**NASA Astrobiology Institute**

**Evolutionary Genomics Focus Group**

**Proposal for Renewal**

Submitted to the ***NAI Executive Council***

AMES Research Center, California

28 March 2004

by

Co-Chairs S. Blair Hedges (Penn State; <sbh1@psu.edu>), and

James A. Lake (UCLA; <lake@mbi.ucla.edu>)

**Contents**

> 1\. Background 2
>
> 1.1. Objective 2
>
> 1.2. Relationship to NASA Astrobiology Roadmap 2
>
> 1.3. Participants 2
>
> 2\. Progress 2
>
> 2.1. Workshops 2
>
> 2.2. Research 3
>
> 2.3. Selected publications 3
>
> 2.4. Web site 4
>
> 3\. Proposal for Continuation 4
>
> 3.1. Overview 4
>
> 3.2. Participants 5
>
> 3.3. Workshops 5
>
> 3.4. Research 5
>
> 3.5. Database activities 6

**1. Background**

**1.1. Objective**

This proposal is for renewal of the *Evolutionary Genomics Focus Group*
for three years. The focus group serves as a forum for discussions and
collaboration among researchers with similar interests, through
workshops, videoconferences, and breakout sessions at annual meetings.
During the renewal period, we will hold three workshops focused on
specific research problems or themes of current interest. National and
international leaders in the research area will be invited to
participate. Arrangements will be made for publication of the workshop
proceedings in an astrobiological journal. New research initiatives and
database activities will be fostered through focus group activities.

**1.2. Relationship to the NASA Astrobiology Roadmap**

Genomes provide a record of the history of life. Therefore, evolutionary
analysis of genomes is fundamental to understanding that history and how
life affected the biosphere. This is **Goal 4** of the NASA Astrobiology
Roadmap (*Earth's early biosphere and its environment*). Other relevant
goals are **Goal 5** (*Understand the evolutionary mechanisms and
environmental limits of life*), **Goal 3** (*Origins of life*), and
**Goal 7** (*Signatures of life*). (See
<http://astrobiology.arc.nasa.gov/roadmap/>).

**1.3. Participants**

Steven A. Benner (U. Florida)

Jack D. Farmer (Arizona State U.)

James R. Garey (U. South Florida)

Eric A. Gaucher (U. Florida)

J. Peter Gogarten (U. Connecticut)

S. Blair Hedges (Penn State)

Christopher H. House (Penn State)

David K. Jacobs (UCLA)

Joseph L. Kirschvink (Caltech)

Sudhir Kumar (Arizona State U.)

James A. Lake (UCLA)

Charles R. Marshall (Harvard)

Monica Riley (Marine Biological Laboratory)

Lynn J. Rothschild (Ames Research Center)

Bruce N. Runnegar (UCLA)

Mitchell L. Sogin (Marine Biological Laboratory)

**2. Progress**

**2.1. Workshops**

Three workshops and symposia were held during the first three years of
the focus group. One workshop took place at UCLA (9--11 March, 2001),
hosted by co-chair Lake, and it focused on discussions of animal origins
and the influence of Neoproterozoic snowball Earth events and
relationship with the Cambrian Explosion of animal phyla in the fossil
record. It was attended by Jim Garey, Blair Hedges, David Jacobs, Jim
Lake, Charles Marshall, Bruce Runnegar; Rose Grymes represented NAI
Central. A focus group symposium (Special Session) was held at the NAI
General Meeting, 10--12 February 2003 at Arizona State University,
chaired by Lake and Hedges. Speakers included Herve Philippe (U.
Montreal), Beverly Green (Vancouver), Lake, Riley, Janet Siefert (Rice
U.), Staley (U. Washington), Hedges, and additional presentations by
graduate students and postdoctoral fellows (Eric Gaucher, Davide Pisani,
Jaime Blair, Maria Rivera, and Cody Nash). Another *Evolutionary
Genomics Focus Group* "special session" was held at the Gordon Research
Conference on the Origin of Life at Bates College, Maine (13--18 July,
2003), chaired by Hedges and Lake. In this case, the 19 speakers were
split into two sessions on separate days: "Origin and Evolution of
Eukaryotes" (Beverly Green, Peter Gogarten, Herve Philippe, Maria
Rivera, Jim Lake, Blair Hedges, Leonid Moroz, Lynn Rothschild, Hyman
Hartman) and "Tree of Life and Horizontal Gene Transfer" (Joe
Kirschvink, Yuri Wolf, Peter Gogarten, Herve Philippe, Richard
Greenblat, Jim Lake, Eugene Koonin, Joshua Rest, Blair Hedges, and Ford
Doolittle).

