DOI: 10.5061/dryad.kprr4xhf7
title: Different mammals, same structure: Co-occurrence structure across the Plio-Pleistocene transition

description: A central goal in ecology is investigating the impact of major
 perturbations, such as invasion, on the structure of biological
 communities. One promising line of inquiry is using co-occurrence analyses
 to examine how species’ traits mediate co-existence and how major
 ecological, climatic, and environmental disturbances can affect this
 relationship, and underlying mechanisms. However, present communities are
 heavily influenced by anthropogenic behaviors and may exhibit greater or
 lesser resistance to invasion than communities that existed before human
 arrival. Therefore, to disentangle the impact of individual disturbances
 on mammal communities, it is important to examine community dynamics prior
 to humans. Here, we use the North American fossil record to evaluate the
 co-occurrence structure of mammals across the Great American Biotic
 Interchange. We compiled 126 paleocommunities from the late Pliocene
 (4–2.5 Ma) and early Pleistocene (2.5–1 Ma). Genus-level co-occurrence was
 calculated to identify significantly aggregated (co-occur more than
 expected) and segregated (co-occur less than expected) genus pairs. A
 functional diversity analysis was used to calculate functional distance
 between genus pairs to evaluate the relationship between pair association
 strength and functional role. We found that the strength distribution of
 aggregating and segregating genus pairs does not significantly change from
 the late Pliocene to the early Pleistocene even with different mammals
 forming the pairs, including immigrant mammals from South America.
 However, we did find that significant pairs, aggregations, and
 segregations, became more similar in their functional roles following the
 Plio-Pleistocene transition. Due to different mammals and ecological roles
 forming significant associations and the stability of co-occurrence
 structure across this interval, our study suggests that mammals have
 fundamental ways of assembling that may have been altered by humans in the
 present.
description: The dataset of mammal occurrences and traits was compiled into a
 csv file from various open-access databases including, the Paleobiology
 Database, the primary literature, the NOW Database, and the MOM Database.
 The dataset that includes information about each genera's continental
 origin was compiled into a csv file from the Paleobiology Database records
 and primary literature. All other datasets are kept in csv files and are
 results extracted from analyses performed in R version 4.3.1. The
 supplementary file includes supporting information about the methods and
 additional plots from supporting analyses.
description: # Different mammals, same structure: Co-occurrence structure across the
 Plio-Pleistocene transition
 [https://doi.org/10.5061/dryad.kprr4xhf7](https://doi.org/10.5061/dryad.kprr4xhf7) ## Description of the data and file structure **Datafile1** contains the occurrence and trait data for each mammal genus in the data set. It also includes the locality data range for each occurrence. The data file also provides the PCoA coordinates for each genus based on the functional diversity analysis. The traits included are body mass category, diet, locomotion, and life habits. The occurrences were compiled from the Paleobiology Database. Trait data were compiled from various online databases and the primary literature. These include the NOW Database, MOM Database, Shupinski et al. 2024, Smith et al. 2018, and the Paleobiology Database.  **Datafile2** includes the co-occurrence results of genus pairs from the co-occurrence analysis performed in R version 4.3.1 including the type of association and strength of association. The data file also includes the PCoA coordinates from the functional diversity analysis as well as the Euclidean distance calculated from those PCoA coordinates. Furthermore, information about the body mass categories, diet categories, continental origins, and survival status of the genus pairs. **Datafile 3** has information about each genus regarding the original body mass before categorization and the genus's temporal extent in the fossil record. The temporal extent of a genus was used to determine if a species survived into the late Pleistocene as well as if the genus is still extant in the modern. This data was compiled from the Paleobiology Database records. Body mass was compiled by Smith et al. 2018 and Shupinski et al. 2024.  ### Files and variables #### File: DataFile3\_NA\_Mammal\_Extinction.csv **Description:**  ##### Variables * Order: The taxonomic order of the mammalian genus * Family: The taxonomic family of the mammalian genus * Accepted.name: The accepted species identification of the mammal occurrence * Genus: The taxonomic genus of the mammal species * Extinct.Exant: Identifies if the genus is extinct or extant * Log.Mass: The species average log body mass (grams) * Reference: The reference for the average body mass * BodyMass.Taxonomic.Level: The taxonomic level that was used to average body mass for the species * Firstapp.max.ma: The earliest date that the genus first appeared in the fossil record (millions of years ago) * Firstapp.min.ma: The latest date that the genus first appeared in the fossil record (millions of years ago) * Lastapp.max.ma: The earliest date that the genus has its last appearance in the fossil record (millions of years ago) * Lastapp.min.ma: The latest date that the genus had its last appearance in the fossil record (millions of years ago) * Plio.Pleistocene.Survival: Determines if the genus survived past the Plio-Pleistocene transition (~2.5 Ma).  * Late.Pleistocene.Survival: Determines if the genus survived into the late Pleistocene (&lt;1.5 Ma) #### File: Datafile1\_Plio\_Pleistocene\_Mammal\_Coords\_All.csv **Description:**  ##### Variables * collection_no: The collection number of the fossil locality as found in the Paleobiology Database * identified_name: The initial species identification in the Paleobiology Database * accepted_name: The accepted species identification after revision in the Paleobiology Database * max_ma: The earliest date estimate for the locality date range (millions of years ago) * Ma: The average date estimate for the locality date range (millions of years ago) * min_ma: The latest date estimate for the locality date range (millions of years ago) * time_bins: Identifies if the locality is from the late Pliocene (Pre) or the early Pleistocene (Post)  * lng: longitude of the locality location * lat: latitude of the locality location * Original_collection_name: The original collection name before combining localities with the same location * collection_name_Edited: The modified collection name after combining localities with the same location * order: The taxonomic order of the species occurrence * family: The taxonomic family of the species occurrence * genus: The taxonomic genus of the species occurrence * Continent_Origin: The continental origin of the genus (South America or North America) to identify it as an immigrant or native genus * Mass_Cat: The body mass category of the genus based on average genus log body mass (grams) * Diet: The diet category of the genus * Locomotion: The locomotion type of the genus * Life.Habit: The life habit of the genus * state: The state that the locality was found in  * paleolng: The paleolongitude location of the locality * paleolat: The paleolatitude location of the locality  * PCoA1: The first PCoA coordinate of the genus based on the functional diversity analysis  * PCoA2: The second PCoA coordinate of the genus based on the functional diversity analysis  * PCoA3: The third PCoA coordinate of the genus based on the functional diversity analysis  * PCoA4: The fourth PCoA coordinate of the genus based on the functional diversity analysis  * Survival_Max: If the genus survived the Plio-Pleistocene transition based on the latest last appearance dates (millions of years ago) * Survival_Min: If the genus survived the Plio-Pleistocene transition based on the earliest last appearance dates (millions of years ago) #### File: DataFile2\_West\_Pairs\_Data.csv **Description:**  ##### Variables * sp1_name: The genus of the first mammal in the pair * sp2_name: The genus of the second mammal in the pair * sp_ID: The combined name of the pair that includes the genus of sp1 and sp2 * Sp1_Continent_Origin: The continental origin of the genus of the first mammal in the pair * Sp2_Continent_Origin: The continental origin of the genus of the second mammal in the pair * Mass_Pair: Combined identification of body mass category for sp1 and sp2 determined by the average body mass in log mass (grams) * Continent_Origin: Combined identification of continental origin for sp1 and sp2 * z_score: The strength of the genus pair after before z-transformed * Pair_Survival: Combined identification of survival status of the Plio-Pleistocene transition for sp1 and sp2 * p.value: The significant p-value for aggregations and segregations * Veech: The type of association as identified by the Veech co-occurrence method * Bin: The time bin the pair are in (late Pliocene, early Pleistocene) * Sp_2PCOA1: The first PCoA coordinate of sp2 * Sp_2PCOA2:  The second PCoA coordinate of sp2 * Sp_2PCOA3: The third PCoA coordinate of sp2 * Sp_2PCOA4: The fourth PCoA coordinate of sp2 * Sp_1PCOA1: The first PCoA coordinate of sp1 * Sp_1PCOA2: The second PCoA coordinate of sp1 * Sp_1PCOA3: The third PCoA coordinate of sp1 * Sp_1PCOA4: The fourth PCoA coordinate of sp1 * Base.FETmP.x: The strength of the genus association before z-transformation * Pair_Type: The type of association based on the strength * Euc.Dist: The Euclidean distance of the genus pair based on the PCoA coordinates * Sp1_Mass_Cat: Body mass category of sp1 based on average genus log body mass (grams) * Sp2_Mass_Cat: Body mass category of sp2 based on average genus log body mass (grams) * Mass_Diff: The difference in body mass categories between the genus pair determined by the average body mass in log mass (grams) * Sp1_Diet: Diet category of sp1 * Sp2_Diet: Diet category of sp2 * Diet_Pair: The combined diet categories of the genus * Sp1_Survival: If sp1 survived the Plio-Pleistocene transition * Sp2_Survival: If sp2 survived the Plio-Pleistocene transition ## Code/software My data are all uploaded in csv files that are accessible in Microsoft Excel and R. My code was run in the R version 4.3.1. The following packages are required to run the code:  if(!require(ggplot2)) install.packages("ggplot2"); library(ggplot2) if(!require(reshape2)) install.packages("reshape2"); library(reshape2) if(!require(cooccur))install.packages("cooccur"); library(cooccur) if(!require(tidyverse)) install.packages("tidyverse"); library(tidyverse) if(!require(dplyr))install.packages("dplyr"); library(dplyr) if(!require(raster))install.packages("raster");library(raster) ## Access information NA