How and Why to Build a Unified Tree of Life.

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

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.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research.

The Fossil Calibration Database-A New Resource for Divergence Dating.

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology.

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies.

Species trees from highly incongruent gene trees in rice.

Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline.

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct 'genome types' (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1-Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL).

The PhyLoTA Browser: processing GenBank for molecular phylogenetics research.

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.

Summarizing a posterior distribution of trees using agreement subtrees.

Bayesian inference of phylogeny is unique among phylogenetic reconstruction methods in that it produces a posterior distribution of trees rather than a point estimate of the best tree. The most common way to summarize this distribution is to report the majority-rule consensus tree annotated with the marginal posterior probabilities of each partition. Reporting a single tree discards information contained in the full underlying distribution and reduces the Bayesian analysis to simply another method for finding a point estimate of the tree.