Uploaded data files and R scripts for Fritz et al. 

If you use these datasets, please cite:



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Files listed alphabetically below. Note that each data file comes with a metadata txt file.

To follow data and analyses in the order presented in the paper, these are the steps with section titles as in the methods description:

Mammalian fossil data: Data_GenusOccurrence.txt is the cleaned occurrence file which genera occur in which location. This was produced using the taxonomy lookup table Data_TaxonomyLookup.xls and the gridded focal regions Data_RegionsGridded.shp.

Estimation of mammalian gamma diversity: Analyses were performed with Rscript_MammalDataProcessing.r. The script produces first versions of the Data_Regions.txt and Data_Continents.txt files, by compiling the raw number of genera in each region/continent and time interval, and by estimating gamma diversity with the estimator algorithms. It also uses the Data_RegionsGridded.shp file to add area (the minimum convex hull around mammalian locations in each time interval) to the data. Supplementary analyses for mammalian gamma diversity presented in the SI are included in R_SupplementaryAnalysesFossilMammals.r and use Data_Suppl_PresentDayOccurrence.txt (and, if you want to recreate exactly the results of simulations in the paper, Output_Suppl_PresentDaySensitivityGamma.RData).

Estimation of present-day diversity and end-Pleistocene and Holocene extinctions: A global file of 1° lat-long grid cells and the mammalian data (present-day richness of the large terrestrial orders used in our paper) and the climate and NPP data (present-day temperature, precipitation, and NPP) was produced with ArcGIS: Data_PresentDay_Global.txt (and also Data_PresentDay_StudyRegions.txt as an excerpt of the global file). The numbers of Pleistocene and Holocene extinct genera are included in the Data_Analyses... files (separately for continents and regions).

Paleobotanical data: Data_Paleoclimate_Regions.txt is the cleaned file for paleo-climatic estimates in locations across our focal regions. This was produced with allocation of stratigraphic stages as recorded in Data_AgeTablePaleoclimate.txt. Supplementary analysis of the two different ways to allocate stratigraphic stages is included in Rscript_ClimateDataProcessing.r and Rscript_ProdDivModelling.r.

Calculation of NPP from paleo-climatic estimates: Analyses were performed with Rscript_ClimateDataProcessing.r. The script produces columns appended to the Data_Regions.txt and Data_Continents.txt files, by summarizing the paleo-climatic estimates in each grid cell and region/continent.

Present-day NPP data and human appropriation: A global file of 1° lat-long grid cells and the mammalian data (present-day richness of the large terrestrial orders used in our paper) and the climate and NPP data (present-day temperature, precipitation, and NPP) was produced with ArcGIS: Data_PresentDay_Global.txt (and also Data_PresentDay_StudyRegions.txt as an excerpt of the global file). Analyses were performed with Rscript_PresentDay.r, which compares present-day NPP values generated with DGVMs and with the Miami model.

Analyses of the mammalian diversity-productivity relationship: Data_Continents.txt and Data_Regions.txt contain all data for all models, which were fitted with Rscript_ProdDivModelling.r. The output saved at the end of this script is also given in Data_AnalysesContinents.txt and Data_AnalysesRegions.txt, which only contain the relevant data for the main models, model residuals, and present-day data for Fig 2 and 3. Note that Rscript_ProdDivModelling.r also fits some supplementary models (Table S2). Spatial models for the present day are fitted with Rscript_PresentDay.r (Fig S6 and S7).


Most figures were produced with Rscript_FiguresFossil.r: Fig. 1-3 and Fig S1-S4.
The remaining data figures (Fig S6 and Fig S7) were produced with Rscript_PresentDay.r. 


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Data_AgeTablePaleoclimate: table showing which stratigraphic stage and land mammal age / zone were allocated to which age estimate given in paleo-climatic data sources.

Data_AnalysesContinents.txt: the data from Data_Continents that are relevant for the main diversity-productivity models in Rscript_ProdDivModelling.r, and our model residuals and present-day data included in Fig. 2 and 3.

Data_AnalysesRegions.txt: the data from Data_Regions that are relevant for the main diversity-productivity models in Rscript_ProdDivModelling.r, and our model residuals and present-day data included in Fig. 2 and 3.

Data_Continents.txt: the processed fossil mammalian and NPP data for each focal continent.

Data_GenusOccurrence.txt: Original mammal data, i.e. a dataset of mammalian genera occurring in locations through the Neogene.

Data_Paleoclimate_Regions.txt: Original paleobotanical data, i.e. a dataset of paleoclimatic localities (mean annual temperatures and/or mean annual precipitation) for focal areas in North America and Europe through the Neogene.

Data_PresentDay_Global.txt: Original present-day data on global richness, geography and environment (climate and NPP) in 1° lat-long grid cells.

Data_PresentDay_StudyRegions.txt: Original present-day data on  richness, geography and environment (climate and NPP) in 1° lat-long grid cells within the study regions.

Data_Regions.txt: the processed fossil mammalian and NPP data for each focal region.

Data_RegionsGridded.shp: The shapefile containing the grid cells for our focal regions and continents.

Data_Suppl_PresentDayOccurrence.txt: Present-day occurrence data of mammals in the fossil Neogene locations.

Data_TaxonomyLookup.xls: The taxonomy lookup tables for unifying taxonomy across the different sources, from which a species list can also be extracted.

Data_TimezonesAmerica.txt: chronology scheme for North American Land Mammal Ages and how they map on our global stratigraphic stages.

Data_TimezonesEUrope.txt: chronology scheme for Neogene Mammal units in Europe and how they map on our global stratigraphic stages.


Output_Suppl_PresentDaySensitivityGamma.RData: Results of simulations for gamma diversity with first-order Jackknife, based on present-day mammal occurrence in fossil Neogene locations.


Rscript_ClimateDataProcessing.r: R script to process the paleobotanical data in Data_Paleoclimate_Regions.txt and produce / modify Data_Regions.txt and Data_Continents.txt.

Rscript_FiguresFossil.r: R script to produce all figures in the main paper and SI figures S1-S4.

Rscript_MammalDataProcessing.r: R script to process the fossil mammalian data in Data_GenusOccurrence.txt and produce Data_Regions.txt and Data_Continents.txt.

Rscript_PresentDay.r: R script to run the present-day analyses and make the plots and maps of Fig. S6 and S7.

Rscript_ProdDivModelling.r: R script to fit the statistical models of the diversity-productivity relationship in the fossil record, using Data_Continents.txt and Data_Regions.txt. Only the regional and continental data relevant to the main model, as well as our model residuals and present-day data, are uploaded in Data_AnalysesContinents.txt and Data_AnalysesRegions.txt.

Rscript_SupplementaryAnalysesFossilMammals.r: R script to run the supplementary analyses for fossil mammalian data.