Silva, Ana Serra;
Siu-Ting, Karen;
Creevey, Christopher J;
Pisani, Davide;
Wilkinson, Mark;
(2025)
Coping with Ineffective Overlap in Multilocus Phylogenetics.
Systematic Biology
, Article syaf044. 10.1093/sysbio/syaf044.
(In press).
Preview |
Text
syaf044.pdf Download (1MB) | Preview |
Abstract
Missing data is a long standing issue in phylogenetic inference, which often results in high levels of taxonomic instability, obscuring otherwise well supported relationships. Multiple approaches have been developed to deal with the negative effects of ineffective overlap on tree resolution, often by identifying taxa for removal. Here we repurpose a heuristic method developed to identify unstable taxa in morphological data matrices, concatabominations, and combine it with a novel gene-tree jackknifing on matrix representation of trees to identify candidates for targeted sequencing. Using a multilocus caecilian dataset we illustrate the method’s capacity to identify candidate taxa and loci for additional sequencing, compare the results to those of the mathematics-based gene sampling sufficiency approach and explore the terrace space associated with the multilocus dataset. We show that our approach yields tractable numbers of loci/taxa for targeted sequencing that successfully mitigate topological instability due to ineffective overlap, even when modest amounts of data are added.
| Type: | Article |
|---|---|
| Title: | Coping with Ineffective Overlap in Multilocus Phylogenetics |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/sysbio/syaf044 |
| Publisher version: | https://doi.org/10.1093/sysbio/syaf044 |
| Language: | English |
| Additional information: | Copyright © The Author(s) 2025. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | Taxonomic instability, ineffective overlap, phylogenomics, matrix representation of splits, terraces, targeted taxon/locus sampling |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10210796 |
Archive Staff Only
 |
View Item |
