Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Synthesis of phylogeny and taxonomy into a comprehensive tree of life
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DOI：
10.1073/pnas.1423041112
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发表时间：
2015-10-13
影响因子：
11.1
通讯作者：
Cranston, Karen A.
中科院分区：
文献类型：
--
作者：
Hinchliff, Cody E.;Smith, Stephen A.;Cranston, Karen A.
重建团结所有血统(生命之树)的系统发育关系是一个巨大的挑战。目前，不同血缘关系的同源特征数据的匮乏使得直接的系统发育推论无法成立。因此，为了重建一棵全面的生命树，我们综合了已发表的系统发育图，以及从未纳入系统发育图的分类群。我们呈现了一棵包含230万条提示的草稿树--开放的生命之树。实现这一树需要汇编两个额外的社区资源：(1)一个全面的全球参考分类法；(2)一个与该分类法相对应的已公布的系统发育树数据库。我们的开源框架促进了社区的评论和贡献，使树能够在新的系统发育和分类数据变得数字化时不断更新。尽管《开放生命树》的数据覆盖范围和系统发育冲突说明了可用于系统发生重建的基础数据和将树作为数字对象出版方面的差距，但这棵树为社区的贡献提供了一个引人注目的起点。这棵综合性的树将推动对生物多样性本质的基础研究，最终为比较生物学、生态学、保护生物学、气候变化、农业和基因组学的下游应用提供最新的系统发生学。
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.