NASA Astrobiology Institute (NAI)

1. Genomic Record of the Earth's Early Biosphere (Hedges)

   Project Investigators:

   Other Project Members

   Fabia Battistuzzi (No Role Selected)

   S. Blair Hedges (No Role Selected)

   Matthew Heinicke (No Role Selected)

   Jaime Blair (Collaborator)

   Sudhir Kumar (Collaborator)

   Summary

   Our research involves molecular evolutionary genetics in an effort to better understand the relationship between planetary history and the evolution of life. We continue to update our public database TimeTree (www.timetree.org), which presents divergence times of organisms. Most of the work during the past year involved editing and contributing to a book, The Timetree of Life, which summarizes the current state of knowledge in the field and presents new data, with 81 chapters and 105 authors (Oxford University Press, in production).

   Astrobiology Roadmap Objectives:

   • Objective 4: Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.
   • Objective 4: Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.
   • Objective 4: Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.

   Project Progress

   Our database TimeTree (www.timetree.org) was released in 2006 it presents divergence times of organisms from the published literature (timetrees are phylogenies scaled to time). The initial development of the database was supported by a grant from NSF. Astrobiologists and others are interested in knowing if there is a consensus in the field regarding a specific divergence time, the range of times proposed, the robustness of a given time estimate, and the researchers working on specific divergence times for particular groups of species. However, there are ~3,000 publications presenting divergence times and the data (timetrees) are multidimensional and hierarchical, requiring a sophisticated tree-traversing knowledgebase. During the past year we identified and coded 400 new studies for addition to TimeTree.

   The PI (Hedges) and collaborator Sudhir Kumar (ASU) were both on sabbatical last year and spent most of that time working on and contributing to a book, The Timetree of Life (Hedges and Kumar, Eds.), which is now in production at Oxford University Press. It has 81 chapters and 105 authors (480 p.) and will be released in early 2009. It summarizes the current state of knowledge in the field, across all groups of organisms down to the family level. Each chapter is authored by one or more experts on the specific group, and timetrees are presented, and thus it is essentially an encyclopedia of the tree of life--the first of its kind. It will be a reference work for biologists and scientists in other fields, including astrobiologists.

Publications

Battistuzzi, F.U. & Hedges, S.B.  (2009).  Archaebacteria.  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Battistuzzi, F.U. & Hedges, S.B.  (2009).  Eubacteria.  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Bhattacharya, D., Yoon, H.S., Hedges, S.B. & Hackett, J.D.  (2009).  Eukaryotes (Eukaryota).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Blair, J.E.  (2009).  Animals (Metazoa).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Blair, J.E.  (2009).  Fungi.  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Hedges, S.B.  (2008).  At the lower limit of size in snakes: two new species of threadsnakes (Squamata: Leptotyphlopidae: Leptotyphlops) from the Lesser Antilles.  Zootaxa, 1841:1-30.

Hedges, S.B.  (2009).  Vertebrate (Vertebrata).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Unknown type: Edited Book (28)

Hedges, S.B. & Kumar, S.  (2009).  Discovering the timetree of life.  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Hedges, S.B. & Vidal, N.  (2009).  Lizards, snakes, and amphisbaenians (Squamata).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Heinicke, M.P., Naylor, G.P. & Hedges, S.B.  (2009).  Cartilaginous fishes (Chondrichthyes).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Heinicke, M.P., Sander, J.M. & Hedges, S.B.  (2009).  Lungfishes (Dipnoi).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.

Vidal, N., Azvolinsky, A., Cruaud, C. & Hedges, S.B.  (2008).  Origin of tropical American burrowing reptiles by transatlantic rafting.  Biology Letters, 4:115-118.

Vidal, N., Rage, J.-C., Couloux, A. & Hedges, S.B.  (2009).  Snakes (Serpentes).  In: S.B. Hedges & S. Kumar (Eds.).  The timetree of life (pp. 000-000).  New York: Oxford University Press.