DOI: 10.5061/dryad.w6m905r1x
title: Supplementary data for: Mass extinction triggered the early radiations of jawed vertebrates and their jawless relatives (gnathostomes)

description: This Dryad folder supports a published analysis (Hagiwara and Sallan,
 2026; Doi: 10.1126:sciadv.aeb2297) of conodont (early cyclostome
 vertebrates) global genus richess and gnathostome (jawed vertebrates and
 relatives) global species richness and faunal composition between the
 Ordovician period (480 Million years ago, Ma) and the end-Devonian (360
 Ma). It includes Data Files S1-S8, which comprises species lists and
 environmental and age information for 169 gnathostome vertebrate
 assemblages (faunas), matrices of species occurrences in 12 taxonomic
 categories in each fauna used in multivariate and ordination analyses and
 to construct histograms, all Ordovician-Devonian gnathostome species
 occurrences (N=1576) used for curves of species and genus richness,
 Ordovician-Silurian conodont species occurrences downloaded from the PBDB
 (N=1398). It also includes all R code, output files for analyses, and
 figure and table files. Please refer to the Materials and Methods of
 Hagiwara and Sallan, 2026 and the Supplementary Materials for details.
 These data provide a basis for examining the influence of extinction,
 incumbency, and biogeography on the initial radiations of
 gnathostomes. 
description: # Supplementary data for: Mass extinction triggered the early radiations
 of jawed vertebrates and their jawless relatives (gnathostomes). (Hagiwara
 and Sallan, 2026) Dataset DOI:
 [10.5061/dryad.w6m905r1x](10.5061/dryad.w6m905r1x) ## Description of the
 data and file structure Hagiwara_and_Sallan_Dryad_Final.zip folder
 contains spreadsheets and text files with species-level occurrences for
 Ordovician and Silurian gnathostomes collected from the literature (See
 Supplementary Data Files folder, Data S1-S8 files). The occurrences were
 used to generate curves of species-level and genus-level diversity by
 stage (see 'Analysis Input and R files' folder and DOI:
 10.1126: sciadv.aeb2297), and a set of gnathostome assemblages (faunas)
 spanning the Ordovician-Silurian (Data S1). This was used to generate a
 histogram of number of species within major groups at each locality (See
 DOI: 10.1126: sciadv.aeb2297). Assemblages with more than 2 species were
 then coded for number of species in each of 13 major groups at each site
 for use in ecological statistical analyses, including Canonical
 Correspondence Analysis (CCA), Non-parametric multidimensional scaling
 (NMDS), Analysis of Similarity (ANOSIM), Similarity Percentage (SIMPER)
 and Cluster Analysis (See 'Analysis Input and R files' folder).
 All results used in the final manuscript are shown in the
 "Supplementary Table Files" folder and the Supplementary
 Material at DOI: 10.1126: sciadv.aeb2297. Please refer to the Materials
 and Methods and Supplementary Materials of Hagiwara and Sallan, 2026 (DOI:
 10.1126: sciadv.aeb2297) for exact details on methods and methodological
 choices, and detailed captions for tables and figures. ### Files and
 Variables **Analysis and Input Files (Folder).** Note that spreadsheets in
 this file are in xslx format, as these were designed to be used with R
 code and included sheets are called explicitly. These exact files were
 used in our analyses. AllMatrix.xlsx - Input matrices of species
 occurrences by group for all gnathostome sites/assemblages
 ("faunas"). Sheet 1 is all faunas, and Sheet 2 is filtered to
 faunas with at least 3 species.   * *Sites -* assemblage (fauna) names *
 *Stage -* geological age * *Series -* ordered numerical geological age *
 *Region -* regional category * *Environment* - Benthic Assemblage Zone  *
 *Remaining Columns* - Taxonomic groups (by name) and Total Occurrences.
 Values indicate number of species in each group. Colorcode.xslx - Color
 codes for all taxonomic groups, regions, and ages used in all figures.
