Herodotools: An R package to integrate macroevolution, biogeography and community ecology

Aim: Speciation, extinction and historical dispersal are the ultimate factors generating and maintaining biodiversity. However, methods of macroevolution used to detect historical processes usually ignore the variation of macroevolutionary processes at scales finer than entire regions. Likewise, biogeography and community ecology often ignore deep-time evolutionary processes. To overcome this problem, it is necessary to integrate data from ancestral state reconstructions, current species distributions and biogeographical regionalization. Herodotools is an R package designed to perform this integration.Location: Global application, with an example from Neotropics.Major taxa studied: Any taxa, with an example from small rodents (genus Akodon and subfamily Sigmodontinae).Methods: Herodotools streamline analyses of historical biogeography, including regionalization, calculation of assemblage age, lineage in situ diversification and community phylogenetic metrics, merging species occurrence with macroevolutionary methods of ancestral area and trait reconstruction. The main functions of our R package are presented with toy examples and by analysing the historical biogeography of small rodent assemblages in the Neotropics.Results: Our package can integrate methods from biogeography, macroevolution and community ecology, allowing us to downscale the effects of historical processes and calculate important historical variables (e.g., age of assemblages, in situ diversification, phylogenetic regionalization, phylogenetic transition zones, metrics of trait macroevolutionary dynamics and new metrics of phylogenetic diversity and endemism) in different scales, from entire regions to communities of co-occurrent species.Main Conclusions: Herodotools is the first platform to streamline the analysis of historical biogeography, enabling a better understanding of historical processes at different levels of organization, from local assemblages to entire biogeographical regions and incorporating macroevolutionary models in commonly used community phylogenetic metrics. This integration bridges the gap between macroevolutionary, biogeography and community ecology methods.