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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.