A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression.

ABSTRACT: Just exactly which tree(s) should we assume when testing evolutionary hypotheses? This question has plagued comparative biologists for decades. Though all phylogenetic comparative methods require input trees, we seldom know with certainty whether even a perfectly estimated tree (if this is possible in practice) is appropriate for our studied traits. Yet, we also know that phylogenetic conflict is ubiquitous in modern comparative biology, and we are still learning about its dangers when testing evolutionary hypotheses. Here, we investigate the consequences of tree-trait mismatch for phylogenetic regression in the presence of gene tree-species tree conflict. Our simulation experiments reveal excessively high false positive rates for mismatched models with both small and large trees, simple a

SUBMITTER: Adams R 

PROVIDER: S-EPMC11884811 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature