DOI: 10.5061/dryad.j126v
title: Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions

description: Drosophila subobscura presents a rich and complex chromosomal inversion
 polymorphism. It can thus be considered a model system i) to study the
 mechanisms originating inversions and how inversions affect the levels and
 patterns of variation in the inverted regions, and ii) to study adaptation
 at both the single-gene and chromosomal inversion levels. It is therefore
 important to infer its demographic history since previous information
 indicated that its nucleotide variation is not at mutation-drift
 equilibrium. For that purpose, we sequenced 16 non-coding regions
 distributed across those parts of the J chromosome not affected by
 inversions in the studied population and possibly either by other
 selective events. The pattern of variation detected in these 16 regions is
 similar to that previously reported within different chromosomal
 arrangements, suggesting that the latter results would, thus, mainly
 reflect recent demographic events rather than the partial selective sweep
 imposed by the origin and frequency increase of inversions. Among the
 simple demographic models considered in our ABC analysis of variation at
 the 16 regions, the model best supported by the data implies a population
 size expansion soon after the penultimate glacial period. This model
 constitutes a better null model and it is therefore an important resource
 for subsequent studies aiming among others to uncover selective events
 across the species genome. Our results also highlight the importance of
 introducing the possibility of multiple hits in the coalescent simulations
 with an outgroup.
description: p18DNA alignment of the p18
 region in Fasta formatp108DNA alignment of the
 p108 region in Fasta formatp148DNA alignment of the
 p148 region in Fasta formatp175DNA sequence alignment
 of the p175 region in Fasta formatp187DNA sequence alignment
 of the p187 region in Fasta formatp203DNA sequence alignment
 of the p203 region in Fasta formatp204DNA sequence alignment
 of the p204 region in Fasta formatp215DNA sequence alignment
 of the p215 region in Fasta formatp220DNA sequence alignment
 of the p220 region in Fasta formatp227DNA sequence alignment
 of the p227 region in Fasta formatp237DNA sequence alignment
 of the p237 region in Fasta formatp248DNA sequence alignment
 of the p248 region in Fasta formatp271DNA sequence alignment
 of the p271 region in Fasta formatp8593DNA sequence alignment
 of the p8593 region in Fasta formatp10849DNA sequence alignment
 of the p10849 region in Fasta formatp32096DNA sequence alignment
 of the p32096 region in Fasta formatp18_5spp18 Fasta alignment for BEAST analysisp108_5spp108 Fasta alignment for BEAST analysisp148_5spp148 Fasta alignment for BEAST analysisp175_5spp175 Fasta alignment for BEAST analysisp187_5spp187 Fasta alignment for BEAST analysisp203_5spp203 Fasta alignment for BEAST analysisp204_5spp204 Fasta alignment for BEAST analysisp215_5spp215 Fasta alignment for BEAST analysisp220_5spp220 Fasta alignment for BEAST analysisp227_5spp227 Fasta alignment for BEAST analysisp237_5spp237 Fasta alignment for BEAST analysisp248_5spp248 Fasta alignment for BEAST analysisp271_5spp271 Fasta alignment for BEAST analysisp8593_5spp8593 Fasta alignment for BEAST analysisp10849_5spp10849 Fasta alignment for BEAST analysisp32096_5spp32096 Fasta alignment for BEAST analysis