Towards an inclusive philosophy for phylogenetic inference

We defend and expand on our earlier proposal for an inclusive philosophical framework for phylogenetics, based on an interpretation of Popperian corro boration that is decoupled from the popular falsificationist interpretation of Popperian philosophy. Any phylogenetic inference method can provide Pop perian "evidence" or "test statements" based on the method's goodness-of-fi t values for different tree hypotheses. Corroboration, or the severity of t hat test, requires that the evidence is improbable without the hypothesis, given only background knowledge that includes elements of chance. This fram ework contrasts with attempted Popperian justifications for cladistic parsi mony-in which evidence is the data, background knowledge is restricted to d escent with modification, and "corroboration," as a by-product of nonfalsif ication, is to be measured by cladistic parsimony. Recognition that cladist ic "corroboration" reflects only goodness-of-fit, not corroboration/severit y, makes it clear that standard cladistic prohibitions, such as restriction s on the evolutionary models to be included in "background knowledge," have no philosophical status. The capacity to assess Popperian corroboration ne ither justifies nor excludes any phylogenetic method, but it does provide a framework in phylogenetics for learning from errors-cases where apparent g ood evidence is probable even without the hypothesis. We explore these issu es in the context of corroboration assessments applied to likelihood method s and to a new form of parsimony. These different forms of evidence and cor roboration assessment point also to a new way to combine evidence-not at th e level of overall fit, but at the level of overall corroboration/severity. We conclude that progress in an inclusive phylogenetics will be well serve d by the rejection of cladistic philosophy.