DOI: 10.5061/dryad.c494p
title: Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification

description: The binary-state speciation and extinction (BiSSE) model has been used in
 many instances to identify state-dependent diversification and reconstruct
 ancestral states. However, recent studies have shown that the standard
 procedure of comparing the fit of the BiSSE model to constant-rate
 birth–death models often inappropriately favours the BiSSE model when
 diversification rates vary in a state-independent fashion. The newly
 developed HiSSE model enables researchers to identify state-dependent
 diversification rates while accounting for state-independent
 diversification at the same time. The HiSSE model also allows researchers
 to test state-dependent models against appropriate state-independent null
 models that have the same number of parameters as the state-dependent
 models being tested. We reanalyse two data sets that originally used BiSSE
 to reconstruct ancestral states within squamate reptiles and reached
 surprising conclusions regarding the evolution of toepads within Gekkota
 and viviparity across Squamata. We used this new method to demonstrate
 that there are many shifts in diversification rates across squamates. We
 then fit various HiSSE submodels and null models to the state and
 phylogenetic data and reconstructed states under these models. We found
 that there is no single, consistent signal for state-dependent
 diversification associated with toepads in gekkotans or viviparity across
 all squamates. Our reconstructions show limited support for the recently
 proposed hypotheses that toepads evolved multiple times independently in
 Gekkota and that transitions from viviparity to oviparity are common in
 Squamata. Our results highlight the importance of considering an adequate
 pool of models and null models when estimating diversification rate
 parameters and reconstructing ancestral states.
description: Figure S1. Plot of the
 posterior and prior distributions from BAMM analysis using an expected
 number of shifts prior of 1.Figure S1. Plot of the
 posterior and prior distributions from BAMM analysis using an expected
 number of shifts prior of 1.Fig. S1 -
 BAMM_prior_posterior.pdfFigure S2. Ancestral
 state reconstruction of viviparity for Liolaemidae using the uncorrected
 sample fractionFigure S2. Ancestral
 state reconstruction of viviparity for Liolaemidae using the uncorrected
 sample fraction from HiSSE model-averaged across all tested models.
 Colored circles at tips and nodes indicate the states of species and
 probability that ancestors were oviparous (black) or viviparous (white).
 The legend in the lower left shows the range of rates, as well as the
 distribution of rates across the tree (upper histogram) and the frequency
 of tips in each state (lower bars).Fig. S2 -
 Liolaemidae_uncorrected_frac_states.pdfFig. S3 - BAMM net diversificationFigure S3. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are net diversification rates.Fig. S3 - BAMM_NetDiv_labelled.pdfFig. S4 - BAMM speciationFigure S4. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are speciation rates.Fig. S5 - BAMM ExtinctionFigure S5. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are extinction rates.Fig. S6 - Gekkota Diversitree BiSSE statesFigure S6. Ancestral state reconstruction of gekkotan toepads using the BiSSE model from Diversitree. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black).Fig. S6 - Gamble_Diversitree_BiSSE_states.pdfFig. S7 - Gekkota BiSSE-like HiSSE statesFigure S7. Ancestral state reconstruction of gekkotan toepads from HiSSE using the BiSSE-like model. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black). Branches are colored by model-averaged diversification rates.Fig. S7 - Gekkota_BiSSE-like_HiSSE_states.pdfFig. S8 - Gekkota HiSSE toepad statesFigure S8. Ancestral state reconstruction of gekkotan toepads from HiSSE model-averaged across all tested models with tip labels. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black). Branches are colored by model-averaged diversification rates.Fig. S8 - Gekkota_toepad_states.pdfFig. S9 - Squamata HiSSE statesFigure S9. Ancestral state reconstruction of viviparity for Squamata with from HiSSE model-averaged across all tested models with tip labels. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S9 - Squamates_states.pdfFig. S10 - Scincoidea HiSSE statesFigure S10. Ancestral state reconstruction of viviparity for Scincoidea from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S10 - Scincoidea_states.pdfFig. S11 - Serpentes HiSSE statesFigure S11. Ancestral state reconstruction of viviparity for Serpentes from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S11 - Snake_states.pdfFig. S12 - Viperidae HiSSE statesFigure S12. Ancestral state reconstruction of viviparity for Viperidae from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S12 - Viper_states.pdfFig. S13 - Anguimorpha HiSSE statesFigure S13. Ancestral state reconstruction of viviparity for Anguimorpha from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S13 - Anguimorpha_states.pdfFig. S14 - Phrynosomatidae HiSSE statesFigure S14. Ancestral state reconstruction of viviparity for Phrynosomatidae from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S14 - Phrynosomatidae_states.pdfFig. S15 - Liolaemidae HiSSE states with corrected sampling fractionFigure S15. Ancestral state reconstruction of viviparity for Liolaemidae using the corrected sampling fraction from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).Fig. S15 - Liolaemidae_states.pdfTable S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fractionTable S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fractionTable S1_uncorrected_sampling_Liolaemidae.xlsxTable S2. Diversitree and BiSSE-like HiSSE Gekkota parameter estimatesTable S2. Parameters estimated using the BiSSE model in Diversitree and the BiSSE-like model in the HiSSE package for Gamble et al. dataset.Table S2 - Gamble parameters.xlsxR code, tree, and data for Gekkota HiSSE analysesThis zip file contains the tree, trait data, and commented R script to run HiSSE analyses. The null-four nine-rate model requires the separately uploaded file containing the modified null-four function.Gekkota_analyses.zipHiSSE.null4.9rate.RNull-four function modified to allow nine transition rates among hidden states. To run this with 9 transition rates, set trans.type = "All.no.dual", all other arguments are identical to the hisse.null4 in the HiSSE package.Viviparity analyses R scriptsThis zip file contains two commented R scripts. One fits HiSSE models to the full squamate dataset. The other fits models to subtrees. See comments in scripts for details. The null-four nine-rate model requires the HiSSE.null4.9rate.R file separately available Dryad. For the location of the tree and data used, see comments in scripts.Viviparity analyses.zip