Articleshttps://doi.org/10.1038/s41559-020-1225-3

Metamorphosis shapes cranial diversity and rate of evolution in salamandersAnne-Claire Fabre   1 ✉, Carla Bardua   1,2, Margot Bon1, Julien Clavel1,3, Ryan N. Felice   4, Jeffrey W. Streicher1, Jeanne Bonnel2, Edward L. Stanley   5, David C. Blackburn   5 and Anjali Goswami1

1Department of Life Sciences, The Natural History Museum, London, UK. 2Department of Genetics, Evolution and Environment, University College London, London, UK. 3Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France. 4Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, UK. 5Florida Museum of Natural History, University of Florida, Gainesville, FL, USA. ✉e-mail: a.fabre@nhm.ac.uk

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Supplementary Information for

Metamorphosis shapes cranial diversity and rate of evolution in salamanders

Anne-Claire Fabre, Carla Bardua, Margot Bon, Julien Clavel, Ryan N. Felice, Jeffrey W.

Streicher, Jeanne Bonnel, Edward L. Stanley, David C. Blackburn, Anjali Goswami

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Supplementary Figures

Supplementary Figure 1: The phylogenetic relationships of the species used in this study

(based on43). The time scale is in millions of years. The different life cycles are indicated by red

circles for biphasic species, yellow circles for direct developers, blue circles for paedomorphic

species, and black circles for strictly viviparous species.

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Supplementary Figure 2: The phylogenetic relationships of the species used in this study

(based on43). The time scale is in millions of years. The different fine-grained classification of

life cycles is indicated as in the legend. Abbreviations are as follows: f-bi pd1 indicates

facultative biphasic species, as some populations can be paedomorphic in these species. When

they are paedomorphic they display external gills, gill slits, a tail fin, no eyelids, no maxillary

bones, no septomaxilla, and no prefrontal; f-bi pd4 indicates facultative biphasic species, as

some populations can be paedomorphic in these species. When they are paedomorphic they

display external gills, gill slits, tail fin, no eyelids, no septomaxilla and with maxillary and

prefrontal bones developing before adulthood; f-bi pd4tri indicates species that are triphasic;

pd1 indicates paedomorphic species with external gills, gill slits, tail fin, no eyelids, no maxillary

bones, no septomaxilla, and no prefrontal; pd2 indicates paedomorphic species with external

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gills, gill slits, tail fin, no eyelids, no septomaxilla, no prefrontal and with maxillary bones

developing before adulthood; pd3 indicates paedomorphic species without external gills but with

gill slits, tail fin, no eyelids, no septomaxilla and with maxillary and prefrontal bones developing

before adulthood; pd4 indicates paedomorphic species with external gills, gill slits, tail fin, no

eyelids, no septomaxilla and with maxillary and prefrontal bones developing before adulthood;

vipu indicates strictly puereparate viviparous species; f-vila indicates facultative larviparate

viviparous species; ovi indicates oviparous species.

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Supplementary Figure 3: The phylogenetic relationships of the species used in this study

(based on43). The time scale is in millions of years. The different microhabitats are indicated as

in legend.

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Supplementary Figure 4: Phylomorphospace of the first two principal component scores

describing the skull shape distribution of Caudata. Data point shapes are coded by family

group and colors represent the size of the specimen, as indicated by the key.

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Supplementary Figure 5: Phylomorphospace of the first two principal component scores

showing the skull shape distribution of Caudata. Data point shapes are coded by family group

and colors represent microhabitats as indicated by the key.

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Supplementary Figure 6: trace plots and comparison of several independent runs for the

whole cranium data set.

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Supplementary Tables

Regression R2 P-value

Paedomorphic 0.145 0.001

Direct developer 0.140 0.001

Biphasic 0.091 0.001

Entire dataset 0.063 0.002

Supplementary Table 1: Results of the PGLS regression performed on the cranial shape

depending on life cycle and for the entire dataset. Results are significant. There is a moderate

impact of centroid size on cranial shape for paedomorphic and direct developing species.

