Data from: Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations

Lewitus E, Morlon H

Date Published: December 14, 2017

DOI: https://doi.org/10.5061/dryad.m96r3

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Title Supplemental Figure 1
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Description Recovered parameter estimates for trees simulated with a constant λ and an exponential dependency of μ on temperature. Simulations with: (A) varying λ0, constant μ0, and constant αμ; (B) constant λ0, varying μ0, and constant αμ; and (C) constant λ0, constant μ0, and varying αμ. Dashed red lines mark the simulated parameter value.
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Title Supplemental Figure 2
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Description Recovered parameter estimates for trees simulated with an exponential dependency of λ and μ on temperature. Dashed red lines mark the simulated parameter value.
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Title Supplemental Figure 3
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Description The effect of undersampling on parameter estimation. Parameter estimates for trees simulated with (a) a positive exponential dependency of λ on temperature and constant extinction (μ = 0.05) and (b) a positive exponential dependency of μ on temperature with constant speciation (λ = 0.5) by fitting the temperature-dependent model. Parameter estimates are shown for trees with increasingly smaller sampling fractions, which were achieved by jackknifing the simulated trees by a fixed % and then fitting the environment-dependent model. Simulated parameters are marked by dashed red lines. Model selection determined by (c) AICc and (d) Akaike weights for trees simulated with a positive exponential dependency of λ on temperature and constant extinction (grey, temperature- dependent model; light blue, time-dependent model; black, constant-rate model). In (d), weights are averaged across all trees within each undersampled bracket.
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Title Supplemental Figure 4
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Description The ability to correctly recover trees simulated under a time-dependent model or temperature-dependent model where the dependence is on extinction. Columns in each plot show the percentage of trees recovered (A,B) or Akaike weights (C,D) for constant-rate (black), time-dependent (light blue), or temperature-dependent extinction (brown) models for a set of trees simulated under (A,C) time-dependence or (B,D) temperature-dependence. Trees simulated under time-dependent extinction (B,D) were also fit with time-dependent speciation models (grey). The x-axis shows the strength of the dependencies (i.e., $\alpha$ value) used to simulate each set of trees. Akaike weights are averaged over all trees simulated with the same $\alpha$.}
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Title Supplemental Figure 5
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Description Parameter estimates for trees simulated with a positive (left) and negative (right) exponential dependency of $\lambda$ on temperature by fitting the temperature-dependent model. Parameter estimates are shown for trees with different species richness. Simulated parameters are marked by dashed red lines. Akaike weights are shown for trees fitted with temperature-dependent models (grey), time-dependent models (light blue), and constant-rate models (black). Weights are averaged across all trees within each species richness bracket.
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Title Supplemental Figure 6
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Description Parameter estimates for (a) λ0, (b) μ0, (c) αμ for trees simulated with a positive exponential dependency of μ on temperature by fitting the temperature- dependent model. Parameter estimates are shown for trees with different species richness. Simulated parameters are marked by dashed red lines. (c, inset) A magnified plot of αμ estimates. (d) Akaike weights averaged over all trees for each species richness cohort for models fitted with temperature-dependent models (grey), time-dependent models (light blue), and constant-rate models (black).
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Title Supplemental Figure 7
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Description Model selection and parameter estimation in temperature- dependent trees under various spline smoothings in the fitted model. (a) Plots of temperature curve splines smoothed by different degrees of freedom. The time-series of temperature data are shown in grey dots and the smoothed curves in black lines. (b,c) Parameter estimates for trees simulated with an exponential dependency of speciation on temperature (b, λ = 0.2e0.05·T(t); C, λ = 0.3e−0.05·T(t)) with temperature curves determined using generalized cross-validation (degrees of freedom=208), where the fitted temperature-dependent models have temperature curve splines smoothed by different degrees of freedom. Simulated parameters are marked by dashed red lines. (d) The percentage of temperature-dependent trees, simulated with a temperature curve determined using generalized cross-validation, best sup- ported by models fit with temperature curve splines smoothed by different degrees of freedom versus constant-rate models and time-dependent models with an exponential dependence on speciation.
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Title Supplemental Figure 8
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Description Mean of the Akaike weights for constant-rate models (black), time-dependent models (light blue), and environment-dependent models (colors correspond to Figure 1) across all environment-dependent λ trees with the same αλ (see Figure 4).
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Title Supplemental Figure 9
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Description Effect of different characteristics on the rate of recovery of environmental curves. The ability to correctly recover the simulated model at different values of αλ for (a) abiotic and biotic variables (see Figure 4) and (b) linear and non-linear environmental curves. (c) Barplots for the slope and intercept for regression models fit to autocorrelation functions for multiple lag-times for each environmental curve; the correlation, slope, and degrees of freedom estimated for generalized least squares (GLS) linear fits to each environmental curve; and the average rate of change of each environmental variable with respect to time. Bars are colored according to panel a.
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Title Supplemental Figure 10
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Description Rate of recovery for trees simulated with an exponential de- pendency of μ on different paleoenvironments, X, (μ = 0.02e^{αμX(t)}) for varying values of αμ and constant λ (λ0 = 0.15). (Top) Simulated trees fitted with models with an exponential dependency of μ on the paleoenvironment and a constant λ. (Bottom) Simulated trees fitted with models with an exponential dependency of λ on the paleoenvironment and a constant μ. Colors correspond to Figure 1.
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Title Supplemental Figure 11
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Description Environment-dependency in Ruminantia computed from the Ruminantia supertree (11). AICc support for different environment-dependent models, a constant-rate birth-death model, and an exponential time-dependent model (without extinction) on a distribution of 5000 posteriorly sampled probabilities of the Ruminantia supertree. All environment-dependent models have an exponential dependency on the environmental variable. Colors correspond to Figure 1.
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When using this data, please cite the original publication:

Lewitus E, Morlon H (2017) Detecting environment-dependent diversi_cation from phylogenies: a simulation study and some empirical illustrations. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx095

Additionally, please cite the Dryad data package:

Lewitus E, Morlon H (2017) Data from: Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations. Dryad Digital Repository. https://doi.org/10.5061/dryad.m96r3
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