Phyloseminar #103: Bjørn Kopperud (LMU Munich) and Andrew Magee (U Washington)

Birth-death congruence classes can be collapsed using Bayesian shrinkage priors

Recently, the discovery of congruent sets of phylogenetic birth-death processes has raised a series of questions as to what diversification patterns we can infer from phylogenetic trees and which are indistinguishable. Many phylogenetic trees are estimated solely from extant samples, and thus yield ultrametric trees that lack critical information (i.e., extinction events) about the tempo of diversification histories. This is the crux of the problem, and makes models in the same congruence class statistically unidentifiable. However, the general behaviour for such classes is not well known. How similar are these classes, are they easy to construct, and is it possible to mimic any plausible diversification history within one single class? To answer this, we simulate a series of phylogenetic trees, both within and across congruence classes, and investigate their properties using state of the art Bayesian inference methods. Our results show that the diversification rates inferred using Bayesian shrinkage priors produce not an arbitrary model from the congruence class. Instead, using Bayesian shrinkage priors collapses the congruence class, yielding a single, simplest model in accordance with the prior expectations. Thus, diversification rate can be inferred from molecular phylogenies when realistic priors are used.