Adams et al. page: 39
Supplemental Material for:
Are rates of species diversification correlated with rates of morphological evolution?
Dean C. Adams, Chelsea M. Berns, Kenneth H. Kozak, and John J. Wiens
Table 1s. Estimates of species diversification rates for 15 clades of plethodontid salamanders, using different estimates of relative extinction rates (“e”) and different numbers of species: “tree” refers to the diversification rate estimate only from the species included in the phylogeny (matching the sampling for estimates of morphological evolution), whereas “clade” refers to the total number of described species in the clade.
Clade / e = 0.0 / e = 0.45 / e = 0.90 / e = 0.0 / e = 0.45 / e = 0.90
(1) Desmognathus and Phaeognathus / 0.0485 / 0.04392 / 0.01865 / 0.07906 / 0.07343 / 0.03994
(2) Aneides / 0.0301 / 0.02679 / 0.00918 / 0.03619 / 0.03220 / 0.01150
(3) Western Plethodon / 0.0360 / 0.03210 / 0.01146 / 0.04940 / 0.04435 / 0.01751
(4) P. cinereus group / 0.0695 / 0.06208 / 0.02302 / 0.08938 / 0.08047 / 0.03264
(5) P. werhlei-welleri group / 0.0552 / 0.04915 / 0.01755 / 0.06299 / 0.05621 / 0.02084
(6) P. glutinosus group / 0.1409 / 0.12880 / 0.06031 / 0.17148 / 0.15849 / 0.08226
(7) Gyrinophilus, Pseudotriton, Stereochilus / 0.0297 / 0.02639 / 0.00868 / 0.03929 / 0.03487 / 0.01195
(8) Eurycea / 0.09476 / 0.08650 / 0.03997 / 0.11358 / 0.10472 / 0.05316
(9) Nototriton / 0.0684 / 0.06079 / 0.02084 / 0.13992 / 0.12685 / 0.05495
(10) Oedipina / 0.0895 / 0.08062 / 0.03270 / 0.14053 / 0.12946 / 0.06518
(11) Chiropterotriton / 0.0754 / 0.06731 / 0.02496 / 0.10789 / 0.09760 / 0.04145
(12) Pseudoeurycea clade / 0.1008 / 0.09343 / 0.04944 / 0.11487 / 0.10717 / 0.06080
(13) Bolitoglossa (Eladinea) / 0.1239 / 0.11278 / 0.05059 / 0.19288 / 0.17988 / 0.10167
(14) Bolitoglossa, (Magnadigita, Oaxakia, Pachymandra) / 0.1167 / 0.10689 / 0.05067 / 0.13101 / 0.12069 / 0.06076
(15) Bolitoglossa, (Bolitoglossa, Mayamandra, Nanotriton) / 0.0859 / 0.07739 / 0.03139 / 0.11431 / 0.10435 / 0.04821
Table 2s. Results of regression analyses of different estimates of lineage diversification rates (see Table 1s) versus morphological rates. Significant results are indicated with boldface and asterisks. “Tree” refers to the diversification rate estimate only from the sampled species on the tree, whereas “clade” refers to the rate estimated from the total number of described species in the clade and “e” refers to the relative extinction rate.
