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 |
|
