Wurdack and Davis — American Journal of Botany 96(8): 1551-1570. 2009. – Data Supplement S1– Page
Wurdack, Kenneth J. and Charles C. Davis. 2009. Malpighiales phylogenetics: Gaining ground on one of the most recalcitrant clades in the angiosperm tree of life. American Journal of Botany 96(8): 1551-1570.
Appendix S1. Data set and tree characteristics for Malpighiales phylogenetic analyses.
Data set
|
cp
atpB
|
cp
matK
|
cp
ndhF
|
cp
rbcL
|
mt
ccmB
|
mt
cob
|
mt
matR
|
mt
nad1B-C
|
mt
nad6
|
No. terminals
|
183
|
178
|
177
|
185
|
169
|
173
|
186
|
178
|
182
|
Aligned length, nt
|
1521
|
1815
|
1349
|
1428
|
569
|
761
|
2838
|
2900
|
554
|
Characters analyzed, nt
|
1429
|
1202
|
1094
|
1398
|
569
|
761
|
1817
|
1640
|
536
|
% missing or
ambiguous data
|
3.63
|
6.79
|
25.5
|
1.16
|
0.945
|
0.392
|
6.02
|
18.2
|
0.780
|
Constant characters, nt
|
701
|
168
|
249
|
718
|
313
|
537
|
681
|
728
|
314
|
Variable characters, nt
|
688
|
1034
|
845
|
680
|
256
|
600
|
1136
|
912
|
222
|
Informative
characters, nt
|
573
|
906
|
725
|
512
|
164
|
161
|
820
|
606
|
148
|
No. MP trees
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
>20,000
|
MP tree length
|
4607
|
8262
|
7229
|
4960
|
676
|
691
|
2973
|
2308
|
698
|
CI
(CI excluding
uninformative sites)
|
0.259
(0.234)
|
0.260
(0.245)
|
0.246
(0.231)
|
0.220
(0.189)
|
0.481
(0.395)
|
0.423
(0.355)
|
0.554
(0.489)
|
0.565
(0.484)
|
0.413
(0.337)
|
RI
|
0.614
|
0.605
|
0.603
|
0.542
|
0.731
|
0.718
|
0.771
|
0.726
|
0.738
|
ML, -ln
|
25843.5018
|
42297.3999
|
35755.4946
|
27608.0444
|
4900.2240
|
5410.5520
|
21658.5258
|
17165.3610
|
5079.6317
|
Data set
|
mt
rps3
|
nu
18S
|
nu
EMB2765
|
nu
PHYC
|
All cp
|
All mt
|
All nu
|
13 gene
full
|
13-gene, no third
positions for
EMB2765
and PHYC
|
No. terminals
|
172
|
188
|
153
|
146
|
186
|
189
|
189
|
190
|
190
|
Aligned length, nt
|
2351
|
1832
|
818
|
1176
|
6113
|
9973
|
3826
|
19912
|
19259
|
Characters analyzed, nt
|
1543
|
1657
|
818
|
1140
|
5123
|
6866
|
3615
|
15604
|
14951
|
% missing or
ambiguous data
|
16.4
|
1.87
|
2.84
|
26.2
|
10.7
|
15.1
|
19.5
|
15.6
|
14.8
|
Constant characters, nt
|
560
|
1176
|
307
|
287
|
1863
|
3133
|
1770
|
6766
|
6745
|
Variable characters, nt
|
983
|
481
|
511
|
853
|
3260
|
3733
|
1845
|
8838
|
8206
|
Informative
characters, nt
|
695
|
374
|
435
|
695
|
2716
|
2594
|
1504
|
6814
|
6187
|
No. MP trees
|
>20,000
|
>20,000
|
629
|
45
|
180
|
5929
|
>20,000
|
2
|
4
|
MP tree length
|
3141
|
2065
|
6290
|
7506
|
25240
|
10840
|
16083
|
52423
|
42153
|
CI
(CI excluding
uninformative sites)
|
0.466
(0.399)
|
0.322
(0.282)
|
0.149
(0.137)
|
0.219
(0.199)
|
0.246
(0.226)
|
0.491
(0.419)
|
0.202
(0.182)
|
0.282
(0.248)
|
0.317
(0.276)
|
RI
|
0.656
|
0.637
|
0.472
|
0.491
|
0.591
|
0.704
|
0.497
|
0.585
|
0.611
|
ML, -ln
|
20941.3314
|
13863.1373
|
28784.6657
|
35345.9258
|
133629.8170
|
78808.7259
|
80273.8615
|
297579.9319
|
253331.7827
| |
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