**2.2. Research**

Most members of the *Evolutionary Genomics Focus Group*, during the
initial three years, were also members of an NAI Lead Team. Some members
of the focus group (Benner, Lake, Jacobs, Riley, Hedges, Marshall)
received augmentation funding through their lead teams during that
period as a result of a joint proposal. The augmentation funding
supported additional personnel to assist with analyses in three areas of
focus: (i) Phylogeny and Timescale, (ii) Gene Function, and (iii)
Horizontal Transfer.

The NAI support proved to be critical for making the discoveries that
were made (see publications below). For example, proteins that existed 3
billion years ago were "resurrected" in the lab and shown to support a
model for early Earth environment (Gaucher et al., 2003). In another
example, major divergences within fungi were estimated to have occurred
deep in the Precambrian (Heckman et al., 2001). Also, a new mechanism
for protein synthesis was proposed that suggests how the current
RNA/Protein world may have started from an RNA world (Simonson and Lake,
2002).

In some cases there were face-to-face meetings, videoconferences, and
direct collaborations, and in other cases the research progressed more
independently. In all cases the resulting research benefited by focus
group activities that facilitated professional interactions and sharing
of ideas. Some of the resulting publications are listed below. A
complete list of publications by focus group members can be found on the
web site ([www.evogenomics.org](http://www.evogenomics.org/)).

**2.3. Selected Publications**

[Benner SA]{.underline}, Caraco MD, Thomson JM, Gaucher EA. 2002.
Planetary Biology: Combining the paleontological, geological, and
molecular records of the history and function of life on Earth.
***Science*** 296:864--868*.*

Fukami-Kobayashi K, Schreiber DR, [Benner SA.]{.underline} 2002.
Detecting compensatory covariation signals in protein evolution using
reconstructed ancestral sequences. ***J Mol Biol*** 319:729-743.  

Gaucher EA, Miyamoto MM, [Benner SA.]{.underline} 2001.
Function-structure analysis of proteins using covarion-based
evolutionary approaches. Elongation factors. ***Proc. Natl. Acad. Sci.
USA*** 98:548--552.

Gaucher EA, Thomson JM, Burgan MF, Benner SA. 2003. Inferring the
palaeoenvironment of ancient bacteria on the basis of resurrected
proteins. ***Nature*** 425:285--288.

Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, [Hedges
SB.]{.underline} 2001. Molecular evidence for the early colonization of
land by fungi and plants. ***Science*** 293:1129--1133.

[Hedges SB]{.underline}. 2002. The origin and evolution of model
organisms. ***Nat Rev Genet*** 3:838--49. 

[Hedges SB]{.underline}, Chen H, Kumar S, Wang DY-C, Thompson AS,
Watanabe H. 2001. A genomic timescale for the origin of eukaryotes.
***BMC Evolutionary Biology*** 1(4):1--10.

[Hedges SB]{.underline}, Kumar S. 2002.Vertebrate genomes compared.
***Science*** 297:1283--5.

[Hedges SB]{.underline}, Kumar S. 2003. Genomic clocks and evolutionary
timescales. ***Trends Genet*** 19:200-206.

[Hedges SB.]{.underline}, Blair JE, Venturi ML, Shoe JL. 2004. A
molecular timescale of eukaryote evolution and the rise of complex
multicellular life. ***BMC Evol. Biol.*** 4(2):1--9.

[Jacobs DK]{.underline}, Gates RD. 2003. Developmental genes and the
reconstruction of metazoan evolution. Implications of evolutionary loss,
limits on inference of ancestry and type 2 errors. **Integrative Comp.
Biol.** 43:11--18.

Jain R, Rivera MC, Moore JE, [Lake JA]{.underline}. 2003. Horizontal
gene transfer accelerates genome innovation and evolution. ***Mol Biol
Evol*** 20:1598--1602.

Liang P, and [Riley M]{.underline}. 2001. A comparative genomics
approach for studying ancestral proteins and evolution. ***Advances in
Applied Microbiology***, 50: 39--72.

Moore JE, [Lake JA]{.underline}. 2003. Gene structure prediction in
syntenic DNA segments. ***Nucleic Acids Res*** 31:7271--7279.

Pisani D, Poling LL, Lyons-Weiler M, [Hedges SB]{.underline}. 2004. The
colonization of land by animals: molecular phylogeny and divergence
times among arthropods. ***BMC Biology*** 2(1):1--10.