 Sheets contain different color codes used in different figures. Sheet 1
 contains colors for geological stages (ages) as hexadecimal RGB code based
 on the international standards. Sheet 2 contains colors for stages (ages)
 as names for use in R, Sheet 3 contains colors for stages (ages) as
 hexadecimal RGB code for use in Figure 2. Sheet 4 contains colors for
 geological series (epochs) as names for use in R.  Sheet 5 contains colors
 for environments as names for use in R.  Sheet 6 contains colors for
 regions as names for use in R.  Sheet 7 contains colors for geological
 series (epochs) as hexadecimal RGB code based on the international
 standards. Sheet 8 contains colors for geological series (epochs) as
 hexadecimal RGB code for use in Figure 2. Sheet 9 contains colors for
 regions as hexadecimal RGB code. Sheet 10 contains colors for
 "species" (taxonomic groups) as hexadecimal RGB code. Sheet 11
 contains colors for "species" (gnathostomes and conodonts) as
 hexadecimal RGB code. Sheet 11 contains colors for "species"
 (jawed fish and jawless fish) as hexadecimal RGB code.  Counting.R - R
 code to get species counts by time bin from the raw occurrence data (Data
 S3 and Data S4) Fig1_Main_Curve_Data.xlsx - Matrices for Genera per stage
 and region used to generate Fig. 1. Sheet 1 (Genus_Gna_Con) is raw genus
 counts for Gnathostomes and Conodonts per geological stage (rows). Sheet 2
 (Rate_Gna_Con) is the same data but divided by stage length in million
 years (per million years). Sheet 3 (Genus_Taxon) is the number of genera
 in each gnathostome taxonomic group (rows) by geological stage (columns).
 Sheet 4 (Genus_Region) is the number of gnathostome genera in region
 (rows) by geological stage. Fig1_Main_Curve_R - R code for generating
 diversity curves from the matrices in Fig1_Main_Curve_Data
 Fig2_Main_Hist_CCA_NMDS.R - R code for generating a histogram of species
 occurrences within taxonomic groups at gnathostome faunas, performing
 Canonical Correspondence Analysis and NMDS using the faunal matrices in
 Fig2_Main_Hist_Statistic.xlsx Fig2_Main_Hist_Statistic.xslx - A
 spreadsheet containing input files to generate Fig. 2. Sheet 1 (Hist) is
 the number of species occurrences in each taxonomic group (rows) per
 sites/"faunas" (columns). Sheet 2 (CCA_Hist) is the same data
 filtered to only include sites with more than 3 species occurrences.
 Fig3_PieChart.R - R code using Fig3_PieChart.xlsx and Color_code.xlsx to
 produce regional pie charts for each geological interval for use in Fig. 3
 Fig4_Main_Hist_Curve.R - R code using All_Matrix.xslx and Color_code.xslx
 to produce the histogram of jawed and jawless gnathostomes at each
 site/fauna and the genus-level stage-binned diversity curves of jawed and
 jawless gnathostomes (raw counts and per million years) used in Fig. 4
 Reanalysis_ANOSIM.R - R code using All_Matrix.xlsx to perform Analysis of
 Similarity (ANOSIM) on gnathostome faunas. Richness_Curve_data.xlsx -
 Spreadsheet containing all input data for genus level and species level
 diversity curves. Sheet 1 (Genus_Gna_Con) is raw genus counts for
 Gnathostomes and Conodonts per geological stage (rows). Sheet 2
 (Rate_Gna_Con) contains the same data but divided by stage length in
 million years (per million years). Sheet 3 (Species_Gna) is raw species
 counts for Conodonts and Gnathostomes per geological stage (rows). Sheet 4
 (Rate_Sp_Gna) contains the same data but divided by stage length in
 million years (per million years). Sheet 5 (Sp_Genus_Gna_Con1) is the
 number of species per genera for conodonts and gnathostomes per stage.
 Sheet 6 (Sp_Genus_Gna_Con2) is the number divided by million years. Sheet
 7 (Genus_taxon) is the number of genera in each gnathostome group per
 stage. Sheet 8 (Genus_Region) is the number of gnathostome genera per
 region in each stage. Sheet 9 (Fig4-B) is the raw jawed versus jawless
 gnathostome genera per stage used to generate the curves in Fig. 4B. Sheet
 10 (Fig4-C) contains the same data with number in each stage divided by
 stage length in million years. Sheet 11 (FigS3-A) contains the species
 counts in each jawless gnathostome taxonomic group (columns) by stage
 (rows) used to generate FigS3A. Sheet 12 (FigS3-C) contains the same data
 with counts divided by the stage length in million years. Sup_ANOSIM.R - R
 code for performing ANOSIM of gnathostome faunas with 3 or more species
 using "All_Matrix.xslx",
 "Fig2_Main_Hist_Statistic.xslx", and "Color_code.xslx"
 Sup_Cluster.R - R code for performing cluster analysis of gnathostome
 faunas with 3 or more species using "All_Matrix.xslx",
 "Fig2_Main_Hist_Statistic.xslx", and "Color_code.xslx"
 Sup_Curve.R - R code for generating species level diversity curves used in
 Figs. S3 and S4 using "Richness_Curve_Data.xslx"
 Sup_FA_SIMPER_Ord-Dat.dat - Input matrix for performing Factor Analysis
 (FA) and Similarity Percentage (SIMPER) on gnathostome faunas with at
 least 3 species occurrences using the program PAST (PASTproject).