Div. rate Tree (e=0.00) vs. Size rate / Tips / 0.198 / 0.178 / 1.108 / 0.288
Div. rate Tree (e=0.00) vs. Size rate / PGLS / 0.200 / 0.142 / 1.414 / 0.181
Div. rate Tree (e=0.45) vs. Size rate / Tips / 0.219 / 0.192 / 1.141 / 0.275
Div. rate Tree (e=0.45) vs. Size rate / PGLS / 0.220 / 0.151 / 1.454 / 0.170
Div. rate Tree (e=0.90) vs. Size rate / Tips / 0.494 / 0.357 / 1.384 / 0.190
Div. rate Tree (e=0.90) vs. Size rate / PGLS / 0.463 / 0.263 / 1.760 / 0.102
Div. rate Clade (e=0.00) vs. Size rate / Tips / 0.095 / 0.135 / 0.701 / 0.496
Div. rate Clade (e=0.00) vs. Size rate / PGLS / 0.078 / 0.111 / 0.702 / 0.495
Div. rate Clade (e=0.45) vs. Size rate / Tips / 0.105 / 0.144 / 0.729 / 0.479
Div. rate Clade (e=0.45) vs. Size rate / PGLS / 0.086 / 0.118 / 0.733 / 0.477
Div. rate Clade (e=0.90) vs. Size rate / Tips / 0.219 / 0.240 / 0.912 / 0.378
Div. rate Clade (e=0.90) vs. Size rate / PGLS / 0.174 / 0.186 / 0.937 / 0.366
Div. rate Tree (e=0.00) vs. Shape rate / Tips / 0.008 / 0.005 / 1.530 / 0.150
Div. rate Tree (e=0.00) vs. Shape rate / PGLS / 0.005 / 0.005 / 1.154 / 0.269
Div. rate Tree (e=0.45) vs. Shape rate / Tips / 0.008 / 0.005 / 1.556 / 0.144
Div. rate Tree (e=0.45) vs. Shape rate / PGLS / 0.006 / 0.005 / 1.203 / 0.251
Div. rate Tree (e=0.90) vs. Shape rate / Tips / 0.018 / 0.010 / 1.753 / 0.103
Div. rate Tree (e=0.90) vs. Shape rate / PGLS / 0.013 / 0.008 / 1.591 / 0.136
Div. rate Clade (e=0.00) vs. Shape rate / Tips / 0.006 / 0.004 / 1.690 / 0.115
Div. rate Clade (e=0.00) vs. Shape rate / PGLS / 0.003 / 0.004 / 0.761 / 0.460
Div. rate Clade (e=0.45) vs. Shape rate / Tips / 0.007 / 0.004 / 1.707 / 0.112
Div. rate Clade (e=0.45) vs. Shape rate / PGLS / 0.003 / 0.004 / 0.793 / 0.442
Div. rate Clade (e=0.90) vs. Shape rate / Tips / 0.012 / 0.006 / 1.787 / 0.097
Div. rate Clade (e=0.90) vs. Shape rate / PGLS / 0.006 / 0.006 / 1.014 / 0.329
Div. rate Tree (e=0.00) vs. Disparity / Tips / -0.102 / 2.270 / -0.045 / 0.965
Div. rate Tree (e=0.00) vs. Disparity / PGLS / -1.140 / 2.047 / -0.557 / 0.587
Div. rate Tree (e=0.45) vs. Disparity / Tips / -0.034 / 2.455 / -0.014 / 0.989
Div. rate Tree (e=0.45) vs. Disparity / PGLS / -1.152 / 2.199 / -0.524 / 0.609
Div. rate Tree (e=0.90) vs. Disparity / Tips / 1.103 / 4.642 / 0.238 / 0.816
Div. rate Tree (e=0.90) vs. Disparity / PGLS / -1.014 / 3.971 / -0.255 / 0.802
Div. rate Clade (e=0.00) vs. Disparity / Tips / -0.397 / 1.669 / -0.238 / 0.816
Div. rate Clade (e=0.00) vs. Disparity / PGLS / -1.405 / 1.493 / -0.941 / 0.364
Div. rate Clade (e=0.45) vs. Disparity / Tips / -0.363 / 1.782 / -0.204 / 0.842
Div. rate Clade (e=0.45) vs. Disparity / PGLS / -1.448 / 1.585 / -0.908 / 0.381
Div. rate Clade (e=0.90) vs. Disparity / Tips / 0.133 / 3.012 / 0.044 / 0.966
Div. rate Clade (e=0.90) vs. Disparity / PGLS / -1.717 / 2.571 / -0.668 / 0.516
