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Table 2 Probabilistic count of Emx gene duplications based on the ML method

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

Cyclostome included

ML tree topology

N bef

N aft

N cyc

N unk

Sea lamprey and hagfish

(((((g3,g1),g2),cB),cA),outgroup);

1.36

1.32

0.09

0.18

Sea lamprey

((((g3,g1),g2),(cB,cA)),outgroup);

1.21

0.93

0.63

0.21

Hagfish

((((cB,g2),(g3,g1)),cA),outgroup);

2.02

0.56

0.02

0.34

  1. Abbreviation: g1 gnathostome Emx1, g2 gnathostome Emx2, g3 gnathostome Emx3, cA cyclostome EmxA, cB cyclostome EmxB. See Kuraku et al. [11] for details of N bef, N aft, N cyc, and N unk.
  2. According to the results of ProtTest3, JTT+I+Γ4 model was employed for the analysis with both sea lamprey and hagfish, while JTT+Γ4 model was employed for the analyses with either of sea lamprey and hagfish.