Affiliation:
1. Departamento de Ecologia e Evolução National Institute of Science and Technology—Ecology, Evolution and Conservation Biology (INCT‐EECBio), Universidade Federal de Goiás Goiânia Brazil
2. Departamento de Ecologia, Avenida Bento Gonçalves, Agronomia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil 90650‐001
3. Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Helsinki Institute for Life Sciences, University of Helsinki Helsinki Finland
4. Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria Santa Maria Brazil
Abstract
AbstractAimSpeciation, 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.LocationGlobal application, with an example from Neotropics.Major taxa studiedAny taxa, with an example from small rodents (genus Akodon and subfamily Sigmodontinae).MethodsHerodotools 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.ResultsOur 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 ConclusionsHerodotools 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.
Funder
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Subject
Ecology,Ecology, Evolution, Behavior and Systematics
Cited by
4 articles.
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