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Positive and Negative Selection on Noncoding DNA in Drosophila simulans Penelope R. Haddrill,* Doris Bachtrog, and Peter Andolfatto
 

Summary: Positive and Negative Selection on Noncoding DNA in Drosophila simulans
Penelope R. Haddrill,* Doris Bachtrog, and Peter Andolfattoā
*Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; Section of
Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego; and āDepartment of Ecology
and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University
There is now a wealth of evidence that some of the most important regions of the genome are found outside those that
encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective
constraint, particularly in Drosophila. Recent work has suggested that these regions may also have been subject to the
action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive
evolution. However, this work has focused on Drosophila melanogaster, which is thought to have experienced
a reduction in effective population size (Ne), and thus a reduction in the efficacy of selection, compared with its closest
relative Drosophila simulans. Here, we examine patterns of evolution at several classes of noncoding DNA in
D. simulans and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of
polymorphism and divergence and a skew in the frequency spectrum toward rare variants. We find that the signature of
negative selection on noncoding DNA and nonsynonymous sites is obscured to some extent by purifying selection acting
on preferred to unpreferred synonymous codon mutations. We investigate the extent to which divergence in noncoding
DNA is inferred to be the product of positive selection and to what extent these inferences depend on selection on
synonymous sites and demography. Based on patterns of polymorphism and divergence for different classes of
synonymous substitution, we find the divergence excess inferred in noncoding DNA and nonsynonymous sites in the
D. simulans lineage difficult to reconcile with demographic explanations.

  

Source: Andolfatto, Peter - Department of Ecology and Evolutionary Biology, Princeton University
Haddrill, Penelope - Institute of Evolutionary Biology, University of Edinburgh

 

Collections: Biology and Medicine