Data from: Methods for the quantitative comparison of molecular estimates of clade age and the fossil record

Clarke JA, Boyd CA

Date Published: December 26, 2014

DOI: http://dx.doi.org/10.5061/dryad.0vk92.2

 

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Title ClarkeBoyd_readme
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Description This text file describes the complete set of supplementary data files and explains in more detail how to implement the metrics we describe.
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Title Table_2_Calculations
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Description 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.
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Title CLARKEBOYDonlineAPPENDIX1
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Description This file contains the fossil ages and their associated references for the analysis of Sphenisciformes.
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Title Table_3_Calculations
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Description 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.
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Title Table_5_MDI_Calculations
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Description 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.
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Title Ostracod_Tree_Fossils_Only
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Description 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.
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Title Penguin_Tree_Fossils_Only
Downloaded 6 times
Description 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.
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Title Penguin_Tree_Combined
Downloaded 6 times
Description 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.
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Title Penguin_Tree_mtDNA_Only
Downloaded 5 times
Description 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.
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Title Penguin_Tree_Rag1_Only
Downloaded 6 times
Description 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.
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Title Sauquet_Scenario_1_Beast
Downloaded 5 times
Description 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.
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Title Sauquet_Scenario_3_Beast
Downloaded 3 times
Description 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.
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Title Sauquet_Scenario_4_Beast
Downloaded 7 times
Description 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.
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Title Sauquet_Scenario_6_Beast
Downloaded 8 times
Description 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.
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Title Sauquet_Scenario_1_ML
Downloaded 3 times
Description 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.
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Title Sauquet_Scenario_4_ML
Downloaded 5 times
Description 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.
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When using this data, please cite the original publication:

Clarke JA, Boyd CA (2015) Methods for the quantitative comparison of molecular estimates of clade age and the fossil record. Systematic Biology 64(1): 25-41. http://dx.doi.org/10.1093/sysbio/syu068

Additionally, please cite the Dryad data package:

Clarke JA, Boyd CA (2014) Data from: Methods for the quantitative comparison of molecular estimates of clade age and the fossil record. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.0vk92.2
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