Phylo-Species-Atlas: a curated atlas of empirical species-level phylogenies and their archival uncertainty

A curated, standardized collection of empirical phylogenetic datasets covering taxonomic groups across Bacteria, Archaea, and Eukaryota. Organized into 62 partitions yielding 264 standardized trees (218 Condamine family-level + 25 further partition-canonical + 21 sub-clade/reference), with tip-label normalized Newick trees, a global standardized-label dictionary, full label mappings, and per-tree provenance (Supplementary Tables S5 and S7 of the accompanying manuscript). Companion deposit to the manuscript 'Where the tree of life is empirically resolved, and where it is not: an open atlas of species-level phylogenies and their archival uncertainty' (Richter, 2026, under review). The underlying trees are permanently archived in their original repositories (Dryad, Figshare, Zenodo, GitHub) as cited in the manuscript; this derivative deposit enables cross-tree interoperability, standardization, and reproducibility of the paper's headline numbers. Releases are tagged on GitHub and the version metadata is auto-populated by Zenodo at deposit time from the git tag. Cite the version-specific DOI for reproducibility; cite the concept DOI 10.5281/zenodo.20127157 when referring to the resource as a whole.