Integrative taxonomy clarifies the evolution of a cryptic primate clade

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar’s biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here, we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation-by-distance. We systematically apply this framework to an entire, taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis ..., This is an interdisciplinary data set, including genomic (RADseq), morphometric, ecological, behavioral and life history data. Please refer to van Elst et al. Nature Ecology & Evolution (2024) for details on data collection and processing., , # Data from: Integrative taxonomy clarifies the evolution of a cryptic primate clade

[https://doi.org/10.5061/dryad.b2rbnzsp3](https://doi.org/10.5061/dryad.b2rbnzsp3)

This repository holds input, configuration and output files for the following analyses conducted as part of the publication van Elst et al. (2024), *Nat. Ecol. Evol.*:

* Genotyping
* Phylogenetic inference
* Species delimitation
* Divergence time estimation
* Biogeographic reconstruction
* Modelling morphological and climatic niche evolution
* Conservation_reassessment

## 1 Description of the data and file structure

### 1.1 Genotyping

`./Genotyping` contains genotypes called with with [GATK v4.1.9.0](https://gatk.broadinstitute.org/hc/en-us) and filtered with [VCFtools v0.1.17](https://vcftools.github.io/index.html) (`Genotype_calls`), phased RAD loci extracted following [Poelstra et al. (2021), *Syst. Biol.*](https://doi.org/10.1093/sysbio/syaa053) (`Loci`), and genotype likelihoods inferred with [ANGSD v0.92](http...