Population Genomics of Drosophila melanogaster Coding Sequences. Grace Y C Lee, David J Begun, Alisha K Holloway, Charles H Langley. Department of Evolution and Ecology, University of California, Davis, CA.
Understanding the evolutionary forces shaping polymorphism and divergence of protein sequences has been a long-standing interest in evolutionary genetics. Here, we used Drosophila melanogaster population genomic data, which consist of 39 genomes from a North American population and 6 from an African population (dpgp.org), to investigate the evolution of annotated D. melanogaster coding regions. Our observations generally support previous findings and theoretical predictions, such as the higher polymorphism in African than non-African populations, faster adaptive protein evolution on the X chromosome, reduced heterozygosity of X chromosomes in cosmopolitan populations, and the effects of linked selection on polymorphism and adaptive protein evolution. In both African and North American populations, we found similar proportion of genes rejecting the null hypothesis of neutral evolution using the McDonald-Kreitman test. Most of the significant MK results for the African population sample were deviated in the direction of adaptive protein evolution. However, in North American samples a substantial fraction of significant MK tests deviated in the direction of excess protein polymorphism. We investigated the effects of sample size difference and demographic history of the two population samples to explain such findings. GO categories related to chromosome biology and reproductions are enriched with genes having evidence of adaptive protein evolution. Interestingly, GO categories associated with light-stimuli related response and circadian cycles are especially exceptional in the African sample.