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

Jackson, Andrew P

doi:10.1186/1471-2148-7-54

BMC Ecology and Evolution

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	-	-	-	-	-	-	-	-	-

* 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.
^† Sequence divergence is expressed using the rate of synonymous (D_s) and non-synonymous (D_n) substitutions per site.
^# 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.

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