DOI: 10.5061/dryad.63xsj3v9x
title: Data and Supplement from: Phylogenetic tree instability after taxon addition: Empirical frequency, predictability, and consequences for online inference

description: 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.
description: The dataset presented here is a subsample of 1,000 alignments of
 the datasets of Harrington et al.: https://doi.org/10.5061/dryad.g4vp6jv
description: # Data and Supplement from: Phylogenetic tree instability after taxon
 addition: Empirical frequency, predictability, and consequences for online
 inference
 [https://doi.org/10.5061/dryad.63xsj3v9x](https://doi.org/10.5061/dryad.63xsj3v9x) ## Description of the data and file structure ### Alignments This dataset of 1,000 nucleotide alignments is a subsample of the datasets presented by Harrington et al., 2021 ([https://doi.org/10.5061/dryad.g4vp6jv](https://doi.org/10.5061/dryad.g4vp6jv), [https://doi.org/10.5061/dryad.b568p21](&lt; https://doi.org/10.5061/dryad.b568p21 &gt;)), which we converted to FASTA files. Originally, these datasets come from three sources: * Brown and Thomson, 2017 ([https://doi.org/10.1093/sysbio/syw101](https://doi.org/10.1093/sysbio/syw101)): Amniotes data containing gene sequences with small numbers of taxa (less than 50 taxa) * we sampled 43 of these alignments * Richards et al., 2018 ([https://doi.org/10.1093/sysbio/syy013](https://doi.org/10.1093/sysbio/syy013)): mtDNA sequences of all 13 protein-coding mitochondrial genes of a variety of tetrapod species giving us alignments containing between 20 and 575 sequences * we sampled 9 of these alignments * Sanderson et al., 2009 ([https://doi.org/10.1080/10635150802158688](https://doi.org/10.1080/10635150802158688)): datasets assembled by Harrington et al. (2021) from the PhyLoTA database, which contain nucleotide alignments with up to 250 sequences curated from GenBank with diverse taxon compositions and sizes. * we sampled 948 of these alignments ### Supplement Additionally, we present the PDF of supplementary information for the article "Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference". ### Files and variables #### File: alignments.zip **Description:** Zipped directory of nucleotide alignments containing characters "A", "C", "G", "T", and "-" in FASTA format. #### File: supplement.pdf **Description:** PDF containing supplementary materials and figures for the main article. ## Access information Data was derived from the following sources: * [https://doi.org/10.5061/dryad.g4vp6jv](https://doi.org/10.5061/dryad.g4vp6jv) * [https://doi.org/10.5061/dryad.b568p21](&lt; https://doi.org/10.5061/dryad.b568p21 &gt;)