Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction.

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 has improved alongside the increased biological realism of these models. However, the field has primarily relied on reconstructions that focus on individual nodes, known as marginal reconstructions. This framework is analytically tractable but may not accurately represent what biologists want in inference, as evolution is dependent, and phenotypic transitions deeper in time can lead to consistent changes later. We argue that evolutionary history is better represented by joint reconstructions, which estimate the full sequence of states across nodes. Traditionally, joint reco

SUBMITTER: Boyko JD 

PROVIDER: S-EPMC12632483 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature