Different mammals, same structure: Co-occurrence structure across the Plio-Pleistocene transition

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.

Methods
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.