DOI: 10.5061/dryad.3hf2q
title: Data from: Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster

description: Examples of clinal variation in phenotypes and genotypes across
 latitudinal transects have served as important models for understanding
 how spatially varying selection and demographic forces shape variation
 within species. Here we examine the selective and demographic
 contributions to latitudinal variation through the largest comparative
 genomic study to date of Drosophila simulans and D. melanogaster, with
 genomic sequence data from 382 individual fruit flies, collected across a
 spatial transect of 19 degrees latitude and at multiple timepoints over
 two years. Consistent with phenotypic studies, we find less clinal
 variation in D. simulans than D. melanogaster, particularly for the
 autosomes. Moreover, we find that clinally varying loci in D. simulans are
 less stable over multiple years than comparable clines in D. melanogaster.
 D. simulans shows a significantly weaker pattern of isolation by distance
 than D. melanogaster and we find evidence for a strong contribution of
 annual re-migration to D. simulans population genetic structure. While
 population bottlenecks and migration can plausibly explain the differences
 in amount and stability of clinal variation between the two species, we
 also observe a significant enrichment of shared clinal genes, suggesting
 that the selective forces associated with climate are acting on the same
 genes and phenotypes in D. simulans and D. melanogaster.
description: D. melanogaster SNP
 allele frequencyD. melanogaster
 population allele frequency (*.freq) and number of chromosomes () for each
 SNP used in the final analyses. These data were originally published in
 Bergland et al 2014. The number of chromosomes is calculated as an
 effective number of chromosomes based on a model of pool-seq error (see
 Methods). The SNPs are in the coordinates of D. melanogaster genome
 release 5.5 (FlyBase).mel_freq_dp_final_Oct2015.txtD. simulans SNP allele frequencyD. simulans population allele frequency (*.freq) and number of chromosomes (*.dp) for each SNP used in the final analyses. The number of chromosomes for the pool-seq populations (*.Np) is calculated as an effective number of chromosomes based on a model of pool-seq error (see Methods). The SNPs are in the coordinates of the D. simulans genome v2 as published in Hu et al 2013.sim_freq_dp_final_Oct2015.txtD. melanogaster median Fst and latitudeD. melanogaster Fst values for pair-wise population comparisons and the latitude of each population. The analysis of isolation by distance used the median Fst (median.Fst) and the difference in latitude (lat.diff) between the two populations being compared.mel_populations_latitude_Fst40.txtD. simulans median Fst and latitudeD. simulans Fst values for pair-wise population comparisons and the latitude of each population. The analysis of isolation by distance used the median Fst (median.Fst) and the difference in latitude (lat.diff) between the two populations being compared.sim_populations_latitude_Fst40.txtD. melanogaster clinal regressionsD. melanogaster results of the regression of allele frequency with latitude, per SNP. The SNPs are in the coordinates of D. melanogaster genome release 5.5 (FlyBase).melclinal_auto2x_Np_Dec2014_qvalue.txtD. simulans clinal regressionsD. simulans results of the regression of allele frequency with latitude, per SNP. The SNPs are in the coordinates of the D. simulans genome v2 as published in Hu et al 2013.simclinal_auto2x_Np_Dec2014_qvalue.txtD. melanogaster and D. simulans shared clinal genesGenes found to have at least one clinal SNP in both D. melanogaster and D. simulans.sharedgenes.txt