Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

重建连接所有演化支系的系统发育关系（即生命之树）是一项极具挑战性的重大课题。当前，亲缘关系迥异的演化支系间同源性状数据的匮乏，使得直接开展系统发育推断难以实现。为构建全面的生命之树，我们整合了已发表的系统发育树，以及从未被纳入系统发育研究的分类单元的分类学归属信息。我们推出了包含230万个终端节点的生命之树草案——开放生命之树（Open Tree of Life）。该生命之树的构建需要额外汇编两项科研社区资源：其一为全面的全球参考分类学体系，其二为已发表的、映射至该分类体系的系统发育树数据库。我们的开源框架支持科研社区的评议与贡献，使得当新的系统发育与分类学数据数字化发布后，该生命之树能够得到持续更新。尽管开放生命之树的数据覆盖范围与系统发育冲突情况，揭示了两方面的不足：一是系统发育重建可用的基础数据存在缺口，二是系统发育树作为数字化成果的发表存在短板，但该生命之树仍为科研社区的后续贡献提供了极具说服力的起点。这一全面的生命之树将推动关于生物多样性本质的基础研究，最终可为比较生物学、生态学、保护生物学、气候变化研究、农业以及基因组学等领域的下游应用提供最新的系统发育数据。