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Abstract 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 coexistence 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 mammalian communities, it is important to examine community dynamics before 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, both 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. 

Understanding the role of humans as ‘ecosystem engineers’ requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no con-ceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional defini-tions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term – ‘Earth system engineering’ – to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate this framework using the fossil record, and show how it can be applied across the tree of life, and throughout Earth history. 

Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects have probably altered mammalian community structure, raising the question of how past perturbations have done so. We used functional diversity (FD) to describe how the structure of North American mammal palaeocommunities changed over the past 66 Ma, an interval spanning the radiation following the K/Pg and several subsequent environmental disruptions including the Palaeocene–Eocene Thermal Maximum (PETM), the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examined three aspects of ecological function: functional evenness, functional richness and functional divergence. We found that shifts in FD were associated with major ecological and environmental transitions. All three measures of FD increased immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of FD were decoupled and responded differently to environmental changes over the last ~56 Myr.