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Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of D. melanogaster. We compiled a dataset of 6,141 autosomal protein coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by ~27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose ~17% of their adaptive substitutions while genes with high mutation rates embedded in gene rich regions lose ~60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation and gene density along the genome affects the HRi effect.
This article was published in the following journal.
Name: Molecular biology and evolution
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The interdisciplinary science that studies evolutionary biology, including the origin and evolution of the major elements required for life, their processing in the interstellar medium and in protostellar systems. This field also includes the study of chemical evolution and the subsequent interactions between evolving biota and planetary evolution as well as the field of biology that deals with the study of extraterrestrial life.
Evolution at the molecular level of DNA sequences and proteins. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
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