Mutation-biased adaptation in Andean house wrens

Stoltzfus, Arlin; McCandlish, David M.

doi:10.1073/pnas.1518490112

Cited by 8 publications

(7 citation statements)

References 20 publications

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“…Candidate cases of experimental and natural adaptation were identified from available reviews of parallel evolution or experimental adaptation ( Wood et al 2005 ; Arendt and Reznick 2008 ; Gompel and Prud’homme 2009 ; Stern and Orgogozo 2009 ; Christin et al 2010 ; Conte et al 2012 ; Martin and Orgogozo 2013 ; Stern 2013 ; Stoltzfus and McCandlish 2015 ; Long et al 2015 ; Lenormand et al 2016 ). We processed cited works opportunistically for each set until we had accumulated cases comprising at least 50 parallelisms.…”

Section: Methodsmentioning

confidence: 99%

“…Though their main result was to find evidence of fixation bias, they also found an effect mutational bias. Recently, Galen et al (2015) argued for the role of a CpG mutational hotspot in changes to hemoglobin linked to altitude adaptation in Andean house wrens ( Troglodytes aedon ; see also Stoltzfus and McCandlish 2015 ). However, as noted by Storz (2016) , the importance of mutational biases in natural cases of parallel adaptation has not been investigated systematically.…”

Section: Introductionmentioning

confidence: 99%

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Mutational Biases Influence Parallel Adaptation

Stoltzfus

McCandlish

2017

Molecular Biology and Evolution

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122

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While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mutational Biases Influence Parallel Adaptation

Stoltzfus

McCandlish

2017

Molecular Biology and Evolution

Self Cite

103

122

View full text Add to dashboard Cite

show abstract

“…Candidate cases of experimental and natural adaptation were identified from available reviews of parallel evolution or experimental adaptation (Wood et al, 2005;Arendt and Reznick, 2008;Gompel and Prud'homme, 2009;Stern and Orgogozo, 2009;Christin et al, 2010;Conte et al, 2012;Martin and Orgogozo, 2013;Stern, 2013;Stoltzfus and McCandlish, 2015;Long et al, 2015;Lenormand et al, 2016). We processed cited works opportunistically for each set until we had accumulated cases comprising at least 50 parallelisms (the resulting numbers were 51 for the natural cases, and 63 for the experimental ones).…”

Section: Casesmentioning

confidence: 99%

“…Though their main result was to find evidence of fixation bias, they also found an e↵ect mutational bias. Recently, Galen et al (2015) argued for the role of CpG mutational hotspot in altitude adaptation of Andean house wrens (Troglodytes aedon; see also Stoltzfus and McCandlish 2015). However, as noted by Storz (2016), the importance of mutational biases in natural cases of parallel adaptation has not been investigated systematically.…”

Section: Introductionmentioning

confidence: 99%

Mutational biases influence parallel adaptation

Stoltzfus

McCandlish

2017

Preprint

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While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be over-represented among documented adaptive substitutions. To test this hypothesis, we assembled a dataset of putatively adaptive amino acid substitutions that have occurred in parallel during evolution in nature or in the laboratory. We find that the frequency of transitions in this dataset is much higher than would be predicted under a null model where mutation has no e↵ect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.

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“…For instance, a region that is prone to structural variation or transposon insertion is likely to undergo repeated rearrangements, thus facilitating certain gene-to-phenotype changes (CHAN et al 2010). Adaptation to high-altitude in Andean house wrens and hummingbirds has been associated with single point mutations in the βA-globin gene and these mutations appear to lie within CpG sites, which are known to be chemically instable and highly mutable (S.C. GALEN et al 2015;A. STOLTZFUS and D.M.…”

Section: The Causes Of Genetic Repetitionmentioning

confidence: 99%

Predicting the genetic loci of past evolution

Courtier‐Orgogozo

Martin

2017

Preprint

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Repetitions in the mutations found to be responsible for independent evolution of similar phenotypes in various taxa have led some biologists to propose that for certain evolutionary changes the causal mutations are predictable. We examine here the nature of the predictions that have been made and their associated arguments. Predictions about the loci of past evolution are retrodictions, i.e. inferences about events that occurred in the past. They are not based on elaborate models and they derive mainly from the observation of repeated cases of genetic evolution. Predictions at the nucleotide level or at the gene level have a higher inference gain than those for broader categories of genetic changes such as cis-regulatory mutations.

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Mutation-biased adaptation in Andean house wrens

Cited by 8 publications

References 20 publications

Mutational Biases Influence Parallel Adaptation

Mutational Biases Influence Parallel Adaptation

Mutational biases influence parallel adaptation

Predicting the genetic loci of past evolution

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