 "Group" refers to the time category while "Dot" shows
 whether they are marine or non marine. All other columns are taxonomic
 groups with values representing number of species in each per site/fauna
 (rows). Stage represents geological stage. Sup_FA_SIMPER_Reanalysis.dat -
 Same file with chondrichthyans and acanthodians assigned to alternative
 groups. Please refer to manuscript for details. Sup_FA.R - R code for
 performing Factor Analysis analysis of gnathostome faunas with 3 or more
 species using "All_Matrix.xslx",
 "Fig2_Main_Hist_Statistic.xslx", and "Color_code.xslx"
 Sup_fauna_Hist.R - R code for generating histograms of species richness in
 each taxonomic group at each fauna using "All_Matrix.xslx",
 "Fig2_Main_Hist_Statistic.xslx", and "Color_code.xslx"
 Sup_reanalysis_1-3.R - R code for performing Canonical Correspondence
 Analysis (CCA) and Nonparametric Multidimensional Scaling (NMDS) using
 alternative assignments of Chondrichthyes and
 Acanthodii using "All_Matrix.xslx",
 "Fig2_Main_Hist_Statistic.xslx", and "Color_code.xslx"
 Sup_reanalysis.R - R code for performing Canonical Correspondence Analysis
 (CCA) and Nonparametric Multidimensional Scaling (NMDS) for final analyses
 using "All_Matrix.xslx" Sup_Shannon.R - R code for obtaining
 summary statistics for species diversity (Shannon-Weiner index, Taxonomic
 Richness, Total Species Counts) at each gnathostome fauna using
 "All_Matrix.xslx". **fauna_references plain text -** Full
 citations for all papers used to compile gnathostome species occurrences
 (Data S1). This is in RIF format but presented in plain text here. 
 **Supplementary Data Files (Folder).** Note: All xslx files saved on the
 Science Advances website (DOI: 10.1126: sciadv.aeb2297) have been split
 into separate sheets in csv format for Dryad. All associated sheets are
 labeled as DataS2-DataS8 and then their sheet name.  *Data_S1_Faunallist
 Final.txt -* Fauna descriptions and gnathostome taxon lists. Detailed all
 faunal information from Ordovician to Silurian (N = 169) and reference
 literatures.* *List of details on all gnathostome faunas including name,
 stratigraphy and location, age, environment (Benthic Assemblage Zone),
 Taxa (Resident species occurrences assigned to taxonomic groups),
 Reference numbers, and References for Age, Environment and Taxa. Numbered
 references at bottom of document. *Data_S2.csv* - Matrix of gnathostome
 occurrences in all faunas. Input matrix for histograms and Tab. S4.
 *Data_S3_Ord_AllGnathostome.csv-* Ordovician gnathostome occurrences. Raw
 occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 *Data_S3_Ord_Arandaspida.csv* - Ordovician arandaspid occurrences. Raw
 occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 *Data_S3_Ord_Astraspida.csv* - Ordovician astraspid occurrences. Raw
 occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 *Data_S3_Ord_Chondrichthyes.csv* - Ordovician chondrichthyan occurrences.
 Raw occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 *Data_S3_Ord_OtherPteraspidomorpha.csv* - Ordovician other pteraspidomorph
 occurrences. Raw occurrence records from the reference literature for the
 Ordovician. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S3_Ord_Thelodonti.csv* - Ordovician thelodont occurrences. Raw
 occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 Data_S3_Ord_Unknown.csv - Ordovician genera of unknown group occurrences.
 Raw occurrence records from the reference literature for the Ordovician.
 Occurrences arranged by genus then species. NA indicates specific data
 were not available in the literature for that occurrence.
 *Data_S4_Sil_Acanthodii.csv -* Silurian acanthodian occurrences. Raw
 occurrence records from the reference literature for Silurian. Occurrences
 arranged by genus then species. NA indicates specific data were not
 available in the literature for that occurrence.
 *Data_S4_Sil_AllGnathostomes.csv -* Silurian gnathostome occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Anaspida.csv -* Silurian anaspid occurrences. Raw occurrence
 records from the the reference literature for Silurian. Occurrences
 arranged by genus then species. NA indicates specific data were not
 available in the literature for that occurrence.
 *Data_S4_Sil_Chondrichthyes.csv -* Silurian chondrichthyan occurrences.
 Raw occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Galeaspida.csv -* Silurian galeaspid occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Heterostraci.csv -* Silurian heterostracan occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Osteichthyes.csv -* Silurian osteichthyan occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Osteostraci.csv -* Silurian osteostracan occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Placodermi.csv -* Silurian placoderm occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Thelodonti.csv -* Silurian thelodont occurrences. Raw
 occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S4_Sil_Unknown.csv -* Silurian genera of unknown group occurrences.
