2025/07/02 by Ana Serra Silva, Karen Siu-Ting, Christopher J. Creevey +2 · 1 voice
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #Genetic diversity and population structure #Genomics and Phylogenetic Studies
paper · pdf · doi:10.1093/sysbio/syaf044
openalex publication_date 2025/07/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.