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TABLE 1. Numerical characters used in phylogenetical analyses, with the corresponding ratios of the original vertebrae of the Kaatedocus siberi SMA 0004, the MM models, and the SAM models. Trends recovered by retrodeformation are compared to the Raphus cucullatus test, green indicates probable real trends for SMA 0004. Abb.: H112, character 112 of Harris (2006); U1, character 1 of Upchurch et al. (2004); W87, character 87 of Whitlock (2011).

 

Character

Borders as set in character

Vertebra

Original

Retrodeformed models

Comparison with trends recovered in Dodo (CS)

Comments

MM

SAM

MM

SAM

H112

 

CV 3

1.29

1.59

1.38

=

SMA 0004 ambiguous, retrodeformation enhances ambiguity, but is questioned by Dodo analysis

CV 4

1.08

1.16

1.05

=


CV 5

1.10

1.04

0.95


H114 (=W90)

4 in Harris (2006), Whitlock (2011) leaves gap: 2.5-3, or 4+ as plesio- or apomorphic states, respectively

CV 6

4.13

3.38

3.20

=

Original ambiguous, retrodeformation shifts mid-cervicals into plesiomorphic state of H114, W90 only applicable with SAM models and original of CV 6, but SAM appears to give false trends according to Dodo analysis

CV 7

3.66

3.81

2.81


=

CV 8

3.31

3.02

2.68

=

CV 9

3.51

3.70

2.83


=

CV 10

3.00

3.66

2.90


=

H115

 

CV 6

1.38

1.42

1.35

=

=

Retrodeformation generally strengthens assignment of SMA 0004 to apomorphic state, although this seems to be the wrong trend, according to Dodo analysis. However, deformation would have to be very strong for SMA 0004 to fall within plesiomorphic state

CV 7

1.29

1.45

1.50

=

CV 8

1.23

1.34

1.28

=

CV 9

1.38

1.41

1.45

=

CV 10

1.32

1.44

1.18

=

=

H118 (=W87)

no explicit border in Harris (2006), but described to be around 1; Whitlock (2011) restricts character to anterior cervicals, but leaves gap: <1, or 1.5 as plesio-, or apomorphic states, respectively

CV 3

0.68

0.60

0.71


=

Retrodeformation ambiguous in its trends in anterior and mid-cervicals, but shifts ratios of posterior cervicals towards upper end of plesiomorphic state of H118. However, this appears to be the wrong trend, according to the Dodo analysis. SMA 0004 can thus be safely scored as plesiomorphic

CV 4

0.72

0.69

0.69


CV 5

0.61

0.55

0.58


CV 6

0.55

0.55

0.52


CV 7

0.60

0.48

0.59


CV 8

0.61

0.66

0.67

=

CV 9

0.67

0.59

0.66


CV 10

0.60

0.52

0.55


CV 11

0.67

0.73

0.78

=

CV 12

0.80

0.86

0.89

=

CV 13

0.84

0.89

0.96

=

CV 14

0.94

0.97

1.00

=

U1

 

CV 3

0.48

0.61

0.62


No changes, weak trend to wider vertebrae through retrodeformation (especially when applying the SAM), which appears to be right according the the Dodo analysis

CV 4

0.62

0.61

0.66

=


CV 5

0.65

0.70

0.69


CV 6

0.64

0.78

0.70


CV 7

0.61

0.61

0.62


CV 8

0.76

0.75

0.82

=

=

CV 9

0.68

0.71

0.75


CV 10

0.69

0.74

0.83


CV 11

0.62

0.62

0.69


CV 12

0.62

0.70

0.71


CV 13

0.73

0.77

0.79


CV 14

0.74

0.68

0.70

=

TABLE 2. Numerical characters used in phylogenetic analyses, with the corresponding ratios of the original vertebra of Raphus cucullatus, the deformed models, the MM models, and the SAM models. The closest fit with the original vertebra is marked with bold numbers. Differences between the deformed/retrodeformed models and the original are given in percent, with high deviations (>50%) marked in red, and low differences (<5%) in green. The similarity of the retrodeformed models with the original vertebra is given compared with the deviance of the deformed model (arrows pointing upwards indicate a closer fit between retrodeformed models and original vertebra, arrows pointing down show that the retrodeformation increased deformation even more; two arrows show higher (green) or lower (red) accuracy of the respective retrodeformation method compared with the other one). Abb.: H112, character 112 of Harris (2006); U1, character 1 of Upchurch et al. (2004); W87, character 87 of Whitlock (2011).

 

Character

Character definitions

Undeformed original

Deformed models

Retrodeformed models

Difference from undeformed original (in percent)

MM

SAM

deformed

MM

SAM

H112

Height/width posterior articular surface

0.61

C

1.27

1.30

1.28

210.20%

215.09%

211.25%

S

0.84

0.75

0.69

139.25%

124.65%

114.11%

CS

1.16

1.18

1.18

190.85%

194.52%

195.19%

H114 (=W90)

Centrum length/height of posterior articular surface

2.00

C

1.45

1.63

1.45

72.32%

81.25%

72.73%

S

2.09

2.33

2.38

104.65%

116.67%

119.23%

CS

1.44

1.23

1.20

72.00%

61.32%

59.80%

H115

Height neural arch/height of posterior articular surface

1.33

C

1.36

1.18

1.29

102.48%

88.91%

97.38%

S

1.33

1.31

1.34

100.00%

98.65%

101.25%

CS

1.42

1.43

1.40

107.35%

108.18%

105.90%

H118 (=W87)

Total height/centrum length

1.47

C

1.76

1.47

1.75

119.57%

100.18%

119.06%

S

1.28

1.16

1.23

86.93%

79.13%

83.40%

CS

2.05

2.22

2.37

139.52%

151.18%

160.92%

U1

Total width/total height

1.31

C

0.87

0.94

0.91

66.17%

71.50%

68.96%

S

1.38

1.49

1.57

104.97%

113.84%

119.73%

CS

0.97

0.92

0.89

73.67%

69.89%

68.14%

TABLE 2 (continued).

 

Character

Comments on character

Retrodeformation trends

Comments on retrodeformation

MM

SAM

H112

highly susceptible, should be deleted

worse

bad

increases transverse compression even more, both MM and SAM indicate trend if shear only

good

better

bad

bad

H114 (=W90)

susceptible, use with care

good

 –

bad performance if shear involved, MM indicates trend if compression only

bad

worse

bad

worse

H115

relatively constant, can be used

worse

bad

generally wrong, inverted trends, but on a low error level

worse

bad

bad

better

H118 (=W87)

especially susceptible if shear and compression combined, should be deleted in this case (or scored '?')

better

good

bad performance if shear involved, MM indicates trend if compression only

worse

bad

bad

worse

U1

susceptible, use with care

 

better

good

bad performance if shear involved, MM indicates trend if compression only

bad

worse

bad

worse

 

TABLE 3. Support values of the performed phylogenetic analyses with and without the questionable characters (H112, H114 for Harris, 2006; W90 for Whitlock, 2011). Abb.: MPT, most parsimonious tree.

 

Phylogenetic analysis

Tree length

Number of MPTs

Consistency index

Retention index

Harris (2006)

with

 965

 50

 44

 62

without

 899

 6

 47

 66

Whitlock (2011)

with

 354

 1

 70

 83

without

 350

 1

 71

 83b

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