Size rate vs. Shape rate / Tips / 0.018 / 0.0006 / 2.796 / 0.015 *
Size rate vs. Shape rate / PGLS / 0.020 / 0.007 / 2.851 / 0.014 *
Size rate vs. Disparity / Tips / 9.818 / 1.992 / 4.928 / 0.0003 *
Size rate vs. Disparity / PGLS / 9.737 / 2.638 / 3.691 / 0.003 *
Shape Evol. vs. Disparity / Tips / 170.617 / 105.218 / 1.622 / 0.129
Shape Evol. vs. Disparity / PGLS / 161.331 / 110.359 / 1.462 / 0.168
Age vs. Disparity / Tips / 0.016 / 0.011 / 1.504 / 0.156
Age vs. Disparity / PGLS / 0.031 / 0.012 / 2.595 / 0.022 *
Alternative clade divisions
Our primary analyses were based on a set of 15 non-overlapping clades. To explore the robustness of our results, we identified an alternative set of seven non-overlapping clades from our phylogeny (Appendix 1). As with the previous clade designations, these clades were selected based on species sampling (a minimum of five species per clade included in our tree), clade support, and monophyly. The seven clades are: (1) Aneides, Desmognathus, Ensatina, Hydromantes, Karsenia, Phaeognathus; (2) Plethodon; (3) Spelerpinae (Eurycea, Gyrinophilus, Pseudotriton, Stereochilus); (4) Bolitoglossa; (5) Pseudoeurycea (Ixalotriton, Lineatriton, Parvimolge, Pseudoeurycea); (6) Bradytriton, Dendotriton, Nototriton, Nyctanolis, Oedipina; (7) Chiropterotriton.
Table 3s. Summary data for seven plethodontid clades (as opposed to 15 clades in the main text): “tree” refers to the diversification rate estimate only from the sampled species on the tree, whereas “clade” refers to the rate estimated from the total number of described species in the clade, “e” refers to the extinction rate, and “mya” refers to millions of years ago.
Clade / e = 0.0 / e = 0.45 / e = 0.90 / e = 0.0 / e = 0.45 / e = 0.90
1 / 0.05256 / 0.04822 / 0.02338 / 0.07367 / 0.06890 / 0.03998
2 / 0.06963 / 0.06467 / 0.03517 / 0.07865 / 0.07355 / 0.04268
3 / 0.06258 / 0.05742 / 0.02784 / 0.08227 / 0.07666 / 0.04300
4 / 0.13158 / 0.12262 / 0.06878 / 0.16435 / 0.15503 / 0.09749
5 / 0.10088 / 0.09343 / 0.04944 / 0.11487 / 0.10717 / 0.06080
6 / 0.06296 / 0.05763 / 0.02732 / 0.08769 / 0.08178 / 0.04623
7 / 0.07543 / 0.06731 / 0.02496 / 0.10789 / 0.09760 / 0.04145
Clade / Crown-group age (mya) / No. species /species in tree / Size rate / Shape rate / Morphological disparity
1 / 44.8 / 54/19 / 0.02578 / 0.000691 / 0.8029
2 / 42.0 / 55/36 / 0.01492 / 0.000515 / 0.5444
3 / 37.7 / 44/22 / 0.08039 / 0.001757 / 1.142
4 / 23.6 / 95/44 / 0.02483 / 0.000793 / 0.4429
5 / 27.6 / 51/32 / 0.05167 / 0.002313 / 0.7794
6 / 35.8 / 46/19 / 0.01888 / 0.001708 / 0.7000
7 / 16.6 / 12/7 / 0.04891 / 0.000431 / 0.7382
Table 4s. Results of regression analyses of rates, disparity, and ages, using seven clades rather than 15. Significant results are indicated with boldface and asterisks.
