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Data and Supplement from: Phylogenetic tree instability after taxon addition: Empirical frequency, predictability, and consequences for online inference

Collienne, Lena1; Barker, Mary1; Suchard, Marc A.2; Matsen, Frederick A.1

Published Nov 01, 2024 on Dryad. https://doi.org/10.5061/dryad.63xsj3v9x

Data files

Nov 01, 2024 version files 5.21 MB

Abstract

Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree.
 
In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1,000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.