CRABS: Congruent rate analyses in birth–death scenarios

Diversification rates inferred from phylogenies are not identifiable if the allowed to vary freely over time. There infinitely many combinations of speciation and extinction rate functions that have exact same likelihood score for a given phylogeny, building congruence class. The specific shape characteristics such classes yet been studied. Whether within class share common features is also known. Prior hypotheses typically render diversification identifiable, but results then depend on these priori assumptions. To test robustness hypotheses, we use two different approaches explore classes: (i) constructing congruent models under alternative (ii) sampling function Our methods implemented in open-source R package CRABS (https://github.com/afmagee/CRABS). provides flexible approach summaries can highlight trends, is, increasing, flat or decreasing rates. Although there equally likely functions, features. be used assess patterns robust despite non-identifiability birth–death model. In our example, clearly identify three phases changes among all which sampled Thus, necessarily problem studying historical biodiversity phylogenies.