Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

While some relationships in phylogenomic studies have remained stable since the Sanger sequencing era, many challenging nodes remain, even with genome-scale data. Incongruence or lack of resolution in the phylogenomic era is frequently attributed to inadequate data modeling and analytical issues that lead to systematic biases. However, few studies investigate the potential for random error or establish expectations for the level of resolution achievable with a given empirical dataset, and integrate uncertainties across methods when faced with conflicting results.
Ants are the most species-rich lineage of social insects and one of the most ecologically important terrestrial animals. Consequently, ants have garnered significant research attention, including their systematics. Despite this, there has been no comprehensive genus-level phylogeny of the ants inferred using genomic data that thoroughly evaluates both signal strength and incongruence. In this study, we provide insight into and ..., , , # Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants

[https://doi.org/10.5061/dryad.547d7wmhb](https://doi.org/10.5061/dryad.547d7wmhb)

This dataset is associated with Borowiec et al. 2025 publication in Systematic Biology titled \"Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants\". It contains supplementary information and data including supplementary figures, tables, assembled contig sequences, trimmed and untrimmed locus alignments, concatenated alignments, log and tree files of phylogenetic, simulation, and visualization analyses, and custom code used.

## Description of the data and file structure

Directory structure of supplementary data:

├── `Supplementary_figures.pdf` # Supplementary figures referred to in the manuscript.
├── `Supplementary_tables.xlsx` # Supplementary tables referred to in the manuscript.
├── `1-assembled-contigs` # Assembled SPADES contigs for newly and previously (...,