# Coping with Ineffective Overlap in Multilocus Phylogenetics

## TL;DR

The paper introduces a new method to handle missing data in phylogenetics by identifying taxa and loci for targeted sequencing to improve tree stability.

## Contribution

The novel approach combines concatabominations with gene-tree jackknifing to identify candidates for additional sequencing.

## Key findings

- The method successfully identifies taxa and loci for targeted sequencing to reduce topological instability.
- It performs well even with modest amounts of added data.
- Results are compared with a mathematics-based gene sampling approach.

## 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 data set, we illustrate the method’s capacity to identify candidate taxa and loci for additional sequencing, compare the results with those of the mathematics-based gene sampling sufficiency approach, and explore the terrace space associated with the multilocus data set. 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.