Skip to main content

Table 1 Tandem gene arrays in Trypanosoma brucei: phylogenetic distributions, sequence variation and results of SH tests.

From: Tandem gene arrays in Trypanosoma brucei: Comparative phylogenomic analysis of duplicate sequence variation

Identifier Description Distribution*: Average sequence divergence: Cladistic criterion#:        
   Tb Tbg Tco Tv Tc Lm D s D n Bootstrap Posterior probability Log Likelihood:     
             Optimal Orthologous Concerted
               Δ-lnL p   Δ-lnL p
3 α and β-tubulin X X X X X   0.0000 0.0000 500 1.00 - - - - - - -
4 histone H3 X X X     0.0000 0.0000 500 1.00 - - - - - - -
6 Tb927.1.4540 X X X X    0.2068 0.1227 423 1.00 -2448.9 -3532.7 -1083.8 0.0001 -2448.9 0 0.759
9 65 kDa invariant surface glycoprotein X X      0.1545 0.0763 - - - - - - - - -
12 Tb927.2.5290 X X      0.1559 0.0775 - - - - - - - - -
13 Tb927.3.2550 X X      0.1557 0.0859 - - - - - - - - -
17 Tb927.3.4070 X X X X X X 0.1680 0.0664 499 1.00 -11194.3 -14196.6 -3002.3 0.0001 -11204.7 -10.4 0.448
18 73 kDa paraflagellar rod protein X X X X X X 0.0010 0.0000 500 0.55 -5510.7 -7529.3 -2018.6 0.0001 -5510.7 0 0.506
20 Tb927.3.5690 X       0.4137 0.2155 - - - - - - - - -
24 serine/threonine-protein phosphatase PP1 X X X X X X 1.5094 0.2409 500 1.00 -5352.4 -6392 -1039.6 0.0001 -6068.6 -716.2 0.0001
26 amino acid transporter X X X X    0.3427 0.1226 493 1.00 -6465.23 -6892.64 -427.41 0.0001 -6465.23 0 0.749
28 receptor-type adenylate cyclase GRESAG 4 X X      0.1041 0.0647 - - - - - - - - -
29 amino acid transporter 10 X X      0.5819 0.2133 - - - - - - - - -
30 UDP-GlcNAc-dependent glycosyltransferase X X X     0.0425 0.0286 500 1.00 -4356.7 -6723.1 -2366.4 0.0001 -4366.8 -10.1 0.423
32 75 kDa invariant surface glycoprotein X X      1.1899 0.4529 - - - - - - - - -
39 histone H4 X X X X X   0.0000 0.0000 500 0.95 - - - - - - -
42 receptor-type adenylate cyclase GRESAG 4 X       0.0262 0.0135 - - - - - - - - -
43 cysteine peptidase X X X X X   0.0000 0.0000 499 1.00 - - - - - - -
44 Tb927.6.1300 X       0.0220 0.0043 - - - - - - - - -
47 S-adenosylmethionine synthetase X X X     0.0000 0.0000 500 1.00 - - - - - - -
55 retrotransposon hot spot protein 7 (RHS7) X X      0.0658 0.0647 - - - - - - - - -
57 histone H2A X X X X X   0.0000 0.0000 500 0.98 - - - - - - -
61 Tb927.7.5930 X X      0.3745 0.1181 - - - - - - - - -
62 receptor-type adenylate cyclase GRESAG 4 X X      0.0490 0.0337 - - - - - - - - -
62a Tb927.7.6110 X X X     0.8373 0.2748 493 na -3876.7 -3991.1 -114.4 0.0001 -3876.7 0 0.501
64a nucleolar RNA-binding protein X X X X X X 0.7310 0.5628 412 1.00 -2830.7 -2822.5 8.2 0.482 -3175.9 -345.2 0.0001
67 major surface protease gp63 X X X     0.0083 0.0090 500 1.00 -4693 -6266 -1573 0.0001 -4677.2 15.8 0.391
72 amino acid transporter X X X X X   0.0127 0.0062 500 na -4798.5 -6752.3 -1953.8 0.0001 -4872.6 -74.1 0.11
