Genomic and historical datasets supporting evolutionary and demographic analyses of Northeast Asian treefrogs

This dataset contains analytical inputs and outputs, supporting data files, and derived results associated with genomic demographic inference, phylogenomic reconstruction, environmental niche modelling, and historical contextual synthesis conducted for Northeast Asian Dryophytes species.

Files are organised into thematic folders corresponding to the major analytical components of the study. Folders structure (alphabteically ordered) and contents independently described as:

1.ABBA-BABA & Patterson’s D test
Results from introgression analyses assessing gene flow among focal Dryophytes taxa. Includes input alignments, test outputs, and summary statistics.

2. Anthropogenic layers signal
Derived spatial datasets and analytical outputs used to evaluate potential associations between anthropogenic environmental change and inferred demographic trajectories of Eastern Palearctic Dryophytes. This folder includes processed anthropogenic raster layers (e.g., historical land use, cropland extent, human population proxies where applicable), extracted summary statistics, and supporting files used for comparative analyses with genomic demographic reconstructions.
3. ENM (Ecological Niche Modelling)
Environmental niche modelling outputs including occurrence data, environmental layers used, model settings, and prediction outputs used to assess historical habitat suitability.

4 Genome-based multilocus species trees
Phylogenomic tree reconstructions derived from genome-wide SNP datasets. Includes alignment matrices, tree files, and associated metadata.

5. Meta-analysis
Compiled historical and environmental records used to contextualize demographic inference, including wetland modification, agricultural expansion, and anthropogenic environmental change across East Asia.

6. Stairway plots
Demographic reconstruction outputs generated using site-frequency spectrum (SFS) approaches. Input files consist of folded or unfolded SFS derived from genome-wide SNP datasets, together with Stairway Plot configuration files, inferred effective population size trajectories, and visualization outputs.

7. TreeMix (outgroup: Dryophytes japonicus)
Population graph analyses modelling genetic drift and migration events among focal species. Includes allele frequency inputs, parameter settings, migration edge outputs, and visualization files.