The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes

Table 4 Results of tests (p-values) comparing the best tree topology with alternatives for data sets with 7 and 11 taxa including all mitochondrial markers (ALL) and excluding the control region (ALL-CR)

Data set	Tree	ALL						ALL-CR
Data set	Tree	AU	NP	BP	PP	SH	wSH	AU	NP	BP	PP	SH	wSH
7 taxa	A	0.892	0.756	0.756	0.995	0.942	0.965	0.841	0.680	0.680	0.986	0.930	0.917
	B	0.257	0.105	0.105	0.003	0.525	0.486	0.183	0.037	0.037	0.003	0.434	0.414
	C	0.008	0.004	0.004	6.0E-12	0.025	0.029	0.020	0.009	0.009	1.0E-08	0.050	0.059
	D	0.075	0.039	0.039	2.0E-06	0.184	0.161	0.303	0.229	0.229	0.006	0.450	0.457
	E	0.225	0.096	0.096	2.0E-03	0.501	0.447	0.171	0.045	0.045	0.004	0.449	0.421
11 taxa	F	0.833	0.500	0.495	0.900	0.976	0.989	0.552	0.160	0.158	0.194	0.926	0.921
	G	0.133	0.014	0.014	5.0E-05	0.525	0.501	0.386	0.056	0.055	0.044	0.883	0.882
	H	0.004	0.001	0.001	7.0E-15	0.031	0.022	0.108	0.056	0.055	6.0E-06	0.310	0.303
	I	0.428	0.150	0.150	0.062	0.820	0.725	0.603	0.188	0.185	0.231	0.942	0.946
	J	1.0E-07	4.0E-08	0.000	8.0E-38	2.0E-05	3.0E-05	0.001	1.0E-04	1.0E-04	1.0E-15	0.008	0.009
	K	5.0E-07	5.0E-08	3.0E-07	9.0E-42	6.0E-06	3.0E-05	0.001	1.0E-04	1.0E-04	4.0E-16	0.007	0.016
	L	0.323	0.101	0.101	0.002	0.671	0.616	0.498	0.113	0.110	0.095	0.894	0.900
	M	0.326	0.095	0.094	0.002	0.702	0.643	0.436	0.080	0.078	0.066	0.889	0.885
	N	0.113	0.009	0.009	4.0E-05	0.497	0.474	0.398	0.054	0.053	0.058	0.886	0.896
	O	0.319	0.085	0.084	0.034	0.809	0.660	0.536	0.132	0.129	0.163	0.935	0.924
	P	0.172	0.025	0.024	9.0E-05	0.530	0.516	0.479	0.104	0.102	0.089	0.888	0.882
	Q	0.180	0.027	0.026	1.0E-04	0.553	0.536	0.411	0.076	0.075	0.061	0.880	0.859

The topologies were presented in Fig. 8. Underlined letters and numbers refer to the best topology for the given data set. The following tests were used: approximately unbiased (AU), bootstrap probability calculated from all sets of the scaled replicates (NP), bootstrap probability calculated from one set of replicates (BP), Bayesian posterior probability calculated by the BIC approximation (PP), Shimodaira-Hasegawa (SH) and weighted Shimodaira-Hasegawa (wSH). Values smaller than 0.05 are shown in bold

ISSN: 2730-7182