 Raw occurrence records from the the reference literature for
 Silurian. Occurrences arranged by genus then species. NA indicates
 specific data were not available in the literature for that occurrence.
 *Data_S5_Dev_AllGnathostomes.csv -* Devonian gnathostome occurrences. Raw
 occurrence records from the reference literature for Devonian. Occurrences
 arranged by genus then species. NA indicates specific data were not
 available in the literature for that occurrence. *Data_S5_Dev_Jawed.csv -*
 Devonian jawed gnathostome occurrences. Raw occurrence records from the
 reference literature for Devonian. Occurrences arranged by genus then
 species. NA indicates specific data were not available in the literature
 for that occurrence. *Data_S5_Dev_Jawless.csv -* Devonian jawless
 gnathostome occurrences. Raw occurrence records from the reference
 literature for Devonian. Occurrences arranged by genus then species. NA
 indicates specific data was not available in the literature for that
 occurrence. *Data_S6_Conodonts_Ord_Dap.csv-* Dapingian Ordovician conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for details. NA
 indicates specific data were not available in the literature for that
 occurrence. *Data_S6_Conodonts_Ord_Dar.csv-* Dariwillian Ordovician
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data_S6_Conodonts_Ord_Flo.csv-* Floian Ordovician conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data_S6_Conodonts_Ord_Hir.csv-* Hirnantian Ordovician
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data_S6_Conodonts_Ord_Kat.csv-* Katian Ordovician conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data_S6_Conodonts_Ord_San.csv-* Sandbian Ordovician
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data_S6_Conodonts_Ord_Tre.csv-* Tremedocian Ordovician
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_Gor.csv -* Gorstian Silurian conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_Hom.csv -* Homerian Silurian conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_Lud.csv -* Ludlow Silurian conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_Pri.csv -* Pridoli Silurian conodont
 occurrences. Raw occurrence records from “The Paleobiology Database”
 website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_She.csv -* Sheinwoodian Silurian
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S7_Conodonts_Sil_Tel.csv -* Telychian Silurian
 conodont occurrences. Raw occurrence records from “The Paleobiology
 Database” website. Used under CC0 license with attribution. See file for
 details. Missing data cells were left blank, as downloaded data has not
 been altered. *Data S8.csv -* Matrix of gnathostome faunal occurrences for
 statistical analysis. Input matrix for statistical analysis including
 cluster analysis, CCA, NMDS, FA, ANOSIM and SIMPER. Faunas with less than
 3 species excluded. **Supplementary Table Files (Folder) -** All csv files
 for the supplementary table sections and results. Please see supplementary
 materials file at the Science Advances website for full captions. 
 *Tab_S1_Species_Occurrence_Ord.csv -* Number of species occurrences in
 each gnathostome class by Ordovician stage.
 *Tab_S1_Species_Occurrence_Sil.csv -* Number of species occurrences in
 each gnathostome class by Silurian stage.
 *Tab_S2_Occurrence_region_Lla_Sil.csv -* Number of species occurrences in
 each region in the Llandovery Silurian.
 *Tab_S2_Occurrence_region_Low_Ord.csv -* Number of species occurrences in
 each region in the Lower Ordovician *Tab_S2_Occurrence_region_Lud_Sil.csv
 -* Number of species occurrences in each region in the Ludlow Silurian
 *Tab_S2_Occurrence_region_Mid_Ord.csv -* Number of species occurrences in
 each region in the Middle Ordovician *Tab_S2_Occurrence_region_Mid_Ord.csv
 -* Number of species occurrences in each region in the Middle Ordovician
 *Tab_S2_Occurrence_region_Pri_Sil.csv -* Number of species occurrences in
 each region in the Pridoli Silurian *Tab_S2_Occurrence_region_Upp_Ord.csv
 -* Number of species occurrences in each region in the Upper Ordovician
 *Tab_S2_Occurrence_region_Wen_Sil.csv -* Number of species occurrences in
 each region in the Wenlock Silurian
 *Tab_S3_Species_Diversity_Ord_Rate.csv* - Species occurrences per million
 years for each taxonomic group in each Ordovician stage.
 *Tab_S3_Species_Diversity_Ord_Raw.csv* - Species occurrences for each
 taxonomic group in each Ordovician stage.
 *Tab_S3_Species_Diversity_Sil_Rate.csv* - Species occurrences per million
 years for each taxonomic group in each Silurian stage.
 *Tab_S3_Species_Diversity_Sil_Raw.csv* - Species occurrences for each
 taxonomic group in each Silurian stage.