Div. rate Tree (e=0.00) vs. Size rate / Tips / -0.062 / 0.380 / -0.162 / 0.878
Div. rate Tree (e=0.00) vs. Size rate / PGLS / -0.199 / 0.386 / -0.516 / 0.628
Div. rate Tree (e=0.45) vs. Size rate / Tips / -0.075 / 0.402 / -0.188 / 0.859
Div. rateTree (e=0.45) vs. Size rate / PGLS / -0.216 / 0.404 / -0.535 / 0.616
Div. rate Tree (e=0.90) vs. Size rate / Tips / -0.224 / 0.622 / -0.359 / 0.734
Div. rate Tree (e=0.90) vs. Size rate / PGLS / -0.390 / 0.593 / -0.657 / 0.540
Div. rate Clade (e=0.00) vs. Size rate / Tips / -0.043 / 0.332 / -0.130 / 0.902
Div. rate Clade (e=0.00) vs. Size rate / PGLS / -0.247 / 0.309 / -0.802 / 0.459
Div. rate Clade (e=0.45) vs. Size rate / Tips / -0.057 / 0.350 / -0.162 / 0.878
Div. rate Clade (e=0.45) vs. Size rate / PGLS / -0.269 / 0.320 / -0.840 / 0.439
Div. rate Clade (e=0.90) vs. Size rate / Tips / -0.193 / 0.499 / -0.388 / 0.714
Div. rate Clade (e=0.90) vs. Size rate / PGLS / -0.439 / 0.411 / -1.068 / 0.335
Div. rate Tree (e=0.00) vs. Shape rate / Tips / 0.002 / 0.012 / 0.152 / 0.885
Div. rate Tree (e=0.00) vs. Shape rate / PGLS / -0.013 / 0.014 / -0.942 / 0.389
Div. rate Tree (e=0.45) vs. Shape rate / Tips / 0.002 / 0.013 / 0.169 / 0.873
Div. rate Tree (e=0.45) vs. Shape rate / PGLS / -0.014 / 0.015 / -0.903 / 0.408
Div. rateTree (e=0.90) vs. Shape rate / Tips / 0.005 / 0.020 / 0.250 / 0.812
Div. rateTree (e=0.90) vs. Shape rate / PGLS / -0.016 / 0.023 / -0.685 / 0.524
Div. rateClade (e=0.00) vs. Shape rate / Tips / -0.001 / 0.010 / -0.057 / 0.957
Div. rateClade (e=0.00) vs. Shape rate / PGLS / -0.018 / 0.010 / -1.743 / 0.142
Div. rate Clade (e=0.45) vs. Shape rate / Tips / 0.000 / 0.011 / -0.033 / 0.975
Div. rate Clade (e=0.45) vs. Shape rate / PGLS / -0.018 / 0.011 / -1.685 / 0.153
Div. rate Clade (e=0.90) vs. Shape rate / Tips / 0.002 / 0.016 / 0.101 / 0.924
Div. rate Clade (e=0.90) vs. Shape rate / PGLS / -0.020 / 0.015 / -1.330 / 0.241
Div. rate Tree (e=0.00) vs. Disparity / Tips / -4.494 / 2.981 / -1.508 / 0.192
Div. rate Tree (e=0.00) vs. Disparity / PGLS / -5.868 / 2.986 / -1.965 / 0.107
Div. rate Tree (e=0.45) vs. Disparity / Tips / -4.788 / 3.148 / -1.521 / 0.189
Div. rate Tree (e=0.45) vs. Disparity / PGLS / -6.170 / 3.135 / -1.968 / 0.106
Div. rate Tree (e=0.90) vs. Disparity / Tips / -7.601 / 4.867 / -1.562 / 0.179
Div. rate Tree (e=0.90) vs. Disparity / PGLS / -9.101 / 4.689 / -1.941 / 0.110
Div. rate Clade (e=0.00) vs. Disparity / Tips / -3.754 / 2.642 / -1.421 / 0.215
Div. rate Clade (e=0.00) vs. Disparity / PGLS / -5.271 / 2.300 / -2.292 / 0.071
Div. rate Clade (e=0.45) vs. Disparity / Tips / -4.008 / 2.777 / -1.443 / 0.209
Div. rate Clade (e=0.45) vs. Disparity / PGLS / -5.525 / 2.383 / -2.318 / 0.068
Div. rate Clade (e=0.90) vs. Disparity / Tips / -5.948 / 3.960 / -1.502 / 0.193
Div. rate Clade (e=0.90) vs. Disparity / PGLS / -7.377 / 3.168 / -2.328 / 0.067
Size rate vs. Shape rate / Tips / 0.014 / 0.012 / 1.157 / 0.299
Size rate vs. Shape rate / PGLS / 0.019 / 0.015 / 1.273 / 0.259
Size rate vs. Disparity / Tips / 7.820 / 2.354 / 3.322 / 0.021 *
Size rate vs. Disparity / PGLS / 8.418 / 2.451 / 3.435 / 0.019 *
Shape rate vs. Disparity / Tips / 143.437 / 117.836 / 1.217 / 0.278
Shape rate vs. Disparity / PGLS / 173.541 / 85.259 / 2.035 / 0.097
Age vs. Disparity / Tips / 0.005 / 0.009 / 0.565 / 0.596
Age vs. Disparity / PGLS / 0.009 / 0.012 / 0.762 / 0.480
Principal Components Analyses
Table 5s. Principal components analysis of the covariance matrix of seven log-transformed measurements for 1,573 adult plethodontid specimens from 260 species. The loadings of each morphological variable on seven principal component axes are shown.
