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.
ClarkeBoyd_readme
This text file describes the complete set of supplementary data files and explains in more detail how to implement the metrics we describe.
Table_2_Calculations
This 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.
CLARKEBOYDonlineAPPENDIX1
This file contains the fossil ages and their associated references for the analysis of Sphenisciformes.
Table_3_Calculations
This 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_Calculations
This 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_Only
This 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_Only
This 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_Combined
This 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_Only
This 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_Only
This 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_Beast
This 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_Beast
This 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_Beast
This 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_Beast
This 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_ML
This 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_ML
This 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.