1 Supplementary Material for:
2
Lungfish diversity in Romer’s Gap: reaction to the end-Devonian extinction
1
3 Timothy R. Smithson, Kelly R. Richards and Jennifer A. Clack
4 Principal component analysis
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Generalised Procrustes analysis calculated in R removed size and orientation differences between taxa. The Geomorph package (Adams et al . 2014) was used to create a data array from Procrustes-corrected data matrix. Component variance was
calculated (Table 1). Components 1 and 2 together represent 87% of the variation.
PC1 PC2 PC3 PC4 PC5 PC6 PC7
2.915e-17 Standard deviation
0.2193 0.0970 0.08335 0.03802 9.021e-17 6.66e-17
Proportion of variance
0.7299 0.1428 0.10543 0.02193 0.00e+00 0.000e+00 0.000e+00
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Cumulative 0.7299 0.8726 0.97807 1.00000 1.00e+00 1.000e+00
Proportion
Table 1. Principal component variation
1.000e+00
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The degree of variation within the landmarks was visualised with a Principal
Component Analysis run in R and PC1 was plotted against PC2.
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The Geomorph package was used to analyse the pattern of disparity between the tooth plates. The centroid (average landmark co-ordinate across all tooth plates was calculated and used to create thin spline plate warps and vector diagrams. Vector diagrams show the direction and distance of movement needed to change the centroid landmark position into that of each tooth plate. Thin spline plate warps show a similar movement but using axis-parallel lines. Their deformation from the x and y axis show the direction and distance of movement required of each landmark to reach the co-ordinate of each tooth plate from the average (centroid) starting

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22 position. The thin spline plate warps and vector diagrams were plotted using
Geomorph.
Tooth ridge angle analysis
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Methods
Variables:
L:W: Length:Width.
Length and width of tooth plates were measured.
Length:width ratio calculated for comparison.
TR angle: Tooth ridge angle. The angle measured between the anterior and posterior tooth ridges (see Main text Fig. 2A-B).
No.r.: Number of ridges. The number of tooth ridges counted
Some tooth plates were missing data due to wear and breakage. These were given surrogate data values averaged from other tooth plates of the same taxa. This decision was taken in order to make use of valuable data from incomplete but rare fossils. Data generated in this way is indicated on the data matrix. Those tooth plate taxa missing data and represented by single tooth plates were removed from the analysis where indicated. PAST v2.17b (Wickham and Chang 2014) was used to test normality of the data using Shapiro-Wilk normality tests and the strength of the relationship between the data using Pearson’s correlation coefficients.
Dataset (Table 2) was read into r as a csv file and variables were plotted. All plots in
R were made using the ggplot2 graphics package (Hammer et al.
2001) unless stated.
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Taxon
Adelargo
Andreyvichthys
Orlovichthys
Reference
Johanson and Richie 2000
Smith and Krupina 2001
Krupina et al. 2001
Pt or pr
Pterygoid
Pterygoid
Pterygoid
TR angle No of ridgesL:W
85
50
65
AMNH 357 (New taxon E) Friedman & Daeschler 2006 Pterygoid 53
ANSP 21542 (New taxon E) Friedman & Daeschler 2006 Pterygoid 110
9
7
4
5
5
1.45
1.9
3.4
2
2.6
ANSP 22127 (New taxon E) Friedman & Daeschler 2006 Pterygoid 115
Dipterus arcanus Krupina 2000 Pterygoid 67
Dipterus pacatus
Dipterus expressus
Chirodipterus interstitus
Occludus romeri
Occludus romeri
Krupina 2000
Krupina 2000
Krupina 2000
Pterygoid 53
Pterygoid 70
Pterygoid 53
Pterygoid
Pterygoid
125
125
5
13
5
7
6
11
12
4
4
2.5
1.33
1.8
1.8
1.6
Occludus romeri
Occludus romeri
Occludus romeri
Occludus romeri
Ballagadus rossi
Coccovedus celatus
Coccovedus celatus
Coccovedus celatus
Ballagadus caustrimi
Ctenodus williei
Ctenodus williei
Ctenodus williei
Ctenodus whitropei
Ctenodus roberti
Xylognathus macrustenus
Xylognathus macrustenus
Xylognathus macrustenus
Xylognathus macrustenus
Uronemus
Ctenodus allodens
Ctenodus interuptus
Tranodis
Ctenodus sp.
Smith et al. 1987
Sharp and Clack 2013
Sharp and Clack 2013
Schultz and Bolt 1996
Turner et al. 1999
Prearticular 120
Prearticular 120
Pterygoid 100
Pterygoid 105
Pterygoid 120
Prearticular 140
Prearticular 135
Prearticular 140
Pterygoid 100
Pterygoid 35
Prearticular 30
Pterygoid 35
Pterygoid 30
Pterygoid 6
Pterygoid 180
Prearticular 165
Prearticular 165
Pterygoid
Pterygoid
Pterygoid
Pterygoid
Pterygoid
175
145
87
28
113
Pterygoid 7
11
12
11
8
7
5
3
5
6
18
18
11
10
7
4
2
2
2
5
8
11
9
8
3
3
4
4
2.4
2.4
2.4
2.4
2.4
1.67
1.46
1.67
1.4
1.4
3.5
3.5
3.5
3.5
9.7
2.1
1.6
2.7
2.7
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Table 2. Lungfish tooth plate morphometric variable dataset. Red colour indicates reconstructed values or probable diagnoses.
46 Results
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Relationship between Length:Width and TR angle. These two variables are plotted against each other in Figure S2. L:W and TR angle are positively correlated as shown by the regression line. As tooth plate length increases in relation to the

