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

Gabriel Nakamura , Arthur Vinícius Rodrigues, André Luíz Luza, Renan Maestri, Vanderlei Debastiani, Leandro da Silva Duarte

Aim: Historical processes like speciation, extinction, and historical dispersal are the ultimate factors generating and maintaining biodiversity in space and time. While detecting the effect of those processes on the distribution of biodiversity has great relevance by itself, how to measure them is critical to interpreting the underlying causes of biological patterns. However, metrics of macroevolution used at biogeographical scales usually ignore the variation of macroevolutionary processes at scales finer than entire regions. Likewise, biogeography and community ecology often ignore deep-time evolutionary processes, giving us a limited picture of the role of historical processes in community assembly. To overcome this problem, it is necessary to integrate data from ancestral state reconstructions, current species distributions, and biogeographical regionalization. We hereby present Herodotools, an R package that integrates macroevolutionary models with data on the distribution of species occurrences in assemblages and biogeographic regions.
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: We developed an R package called Herodotools, designed to streamline analyses of historical biogeography, including regionalization, calculation of assemblage age, lineage in situ diversification, and community phylogenetic metrics, which merge species occurrence with macroevolutionary methods of ancestral area and trait reconstruction. We described the main functions of our R package through toy examples and illustrated the use of our new package by analyzing the historical biogeography from small rodent assemblages in the Neotropics.
Results: We showed that our methods 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) in different scales, from entire regions to communities of co-occurrent species.
Main Conclusions: Our package provides 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.