Resolving competing evolutionary histories in joint ancestral state reconstruction.

ABSTRACT: Ancestral state reconstruction (ASR) is a foundational tool in comparative biology, offering insights into the evolutionary history of lineages. With each new evolutionary model, our ability to estimate ancestral states with increased biological realism has improved. However, the field has primarily relied on marginal reconstructions, which focus on individual nodes. This framework is analytically tractable and appropriate for node-specific hypotheses, but it is not designed to identify the most probable sequence of evolutionary events across a tree. We argue that for researchers interested in evolutionary trajectories, joint reconstructions provide a more effective way to characterize the full history of transitions. Traditionally, joint reconstruction algorithms focused only on the singl

SUBMITTER: Boyko JD 

PROVIDER: S-EPMC13079920 | biostudies-literature | 2026 Apr

REPOSITORIES: biostudies-literature