DOI: 10.5061/dryad.mp48001
title: Data from: Death is on our side: paleontological data drastically modify phylogenetic hypotheses

description: Fossils are the only remaining evidence of the majority of species that
 have ever existed, providing a direct window into events in evolutionary
 history that shaped the diversification of life on Earth. Phylogenies
 underpin our ability to make sense of evolution but are routinely inferred
 using only data available from living organisms. Although extinct taxa
 have been shown to add crucial information for inferring macroevolutionary
 patterns and processes (such as ancestral states, paleobiogeography and
 diversification dynamics), the role fossils play in reconstructing
 phylogeny is controversial. Since the early years of phylogenetic
 systematics, different studies have dismissed the impact of fossils due to
 their incompleteness, championed their ability to overturn phylogenetic
 hypotheses or concluded that their behavior is indistinguishable from that
 of extant taxa. Based on taxon addition experiments on empirical data
 matrices, we show that the inclusion of paleontological data has a
 remarkable effect in phylogenetic inference. Fossils often have higher
 levels of topological influence than extant taxa, while inducing unique
 topological rearrangements. Previous studies have proposed a suite of
 explanations for the topological behavior of fossils, such as their
 retention of unique morphologies or their ability to break long branches.
 We develop predictive models that demonstrate that the possession of
 distinctive character state combinations is the primary predictor of the
 degree of induced topological change, and that the relative impact of taxa
 (fossil and extant) can be predicted to some extent before any
 phylogenetic analysis. Our results bolster the consensus of recent
 empirical studies by showing the unique role of paleontological data in
 phylogenetic inference, and provide the first quantitative assessment of
 its determinants, with broad consequences for the design of taxon sampling
 in both morphological and total-evidence analyses.
description: SI File 1:
 DatasetsModified morphological
 datasets used for all analyses.SI File 1
 (Datasets).rarSI File 2: Supplementary
 MethodsFurther methodological
 details on dataset processing, subsampling procedure, estimation of
 determinants of topological impact and comparisons between parsimony and
 Bayesian inferenceSI File 2 (Supplementary
 Methods).docxSI File 3: Supplementary
 FiguresFigs.
 S1-S8SI
 File 3 (Supplementary
 Figures).docxSI File 4: Example TNT
 batch fileFile to run all maximum
 parsimony analyses of a given dataset. This provides a template that can
 be easily modified for the analysis of thousands of matrices in TNT
 format.fossilsensitivityTNT.runSI File 5: R scriptThe code contains all functions used in the manuscript, including those necessary for subsampling datasets and estimating topological impacts and its determinats. It also performs all statistical analysis and plots all of the results. Alongside SI File 1 (Datasets) and SI File 6 (Results) it allows all stages of the study to be replicated.fossil_impact.RSI File 6: ResultsResults of the assessment of topological impact (across extant, fossil and pseudoextinct terminals, as well as for each taxon individually). The data can be uploaded into R using code in SI File 5 and used to replicate the statistical analyses.SI File 6 (Results).rarSI File 7: Supplementary TablesTables S1-S2SI File 7 (Supplementary Tables).docx