Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes

Table 1 ML analysis of vertebrate Emx gene phylogeny

Rank	Tree topology	log L	Δlog L ± SE	P value
Rank	Tree topology	log L	Δlog L ± SE	1sKH	SH
1	(((((g1,g3),g2),cB),cA),outgroup)	-1909.94	ML	1.00	1.00
2	(((((g1,g3),cB),g2),cA),outgroup)	-1910.93	0.99 ± 1.84	0.27	0.82
3	((((g1,g3),(g2,cB)),cA),outgroup)	-1910.93	0.99 ± 1.84	0.26	0.82
4	(((((g1,g3),g2),cA),cB),outgroup)	-1911.62	1.68 ± 2.27	0.22	0.74
5	((((g1,g3),g2),(cA,cB)),outgroup)	-1911.62	1.68 ± 2.27	0.20	0.74
6	((((g1,g3),(cA,cB)),g2),outgroup)	-1912.39	2.45 ± 2.56	0.17	0.63
7	(((g1,g3),((cA,cB),g2)),outgroup)	-1912.39	2.46 ± 2.55	0.17	0.63
8	((((g1,g3),(g2,cB)),cA),outgroup)	-1912.61	2.68 ± 2.91	0.17	0.60
9	((((g1,g3),cB),(g2,cA)),outgroup)	-1912.61	2.68 ± 2.91	0.16	0.60
10	(((((g1,g3),cA),g2),cB),outgroup)	-1912.61	2.68 ± 2.91	0.17	0.60
11	((((g1,g3),cA),(g2,cB)),outgroup)	-1912.61	2.68 ± 2.91	0.17	0.60
12	(((((g1,g3),cB),cA),g2),outgroup)	-1912.61	2.68 ± 2.91	0.19	0.60
13	(((g1,g3),((g2,cB),cA)),outgroup)	-1912.61	2.68 ± 2.91	0.18	0.60
14	(((g1,g3),((g2,cA),cB)),outgroup)	-1912.61	2.68 ± 2.91	0.18	0.60
15	(((((g1,g3),cA),cB),g2),outgroup)	-1912.61	2.68 ± 2.91	0.19	0.60

Abbreviation: SE standard error, 1sKH One-sided Kishino-Hasegawa test, SH Shimodaira-Hasegawa test, g1 gnathostome Emx1, g2 gnathostome Emx2, g3 gnathostome Emx3, cA cyclostome EmxA, cB cyclostome EmxB.

ISSN: 2730-7182