Beyond Congruence: Evidential Integration and Inferring the Best Evolutionary Scenario

Abstract

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.

The Integrative Approach to Inferring Homology: Morphology and Development Combined

“…Thus, the integration of the correlational approach with a causal/mechanistic approach is necessary for making robust homology inferences (Fig. 3), which in turn both inform and are informed by tree inferences to arrive at integrative evolutionary scenarios of biological evolution (Nejad Kourki, 2021).…”