Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification

Harrington S, Reeder TW

Date Published: October 26, 2016

DOI: http://dx.doi.org/10.5061/dryad.c494p

 

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Title Figure S1. Plot of the posterior and prior distributions from BAMM analysis using an expected number of shifts prior of 1.
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Description Figure S1. Plot of the posterior and prior distributions from BAMM analysis using an expected number of shifts prior of 1.
Download Fig. S1 - BAMM_prior_posterior.pdf (5.017 Kb)
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Title Figure S2. Ancestral state reconstruction of viviparity for Liolaemidae using the uncorrected sample fraction
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Description Figure 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).
Download Fig. S2 - Liolaemidae_uncorrected_frac_states.pdf (137.7 Kb)
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Title Fig. S3 - BAMM net diversification
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Description Figure S3. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are net diversification rates.
Download Fig. S3 - BAMM_NetDiv_labelled.pdf (1.284 Mb)
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Title Fig. S4 - BAMM speciation
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Description Figure S4. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are speciation rates.
Download Fig. S4 - BAMM speciation.pdf (1.214 Mb)
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Title Fig. S5 - BAMM Extinction
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Description Figure S5. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are extinction rates.
Download Fig. S5 - BAMM Extinction.pdf (1.189 Mb)
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Title Fig. S6 - Gekkota Diversitree BiSSE states
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Description Figure 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).
Download Fig. S6 - Gamble_Diversitree_BiSSE_states.pdf (245.3 Kb)
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Title Fig. S7 - Gekkota BiSSE-like HiSSE states
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Description Figure 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.
Download Fig. S7 - Gekkota_BiSSE-like_HiSSE_states.pdf (145.8 Kb)
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Title Fig. S8 - Gekkota HiSSE toepad states
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Description Figure 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.
Download Fig. S8 - Gekkota_toepad_states.pdf (346.0 Kb)
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Title Fig. S9 - Squamata HiSSE states
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Description Figure 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).
Download Fig. S9 - Squamates_states.pdf (4.018 Mb)
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Title Fig. S10 - Scincoidea HiSSE states
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Description Figure 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).
Download Fig. S10 - Scincoidea_states.pdf (341.2 Kb)
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Title Fig. S11 - Serpentes HiSSE states
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Description Figure 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).
Download Fig. S11 - Snake_states.pdf (1.355 Mb)
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Title Fig. S12 - Viperidae HiSSE states
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Description Figure 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).
Download Fig. S12 - Viper_states.pdf (265.4 Kb)
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Title Fig. S13 - Anguimorpha HiSSE states
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Description Figure 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).
Download Fig. S13 - Anguimorpha_states.pdf (127.7 Kb)
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Title Fig. S14 - Phrynosomatidae HiSSE states
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Description Figure 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).
Download Fig. S14 - Phrynosomatidae_states.pdf (135.1 Kb)
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Title Fig. S15 - Liolaemidae HiSSE states with corrected sampling fraction
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Description Figure 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).
Download Fig. S15 - Liolaemidae_states.pdf (137.2 Kb)
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Title Table S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fraction
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Description Table S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fraction
Download Table S1_uncorrected_sampling_Liolaemidae.xlsx (9.286 Kb)
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Title Table S2. Diversitree and BiSSE-like HiSSE Gekkota parameter estimates
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Description Table S2. Parameters estimated using the BiSSE model in Diversitree and the BiSSE-like model in the HiSSE package for Gamble et al. dataset.
Download Table S2 - Gamble parameters.xlsx (10.46 Kb)
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Title R code, tree, and data for Gekkota HiSSE analyses
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Description This 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.
Download Gekkota_analyses.zip (13.95 Kb)
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Title HiSSE.null4.9rate.R
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Description Null-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.
Download HiSSE.null4.9rate.R (37.90 Kb)
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Title Viviparity analyses R scripts
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Description This 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.
Download Viviparity analyses.zip (5.838 Kb)
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When using this data, please cite the original publication:

Harrington S, Reeder TW (2016) Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification. Journal of Evolutionary Biology 30(2): 313-325. http://dx.doi.org/10.1111/jeb.13004

Additionally, please cite the Dryad data package:

Harrington S, Reeder TW (2016) Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.c494p
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