Using phylogenetic data for island biogeography analyses: The DAISIEprep package

Molecular Phylogenetics and Evolution, vol. 206, pp. 108324

Abstract

• Phylogenetic approaches to infer biogeography and diversification often employ unconventional data structures that pose a barrier to their use. • DAISIE is an island biogeography model that can estimate rates of colonisation, speciation and extinction from phylogenetic data of island communities. • We describe the DAISIEprep R package, a set of tools to aid the extraction of data in a format interpretable by DAISIE for the application of island biogeography inference models. • DAISIEprep enables reproducible and user-friendly data extraction, formatting, and visualisation of phylogenetic data in a diverse range of scenarios. • This will facilitate addressing questions about island biogeography, diversification, and anthropogenic impacts in insular systems. New methodologies to infer past evolutionary, ecological and biogeographical processes from molecular phylogenies are rapidly being developed. However, these often employ unfamiliar data structures that may pose a barrier to their use. DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from molecular phylogenetic data across insular assemblages. The method uses an unconventional phylogenetic data structure: instead of considering a single island lineage, it focuses on multiple independent lineages descending from different colonisation events of the island. While analyzing phylogenies from this perspective has plenty of potential, this comes with challenges for the user. Here we describe software DAISIEprep, an R package to aid the extraction of data from one or many phylogenetic trees to generate and visualise data in a format interpretable by macroevolutionary and biogeographical inference models. DAISIEprep includes simple algorithms to extract data on island colonists and account for biogeographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when molecular data are not available. The software enables reproducible and user-friendly data extraction, formatting and visualisation of phylogenetic data from island lineages, and will facilitate addressing questions about island evolution, community ecology and anthropogenic impacts in insular systems. The tools presented here will also be useful for researchers who do not plan to use DAISIE but are interested in how to interpret, visualize and analyze phylogenetic datasets of islands species or island-like environments.

Authors 5

1. Joshua W. Lambert

   University of Groningen

   Affiliation as printed

   Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands

2. Lizzie Roeble Aachen

   Naturalis Biodiversity Center · University of Groningen

   Affiliation as printed

   Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands

3. Théo Pannetier

   University of Stirling · University of Groningen

   Affiliation as printed

   Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands; Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom

4. Rampal S. Etienne

   University of Groningen

   Affiliation as printed

   Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands

5. Luís Valente corresponding Aachen

   Naturalis Biodiversity Center · University of Groningen

   Affiliation as printed

   Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands. Electronic address: l.m.lima.valente@rug.nl