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

Molecular phylogenetics plays a key role in comparative genomics and has an increasingly-significant impacts on science, industry, government, public health, and society. In this opinion 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 our 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. Dedication To the memory of Rossiter H. Crozier (1943-2009), an evolutionary biologist, who, with his great generosity and wide-reaching inquisitiveness, inspired students and scientists in Australia, and abroad.