DOI: 10.5061/dryad.0vk92
title: Data from: Methods for the quantitative comparison of molecular estimates of clade age and the fossil record

description: Approaches quantifying relative congruence, or incongruence, of molecular
 divergence estimates and the fossil record have been limited. Previously
 proposed methods are largely node specific, assessing incongruence at
 particular nodes for which both fossil data and molecular divergence
 estimates are available. These existing metrics, and other methods that
 quantify incongruence across topologies including entirely extinct clades,
 have so far not taken into account uncertainty surrounding both the
 divergence estimates and the ages of fossils. They have also treated
 molecular divergence estimates younger than previously assessed fossil
 minimum estimates of clade age as if they were the same as cases in which
 they were older. However, these cases are not the same. Recovered
 divergence dates younger than compared oldest known occurrences require
 prior hypotheses regarding the phylogenetic position of the compared
 fossil record and standard assumptions about the relative timing of
 morphological and molecular change to be incorrect. Older molecular dates,
 by contrast, are consistent with an incomplete fossil record and do not
 require prior assessments of the fossil record to be unreliable in some
 way. Here, we compare previous approaches and introduce two new
 descriptive metrics. Both metrics explicitly incorporate information on
 uncertainty by utilizing the 95% confidence intervals on estimated
 divergence dates and data on stratigraphic uncertainty concerning the age
 of the compared fossils. Metric scores are maximized when these ranges are
 overlapping. MDI (minimum divergence incongruence) discriminates between
 situations where molecular estimates are younger or older than known
 fossils reporting both absolute fit values and a number score for
 incompatible nodes. DIG range (divergence implied gap range) allows
 quantification of the minimum increase in implied missing fossil record
 induced by enforcing a given set of molecular-based estimates. These
 metrics are used together to describe the relationship between time trees
 and a set of fossil data, which we recommend be phylogenetically vetted
 and referred on the basis of apomorphy. Differences from previously
 proposed metrics and the utility of MDI and DIG range are illustrated in
 three empirical case studies from angiosperms, ostracods, and birds. These
 case studies also illustrate the ways in which MDI and DIG range may be
 used to assess time trees resultant from analyses varying in calibration
 regime, divergence dating approach or molecular sequence data analyzed.
description: ClarkeBoyd_readmeThis text file describes the complete set of supplementary data files and explains in more detail how to implement the metrics we describe.Table_2_CalculationsThis file contains the raw data and calculations used to produce the values of WSS, SEA, and MDI reported in Table 2 (from analysis of the Tinn and Oakley [2008] ostracod dataset.CLARKEBOYDonlineAPPENDIX1This file contains the fossil ages and their associated references for the analysis of Sphenisciformes.Table_3_CalculationsThis file contains the raw data and calculations used to produce the values of WSS, SEA, and MDI reported in Table 3 from analysis of the sphenisciform dataset.Table_5_MDI_CalculationsThis file contains the raw data and calculations used to produce the values of MDI reported in Table 5 from analysis of the data presented in Sauquet et al. (2012). There are three sheets in this file. The ‘MDI Scores’ sheet contains a table of the final scores reported in Table 5, while the ‘MDI Calculations’ sheet contains the formulae used to derive those values. The ‘Molec Data’ sheet contains the raw data used in the calculations.Ostracod_Tree_Fossils_OnlyThis is the file used by the ASCC program (see citation in paper) to calculate the MIG values for the ostracod dataset reported in Table 4. File contains the tree topology and age ranges used for all taxa and nodes.Penguin_Tree_Fossils_OnlyThis is the file used by the ASCC program (see citation in paper) to calculate the MIG values for the sphenisciform dataset reported in Table 4. File contains the tree topology and age ranges used for all taxa and nodes.Penguin_Tree_CombinedThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values for the sphenisciform dataset reported in Table 4. File contains the tree topology and age ranges used for all taxa and nodes, with node ages set equal to the molecular-based ages obtained using by Baker et al. (2006) using the combined mtDNA and Rag1 dataset.Penguin_Tree_mtDNA_OnlyThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values for the sphenisciform dataset reported in Table 4. File contains the tree topology and age ranges used for all taxa and nodes, with node ages set equal to the molecular-based ages obtained by Baker et al. (2006) using only the mtDNA dataset.Penguin_Tree_Rag1_OnlyThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values for the sphenisciform dataset reported in Table 4. File contains the tree topology and age ranges used for all taxa and nodes, with node ages set equal to the molecular-based ages obtained by Baker et al. (2006) using only the Rag1 dataset.Sauquet_Scenario_1_BeastThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 1 of the Sauquet et al. (2012) study using the program BEAST. File contains the tree topology and age ranges used for all taxa and nodes.Sauquet_Scenario_3_BeastThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 3 of the Sauquet et al. (2012) study using the program BEAST. File contains the tree topology and age ranges used for all taxa and nodes.Sauquet_Scenario_4_BeastThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 4 of the Sauquet et al. (2012) study using the program BEAST. File contains the tree topology and age ranges used for all taxa and nodes.Sauquet_Scenario_6_BeastThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 6 of the Sauquet et al. (2012) study using the program BEAST. File contains the tree topology and age ranges used for all taxa and nodes.Sauquet_Scenario_1_MLThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 1 of the Sauquet et al. (2012) study using the program r8s. File contains the tree topology and age ranges used for all taxa and nodes.Sauquet_Scenario_4_MLThis is the file used by the ASCC program (see citation in paper) to calculate the DIG values reported in Table 5 for scenario 4 of the Sauquet et al. (2012) study using the program r8s. File contains the tree topology and age ranges used for all taxa and nodes.