Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

摘要

Author summary Synthetic platforms for phylogenomic knowledge tend to manage conflict between different evolutionary reconstructions in the following way: "If we do not agree, then it is either our view over yours, or we just collapse all conflicting node concepts into polytomies". We argue that this is not an equitable way to realize synthesis in this domain. For instance, it would not be an adequate solution for building a unified data environment where authors can endorse and yet also reconcile their diverging perspectives, side by side. Hence, we develop a novel system for verbalizing i.e., consistently identifying and aligning incongruent node concepts that reflects a more forward-looking attitude: "We may not agree with you, but nevertheless we understand your phylogenomic inference well enough to express our disagreements in a logic-compatible syntax. We can therefore maximize the translatability of data linked to our diverging phylogenomic hypotheses". We show that achieving phylogenomic synthesis fundamentally depends on the application of trained expert judgment to assert parent node congruence in spite of incongruently sampled children.