Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps

We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions on the structure of the alignment. Under these assumptions, maximum likelihood will asympto...

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Main Authors:	Truszkowski, Jakub, Goldman, Nick
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748752/

id	pubmed-4748752
recordtype	oai_dc
spelling	pubmed-47487522016-02-11 Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps Truszkowski, Jakub Goldman, Nick Regular Articles We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions on the structure of the alignment. Under these assumptions, maximum likelihood will asymptotically recover the tree with edge lengths corresponding to the mean number of substitutions per site on each edge. This refutes Warnow's recent suggestion (Warnow 2012) that maximum likelihood phylogenetic inference might be statistically inconsistent when gaps are treated as missing data, even if the MSA is correct. We also derive a simple new proof of maximum likelihood consistency of ungapped alignments. Oxford University Press 2016-03 2015-11-28 /pmc/articles/PMC4748752/ /pubmed/26615177 http://dx.doi.org/10.1093/sysbio/syv089 Text en © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Truszkowski, Jakub Goldman, Nick
spellingShingle	Truszkowski, Jakub Goldman, Nick Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
author_facet	Truszkowski, Jakub Goldman, Nick
author_sort	Truszkowski, Jakub
title	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
title_short	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
title_full	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
title_fullStr	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
title_full_unstemmed	Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
title_sort	maximum likelihood phylogenetic inference is consistent on multiple sequence alignments, with or without gaps
description	We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions on the structure of the alignment. Under these assumptions, maximum likelihood will asymptotically recover the tree with edge lengths corresponding to the mean number of substitutions per site on each edge. This refutes Warnow's recent suggestion (Warnow 2012) that maximum likelihood phylogenetic inference might be statistically inconsistent when gaps are treated as missing data, even if the MSA is correct. We also derive a simple new proof of maximum likelihood consistency of ungapped alignments.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748752/
_version_	1613536749038862336

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps

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