Synthesis of phylogeny and taxonomy into a comprehensive tree of life

By Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Burleigh, R. Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jia-bin Deng, B. Drew, Romina Gazis and 12 more. 2014

659 citations recorded by the source corpus.

Significance Scientists have used gene sequences and morphological data to construct tens of thousands of evolutionary trees that describe the evolutionary history of animals, plants, and microbes. This study is the first, to our knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life. This tree and the underlying data are available to browse and download from the Internet, facilitating subsequent analyses that require evolutionary trees. The tree can be easily updated with newly published data. Our analysis of coverage not only reveals gaps in sampling and naming biodiversity but also further demonstrates that most published phylogenies are not available in digital formats that can be summarized into a 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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

The Unreasonable Effectiveness of Noisy Data for Fine-Grained Recognition (2015, background): “Even worse, manual labeling does not scale—in the animal kingdom alone, [20] has estimated over 14,000 species of birds in the world (Fig.”
SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? (2017, methodology): “Taxonomies are sourced from IndexFungorum [29], SILVA, NCBI, Global Biodiversity Information Facility [30], Interim Register of Marine and Nonmarine Genera [31] and some clade specific resources [9].”
Miniaturization of biologgers is not alleviating the 5% rule (2018, methodology): “Species names were checked against the taxonomic reference associated with the online tree of life (Hinchliff et al., 2015) using the rotl package (Michonneau, Brown, & Winter, 2016) of r (R Core Team 2016).”
What we (don’t) know about global plant diversity (2018, neutral): “General databases for all organisms exist for genes (GenBank; Benson et al. , 2013), phylogenetic relationships based on those genes (The Open Tree of Life; Hinchliff et al. , 2015) and spatial observations (GBIF; http://gbif.org/ ).”
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018, background): “Apart from inferring rooted time trees, which are valuable in and of themselves [10], BEAST also allows addressing many kinds of micro- and macroevolutionary questions, such as determining the age and location of the origin of species and cultures, rates of mutation and migration, and rate of spread”
The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics (2017, background): “They span a continuum from recent divergences at the phylogeographic level (Hickerson et al. 2010, Edwards et al. 2016a) to ancient diversification among the major lineages of life (Hinchliff et al. 2015, Hug et al. 2016).”
Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera) (2018, background): “…M, U and KK in Table 3 have been corrected in this current version.] branch will ultimately allow meta-analysis at multiple scales, helping to understand the immense diversity of life as well as common evolutionary processes (Watson et al., 2014; Hinchliff et al., 2015; Nelson-Sathi et al., 2015).”