publication . Article . Preprint . 2017

Multinucleotide mutations cause false inferences of lineage-specific positive selection

Aarti Venkat; Matthew W. Hahn; Joseph W. Thornton;
Open Access
  • Published: 20 Jul 2017 Journal: Nature Ecology & Evolution, volume 2, pages 1,280-1,288 (eissn: 2397-334X, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
<jats:title>ABSTRACT</jats:title><jats:p>Phylogenetic tests of adaptive evolution, which infer positive selection from an excess of nonsynonymous changes, assume that nucleotide substitutions occur singly and independently. But recent research has shown that multiple errors at adjacent sites often occur in single events during DNA replication. These multinucleotide mutations (MNMs) are overwhelmingly likely to be nonsynonymous. We therefore evaluated whether phylogenetic tests of adaptive evolution, such as the widely used branch-site test, might misinterpret sequence patterns produced by MNMs as false support for positive selection. We explored two genome-wide ...
Subjects
free text keywords: Molecular evolution, Gene, Evolutionary biology, Population genetics, Positive selection, Human evolutionary genetics, Phylogenetic tree, DNA replication, Phylogenetics, Biology, Genetics, Bioinformatics, Nonsynonymous substitution, Article, adaptation, adaptive evolution, branch-site test, codon models, transversions
60 references, page 1 of 4

1.Goldman N & Yang Z A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11, 725–736 (1994).7968486 [OpenAIRE] [PubMed]

2.Murrell B Gene-wide identification of episodic selection. Mol Biol Evol 32, 1365–1371 (2015).25701167 [OpenAIRE] [PubMed]

3.Murrell B Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8, e1002764 (2012).22807683 [OpenAIRE] [PubMed]

4.Smith MD Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 32, 1342–1353 (2015).25697341 [OpenAIRE] [PubMed]

5.Yang Z & Nielsen R Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19, 908–917 (2002).12032247 [PubMed]

6.Zhang J, Nielsen R & Yang Z Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22, 2472–2479 (2005).16107592 [PubMed]

7.Pond SL, Frost SD & Muse SV HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676–679 (2005).15509596 [OpenAIRE] [PubMed]

8.Kosiol C, Holmes I & Goldman N An empirical codon model for protein sequence evolution. Mol Biol Evol 24, 1464–1479 (2007).17400572 [OpenAIRE] [PubMed]

9.Whelan S & Goldman N Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167, 2027–2043 (2004).15342538 [OpenAIRE] [PubMed]

10.Muse SV & Gaut BS A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11, 715–724 (1994).7968485 [OpenAIRE] [PubMed]

11.Han MV, Demuth JP, McGrath CL, Casola C & Hahn MW Adaptive evolution of young gene duplicates in mammals. Genome Res 19, 859–867 (2009).19411603 [OpenAIRE] [PubMed]

12.Consortium DG Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007).17994087 [OpenAIRE] [PubMed]

13.Foote AD Convergent evolution of the genomes of marine mammals. Nat Genet 47, 272–275 (2015).25621460 [OpenAIRE] [PubMed]

14.Kosiol C Patterns of positive selection in six Mammalian genomes. PLoS Genet 4, e1000144 (2008).18670650 [OpenAIRE] [PubMed]

15.Roux J Patterns of positive selection in seven ant genomes. Mol Biol Evol 31, 1661–1685 (2014).24782441 [OpenAIRE] [PubMed]

60 references, page 1 of 4
Abstract
<jats:title>ABSTRACT</jats:title><jats:p>Phylogenetic tests of adaptive evolution, which infer positive selection from an excess of nonsynonymous changes, assume that nucleotide substitutions occur singly and independently. But recent research has shown that multiple errors at adjacent sites often occur in single events during DNA replication. These multinucleotide mutations (MNMs) are overwhelmingly likely to be nonsynonymous. We therefore evaluated whether phylogenetic tests of adaptive evolution, such as the widely used branch-site test, might misinterpret sequence patterns produced by MNMs as false support for positive selection. We explored two genome-wide ...
Subjects
free text keywords: Molecular evolution, Gene, Evolutionary biology, Population genetics, Positive selection, Human evolutionary genetics, Phylogenetic tree, DNA replication, Phylogenetics, Biology, Genetics, Bioinformatics, Nonsynonymous substitution, Article, adaptation, adaptive evolution, branch-site test, codon models, transversions
60 references, page 1 of 4

1.Goldman N & Yang Z A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11, 725–736 (1994).7968486 [OpenAIRE] [PubMed]

2.Murrell B Gene-wide identification of episodic selection. Mol Biol Evol 32, 1365–1371 (2015).25701167 [OpenAIRE] [PubMed]

3.Murrell B Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8, e1002764 (2012).22807683 [OpenAIRE] [PubMed]

4.Smith MD Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 32, 1342–1353 (2015).25697341 [OpenAIRE] [PubMed]

5.Yang Z & Nielsen R Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19, 908–917 (2002).12032247 [PubMed]

6.Zhang J, Nielsen R & Yang Z Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22, 2472–2479 (2005).16107592 [PubMed]

7.Pond SL, Frost SD & Muse SV HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676–679 (2005).15509596 [OpenAIRE] [PubMed]

8.Kosiol C, Holmes I & Goldman N An empirical codon model for protein sequence evolution. Mol Biol Evol 24, 1464–1479 (2007).17400572 [OpenAIRE] [PubMed]

9.Whelan S & Goldman N Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167, 2027–2043 (2004).15342538 [OpenAIRE] [PubMed]

10.Muse SV & Gaut BS A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11, 715–724 (1994).7968485 [OpenAIRE] [PubMed]

11.Han MV, Demuth JP, McGrath CL, Casola C & Hahn MW Adaptive evolution of young gene duplicates in mammals. Genome Res 19, 859–867 (2009).19411603 [OpenAIRE] [PubMed]

12.Consortium DG Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203–218 (2007).17994087 [OpenAIRE] [PubMed]

13.Foote AD Convergent evolution of the genomes of marine mammals. Nat Genet 47, 272–275 (2015).25621460 [OpenAIRE] [PubMed]

14.Kosiol C Patterns of positive selection in six Mammalian genomes. PLoS Genet 4, e1000144 (2008).18670650 [OpenAIRE] [PubMed]

15.Roux J Patterns of positive selection in seven ant genomes. Mol Biol Evol 31, 1661–1685 (2014).24782441 [OpenAIRE] [PubMed]

60 references, page 1 of 4
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publication . Article . Preprint . 2017

Multinucleotide mutations cause false inferences of lineage-specific positive selection

Aarti Venkat; Matthew W. Hahn; Joseph W. Thornton;