Abstract

Historical processes like speciation, extinction and historical dispersal are the ultimate factors generating and maintaining biodiversity. Therefore, understanding how these factors affect the distribution of biodiversity is of great importance. To do so, it is necessary to integrate information from ancestral state reconstructions and current species distribution data and traits. Studies that integrated both information proved effective in unveiling questions in the intersection of macroecology, macroevolution, and community ecology. However, up to now, numerical methods that perform this integration are scattered, making integration difficult and hampering advances in these research fields. Here we developed Herodotools, an R package that integrates the macroevolutionary models with the distribution of species occurrence in assemblages to provide metrics that represent historical information, such as in-situ diversification, historical dispersal, and age of assemblages. We described the main functions and illustrated the use of our new package by analyzing the historical biogeography of the genus Akodon, a South American small rodent. Our package provides the first platform to investigate questions that require the integration of macroevolutionary information with ecological data (as species occurrence) and streamline analysis of historical biogeography, leveraging the investigation of the effects of historical processes in different levels of organization, from local assemblages to bioregions.

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