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

Lars S Jermiin; Renee A Catullo; Barbara R Holland

doi:10.1093/nargab/lqaa041

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

NAR Genom Bioinform. 2020 Jun 23;2(2):lqaa041. doi: 10.1093/nargab/lqaa041. eCollection 2020 Jun.

Authors

Lars S Jermiin¹, Renee A Catullo¹, Barbara R Holland²

Affiliations

¹ CSIRO Land & Water, Canberra, ACT 2601, Australia.
² School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia.

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.