Table 1 |
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|
Support for monophyly of the genus Trypanosoma in protein phylogenies constructed by three different methods. |
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|
Family |
Aligned sites |
Trypanosoma species 1 |
ME 2 |
MP |
QML |
|
|
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|
Actin |
375 |
Tb, Tcr |
yes (A,71) 3 |
yes (A,71) |
yes (A,100) |
|
Adenylate cyclase |
1142 |
Tb,Tcr |
yes (A, 63) |
yes (A, 94) |
no |
|
ATPase, subunit 6 |
225 |
Tb,Tcr |
no (B,37) |
yes (A, 92) |
no |
|
α tubulin |
451 |
Tb,Tcr |
yes (A,99) |
yes (A,99) |
yes (A,100) |
|
β tubulin |
442 |
Tb,Tcr |
yes (A,98) |
yes (A,96) |
yes (A,100) |
|
Calreticulin |
393 |
Tco,Tcr |
yes (A,95) |
yes (A,97) |
yes (A,100) |
|
Cdc2-related kinase 3 |
290 |
Tb,Tcr |
yes (A,97) |
yes (A,68) |
yes (A,99) |
|
CDKRS |
73 |
Tb,Tcr |
yes (A,96) |
yes (A,72) |
yes (A,100) |
|
CRK1 |
289 |
Tb,Tco,Tcr |
yes (A,100) |
yes (A,99) |
yes (A,98) |
|
Cyclophilin A |
164 |
Tb,Tco,Tcr, Tvi |
no (B,34) |
no (B,49) |
no |
|
Cysteine proteinase |
223 |
Tb,Tco,Tcr,Tr |
yes (A,98) |
yes (A,98) |
yes (A,98) |
|
Cytochrome b |
171 |
Tb,Tcr |
no |
no (B,60) |
no |
|
Cytochrome-c oxidase II |
198 |
Tb,Tcr |
no (B,66) |
no (B,35) |
no (B,87) |
|
DHFR-TS |
455 |
Tb,Tcr,Tve |
no (B,49) |
no (B,65) |
yes (A,100) |
|
DNA-directed RNA polymerase II, large subunit |
1599 |
Tb,Tcr |
yes (A,99) |
yes (A,100) |
yes (A,100) |
|
DNA topoisomerease II |
1171 |
Tb,Tcr |
yes (A,100) |
yes (A,100) |
yes (A,100) |
|
EFH5 |
147 |
Tb,Tcr |
yes (A,78) |
yes (A,67) |
no |
|
EF-1a |
444 |
Tb,Tcr |
yes (A,99) |
yes (A,93) |
yes (A,100) |
|
GAPDH |
337 |
Tb,Tcr,Tev, Tr,Tvi |
yes (A,98) |
yes (A,94) |
yes (A,100) |
|
Glucose-6-phosphate isomerase |
550 |
Tb,Tcr |
yes (A,97) |
yes (A,70) |
yes (A,100) |
|
GRP78 |
624 |
Tb,Tco,Tcr |
yes (A,98) |
yes (A,97) |
yes (A,100) |
|
HEXBP |
161 |
Teq,Tcr |
yes (A,100) |
yes (A,100) |
yes (A,100) |
|
HGPRT |
177 |
Tb,Tcr |
yes (A,96) |
yes (A,60) |
yes (A,94) |
|
HSP60 |
557 |
Tb,Tcr |
yes (A,85) |
yes (A,96) |
yes (A,100) |
|
HSP70 |
511 |
Tb,Tcr |
yes (A,79) |
yes (A,50) |
yes (A,100) |
|
HSP90 |
613 |
Tb,Tcr |
yes (A,99) |
yes (A,100) |
yes (A,100) |
|
Malate dehydrogenase |
310 |
Tb,Tcr |
yes (A,64) |
yes (A,57) |
no |
|
MDR-A |
877 |
Tb,Tcr |
yes (A,99) |
yes (A,100) |
yes (A,100) |
|
MDR-E |
877 |
Tb,Tcr |
yes (A,100) |
yes (A,100) |
yes (A,100) |
|
Oligopeptidase B |
667 |
Tb,Tcr |
yes (A,99) |
yes (A,100) |
yes (A,100) |
|
PAR-2 |
328 |
Tb,Tcr |
yes (A,81) |
yes (A,81) |
no (B,87) |
|
PAR-3 |
328 |
Tb,Tcr |
yes (A,58) |
yes (A,66) |
yes (A,51) |
|
Periredoxin |
188 |
Tb,Tcr |
yes (A,90) |
yes (A,51) |
yes (A,99) |
|
Proteasome subunit α-5 |
237 |
Tb,Tcr |
yes (A100) |
yes (A,99) |
yes (A,100) |
|
Protein kinase A reg. subunit |
372 |
Tb,Tcr |
yes (A,97) |
yes (A,99) |
yes (A,100) |
|
Pteridine reductase |
238 |
Tb,Tcr |
yes (A,94) |
yes (A,55) |
yes (A,100) |
|
P-type H+-ATPase |
832 |
Tb,Tcr |
yes (A,76) |
no (B,53) |
no (B,91) |
|
Ribosomal protein P0 |
312 |
Tb,Tcr |
yes (A,97) |
yes (A,97) |
yes (A,100) |
|
S-adenosyl methionine decarboxylase |
324 |
Tb,Tcr |
yes (A,63) |
no (B,68) |
yes (A,72) |
|
THT |
432 |
Tb,Tco,Tcr, Tvi |
no (B,94) |
no (B,86) |
no (B,96) |
|
TPIS |
247 |
Tb,Tcr |
yes (A,98) |
yes (A,95) |
yes (A,92) |
|
Trypanothione reductase |
407 |
Tb, Tco, Tcr, Tve |
yes (A,100) |
no (B,100) |
yes (A,100) |
|
|
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|
1 Species abbreviations: Tb = Trypanosoma brucei; Tco = T. congolense; Tcr = T. cruzi; Teq = T. equiperdum; Tev = T. evansi; Tr = T. rangeli; Tve = T. vespertilionis; Tvi = T. vivax. 2 Phylogenetic methods: ME = minimum evolution [9]; MP = maximum parsimony [11]; QML = quartet maximum likelihood [10]. ME trees were constructed using the gamma-corrected amino acid distance [15], and the parameter of the gamma distribution was estimated by the TREEPUZZLE program [10]. QML trees were constructed assuming the JTT model of amino acid evolution [21] and that rates varied among sites following a gamma distribution. Amino acid sequences were aligned using the CLUSTALW program [22]. 3 Table entries indicate whether tree supported ("yes") or did not support ("no") monophyly of Trypanosoma. "A" and "B" refer to the alternative topologies illustrated in Figure 3. The numbers indicate the confidence level for the interior branch in the trees. For ME and MP, support is the percentage of 1000 bootstrap pseudo-samples supporting the interior branch. For QML, support is the percent of puzzling steps supporting the interior branch. |
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|
Hughes and Piontkivska Kinetoplastid Biology and Disease 2003 2:15 doi:10.1186/1475-9292-2-15 |
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