Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

River barriers have long played a central role in diversification models of tropical regions, including the exceptionally biodiverse island of Madagascar. Although their role is best understood by integrating additional factors such as elevation and the ecological niche of a species, empirical studies integrating these variables remain rare. We used restriction site-associated DNA sequencing to assess the combined effect of rivers, topography, climate, and forest cover on the distributions and diversity of four Microcebus and two Avahi species (Primates, Lemuriformes) in northeastern Madagascar. We inferred population structure, gene flow, and genetic diversity, and assessed the association of these ecogeographic variables and genetic differentiation using isolation-by-resistance models. Our results show that significant differences in genetic diversity and connectivity among species can be explained by species-specific responses to landscape features and phylogeographic histories. Spec..., , # Data from: Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

[https://doi.org/10.5061/dryad.4xgxd25nt](https://doi.org/10.5061/dryad.4xgxd25nt)

The archive `vanElstetal_2026_MolEcol.tar.gz` holds input, configuration, and output files for the following analyses conducted as part of the publication [van Elst et al. (2026),](https://doi.org/10.1111/mec.70195) *[Mol. Ecol.](https://doi.org/10.1111/mec.70195)*:

* RAD genotyping
* Phylogenetic inference
* Population structure and gene flow
* Drivers of population structure
* Genetic diversity

## 1 Description of the data and file structure

### 1.1 RAD genotyping

For the genus *Avahi*, `./RAD_genotyping` contains catalog output files (directories `stacks.m*.M*/catalog.m*.M*.n*/populations.r*`) and summary statistics (`count_fixed_variant.tsv` and `n_snps_per_locus.tsv`) of the *de novo* parameter tuning pipeline with va...,