Abstract
Dedication To the memory of Rossiter H. Crozier (1943-2009), an evolutionary biologist, who with his generosity and inquisitiveness inspired many students and scientists, in Australia and abroad.
Molecular phylogenetics plays a key role in comparative genomics and has an increasingly-significant impact on science, industry, government, public health, and society. We report that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence the phylogenetic estimates. Based on the potential offered by well-established but under-used procedures (i.e., assessment of phylogenetic assumptions and test of goodness-of-fit), we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.