Dataset DOI: 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 files can be viewed in R  or any text reader. xlsx files can be viewed in Excel, Google Docs, or R. csv files can be viewed in any text reader.

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