Whole‐genome sequencing of two N orth A merican D rosophila melanogaster populations reveals genetic differentiation and positive selection

• Published in: Molecular ecology 2013-10, Vol.22 (20), p.5084-5097
• Main Authors: Campo, D., Lehmann, K., Fjeldsted, C., Souaiaia, T., Kao, J., Nuzhdin, S. V.
• Format: Article
• Language: English
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.12468

The prevailing demographic model for D rosophila melanogaster suggests that the colonization of N orth A merica occurred very recently from a subset of E uropean 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 N orth A merican 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 ( W inters, C alifornia, USA ) and compared them with a public genome data set from Raleigh ( R aleigh, N orth C arolina, USA ). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two N orth A merican 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 3 L 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.