DOI: 10.5061/dryad.kt062
title: Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

description: The prevailing demographic model for Drosophila melanogaster suggests that
 the colonization of North America occurred very recently from a subset of
 European flies that rapidly expanded across the continent. This model
 implies a sudden population growth and range expansion consistent with
 very low or no population subdivision. As flies adapt to new environments,
 local adaptation events may be expected. To describe demographic and
 selective events during North American colonization, we have generated a
 data set of 35 individual whole-genome sequences from inbred lines of D.
 melanogaster from a west coast US population (Winters, California, USA)
 and compared them with a public genome data set from Raleigh (Raleigh,
 North Carolina, USA). We analysed nuclear and mitochondrial genomes and
 described levels of variation and divergence within and between these two
 North American D. melanogaster populations. Both populations exhibit
 negative values of Tajima's D across the genome, a common signature
 of demographic expansion. We also detected a low but significant level of
 genome-wide differentiation between the two populations, as well as
 multiple allele surfing events, which can be the result of gene drift in
 local subpopulations on the edge of an expansion wave. In contrast to this
 genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm
 3L that showed all the hallmarks of a soft selective sweep in both
 populations. A comparison of allele frequencies within this divergent
 region among six populations from three continents allowed us to cluster
 these populations in two differentiated groups, providing evidence for the
 action of natural selection on a global scale.
description: COI sequences
 alignmentAlignment of mt COI
 sequences from inbred Drosophila melanogaster genotypes from Raleigh,
 Winters, and some locations from the South East US and Caribbean. Please
 refer to the manuscript for more information.All_COI.fasObst-F sequences alignmentAlignment of Obst-F gene sequences from inbred Drosophila melanogaster genotypes from Raleigh, Winters, and some locations from the South East US and Caribbean. Please refer to the manuscript for more information.All_Obst-F.fasSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xaa.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xab.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xac.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xad.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xae.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xaf.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xag.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xah.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xai.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xaj.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xak.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xal.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xam.tarSNP data for Raleigh/Winters genotypesSNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.xan.tar