TABLE 2

Phylogenetic analysis of mtDNA-encoded proteins

Type of
alignmentb
No. of
sites
No. of
constant sites
[(hemi, ech), chor]a[(hemi, chor), ech][hemi, (chor, ech)]
ln LcBPdΔ ln L ± SEBPΔ ln L ± SEBP
<82814852- 54073.4901221.1 ± 16.190630.8 ± 14.5*82
< 42520845-43011.2913422.6 ± 16.886342.1 ± 13.9*3
<8 (-KM)2065807-30143.260906.1 ± 11.724137.6 ± 11.11497
< 4 (-KM)1928800- 25661.548870.1 ± 11.4483111.4 ± 8.9282
  • a Three different topologies relating hemichordates (hemi), echinoderms (ech), and a cephalochordates-vertebrates clade (chor). The first topology is the preferred one by the maximum-likelihood criterion with allthe alignments.

  • b The alignments contain either <8 or <4 contiguous nonconserved sites. In the last two alignments (-KM), all positions with Met and Lys residues were removed.

  • c Log-likelihood values of the preferred topology (ln L), and difference in log likelihood and one standard error of that difference (Δ ln L ± SE) relative to the preferred topology. * The difference is significant.

  • d Bootstrap proportions supporting each of the three topologies in 10,000 replicates calculated by the RELL method.