Assembling, Visualizing, and Analyzing the Tree of Life

F.A.Q.

How can I get involved?

How do I incorporate my phylogeny into Open Tree of Life?

  • We haven’t yet rolled out our tree curation / validation interface (but plan to do so in late 2013 / early 2014). In the meantime, this page describes the OpenTree requirements. You can put your data into a data repository, such TreeBASE or Dryad and we will be able to incorporate it from there.

Who is in the group (names, affiliations)?

• Gordon Burleigh, University of Florida
• Tiffani Williams, Texas A&M
• Rick Ree, Field Museum
• Doug Soltis, University of Florida
• Mark Holder, University of Kansas
• David Hibbett, Clark University
• Keith Crandall, Brigham Young University
• Stephen Smith, University of Michigan
• Karen Cranston, NESCent
• Laura Katz, Smith College,
• Karl Gude, Michigan State University

What is the problem or question being addressed?

Despite 150 years of effort, 55 AToL projects, and numerous other funded projects on diverse groups, we still lack a comprehensive ToL. The practice of systematics currently emphasizes disjointed efforts on separate clades, and lacks a culture of synthesis.  Despite the availability of repositories (GenBank, TreeBASE), the majority of systematic knowledge continues to be published in formats that prohibit the sharing and reuse of trees and data. Finally, the pace of species description is much too slow; many undescribed species are being detected with environmental sequences, but there is no systematic process for integrating these into the ToL.

What is your solution? What are you going to do (your specific objectives)?

We propose to:

1) Within one year create a comprehensive first draft ToL (the “Big Bang” Tree) by synthesizing current knowledge on evolutionary relationships.

2) Enable and encourage the community to subsequently annotate, modify and add to this tree by providing a suite of useful tools and by engaging in diverse outreach activities.

3) Begin to transform the culture and practices in systematics toward one of grand synthesis. Producing a comprehensive ToL will be a community-enabled endeavor. As incentives for community involvement, we will design software to provide much-needed services that enhance systematic workflows, as well as facilitate rapid development of new, customized tools. A major research focus will be to create novel mechanisms for automated updating of the ToL, resulting in a perpetually-growing, maximally inclusive view – this will facilitate the rapid discovery of new biodiversity at unprecedented rates.  We will also enable the development of the analytical tools that capture processes that shaped the deepest nodes on the tree of life; to this end, we will enhance methods to infer species trees from individual gene trees, and enable estimates of the lateral transfer events between major portions of the tree of life (e.g., among microorganisms).  We will also host workshops and use other means to engage the broader community. Further, we will provide resources for educators to teach about the ToL, and for students to contribute to the growth of the ToL.

How important is this idea to advancing knowledge and understanding within the field or across different fields?

The availability of the ToL and tools to engage the phylogenetics community will impact a multitude of audiences including: the general public, educators, biologists and systematics. For the first time global analyses will be possible.  These analyses will advance our understanding of biodiversity, ecology, genomics, evolutionary biology and impact areas of study including epidemiology and climate change.

What are the potentially transformative innovations in assembling, visualizing, or carrying out analyses on the tree of life?

We will produce the first draft tree of life that links the single origin of life with all named species.  This tree will be provided in a flexible format that will be attractive, stimulating, and accessible to diverse communities. This will be the moon-shot achievement for biodiversity in its own right. This “Big Bang” tree will then be the starting point for community involvement and annotation. By enabling the community to work on the tree through useful tools provided in an easy to use format, including automated data updating features, the tree will continue to grow and improve. Automatically placing environmental sequences onto the tree will dramatically accelerate the discovery of biodiversity.  This will transform not only how systematics is done but the availability of the tree will impact much of biology.

What are the broader impacts of the proposed project (i.e. integration of research and education, broadening participation, building infrastructure, promoting public understanding, and/or benefits to society)?

This tree of life provides a new lens through which to map biodiversity on Earth, to interpret the patterns and processes of evolution, as well as to identify, evaluate, and assess biodiversity.  Such a perspective is critical for predicting the responses of life to rapid environmental change. Broad knowledge of evolutionary relationships is fundamental to all of biology, providing crucial information for the diverse fields of comparative genomics, molecular evolution, and development, while also enlightening the study of adaptation, speciation, community assembly, and ecosystem functioning. Just as sequencing the entire human genome led to numerous, largely unanticipated biological discoveries, reconstructing the entire tree of life will fuel fundamental research and the development of practical tools to sustain biological diversity. There is a huge public outreach component–since Darwin, the tree of life has proven to be a very accessible visual metaphor for nonscientists, providing an elegant opening for communicating scientific information to people with diverse backgrounds.  Further, the draft tree of life will be a stepping off point as we train students through new courses and research experiences.

What is the “so what”/wow factor?  Why should this idea excite us?

A comprehensive tree of life has the potential to profoundly accelerate the pace of biodiversity discovery. Mapping all of biodiversity on Earth onto a single tree will be transformative to diverse communities (e.g. researchers, teachers, general public). The impact of the first draft tree will be comparable to that that of the completion of the first draft of the human genome, or the first photographs of Earth from the moon. It will provide the icon for life on Earth. Research across all of the life sciences will benefit in fundamental ways from new methods of visualizing large data sets in the context of the tree of life.  In sum, these efforts will engage the public and transform research capabilities across much of biology.

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