Does ecology predict taxonomy? How ecological differentiation can be used to spatially infer intra-specific diversity

Assessing the true dimension of biodiversity is a major challenge. Many species hide within them a diversity that is now being uncovered using molecular data. However, population genetic studies tend to be resource-consuming and more difficult to apply to a broader range of taxa, limiting scalability. Moreover, the growing shortage of trained taxonomists makes it difficult to rely on comparative morphological studies to assess divergence and speciation processes for the vast majority of species-rich taxonomic groups. Here, we explore the usefulness of the “ecological speciation” concept and explore how these hidden lineages tend to occupy a distinct environmental niche that can be used to identify natural groups in the geographical space. From a total of 298 species complexes, we assess the accuracy of five clustering methods and Random Forest models for correctly classifying the occurrences of the different subspecies based only on environmental data. For the best performing clustering..., , # Does ecology predict taxonomy? How ecological differentiation can be used to spatially infer intra-specific diversity

Dataset DOI: [10.5061/dryad.6q573n6c2](https://doi.org/10.5061/dryad.6q573n6c2)

## Description of the data and file structure

The code ClusterStabilityFunction.R is used to clusterize environmental data extracted for each occurrence point (see OccDataAnalysisWithVars.RData) to check correspondence with recognized taxonomic units. The code is designed to perform 500 replicates and is intended to run in parallel.

taxonKey: Identifier for each unique group of taxa, used to differentiate between subspecies.\
speciesKey: Identifier at the species level, which can include multiple subspecies (taxonKey).

## Code/software

The file is developed for the R programming language.,