SOUPE : An R package to test and optimise the phylogenetic and ecological representativeness of a taxonomic sample

Abstract In the field of evolutionary biology, the selection of a phylogenetically representative sample is a crucial step to have a complete and accurate understanding of the studied group and the evolution of its traits. However, this step is often overlooked, and there is currently no objective way to assess the relevance of a sample for a given study. Here, we propose a simple and versatile methodology based on Faith's Phylogenetic Diversity index (PD Faith ). The method helps in assessing the representativeness of existing samples and facilitates the creation of new ones, taking into account the phylogeny as well as ecological and phenotypic traits. An R package was developed to enable the evaluation of the phylogenetic coverage and relevance of an existing sample, and the integration of weighted traits and availability constraints when creating a sample. The package is also open to broader applications needing phylogenetically relevant samples. The usefulness of the proposed methodology is demonstrated through two case studies: testing a published dataset on bird locomotion and developing a digitisation strategy for French natural history collections. A comprehensive workflow is provided to facilitate the implementation of the methodology in future studies. This instrument provides an operational and reproducible framework for evolutionary biologists and collection managers, offering a standard that can be broadly applied across disciplines.