Table 1 Summary statistics for the data matrices corresponding maximum likelihood trees.

From: Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa)

Analysis

16S18S28S

16S18S28S_N

16S18S28S_Nrw4

16S

16S_N

16_Nrw4

Terminal taxa

263

263

263

254

254

254

Total sites

6,254

5,608

4,548

647

582

452

Conserved sites

2,522

2,463

2,413

118

117

112

Variable sites

3,677

3,131

2,132

526

465

340

Informative sites (parsimony)

2,861

2,478

1,551

462

417

300

Singleton sites

757

637

581

61

46

40

Gaps and missing data (%)

38.55

33.02

28.94

15.97

8.72

3.64

Maintained sites (Aliscore, in %)

 

89.67

72.72

 

89.95

69.86

Log-likelihood (RAxML)

−169046.88

−151027.90

−71717.62

−39040.32

−36397.24

−19898.97

Freq A C G T (PhyML)

0.28 0.19

0.28 0.19

0.29 0.19

0.40 0.12

0.40 0.12

0.38 0.13

0.26 0.26

0.26 0.25

0.26 0.25

0.15 0.31

0.15 0.31

0.17 0.30

Invariant proportion: MEGA (Gamma+I. “use all sites”)

~36%

~39%

~43%

~16%

~18%

~21%

Parameters: (alpha PhyML) [Gamma MEGA]

(0.344) [0.647]

(0.325) [0.651]

(0.294) [0.548]

(0.424) [0.587]

(0.425) [0.571]

(0.6361) [0.443]

Analysis

18S

18S_N

18S Nrw4

28S

28S N

28S Nrw4

Terminal taxa

207

207

207

181

181

181

Total sites

1,955

1,802

1,566

3,652

3,224

2,530

Conserved sites

888

862

848

1,516

1,484

1,453

Variable sites

1,050

940

718

2,101

1,726

1,074

Informative sites (parsimony)

782

708

506

1.617

1.353

745

Singleton sites

262

229

212

434

362

329

Gaps and missing data (%)

14.40

7.93

2.86

20.39

12.67

7.31

Maintained sites (Aliscore, in %)

 

92.17

80.10

 

88.28

69.28

Log-likelihood (RAxML)

−37348.89

−35029.30

−21383.44

−91649.78

−78681.31

−29528.53

Freq A C G T (PhyML)

0.26 0.19

0.26 0.19

0.27 0.19

0.26 0.21

0.26 0.21

0.27 0.20

0.26 0.26

0.26 0.26

0.26 0.26

0.28 0.24

0.28 0.23

0.27 0.23

Invariant proportion: MEGA (Gamma+I; “use all sites”)

~38%

~40%

~42%

~38%

~42%

~44%

Parameters: (alpha PhyML) [Gamma MEGA]

(0.296) [0.601]

(0.296) [0.595]

(0.273) [0.561]

(0.319) [0.633]

(0.295) [0.643]

(0.247) [0.530]

  1. (multilocus: 16S1828S, 16S18S28S_N, 16S18S28S_Nrw4, single locus: 16S, 16S_N, 16S_Nrw4, 18S, 18S_N, 18S_Nrw4, 28S, 28S_N, 28S_Nrw4). The log-likelihoods were calculated in RAxML under the GTR+GAMMA model. Nucleotide frequencies and proportion of invariant sites calculated in PhyML and MEGA (together with the estimate of the alpha and gamma parameters in both programs). Cells were left empty when non-applicable.
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