 *Tab_S4_Genus_Diversity_Ord_Rate.csv* - Genus occurrences per million
 years for each taxonomic group in each Ordovician stage.
 *Tab_S4_Genus_Diversity_Ord_Raw.csv* - Genus occurrences for each
 taxonomic group in each Ordovician stage.
 *Tab_S4_Genus_Diversity_Sil_Rate.csv* - Genus occurrences per million
 years for each taxonomic group in each Silurian stage.
 *Tab_S4_Genus_Diversity_Sil_Raw.csv* - Genus occurrences for each
 taxonomic group in each Silurian stage. *Tab_S5_Fauna_number_Ord.csv -*
 Number of faunas in each Ordovician stage. Asterisk indicates that some
 faunas occurred in two stages. *Tab_S5_Fauna_number_Sil.csv -* Number of
 faunas in each Silurian stage. Asterisk indicates that some faunas
 occurred in two stages. *Tab_S6_Richness_by_Region_Jawed_Rate_Ord.csv
 -* Number of jawed gnathostome species in each region in each Ordovician
 stage per million years. *Tab_S6_Richness_by_Region_Jawed_Rate_Sil.csv
 -* Number of jawed gnathostome species in each region in each Silurian
 stage per million years. *Tab_S6_Richness_by_Region_Jawed_Raw_Ord.csv
 -* Number of jawed gnathostome species in each region in each Ordovician
 stage. *Tab_S6_Richness_by_Region_Jawed_Raw_Sil.csv -* Number of jawed
 gnathostome species in each region in each Silurian stage.
 *Tab_S6_Richness_by_Region_Jawless_Rate_Ord.csv -* Number of jawless
 gnathostome species in each region in each Ordovician stage per million
 years. *Tab_S6_Richness_by_Region_Jawless_Rate_Sil.csv -* Number of
 jawless gnathostome species in each region in each Silurian stage per
 million years. *Tab_S6_Richness_by_Region_Jawless_Raw_Ord.csv -* Number of
 jawless gnathostome species in each region in each Ordovician stage.
 *Tab_S6_Richness_by_Region_Jawless_Raw_Sil.csv -* Number of jawless
 gnathostome species in each region in each Silurian stage.
 *Tab_S7_Shannon_Faunas.csv -* Shannon diversity, Genus richness
 (Richness), and Species counts for all gnathostome faunas ordered by age
 from oldest to youngest. *Tab_S7_Shannon_Stages.csv -* Mean, Standard
 Deviation (SD), and Median Values for Species counts, Shannon-Weiner
 Diversity (count), and Taxonomic Richness for all faunas in each
 geological stage. *Tab_S8_CCA_Scores_Eigen_Trace.csv -* Importance and
 significance of the canonical axes (Axis 1, Axis 2, Axis 3) in a Canonical
 Correspondence Analysis of all gnathostome faunas with at least 2 species.
 Eigenvalue - amount of constrained variance (inertia) explained by each
 axis. X.% of constrained inertia - percentage of total constrained
 variation explained by each axis. X.% of total inertia - percentage of all
 variation explained by each axis. p - p-value.
 *Tab_S8_CCA_Scores_Faunas_Taxa.csv -* Scores for taxonomic groups
 (species) and faunas (sites) along Canonical Correspondence Axis 1 (CCA1)
 and Canonical Correspondence Axis 2 (CCA2) from a Canonical Correspondence
 Analysis (CCA) of all gnathostome faunas with with at least 2 species. 
 *Tab_S9_FA_All_Faunas.csv -* Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each Ordovician-Silurian gnathostome fauna from
 Factor Analysis (FA). *Tab_S9_FA_All_Summary.csv -* Importance and
 significance of axes (PCs or factors, equal to FA1, FA2, etc) as
 determined by a Factor Analysis (FA) of Ordovician-Silurian gnathostome
 faunas. Eigenvalue - the amount of variance explained by each factor. %
 variance - percentage of total variance explained by each factor. 
