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

Author:

Jermiin Lars S1234,Catullo Renee A125,Holland Barbara R6

Affiliation:

1. CSIRO Land & Water, Canberra, ACT 2601, Australia

2. Research School of Biology, Australian National University, Canberra, ACT 2601, Australia

3. School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland

4. Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland

5. School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia

6. School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia

Abstract

AbstractMolecular 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.

Funder

Australian Government’s Commonwealth Scientific Industrial Research Organisation

Publisher

Oxford University Press (OUP)

Subject

General Medicine

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