DOI: 10.5061/dryad.5v3b5
title: Data from: Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation.

description: The assumption of strictly neutral evolution is fundamental to the
 multispecies coalescent model and permits the derivation of gene tree
 distributions and coalescent times conditioned on a given species tree. In
 this study, we conduct computer simulations to explore the effects of
 violating this assumption in the form of species-specific positive
 selection when estimating species trees, species delimitations, and
 coalescent parameters under the model. We simulated datasets under an
 array of evolutionary scenarios that differ in both speciation parameters
 (i.e., divergence times, strength of selection) and experimental design
 (i.e., number of loci sampled) and incorporated species-specific positive
 selection occurring within branches of a species tree to identify the
 effects of selection on multispecies coalescent inferences. Our results
 highlight particular evolutionary scenarios and parameter combinations in
 which inferences may be more, or less, susceptible to the effects of
 positive selection. In some extreme cases, selection can decrease error in
 species delimitation and increase error in species tree estimation, yet
 these inferences appear to be largely robust to the effects of positive
 selection under many conditions likely to be encountered in empirical
 datasets.
description: FigureS1FIGURE S1. The effects of species-specific positive selection on effective population size and divergence time estimates of the shallow (top) and moderate-depth (bottom) species tree models. Results are shown for (a-c), (d-f), (g-i), and (j-l) for simulated datasets consisting of 1-locus (a, d, g, j), 2-loci (b, e, h, k), and 10-loci (c, f, i, l). The mean (points) and standard deviation (error bars) of parameter estimates based on 200 replicates are shown for three different Species-AB divergence times: recent (blue), medium (black), and ancient (red). Each panel is split into two subpanels representing 5 (left of dotted line) or 20 (right of dotted line) haplotypes sampled per species. A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01), strong (“S”, s = 0.10), and very strong (“VS”, s = 0.5) selection coefficients.FigureS2FIGURE S2. The effects of species-specific positive selection on effective population size and divergence time estimates of the deep species tree model. Results are shown for (a-c), (d-f), (g-i), and (j-l) for simulated datasets consisting of 1-locus (a, d, g, j), 2-loci (b, e, h, k), and 10-loci (c, f, i, l). The mean (points) and standard deviation (error bars) of parameter estimates based on 200 replicates are shown for three different Species-AB divergence times: 0.001 (blue), 0.005 (black), and 0.009 (red). Each panel is split into two subpanels representing 5 (left of dotted line) or 20 (right of dotted line) haplotypes sampled per species. A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01), strong (“S”, s = 0.10), and very strong (“VS”, s = 0.5) selection coefficients.FigureS3FIGURE S3. The effects of species-specific positive selection on posterior probabilities of species hypotheses of the shallow and moderate-depth species tree models. Results are shown for simulated datasets consisting of 1-locus (a, d, g, j), 2-loci (b, e, h, k), and 10-loci (c, f, i, l). The mean (points) and standard deviation (error bars) of parameter estimates based on 200 replicates are shown for three different Species-AB divergence times: recent (blue), medium (black), and ancient (red). Each panel is split into two subpanels representing 5 (left of dotted line) or 20 (right of dotted line) haplotypes sampled per species. A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01), strong (“S”, s = 0.10), and very strong (“VS”, s = 0.5) selection coefficients.FigureS4FIGURE S4. The effects of species-specific positive selection on posterior probabilities of species hypotheses of the deep species tree model. Results are shown for simulated datasets consisting of 1-locus (a, d, g, j), 2-loci (b, e, h, k), and 10-loci (c, f, i, l). The mean (points) and standard deviation (error bars) of parameter estimates based on 200 replicates are shown for three different Species-AB divergence times: 0.001 (blue), 0.005 (black), and 0.009 (red). Each panel is split into two subpanels representing 5 (left of dotted line) or 20 (right of dotted line) haplotypes sampled per species. A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01), strong (“S”, s = 0.10), and very strong (“VS”, s = 0.5) selection coefficients.FigureS5FIGURE S5. The effects of selection on species tree estimates for the moderate species tree simulations. Violin plots show the distribution of posterior probabilities of the correct rooted species topology (PABC, blue) and incorrect topology (PBCA, yellow) across 200 replicates (mean shown in black) for datasets consisting of 1-locus (bottom), 2-loci (middle), and 10-loci (top) that were simulated with either 5 (left) or 20 samples per species (right) under three different Species-AB divergence times (from left to right): 0.0001 (blue), 0.0005 (black), and 0.0009 (red). A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01, light red), strong (“S”, s = 0.10, medium red), and very strong (“VS”, s = 0.5, dark red) selection coefficients.FigureS6FIGURE S6. The effects of selection on species tree estimates for the deep species tree simulations. Violin plots show the distribution of posterior probabilities of the correct rooted species topology (PABC, blue) and incorrect topology (PBCA, yellow) across 200 replicates (mean shown in black) for datasets consisting of 1-locus (bottom), 2-loci (middle), and 10-loci (top) that were simulated with either 5 (left) or 20 samples per species (right) under three different Species-AB divergence times (from left to right): 0.001 (blue), 0.005 (black), and 0.009 (red). A color gradient ranging from white to dark gray is used to indicate the different percentages of loci under selection: 0% (neutral, white), 10%, 20%, 50% and 100% (dark gray). For simulations with selection, we varied the strength of selection: weak (“W”, s = 0.01, light red), strong (“S”, s = 0.10, medium red), and very strong (“VS”, s = 0.5, dark red) selection coefficients.