Reproductive barriers and genomic hotspots of adaptation during allopatric species divergence: datasets for all phylogenetic reconstructions represented in Fig 2

Theory predicts that in allopatric populations, genomic divergence and reproductive barriers may be driven by random genetic drift, and thereby evolve slowly in large populations. However, local adaptation and divergence under selection may also play important roles, which remain poorly characterised. Here we address three key questions in young allopatric species: (a) How widespread are genomic signatures of adaptive divergence?, (b) What is the functional space along which young sister species show divergence at the genomic level?, and (c) How quickly might prezygotic and postzygotic reproductive barriers evolve? Analysis of 82 re-sequenced genomes of the Oriental Papilio polytes species group revealed surprisingly widespread hotspots of intense selection and selective sweeps at hundreds of genes, and spanning all chromosomes, rather than divergence only in a few genomic islands. These genes are involved in diverse ecologically important adaptive functions such as wing development, co..., Phylogenetic reconstruction was performed using sequences of individuals from the Papilio polytes species group., , # Reproductive barriers and genomic hotspots of adaptation during allopatric species divergence: datasets for all phylogenetic reconstructions represented in Fig 2

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

## Description of the data and file structure

Each sub-folder contains the alignment files, partition files and tree files for each phylogeny from Fig. 2. There are five sub-folders, one larger folder for extracted fasta files of individual genes (`2. single_genes`), and one for each type of dataset: nuclear markers (*thiolase*, *carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), catalase (CAT), dopa decarboxylase (DDC), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), isocitrate dehydrogenase (IDH), malate dehydrogenase (MDH), ribosomal protein S2 (RPS2), ribosomal protein S5 (RPS5), hairy cell leukemia protein 1 (HCL),* *elongation factor-I alpha (EF1-a), and* wingless) (`3. nuclear`), mitochondrial ma...