Coping with ineffective overlap in multilocus phylogenetics
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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 ..., , , # Coping with ineffective overlap in multilocus phylogenetics
Supplementary data for:
Serra Silva, A. et al. (2025). Coping with Ineffective Overlap in Multilocus Phylogenetics. *In press.*
Detailed descriptions of analyses and parameters can be found in the main document and its supplemental information, but all folders below include the scripts necessary to repeat the analyses.
File extensions and naming conventions are shared between zipped folders and are explained below using the Dobrin_etal2018_CC0compliant.zip as an example.
If the geneTrees subfolder includes subfolders named after phylogenetic inference software and no additional listing of files is given, then ALL file extensions correspond to the software's default output.
### Contents of each folder
* Dobrin_etal2018_CC0compliant.zip: contains the analyses based on the datasets used in [Dobrin et al.](https://link.springer.com/article/10.1186/s12862-018-1162-9) (2018)
* Each dataset subfolder has the following organ...,
创建时间：
2025-06-28
