DOI: 10.5061/dryad.b2rbnzsp3
title: Data from: Integrative taxonomy clarifies the evolution of a cryptic primate clade

description: 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 within the genus is best explained by a model of
 morphological stasis imposed by stabilising selection and a neutral
 process of niche diversification. Finally, by clarifying species limits
 and defining evolutionarily significant units, we provide new conservation
 priorities, bridging fundamental and applied objectives in a generalisable
 framework.
description: This is an interdisciplinary data set, including genomic
 (RADseq), morphometric, ecological, behavioral and life history data.
 Please refer to van Elst et al. <em>Nature Ecology &
 Evolution</em> (2024) for details on data collection and
 processing.
description: # 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://www.popgen.dk/angsd/index.php/ANGSD) (`Genotype_likelihoods`). ### 1.2 Phylogenetic inference `./phylogenetic_inference` contains data for maximum likelihood and quartet-based phylogenetic inference with [IQ-TREE v2.2.0](http://www.iqtree.org/#download) (`IQ-TREE`) and [SVDquartets of PAUP* v4.0a](https://paup.phylosolutions.com/) (`SVDquartets`), respectively. ### 1.3 Species delimitation `./Species_delimitation` contains the following subdirectories: `./Genomics` contains data for genomic tests for patterns of isolation-by-distance across species subsets (`Isolation-by-distance` and directories for each species subset therein), individual ancestry inference with [NGSadmix v32](https://www.popgen.dk/software/index.php/NgsAdmix) (`Admixture`), and estimation of genealogical divergence indices (*gdi*) between candidate species (`Gdi`). `./Morphometry` contains data for estimation of overlap in morphometry in the R package ['dynRB' v0.18](https://cran.r-project.org/web/packages/dynRB/index.html) (`Overlap`) and for morphometric tests for patterns of isolation-by-distance (`Isolation-by-distance`). In `Overlap/01_Microcebus_morphological_data.xlsx` and `Isolation-by-distance/data.xlsx`, morphometric data are given in mm, elevation is given in m, and bioclimatic parameters and units are detailed at [https://chelsa-climate.org/bioclim/](https://chelsa-climate.org/bioclim/). `./Climatic_niche` contains data for inference of climatic niche models and estimation of differentiation among these with the R package ['ENMtools' v1.0.7](https://github.com/danlwarren/ENMTools). `./Acoustic_communication` contains data for estimation of differentiation in acoustic communication. Parameters in `Acoustic_data.xlsx` and their units are described in detail in Supplementary Table S23 of the associated original publication. `./Reproductive_activity` contains data for estimation of differentiation in reproductive activity. ### 1.4 Divergence time estimation `./Divergence_time_estimation` contains data for inference of divergence times from phased RAD loci under a coalescent model in [BPP v4.4.1](https://github.com/bpp/bpp). ### 1.5 Biogeographic reconstruction `./Biogeographic_reconstruction` contains data for ancestral biogeogeography reconstruction in the R package ['BioGeoBEARS' v1.1.2](https://github.com/nmatzke/BioGeoBEARS) under three alternative classification schemes: (1) dry vs. humid forest (`Dry_humid`), (2) five major ecoregions as in [Yoder et al. (2016), *PNAS*](https://doi.org/10.1073/pnas.1601081113) (`Five_ecoregions`) and (3) the Köppen-Geiger climate classification [(Beck et al. 2018, *Sci. Data*)](https://doi.org/10.1038/sdata.2018.214) (`Koeppen_Geiger`). ### 1.6 Modelling morphological and climatic niche evolution `./Modelling_morphological_and_climatic_niche_evolution` contains the following subdirectories: `./Climatic_niche_evolution` contains data for modelling the evolution of climatic niches along the inferred *Microcebus* phylogeny. `./Morphological_evolution` contains data for modelling the evolution of morphology along the inferred *Microcebus* phylogeny, including cross-validation (`Cross_validation`) with simulations under Brownian motion (`BM_simulation`) and Ornstein–Uhlenbeck (`OU_simulation`) models (data for each simulation is given in a separate directory therein). Modelling was conducted with the R packages ['phytools' v2.3-0](https://cran.r-project.org/web/packages/phytools/index.html), ['dynRB' v0.18](https://cran.r-project.org/web/packages/dynRB/index.html), ['phyloclim' v0.9.5](https://cran.r-project.org/web/packages/phyloclim/index.html), ['mvMORPH' v1.1.9](https://github.com/JClavel/mvMORPH), ['tmvtnorm' v1.6](https://github.com/cran/tmvtnorm). ### 1.7 Conservation\_reassessment `./Conservation_reassessment` contains data for reassessing conservation status of revised *Microcebus* species, using [ArcGIS Pro v3.1.0](https://www.esri.com/en-us/arcgis/products/arcgis-pro/overview), including climatic niche models (`climatic_niche_models`). Estimates in `Output.xlsx` are given in km². ## 2 Sharing/Access information All new raw sequencing data have been made available through NCBI BioProjects PRJNA560399 and PRJNA807164. Individual BioSample accessions are given in Supplementary Table S13 of the original publication. ## 3 Code/Software Associated scripts are found at [GitHub](https://github.com/t-vane/vanElst_et_al_2024_Cryptic_diversification). For detailed information on used software, please see the GitHub repository and the original publication.