 *Tab_S9_FA_All_Taxa.csv - *Scores for each significant factor (axis, FA1,
 FA2, FA3, FA4) for each gnathostome taxonomic group in Ordovician
 -Silurian gnathostome faunas from Factor Analysis (FA)
 *Tab_S9_FA_Lla-Wen_Faunas.csv -* Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each Llandovery-Wenlock Silurian gnathostome fauna
 from Factor Analysis (FA). *Tab_S9_FA_Lla-Wen_Summary.csv -* Importance
 and significance of axes (PCs or factors, equal to FA1, FA2, etc) as
 determined by a Factor Analysis (FA) of Llandovery-Wenlock Silurian
 gnathostome faunas. Eigenvalue - the amount of variance explained by each
 factor. % variance - percentage of total variance explained by each
 factor.  *Tab_S9_FA_Lla-Wen_Taxa.csv - *Scores for each significant factor
 (axis, FA1, FA2, FA3, FA4) for each gnathostome taxonomic group in
 Llandovery-Wenlock Silurian gnathostome faunas from Factor Analysis (FA)
 *Tab_S9_FA_Lud-Pri_Faunas.csv -* Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each Ludlow-Pridoli Silurian gnathostome fauna
 from Factor Analysis (FA). *Tab_S9_FA_Lud-Pri_Summary.csv -* Importance
 and significance of axes (PCs or factors, equal to FA1, FA2, etc) as
 determined by a Factor Analysis (FA) of Ludlow-Pridoli Silurian
 gnathostome faunas. Eigenvalue - the amount of variance explained by each
 factor. % variance - percentage of total variance explained by each
 factor.  *Tab_S9_FA_Lud-Pri_Taxa.csv - *Scores for each significant factor
 (axis, FA1, FA2, FA3, FA4) for each gnathostome taxonomic group in
 Ludlow-Pridoli Silurian gnathostome faunas from Factor Analysis (FA).
 *Tab_S9_FA_Mid-Upp_Faunas.csv -* Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each Middle-Upper Ordovician gnathostome fauna
 from Factor Analysis (FA). *Tab_S9_FA_Mid-Upp_Summary.csv -* Importance
 and significance of axes (PCs or factors, equal to FA1, FA2, etc) as
 determined by a Factor Analysis (FA) of Middle-Upper Ordovician
 gnathostome faunas. Eigenvalue - the amount of variance explained by each
 factor. % variance - percentage of total variance explained by each
 factor.  *Tab_S9_FA_Mid-Upp_Taxa.csv - *Scores for each significant factor
 (axis, FA1, FA2, FA3, FA4) for each gnathostome taxonomic group in
 Middle-Upper Ordovician gnathostome faunas from Factor Analysis (FA)
 *Tab_S9_FA_Upp-Lla_Faunas.csv -* Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each Upper Ordovician - Llandovery Silurian
 gnathostome fauna from Factor Analysis (FA).
 *Tab_S9_FA_Upp-Lla_Summary.csv -* Importance and significance of axes (PCs
 or factors, equal to FA1, FA2, etc) as determined by a Factor Analysis
 (FA) of Upper Ordovician-Llandovery Silurian gnathostome faunas.
 Eigenvalue - the amount of variance explained by each factor. % variance -
 percentage of total variance explained by each factor. 
 *Tab_S9_FA_Upp-Lla_Taxa.csv - *Scores for each significant factor (axis,
 FA1, FA2, FA3, FA4) for each gnathostome taxonomic group in Upper
 Ordovician - Llandovery Silurian gnathostome faunas from Factor Analysis
 (FA). *Tab_S9_FA_Wen-Lud_Faunas.csv -* Scores for each significant factor
 (axis, FA1, FA2, FA3, FA4) for each Wenlock-Ludlow Silurian gnathostome
 fauna from Factor Analysis (FA). *Tab_S9_FA_Wen-Lud_Summary.csv
 -* Importance and significance of axes (PCs or factors, equal to FA1, FA2,
 etc) as determined by a Factor Analysis (FA) of Wenlock-Ludlow Silurian
 gnathostome faunas. Eigenvalue - the amount of variance explained by each
 factor. % variance - percentage of total variance explained by each
 factor.  *Tab_S9_FA_Wen-Lud_Taxa.csv - *Scores for each significant factor
 (axis, FA1, FA2, FA3, FA4) for each gnathostome taxonomic group in
 Wenlock-Ludlow Silurian gnathostome faunas from Factor Analysis (FA).
 *Tab_S10_ANOSIM_P_Values.csv -* P-values for compositional differences
 between gnathostome faunas with at least 3 in successive geological ages,
 based on pairwise Analysis of Similarity (ANOSIM) using different
 dissimilarity metrics. Comparison - compared groups of faunas, Overall
 Mean - mean p-value for difference based on all metrics. Abundance mean -
 mean p-value based only on metrics which use actual species counts within
 taxonomic groups at each fauna rather than presence-absence of groups. See
 supplementary material at the Science Advances website for explanation of
 dissimilarity metrics.  *Tab_S10_ANOSIM_R_Values.csv -* R-values for
 compositional differences between gnathostome faunas with at least 3 in
 successive geological ages, based on pairwise Analysis of Similarity
 (ANOSIM) using different dissimilarity metrics. R is measure of similarity
 between groups, with R closer to 1 meaning larger differences and negative
 R indicating within group differences are greater than between group
 differences. Comparison - compared groups of faunas, Overall Mean - mean
 R-value for difference based on all metrics. Abundance mean - mean R-value
 based only on metrics which use actual species counts within taxonomic
 groups at each fauna rather than presence-absence of groups. See
 supplementary material at the Science Advances website for explanation of
 dissimilarity metrics.  *Tab_S11-12_SIMPER_Bray_Past_All.csv -* The
 results of Similarity Percentage analysis of faunas in successive
 geological ages using Bray-Curtis dissimilarity. Average dissimilarity
 between faunas in two adjacent ages shown. 