PC1 / PC2 / PC3 / PC4 / PC5 / PC6 / PC7SVL / 0.324 / -0.233 / 0.225 / -0.314 / 0.539 / -0.524 / -0.355
Tail length / 0.274 / -0.898 / -0.148 / 0.178 / -0.198 / 0.137 / 0.084
Head length / 0.365 / 0.070 / -0.103 / -0.738 / -0.033 / 0.216 / 0.508
Snout-eye / 0.362 / 0.150 / 0.205 / -0.151 / -0.749 / -0.126 / -0.454
Body width / 0.385 / 0.098 / 0.748 / 0.344 / 0.143 / 0.289 / 0.247
Forelimb length / 0.440 / 0.237 / -0.347 / 0.402 / -0.063 / -0.555 / 0.396
Hindlimb length / 0.462 / 0.215 / -0.442 / 0.148 / 0.292 / 0.502 / -0.430
Table 6s. Summary of results from a principal components analysis of the covariance matrix of seven log-transformed measurements for 1,573 adult plethodontid specimens from 260 species. The proportion of variation explained by each principal component axis is shown.
Standard deviation / 0.908 / 0.341 / 0.192 / 0.140 / 0.095 / 0.088 / 0.078
Proportion of variance / 0.808 / 0.114 / 0.036 / 0.019 / 0.009 / 0.008 / 0.006
Cumulative proportion / 0.808 / 0.922 / 0.958 / 0.977 / 0.986 / 0.994 / 1.000
Figure 1s. Principal component plot of morphometric data (A) PC1 versus PC2 and (B) PC2 versus PC3. PC1 represents generalized size, while PC2 and PC3 are two primary components of shape. PC2 describes a relative contrast in relative limb lengths and relative tail length (i.e. salamanders with relatively elongate tails and shorter limbs versus the converse), while PC3 primarily describes a contrast between body width and limb length. Species from major plethodontid clades are shown in similar colors; symbol and color combinations signify 15 clades examined in this study. Clades are: 1: Desmognathus, Phaeognathus (gray circle), 2: Aneides (gray square), 3: Western Plethodon (blue down triangle), 4: P. cinereus group (blue circle), 5: P. wehrlei-welleri group (blue up triangle), 6: P. glutinosus group (blue square), 7: Pseudotriton, Gyrinophilus, Stereochilus (Spelerpinae: red square), 8: Eurycea (Spelerpinae: red circle), 9: Nototriton (yellow square), 10: Oedipina (yellow circle), 11: Chiropterotriton (green circle), 12: Pseudoeurycea clade (Ixalotriton, Lineatriton, Parvimolge, Pseudoeurycea) (white circle), 13: Bolitoglossa (subgenus Eladinea) (black circle), 14: Bolitoglossa (subgenera Magnadigita, Oaxakia, and Pachymandra) clade (black up triangle), 15: Bolitoglossa (subgenera Bolitoglossa, Mayamandra, and Nanotriton) (black square).