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.本合集包含49个经人工甄选并标准化的实证系统发育数据集，覆盖细菌域（Bacteria）、古菌域（Archaea）与真核生物域（Eukaryota）下的47个分类群。该合集提供带有数字标识符的末梢标签标准化Newick树（Newick tree）、包含641763个唯一标准化标签的全局物种词典、完整标签映射表与元数据。原始系统发育树已如随刊文献所引，永久归档于其原始存储库（Dryad、Figshare、Zenodo、GitHub）；本衍生合集可实现不同系统发育树间的互操作性与标准化。本合集采用版本控制机制，将随更完善的系统发育数据发布进行更新。版本发布通过GitHub进行标记；若用户需要用于可复现研究的静态快照，需引用特定版本与数字对象唯一标识符（Digital Object Identifier，DOI）。本数据集配套论文《系统发育暗物质：实证树图集揭示生命之树物种覆盖度的巨大不对称性》（Richter，待刊）。