 *Tab_S11-12_SIMPER_Bray_Past_Lla-Wen.csv -* The results of Similarity
 Percentage analysis of faunas in the Llandovery and Wenlock Silurian using
 Bray-Curtis dissimilarity. Taxa (Taxon) are ranked by contribution to
 dissimilarity between faunas grouped into age intervals. Average
 Dissimilarity (Av. dissim) shows how the average Bray-Curtis dissimilarity
 between ages is attributable to each taxon. Contribution percentage
 (Contrib. %) shows the percentage of the total dissimilarity attributable
 to each taxon. Cumulative percentage (Cumulative %) shows the running
 total of dissimilarity explained by all taxa to that row. Mean abundance
 shows the mean abundance of each taxon in faunas of each age. Overall
 average dissimilarity is for all faunas.
 *Tab_S11-12_SIMPER_Bray_Past_Lud-Pri.csv -* The results of Similarity
 Percentage analysis of faunas in the Ludlow and Pridoli Silurian using
 Bray-Curtis dissimilarity. Taxa (Taxon) are ranked by contribution to
 dissimilarity between faunas grouped into age intervals. Average
 Dissimilarity (Av. dissim) shows how the average Bray-Curtis dissimilarity
 between ages is attributable to each taxon. Contribution percentage
 (Contrib. %) shows the percentage of the total dissimilarity attributable
 to each taxon. Cumulative percentage (Cumulative %) shows the running
 total of dissimilarity explained by all taxa to that row. Mean abundance
 shows the mean abundance of each taxon in faunas of each age. Overall
 average dissimilarity is for all faunas.
 *Tab_S11-12_SIMPER_Bray_Past_Mid-Upper_Ord.csv -* The results of
 Similarity Percentage analysis of faunas in the Middle and Upper
 Ordovician using Bray-Curtis dissimilarity. Taxa (Taxon) are ranked by
 contribution to dissimilarity between faunas grouped into age intervals.
 Average Dissimilarity (Av. dissim) shows how the average Bray-Curtis
 dissimilarity between ages is attributable to each taxon. Contribution
 percentage (Contrib. %) shows the percentage of the total dissimilarity
 attributable to each taxon. Cumulative percentage (Cumulative %) shows the
 running total of dissimilarity explained by all taxa to that row. Mean
 abundance shows the mean abundance of each taxon in faunas of each age.
 Overall average dissimilarity is for all faunas.
 *Tab_S11-12_SIMPER_Bray_Past_UpperOrd-Lla.csv -* The results of Similarity
 Percentage analysis of faunas in the Upper Ordovician and Llandovery
 Silurian using Bray-Curtis dissimilarity. Taxa (Taxon) are ranked by
 contribution to dissimilarity between faunas grouped into age intervals.
 Average Dissimilarity (Av. dissim) shows how the average Bray-Curtis
 dissimilarity between ages is attributable to each taxon. Contribution
 percentage (Contrib. %) shows the percentage of the total dissimilarity
 attributable to each taxon. Cumulative percentage (Cumulative %) shows the
 running total of dissimilarity explained by all taxa to that row. Mean
 abundance shows the mean abundance of each taxon in faunas of each age.
 Overall average dissimilarity is for all faunas.
 *Tab_S11-12_SIMPER_Bray_Past_Wen-Lud.csv -* The results of Similarity
 Percentage analysis of faunas in the Wenlock and Ludlow Silurian using
 Bray-Curtis dissimilarity. Taxa (Taxon) are ranked by contribution to
 dissimilarity between faunas grouped into age intervals. Average
 Dissimilarity (Av. dissim) shows how the average Bray-Curtis dissimilarity
 between ages is attributable to each taxon. Contribution percentage
 (Contrib. %) shows the percentage of the total dissimilarity attributable
 to each taxon. Cumulative percentage (Cumulative %) shows the running
 total of dissimilarity explained by all taxa to that row. Mean abundance
 shows the mean abundance of each taxon in faunas of each age. Overall
 average dissimilarity is for all faunas.