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4 width, the TR angle increases. Comparison of the plot and the data table shows that all tooth plates in this analysis have a greater length than width, as denoted by a L:W greater than 1. Most tooth plates fall between 1.4 and 4. Uronemus has an exceptionally high L:W ratio of 9.7. As the correlation would predict, Uronemus also has the second highest TR angle, indicating that this tooth plate is long with a high angle between the first and last tooth row. This plot shows the TR angle pattern over time noted in Fig. 5B and shows that there is no clear correlation between L:W ratio and time bin.
58 Lungfish diversity from the Famennian to the Visean.
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Lungfish show a dramatic decrease in diversity at the generic and specific level following the end of the Devonian (Fig. S3). Genera in this analysis tend to be
monospecific and so the diversity pattern and the absolute counts (see Table 3) at
the two taxonomic levels are almost identical. New taxa were counted at the genus level.
Famennian
Tournaisian
Visean
No of species
26
8
6
No of genera
24
8
4
65
70
71
72
73
66
67
68
69
74
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Shapiro-Wilk normality test (Shapiro and Wilk 1965)
Null hypothesis H
0
is that data is normally distributed, null hypothesis is rejected if p is less than 0.05 (applies throughout these analyses). No taxa were omitted from this
analysis. Our results (Table 4) show that L:W data and Tooth Ridge number data are
normally distributed.
The absence of a normal distribution in TR angle implies that some angles or one range of angles occurs more or less than expected in a single natural population.

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Data variable L:W TR angle
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N (No. of data points) 37
W (normality score) 0.6929
P - value 1.668E-07
Normally distributed? Probably
Table 4. Shapiro Wilk normality tests
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Correlation coefficient using Pearson’s r
.
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0.9628
0.2475
Probably not
No. of tooth ridges
37
0.9396
0.04482
Probably
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The H
0
is that data is uncorrelated. No taxa were omitted from this analysis. Our
results (Table 5) show correlation beyond chance between two pairs of variables: TR
angle – L:W and TR angle – No. of tooth ridges. This result emphasises the significance of TR angle in the statistical differentiation between the tooth plates in this analysis.
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Data Variable L:W
L:W
TR angle 0.51855
No. of tooth ridges -0.26409
TR angle
0.0010094
-0.47942
No. of tooth ridges
0.11424
0.0026793
Table 5. Correlation coefficients. Coefficient value is shown in the bottom left triangle and associated P-values are shown in the top right triangle.
85 Supplementary Material: References
86 ADAMS, D., COLLYER, M., OTAROLA-CASTILLO, E. and SHERRATT, E. 2014.
87 Geometric morphometric analyses of 2d/3d landmark data. CRAN.
88 FRIEDMAN, M. and DAESCHLER, E. B. 2006. Late Devonian (Famennian )
89 lungfishes from the Catskill Formation of Pennsyvania, USA. Palaeontology, 49 :
90 1167-1184.

91 HAMMER,
Ø., HARPER, DAT and RYAN, P. D. 2001. PAST: Paleontological
92 statistics software package for education and data analysis. Palaeontologia
93 Electronica, 4: 9pp
94 JOHANSON, Z. and RICHIE. A. 2000. A new Late Fammenian lungfish from New
95 South Wales, Australia, and its bearing on Australian-Asian terrain relations.
96 Alcheinga, 24 : 99-118.
97 KRUPINA, N.I. 2000. Dipnoans from the Upper Devonian locality Rybnitsa in the
98 Oryol Region. Paleontolgical Journal, 34 : 527-533.
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99 --- REISZ, R. R. and SCOTT, D. 2001. The skull and tooth system of Olovichthys
100 limnatus , a late Devonian dipnoan from Russia. Canadian Journal of Earth Science,
101 38 : 1301-1311.
102 SCHULTZE, H. P. and BOLT, J. R. 1996. The lungfish Tranodis and the tetrapod
103 fauna from the upper Mississippian of North America. Special Papers in
104 Palaeontology, 52 : 31-54.
105 SHAPIRO, S. S. and WILK, M. B. 1965. An analysis of variance test for normality
106 (complete samples). Biometrika, 52 : 591-611.
107 SHARP, E. L. and CLACK, J. A. 2013. A review of the Carboniferous lungfish genus
108 Ctenodus Agassiz 1838 from the United Kingdom, with new data from an articulated
109 specimen of Ctenodus interruptus Barkas 1869. Transactions of the Royal Society of
110 Edinburgh Earth and Environmental Science , 104 : 169-204.
111 SMITH, M.M., SMITHSON, T. R. and CAMPBELL, K. S. W. 1987. The relationships
112 of Uronemus : a Carboniferous Dipnoan with highly modified tooth plates.
113 Philosophical Transactions of the Royal Society London, B 317 : 299-327.

114 --- KRUPINA, N. I. 2001. Conserved developmental processes constrain evolution
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115 of lungfish dentitions. Journal of Anatomy, 199 : 161-168.
116 TURNER, S., KEMP, A. and WARREN, A. A. 1999. First Early Carboniferous
117 lungfish (Dipnoi, Ctenodontidae) from central Queensland. Alcheringa, 23 :177-183.
118 WICKHAM, H. and CHANG, W. 2014. An implementation of the Grammar of
119 Graphics. CRAN.
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121 Supplementary Material: Figure Legends
122 Figure S1
123 Principal component analysis with thin spline plate warps and vector diagrams for
124 the landmarks of tooth plates used in the principal component analysis.
125 Figure S2
126 Relationship between tooth plate length:width and tooth ridge angle. The y axis,
127 length:width ratio, uses a Log scale.
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129
Figure S3
Lungfish taxonomic diversity from the Famennian to the Vis
éan. Diversity is a
130 measure of the number of genera.
131 Supplementary Material: Figures
132 Figure S1

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140 Figure S2
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142 Figure S3
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