DOI: 10.5061/dryad.1g1jwsv69
title: Data and scripts from: Most mammals do not wander: few species escape continental endemism

description: Terrestrial mammals are found nearly everywhere on earth. Yet, most taxa
 are endemic to a single continent; geological, evolutionary, ecological or
 physiological filters constrain geographic distributions. Here, we
 synthesize data on geography, taxonomy, lineage age, dispersal, body size,
 and diet for &gt;4,000 terrestrial mammals prior to detectable
 human-mediated biodiversity losses and quantify factors correlated with
 the likelihood of dispersal between continents. We confirm the uniqueness
 of being on multiple continents: excluding humans and commensals, only 260
 mammals are found on two continents, while six span three or more
 continents (the red deer, red fox, brown bear, least weasel, and common
 bent-wing bat), and just a single species—the lion—once had a geographic
 range that included four continents. Clearly, the challenges of colonizing
 and persisting on multiple continents are severe. No single characteristic
 enables taxa to be on more than one continent. Rather, a suite of
 prerequisite conditions under some circumstances lead to distributions
 spanning multiple continents. Interestingly, the suite of factors
 facilitating the occupation of two continents, like being volant, is
 distinct from those that lead to the occupation of three or more, which
 are primarily faunivores. Other than humans and our commensals, very few
 species have become truly cosmopolitan over evolutionary time and
 geographic space.
description: <strong>Data Collection</strong>
 We used the updated Body Mass of Late Quaternary Mammals dataset
 (Smith et al.
 2003) to version 11.1. See supplemental information of manuscript for deatils. We additionally collected contitnet of family origin ("familyOrigin_Oct2024.csv"). We also added in generic first appearance from the PaleobioDB (see Analysis.R) and Faurby et al. 2018 (PHYLACINE). We also combined data about geographic range, home range, and age of dispersal from Jones et al. 2009 (PanTHERIA), natural ranges from Faurby et al. 2018 (PHYLACINE), as well as generation length from Pacifici et al. 2013. We do not republish existing datasets here. <strong>Data cleaning</strong> <em><strong>Data for Analysis</strong></em> We removed all species records not on a continent (i.e., insular and marine species). We also removed non-native species, including introduced and domesticated species. This is in "Analysis.R" under "TRIM DATA". Since we do not include previously published data, the script “Analysis.R” includes instructions for finding and uploading other datasets used. <em><strong>Data Manipulation</strong></em> All data manipulation can be found in "Analysis.R". We first standardized diet categories under "FIX DIET". We then filled in missing diet by creating generic and above diet categories, under "MAKE GENERIC & FAMILY AVERAGES". <strong>Analysis</strong> The script for all analyses is "Balk_etal_GlobeTrotters.R". These include sections, "NUM SP PER CONTINENT", "CONNECTIVITY", "FAMILY ORIGIN", "DIVERSITY OF CLADE", "BODY SIZE:, "DIET", "HABITAT MODE", "DECISION TREE", "LOG ODDS", and "GEOGRAPHIC RANGE SIZE".
description: # Data and scripts for Most mammals do not wander: little taxonomic
 overlap among continents
 [https://doi.org/10.5061/dryad.1g1jwsv69](https://doi.org/10.5061/dryad.1g1jwsv69) ## Description of the data and file structure ### Files and variables #### File: familyOrigin_Oct2024.xlsx **Description:** A dataset of mammalian families and the continent of first fossil occurrence to as of Oct. 2024. Sheet 1 has the data; Sheet 2 "origin of place reference" contains the references used to determine continent of origin for the family; Sheet 3 "origin of date reference" contains the references for the first occurrence of that family. Empty cells indicate that no data was available at the time of the dataset's creation. ##### Variables for Sheet 1 * family: Accepted mammalian family based off Wilson & Reeder 2005 or the literature * continent: Continent where the family originated, which can be Eurasia, Africa, Australia, North America (North.America), or South America (South.America). * continent_reference: A number that corresponds to a reference in Sheet 2 "origin of place reference". * first origin time mya: A number in millions of years or an interval of the first occurrence of a species of that family. * time_reference: A number that corresponds to a reference in Sheet 2 "origin of date reference". * notes: An open field for comments. #### File: familyOrigin_Oct2024.csv **Description:** A .csv version of only the data values (i.e., not references) of familyOrigin_Oct2024.xlsx.  ##### Variables for Sheet 1 * see above ## Code/software ### Setup Follow these steps to set up the project: #### Download associated data 1. Download data `Supplementary_Files.zip`. Unzip 2. Download data and convert to appropriate file types following the instructions in "Analysis.R". These are commented in the script. #### Download data 1. In `Supplementary_Files.zip`, there is also a file "familyOrigin_Oct2024.xlsx". 2. Convert .xlsx file to .csv [CSV UTF-8 (Comma delimited) (.csv)]. This file is also provided. #### Set up the environment 1. Open R. Set your directory to your files locations. 2. Be sure to install the following packages: * dplyr (1.1.4) * purrrlyr (0.0.8) * tidyverse (2.0.0) * tidyr (1.3.1) * reshape2 (1.4.4) * ggplot2 (3.5.1) * stringr (1.5.1) * gcookbook (2.0) * scales (1.3.0) * rpart (4.1.23) * rpart.plot (3.1.2) * randomForest (4.7.1.1) * caret (6.0.94) * MASS (7.3.60.2) * mfx (1.2.2) * stargazer (5.2.3) * raster (3.6.30) * data.table (1.15.4) * tiff (0.1.12) * paleobioDB (1.0.0) * ape (5.8) * doParrallel (1.0.17) 3. Run the scripts. ## Access information Data was derived from the following sources: * [https://github.com/SmithLabUNM/MOM-Database/tree/MOMv11.1](https://github.com/SmithLabUNM/MOM-Database/tree/MOMv11.1) * Smith, F.A., Lyons, S.K., Ernest, S.M., Jones, K.E., Kaufman, D.M., Dayan, T., Marquet, P.A., Brown, J.H. and Haskell, J.P., 2003. Body mass of late quaternary mammals: ecological archives E084‐094. *Ecology*, *84*(12), 3403-3403. [https://doi.org/10.1890/02-9003](https://doi.org/10.1890/02-9003) * Faurby, S., Davis, M., Pedersen, R.Ø., Schowanek, S.D., Antonelli, A. and Svenning, J.C., 2018. PHYLACINE 1.2: the phylogenetic atlas of mammal macroecology. Ecology, 99(11), 2626. [https://zenodo.org/records/1250504](https://zenodo.org/records/1250504) * Pacifici, M., Santini, L., Di Marco, M., Baisero, D., Francucci, L., Marasini, G.G., Visconti, P. and Rondinini, C., 2013. Generation length for mammals. *Nature Conservation*, *5*, 89-94. [https://doi.org/10.3897/natureconservation.5.5734](https://doi.org/10.3897/natureconservation.5.5734) * Jones, K.E., Bielby, J., Cardillo, M., Fritz, S.A., O'Dell, J., Orme, C.D.L., Safi, K., Sechrest, W., Boakes, E.H., Carbone, C. and Connolly, C., 2009. PanTHERIA: a species‐level database of life history, ecology, and geography of extant and recently extinct mammals: Ecological Archives E090‐184. *Ecology*, *90*(9), 2648-2648. [https://doi.org/10.1890/08-1494.1](https://doi.org/10.1890/08-1494.1)