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    Twisted trees and inconsistency of tree estimation when gaps are treated as missing data – The impact of model mis-specification in distance correction

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    Issue Date
    2015-04-28
    Author
    McTavish, Emily Jane
    Steel, Mike
    Holder, Mark T.
    Publisher
    Elsevier
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
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    Abstract
    Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two \long branch repulsion" trees will be preferred over the true tree { though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolvewith independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data.
    URI
    http://hdl.handle.net/1808/20870
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    • Ecology & Evolutionary Biology Scholarly Works [1493]
    Citation
    Mctavish, Emily Jane, Mike Steel, and Mark T. Holder. "Twisted Trees and Inconsistency of Tree Estimation When Gaps Are Treated as Missing Data – The Impact of Model Mis-specification in Distance Corrections." Molecular Phylogenetics and Evolution 93 (2015): 289-95.

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    KU Libraries
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    785-864-8983

    KU Libraries
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    Lawrence, KS 66045
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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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