Supplementary Materials include results of simulation experiments to investigate the impact of phylogenetic regression with model violations.

Modern comparative biology owes much to phylogenetic regression. At its conception, this technique sparked a revolution that armed biologists with phylogenetic comparative methods (PCMs) for disentangling evolutionary correlations from those arising from hierarchical phylogenetic relationships. Over the past few decades, the phylogenetic regression framework has become a paradigm of modern comparative biology that has been widely embraced as a remedy for shared ancestry. However, recent evidence has sown doubt over the efficacy of phylogenetic regression, and PCMs more generally, with the suggestion that many of these methods fail to provide an adequate defense against unreplicated evolution—the primary justification for using them in the first place. Importantly, some of the most compelling examples of biological innovation in nature result from abrupt lineage-specific evolutionary shifts, which current regression models are largely ill-equipped to deal with. Here we explore a solution..., , , # Supplementary Material and figures showing results of simulation experiments and phylogenetic case studies

[https://doi.org/10.5061/dryad.xpnvx0kn1](https://doi.org/10.5061/dryad.xpnvx0kn1)

Supplementary Figures include results of simulation experiments to investigate the impact of phylogenetic regression with mismatched trees.

## Supplementary Details associated with manuscript \"Robust Phylogenetic Regression\"

Supplementary Materials include results of simulation experiments to investigate the impact of phylogenetic regression with model violations. 

# Brief Description of Supplementary Figures (see documents for further information)

SUPPLEMENTARY FIGURE 1. Diagnostic plots depicting studentized residuals as a function of leverage for the L2 estimator applied to the example datasets shown in Figure 2 with PIC (a) and PGLS (b) regression.

SUPPLEMENTARY FIGURE 2. Histograms illustrating distributions of RPKM values across species (rows) and tissues (columns) for male (left colu...