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Modeling the effect of changing selective pressures on polymorphism and divergence

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  • Benger, Etam
  • Sella, Guy

Abstract

The most common models of sequence evolution used to make inferences about adaptation rely on the assumption that selective pressures at a site remain constant through time. Instead, one might plausibly imagine that a change in the environment renders an allele beneficial and that when it fixes, the site is now constrained—until another change in the environment occurs that affects the selective pressures at that site. With this view in mind, we introduce a simple dynamic model for the evolution of coding regions, in which non-synonymous sites alternate between being fixed for the favored allele and being neutral with respect to other alleles. We use the pruning algorithm to derive closed forms for observable patterns of polymorphism and divergence in terms of the model parameters. Using our model, estimates of the fraction of beneficial substitutions α would remain similar to those obtained from existing approaches. In this framework, however, it becomes natural to ask how often adaptive substitutions originate from previously constrained or previously neutral sites, i.e., about the source of adaptive substitutions. We show that counts of coding sites that are both polymorphic in a sample from one species and divergent between two others carry information about this parameter. We also extend the basic model to include the effects of weakly deleterious mutations and discuss the importance of assumptions about the distribution of deleterious mutations among constrained non-synonymous sites. Finally, we derive a likelihood function for the parameters and apply it to a toy example, variation data for coding regions from chromosome 2 of the Drosophila melanogaster subgroup. This modeling work underscores how restrictive assumptions about adaptation have been to date, and how further work in this area will help to reveal unexplored and yet basic characteristics of adaptation.

Suggested Citation

  • Benger, Etam & Sella, Guy, 2013. "Modeling the effect of changing selective pressures on polymorphism and divergence," Theoretical Population Biology, Elsevier, vol. 85(C), pages 73-85.
  • Handle: RePEc:eee:thpobi:v:85:y:2013:i:c:p:73-85
    DOI: 10.1016/j.tpb.2012.10.001
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    References listed on IDEAS

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    1. Cathy Haag-Liautard & Mark Dorris & Xulio Maside & Steven Macaskill & Daniel L. Halligan & Brian Charlesworth & Peter D. Keightley, 2007. "Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila," Nature, Nature, vol. 445(7123), pages 82-85, January.
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    3. Justin C. Fay & Gerald J. Wyckoff & Chung-I Wu, 2002. "Testing the neutral theory of molecular evolution with genomic data from Drosophila," Nature, Nature, vol. 415(6875), pages 1024-1026, February.
    4. Nick G. C. Smith & Adam Eyre-Walker, 2002. "Adaptive protein evolution in Drosophila," Nature, Nature, vol. 415(6875), pages 1022-1024, February.
    5. Pleuni S Pennings & Joachim Hermisson, 2006. "Soft Sweeps III: The Signature of Positive Selection from Recurrent Mutation," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-15, December.
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