DOI: 10.5061/dryad.4xgxd25nt
title: Data from: Species-specific responses to paleoclimatic changes and landscape barriers drive contrasting phylogeography of co-distributed lemur species in northeastern Madagascar

description: 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. Specifically, rivers present general barriers
 to gene flow, but dispersal between inter-river systems is possible via
 high-elevation headwater regions. While this led to high connectivity and
 genetic diversity in M. lehilahytsara and A. laniger, gene flow among M.
 jonahi populations is limited by low climatic niche suitability at higher
 elevations. Moreover, the more restricted distributions of M. macarthurii,
 M. simmonsi and A. mooreorum likely resulted from refugial dynamics and
 sea level fluctuations leading to allopatric divergence and microendemism.
 Together, the findings illustrate how ecological differences among species
 and temporal landscape dynamics mediate the role of rivers as dispersal
 barriers. They also highlight the importance of prioritizing river
 headwaters and topographically complex regions, which were shown to
 promote connectivity, in conservation efforts.
description: # 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 varying combinations of the [Stacks v2.53](https://catchenlab.life.illinois.edu/stacks/) parameters *m*, *M*, *n* and *r* (see [Paris et al., 2017](https://doi.org/10.1111/2041-210X.12775)) for the full and species-specific (*A. laniger*) sample sets. Output files of the chosen best catalogs are given in the directories `final` (raw VCF files are `populations.snp.vcf`), together with the final filtered VCF files (`populations.snps.filtered06.mac3.vcf`), which were used in downstream analyses, and missingness statistics (`populations.snps.filtered06.mac3.vcf.imiss`). For the genus *Microcebus*, `./RAD_genotyping` contains output files of the reference-guided [Stacks v2.53](https://catchenlab.life.illinois.edu/stacks/) genotype calling pipeline (directories `populations`; raw VCF files are `populations.snp.vcf`) and the final filtered VCF files (`populations.snps.filtered06.mac3.vcf`) with missingness statistics (`populations.snps.filtered06.mac3.vcf.imiss`) for the full and species-specific (*M. jonahi*+*M.macarthurii*, *M. lehilahytsara*, *M. simmonsi*) samples sets, which were used in downstream analyses. ### 1.2 Phylogenetic inference `./phylogenetic_inference` contains output files of maximum likelihood phylogenetic inference with [IQ-TREE v2.2.0](https://iqtree.github.io/), conducted on the full *Avahi* and *Microcebus* genotype call sets. ### 1.3 Population structure and gene flow `./clustering_analysis` contains output files (`*.P` and `*.Q` across different number of clusters *K* and cross validation errors `crossval.txt`) of clustering analysis conducted on the species-specific genotype call sets (*A. laniger*, *M. jonahi*+*M.macarthurii*, *M. lehilahytsara*, *M. simmonsi*) with [ADMIXTURE v1.3.0](https://dalexander.github.io/admixture/). `./gene_flow` contains geographic sample coordinates and genetic distances (*D_PS*) between samples of the species-specific genotype call sets (*A. laniger*, *M. jonahi*, *M. lehilahytsara*, *M. simmonsi*), which were used as input to estimation of gene flow rates under a coalescent model with the R package ['gene.flow.inference' v0.0.0.9](https://github.com/elundgre/gene-flow-inference). In addition, it contains R workspace images (`*.RData`) of the analyses. Results are also given in Supplementary Tables S8-S11 of the original publication. `./excess_allele_sharing` contains output (`out_*`) and configuration (`SETS.txt` and `tree.nwk`) files for tests of excess allele sharing between specific *Avahi* and *Microcebus* populations with [Dsuite v0.4 r38](https://github.com/millanek/Dsuite) as described in the original publication. ### 1.4 Drivers of population structure `./isolation_by_distance` contains geographic and genetic (*D_PS*) distances between samples (`*_ind.txt`) and populations (`*_pop.txt`) of the species-specific genotype call sets (*A. laniger*, *M. jonahi*, *M. lehilahytsara*, *M. simmonsi*), which were used as input to isolation-by-distance tests with the R package ['vegan' v2.5-7](https://vegandevs.github.io/vegan/). Results are given in Supplementary Figs. S26 and S27 of the original publication. `./estimated_effective_migration_surfaces` contains input, configuration (`*.ini`) and output files (directories `results`) for visualizations of spatial deviations from a model of isolation-by-distance based on the species-specific genotype call sets (*A. laniger*, *M. jonahi*, *M. lehilahytsara*, *M. simmonsi*) with [EEMS](https://github.com/dipetkov/eems). `./isolation_by_resistance` contains raster files (`*.tif`) as well as geographic sample coordinates and genetic distances (*D_PS*) between samples of the species-specific genotype call sets (*A. laniger*, *M. jonahi*, *M. lehilahytsara*, *M. simmonsi*), which were used as input to isolation-by-resistance modeling with the R package ['radish' v0.0.2](https://github.com/nspope/radish). Common raster files used in all analyses are found in the directory `common_rasters`. Raster files were created with the R packages ['terra' v1.6.47](https://rspatial.github.io/terra/), ['rasterdiv' v0.3.4](https://mattmar.github.io/rasterdiv/), ['whitebox' v2.2.0](https://whiteboxr.gishub.org/), ['ENMtools' v1.1.2](https://github.com/danlwarren/ENMTools) and ['ENMeval' v2.0.4](https://jamiemkass.github.io/ENMeval). Modeling results are given in Supplementary Tables S4-S7 of the original publication. ### 1.5 Genetic diversity `./genetic_diversity` contains individual observed heterozygosities estimated from the full *Avahi* and *Microcebus* genotype call sets with [VCFtools v0.1.17](https://vcftools.github.io/index.html). Results are also given in Supplementary Tables S12 and S13 of the original publication. ## 2 Sharing/access information All new sequencing data have been made available through NCBI BioProject PRJNA807164. Individual BioSample accessions are given in Supplementary Table S1 of the original publication. ## 3 Code/Software Associated scripts are found at [GitHub](https://github.com/t-vane/vanElst_et_al_2026_Lemur_phylogeography). For detailed information on used software, please see the GitHub repository and the original publication.