Using phylogenetic data for island biogeography analyses: The DAISIEprep package

Area of Science:

• Ecology
• Evolutionary Biology
• Biogeography

Background:

• Molecular phylogenies are increasingly used to infer evolutionary, ecological, and biogeographical processes.
• Novel data structures in phylogenetic analyses can present a barrier to researchers.
• The Dynamic Assembly of Islands through Speciation, Immigration and Extinction (DAISIE) model requires specific phylogenetic data formats.

Purpose of the Study:

• To introduce DAISIEprep, an R package designed to facilitate data extraction and visualization for macroevolutionary and biogeographical models.
• To address user challenges associated with the unconventional data structures required by models like DAISIE.
• To enable reproducible and user-friendly preparation of phylogenetic data for island biogeography research.

Main Methods:

• DAISIEprep processes molecular phylogenetic data from insular assemblages.
• The software extracts data on island colonists and accounts for various uncertainties (biogeographical, topological, taxonomic).
• It allows flexible incorporation of missing species or entire insular lineages.

Main Results:

• DAISIEprep generates and visualizes data in a format interpretable by macroevolutionary and biogeographical inference models.
• The package provides simple algorithms for data extraction and uncertainty handling.
• It supports the inclusion of incomplete data, such as missing species or lineages.

Conclusions:

• DAISIEprep enhances the accessibility and usability of phylogenetic data for island biogeography studies.
• The software streamlines data preparation, enabling researchers to address complex questions in island evolution and ecology.
• These tools are valuable for researchers using DAISIE and those analyzing island species phylogenetic datasets.