A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics

Lars S. Jermiin*, Renee A. Catullo, Barbara R. Holland

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    14 Citations (Scopus)

    Abstract

    Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.

    Original languageEnglish
    Article numberlqaa041
    JournalNAR Genomics and Bioinformatics
    Volume2
    Issue number2
    DOIs
    Publication statusPublished - 1 Jun 2020

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