However, allometry is less strong in biphasic species. Overall, the impact of the centroid size on

cranial shape for the entire dataset is low.

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Life cycle

Fine-grained life

cycle

F P-value F P-value

Premaxilla 2.600 0.003 1.59 0.007

Frontal 2.950 0.001 1.24 0.080

Parietal 2.600 0.003 1.08 0.300

Squamosal 2.600 0.004 1.17 0.170

Quadrate 3.190 0.001 0.37 0.057

Parasphenoid 5.200 0.001 1.66 0.001

Vomer 6.300 0.001 2.06 0.001

Occipital 6.870 0.001 1.83 0.003

Otic region 4.676 0.001 1.54 0.006

Nasal 7.565 0.001 2.23 0.001

Maxilla 11.524 0.001 3.14 0.001

Orbitosphenoid 4.350 0.001 1.56 0.012

Prefrontal 7.719 0.001 2.06 0.001

Pterygoid 9.739 0.001 3.23 0.001

Overall head shape 5.558 0.001 1.84 0.001

Supplementary Table 2: Results of the phylogenetic MANOVAs for each bone testing for

shape differences depending on life cycle (biphasic, paedomorphic and direct developers)

and on subcategories of life cycles (biphasic; facultative biphasic: f-bi pd1, f-bi pd4, f-bi

pd4tri ; direct developers; paedomorphic: pd1, pd2, pd3, pd4; viviparous: vipu,vila;

oviparous). The analyses for life cycle were run on the whole data set excluding the strictly

viviparous species.

Results in bold are significant. Nevertheless, it is important to note that some fine-grained life

cycle categories have less than 5 species (f-vila, vipu, ovi, f-bi pd1) and that the results have to

be interpreted with caution.

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F P-value

Premaxilla 0.9 0.5

Frontal 0.9 0.52

Parietal 1 0.39

Squamosal 1.5 0.02

Quadrate 1.2 0.18

Parasphenoid 1.7 0.004

Vomer 1.4 0.046

Occipital 1.3 0.16

Otic region 1.1 0.2

Nasal 0.7 0.9

Maxilla 1.8 0.01

Orbitosphenoid 1.1 0.25

Prefrontal 1.3 0.16

Pterygoid 0.9 0.5

Overall head shape 1.3 0.03

Supplementary Table 3: Results of the phylogenetic MANOVAs for each bone testing for

shape differences depending on microhabitats (aquatic, semi-aquatic, semi-fossorial,

terrestrial, arboreal species and species inhabiting cave).

Results in bold are significant. Nevertheless, it is important to note that some microhabitat

categories have less than 5 species (semi-fossorial and aquatic species inhabiting cave category)

and that the results have to be taken cautiously.

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Equal rates model Symmetric model All rates different model

AIC 133.2147 130.4413 134.1485

AICc 133.2421 131.037 136.4596

k 1 6 12

Supplementary Table 4: Results of the Akaike information criterion (AIC) and Akaike

information criterion with correction (AICc) for each model fit of the ancestral state

reconstruction of life cycle. The best model selected is the symmetric one.

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Equal rates model Symmetric model All rates different model

AIC 315.3114 263.5621 309.8952

AICc 315.3388 264.1579 312.2063

k 1 6 12

Supplementary Table 5: Results of the Akaike information criterion (AIC) and Akaike

information criterion with correction (AICc) for each model fit of the ancestral state

reconstruction of fine-grained classifications life cycle. The best model selected is the

symmetric one.

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Lh Lh+Prior No.Pram Alpha Sigma.2

First run 316.522 631.773 246.381 2221.19 1774.52

Second run 357.8 688.392 167.648 4340.82 3620.76

Supplementary Table 6: Effective sample size for the first run and second run of the whole

cranium.

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Point

est.

Upper

C.I.

Lh 1 1.01

Lh...Prior 1 1.01

No.Pram 1 1

Alpha 1 1

Sigma.2 1 1

Multivariate psrf 1.08

Supplementary Table 7: test comparing several independent runs using Gelman and

Rubin's convergence diagnostic.

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