 *Tab_S13_Reanalysis1_CCA_Scores_Eigen_Trace.csv -* Importance and
 significance of the canonical axes (Axis 1, Axis 2, Axis 3) in a Canonical
 Correspondence Analysis of all gnathostome faunas with at least 2 species,
 where all Ordovician chondrichthyans are reassigned as "Unknown"
 (Reanalysis 1). Eigenvalue - amount of constrained variance (inertia)
 explained by each axis. X.% of constrained inertia - percentage of total
 constrained variation explained by each axis. X.% of total inertia -
 percentage of all variation explained by each axis. p - p-value.
 *Tab_S13_Reanalysis1_CCA_Scores_Faunas_Taxa.csv -* Scores for taxonomic
 groups (species) and faunas (sites) along Canonical Correspondence Axis 1
 (CCA1) and Canonical Correspondence Axis 2 (CCA2) from a Canonical
 Correspondence Analysis (CCA) of all gnathostome faunas with with at least
 2 species, where all Ordovician chondrichthyans are reassigned as
 "Unknown" (Reanalysis 1). 
 *Tab_S13_Reanalysis2_CCA_Scores_Eigen_Trace.csv -* Importance and
 significance of the canonical axes (Axis 1, Axis 2, Axis 3) in a Canonical
 Correspondence Analysis of all gnathostome faunas with at least 2 species,
 where all acanthodians are reassigned as chondrichthyans (Reanalysis 2). 
 Eigenvalue - amount of constrained variance (inertia) explained by each
 axis. X.% of constrained inertia - percentage of total constrained
 variation explained by each axis. X.% of total inertia - percentage of all
 variation explained by each axis. p - p-value.
 *Tab_S13_Reanalysis2_CCA_Scores_Faunas_Taxa.csv -* Scores for taxonomic
 groups (species) and faunas (sites) along Canonical Correspondence Axis 1
 (CCA1) and Canonical Correspondence Axis 2 (CCA2) from a Canonical
 Correspondence Analysis (CCA) of all gnathostome faunas with with at least
 2 species, where all acanthodians are reassigned as chondrichthyans
 (Reanalysis 2).  *Tab_S13_Reanalysis3_CCA_Scores_Eigen_Trace.csv
 -* Importance and significance of the canonical axes (Axis 1, Axis 2, Axis
 3) in a Canonical Correspondence Analysis of all gnathostome faunas with
 at least 2 species, where all acanthodians are reassigned as
 chondrichthyans and all Ordovician chondrichthyans are reassigned as
 "Unknown" (Reanalysis 3). Eigenvalue - amount of constrained
 variance (inertia) explained by each axis. X.% of constrained inertia -
 percentage of total constrained variation explained by each axis. X.% of
 total inertia - percentage of all variation explained by each axis. p -
 p-value. *Tab_S13_Reanalysis3_CCA_Scores_Faunas_Taxa.csv -* Scores for
 taxonomic groups (species) and faunas (sites) along Canonical
 Correspondence Axis 1 (CCA1) and Canonical Correspondence Axis 2 (CCA2)
 from a Canonical Correspondence Analysis (CCA) of all gnathostome faunas
 with with at least 2 species, where all acanthodians are reassigned as
 chondrichthyans and all Ordovician chondrichthyans are reassigned as
 "Unknown" (Reanalysis 3). 
 *Tab_S14_Reanalysis1_FA_Upp-Lla_Faunas.csv -* Scores for each significant
 factor (axis, FA1, FA2, FA3, FA4) for each Upper Ordovician - Llandovery
 Silurian gnathostome fauna from Factor Analysis (FA) where all Ordovician
 chondrichthyans are reassigned as "Unknown" (Reanalysis 1).
 *Tab_S14_Reanalysis1_FA_Upp-Lla_Summary.csv -* Importance and significance
 of axes (PCs or factors, equal to FA1, FA2, etc) as determined by a Factor
 Analysis (FA) of Upper Ordovician-Llandovery Silurian gnathostome faunas
 where all Ordovician chondrichthyans are reassigned as "Unknown"
 (Reanalysis 1). . Eigenvalue - the amount of variance explained by each
 factor. % variance - percentage of total variance explained by each
 factor.  *Tab_S14_Reanalysis1_FA_Upp-Lla_Taxa.csv -* Scores for each
 significant factor (axis, FA1, FA2, FA3, FA4) for each gnathostome
 taxonomic group in Upper Ordovician - Llandovery Silurian gnathostome
 faunas from Factor Analysis (FA) where all Ordovician chondrichthyans are
 reassigned as "Unknown" (Reanalysis 1).  ## Code/software R
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 Access information Data were derived from the following sources: *
 Paleobiology Database * References listed in Data S1, Data S3-Data S7,
 'fauna_references plain text.txt