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Multinucleotide mutations cause false inferences of lineage-specific positive selection

Nature Ecology & Evolution volume 2, pages 1280–1288 (2018)Cite this article

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Abstract

Phylogenetic tests of adaptive evolution, such as the widely used branch-site test (BST), assume that nucleotide substitutions occur singly and independently. Recent research has shown that errors at adjacent sites often occur during DNA replication, and the resulting multinucleotide mutations (MNMs) are overwhelmingly likely to be non-synonymous. To evaluate whether the BST misinterprets sequence patterns produced by MNMs as false support for positive selection, we analysed two genome-scale datasets—one from mammals and one from flies. We found that codons with multiple differences account for virtually all the support for lineage-specific positive selection in the BST. Simulations under conditions derived from these alignments but without positive selection show that realistic rates of MNMs cause a strong and systematic bias towards false inferences of selection. This bias is sufficient under empirically derived conditions to produce false positive inferences as often as the BST infers positive selection from the empirical data. Although some genes with BST-positive results may have evolved adaptively, the test cannot distinguish sequence patterns produced by authentic positive selection from those caused by neutral fixation of MNMs. Many published inferences of adaptive evolution using this technique may therefore be artefacts of model violation caused by unincorporated neutral mutational processes. We introduce a model that incorporates MNMs and may help to ameliorate this bias.

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Fig. 1: CMDs drive branch-site signatures of selection.
Fig. 2: Incorporating MNMs into the branch-site model eliminates the signature of positive selection in many genes.
Fig. 3: MNMs cause a strong bias in the BST under realistic conditions.
Fig. 4: Transversion enrichment in CMDs biases the BST.
Fig. 5: CMDs implying multiple non-synonymous steps drive the BST.

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Acknowledgements

We are grateful to the members of the Thornton laboratory for discussion and helpful comments. We thank the Beagle2, Midway2 and Tarbell supercomputing clusters at the University of Chicago. We also thank the developers of HyPhy for presenting an open source platform that allows customization of standard analyses. Funding was provided by NIH R01GM104397 and R01GM121931 (to J.W.T.), NSF DEB-1601781 (to J.W.T. and A.V.), NSF DBI-1564611 (to M.W.H.), and the Precision Health Initiative of Indiana University (to M.W.H.).

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Authors and Affiliations

  1. Department of Human Genetics, University of Chicago, Chicago, IL, USA

    Aarti Venkat & Joseph W. Thornton

  2. Department of Biology, Indiana University, Bloomington, IN, USA

    Matthew W. Hahn

  3. Department of Computer Science, Indiana University, Bloomington, IN, USA

    Matthew W. Hahn

  4. Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA

    Joseph W. Thornton

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  1. Aarti Venkat
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The analyses were designed by all authors, performed by A.V. and interpreted by all authors. The manuscript was written by A.V. and J.W.T. with contributions from M.W.H.

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Correspondence to Joseph W. Thornton.

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Venkat, A., Hahn, M.W. & Thornton, J.W. Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol 2, 1280–1288 (2018). https://doi.org/10.1038/s41559-018-0584-5

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