaculatrix, Eleutheronema rhadinum and Polydactylus sextarius	99
1N2N	6	No	90	Centropomidae	90	Pleuronectiformes+Other Carangimorpha excluding Eleutheronema rhadinum and Polydactylus sextarius	66
p4 Multiple Composition Vectors and Rate Matrices
1N2N3N	6	No	61	Centropomidae	56	Eleutheronema rhadinum + Polydactylus sextarius	100
1N2N3RY	6	No	100	Centropomidae	97	Other Carangimorpha excluding Toxotes jaculatrix, Eleutheronema rhadinum and Polydactylus sextarius	99
1N2N	6	No	98	Centropomidae	100	Other Carangimorpha excluding Toxotes jaculatrix, Eleutheronema rhadinum and Polydactylus sextarius	65
BEAST
1N2N3RY	6	No	1	Centropomidae	0.98	Toxotes jaculatrix	0.52