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High-throughput Analysis of Locomotor Behavior in the Drosophila Island Assay

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Using phylogenetic data for island biogeography analyses: The DAISIEprep package.

Joshua W Lambert¹, Lizzie Roeble², Théo Pannetier³

¹Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, the Netherlands.

Molecular Phylogenetics and Evolution

|March 11, 2025

Summary

New software, DAISIEprep, simplifies extracting and visualizing phylogenetic data for island biogeography models. This R package aids macroevolutionary and ecological studies by overcoming data structure challenges in evolutionary inference.

Keywords:

DAISIE Data science Island biogeography Macroevolution Phylogenetics R package

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Last Updated: May 23, 2025

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Published on: February 5, 2014

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.