73 PFR2 69 kDa paraflagellar rod protein X X X X X X 0.0000 0.0000 500 1.00 - - - - - - -
75 Tb927.8.6700 X X X X X X 0.7726 0.3661 500 1.00 -15754.1 -18536.1 -2782 0.0001 -15812.6 -58.5 0.194
80 amino acid transporter X X X     0.7609 0.1607 497 1.00 -5761 -6677.5 -916.5 0.0001 -6844.1 -1083.1 0.0001
80a receptor-type adenylate cyclase GRESAG 4 X X X     0.0624 0.0361 480 1.00 -19488.9 -25099.5 -5610.6 0.0001 -19498.2 -9.3 0.468
82 fatty acyl CoA syntetase X X X X X X 1.2045 0.3632 na na -19561.6 -19987.6 -426 0.001 -21771.5 -2209.9 0.0001
85 Tb09.v1.0470 X X      0.5568 0.2667 - - - - - - - - -
87a Tb09.211.1000 X X X X    0.1673 0.0786 500 1.00 -7085 -8471 -1386 0.0001 -7092.9 -7.9 0.42
89 glycerol kinase X X X X X X 0.0050 0.0012 374 1.00 -3369.3 -3883.5 -514.2 0.0001 -3379.3 -10 0.425
90 ADP-ribosylation factor X X X X X   0.0119 0.0012 500 1.00 -1805.1 -2709.1 -904 0.0001 -1805.1 0 0.736
93 Bloodstream Alanine Rich Protein (BARP) X X X     0.5033 0.2534 500 na -4060.3 -4639.6 -579.3 0.0001 -4063.4 -3.1 0.457
103 Tb10.70.0040 X X X X X X 0.4821 0.2926 500 1.00 -9380.5 -10906.8 -1526.3 0.0001 -9380.5 0 0.773
105a expression site-associated gene (ESAG) protein X X X X    0.5109 0.4099 500 1.00 -8318.4 -10357.7 -2039.3 0.0001 -8384.3 -65.9 0.104
106 procyclin-associated gene X X X     1.6527 0.9281 346 0.91 -8085.9 -8130.6 -44.7 0.014 -8221.1 -135.2 0.0001
107 histone H2B X X X X X   0.0000 0.0000 499 0.99 - - - - - - -
109c Tb10.389.0830 X X X X X   1.8231 0.6691 na na -6267.9 -7327.1 -1059.2 0.0001 -6387 -119.1 0.017
112 DNA polymerase kappa X X X X X X 0.2129 0.0892 500 1.00 -5710 -6440.8 -730.8 0.0001 -5710 0 0.511
113 cation transporter X X X X X X 1.6028 0.2454 na 1.00 -4974.1 -7292.3 -2318.2 0.0001 -4982.4 -8.3 0.444
117 calmodulin X X X X X X 0.0056 0.0000 414 1.00 - - - - - - -
x1 ribonucleoside-diphosphate reductase small chain X X      0.0101 0.0126 - - - - - - - - -
  1. * Codes for species names: Tb: T. brucei; Tbg: T. b. gambiense; Tco: T. congolense; Tv: T. vivax; Tc: T. cruzi; Lm: L. major. Presence of a homologous locus within conserved gene order is shown by a cross X.
  2. Sequence divergence is expressed using the rate of synonymous (Ds) and non-synonymous (Dn) substitutions per site.
  3. # Monophyly of array copies was assessed through non-parametric bootstraps of a ML phylogeny (500 replicates) and posterior probabilities in a Bayesian phylogeny ('na' denotes that monophyly was not recovered by the Bayesian tree). SH tests compared the likelihood of an optimal topology with 'orthologous' and 'concerted' scenarios; significant p-values are shown in bold and indicate that the scenario concerned was significantly less likely that the optimal topology. The cladistic criterion was only applied to arrays with widespread distributions.