Simonson AB, [Lake JA.]{.underline} 2002. The Transorientation
hypothesis for codon recognition during protein synthesis. ***Nature***
416: 281--285.

Tavare S, [Marshall CR]{.underline}, Will O, Soligo C, Martin RD. 2002.
Using the fossil record to estimate the age of the last common ancestor
of extant primates. ***Nature ***416:726--729.

**2.4. Web site** ([www.evogenomics.org](http://www.evogenomics.org/))

Our web site describes the function of the *Evolutionary Genomics Focus
Group*, members and contact information, and research undertaken by the
members. Publications of the focus group members since creation of NAI
in 1998 are listed by year, and electronic copies of the papers are
linked to the citations. One web page presents links to computational
tools. Undergraduate, graduate, and postdoctoral research and
educational opportunities are presented on separate pages. Finally, a
calendar page lists links to upcoming meetings and events of interest to
astrobiologists and members of the focus group and evolutionary genomics
community.

**3. Proposal for Continuation**

**3.1. Overview**

We wish to renew the *Evolutionary Genomics Focus Group* for three
additional years. We propose to hold three workshops during the renewal
period in addition to other meetings of participants and research
activities. The workshops will differ from those in the past in being
more structured, in focusing on specific research problems of wide
interest in the field, and involving national and international leaders
(NAI and non-NAI members). Additionally, the proceedings of the
workshops will be published in a timely manner in an astrobiological
journal. Finally, an explicit goal of the workshops and other meetings
of focus group participants will be to identify specific research areas
of astrobiological relevance that might lead to collaborations and new
NAI-supported research initiatives.

**3.2. Participants and organization**

If renewed, The *Evolutionary Genomics Focus Group* will meet informally
during AbSciCon 2004 to discuss future workshops, new initiatives,
potential collaborations, and identify new focus group members. A
videoconference may be scheduled as a follow-up to continue discussions
after the conference.

**3.3. Workshops**

At least three workshops will be organized and held during the renewal
period. Each workshop will be hosted by a different member (or members)
of the *Evolutionary Genomics Focus Group*, although the research focus
and participant list will be determined by discussions among members of
the focus group and both co-chairs. The co-chairs will then submit the
workshop proposal and participant list to NAI Central for approval. The
themes of each workshop will be timely and pertain to key issues in
evolutionary genomics, with relevance to astrobiology. Examples of some
possible themes are: (i) molecular phylogenies and the early history of
life, (ii) prokaryote genomes and phylogeny, (iii) molecular evidence
for the origin of eukaryotes, (iv) a timescale of Precambrian evolution,
(v) evolutionary genomics and the Cambrian explosion, and (vi)
horizontal gene transfers in early evolution.

For example, the workshop on a "Timescale of Precambrian evolution"
might involve 5--10 researchers who use and/or develop molecular clock
methodology and 5--10 paleontologists and experts on biomarkers who
contribute temporal information and/or calibrations for molecular
clocks. Graduate students also would be encouraged to attend.

It is anticipated that at least one-half of workshop participants will
be members of the focus group and/or NAI. However, non-NAI participants
will be invited, including those from other countries. Each workshop
host will ensure that participants submit manuscripts of their
presentations soon after the workshop. Arrangements will be made with an
astrobiology journal (e.g., *Astrobiology*, *International Journal of
Astrobiology*), or a related journal (e.g., *Geobiology*,
*Gene-Evolutionary Genomics*) to publish the proceedings of the
workshop.

**3.4. Research**

At this time, we have no specific proposals for research by the
*Evolutionary Genomics Focus Group*. We expect that such proposals will
emerge from focus group membership during the renewal period, as they
did during the initial period. The co-chairs will facilitate development
of those proposals by helping to arrange for meetings, breakout
sessions, and videoconferences as needed. In some cases, the focus group
may serve only as a forum for discussion of a research topic later
submitted to another agency as a grant proposal. In other cases, partial
funding or co-funding may be requested from NAI.

**3.5. Database activities**

Several members of the focus group are involved in developing and/or
curating internet databases of interest to the astrobiology community.
The Marine Biological Laboratory (Mitch Sogin, Monica Riley) hosts
several public databases, including GenProtEC
(<http://genprotec.mbl.edu/>) which presents functional data for
proteins of the eubacterium *E. coli*, and Microscope
(<http://microscope.mbl.edu/reflections/baypaul/microscope/general/page_01.htm>),
which contains images, classification schemes, and educational resources
pertaining to microbes. The Paleobiology Database
(http://www.paleodb.org/) is being developed by a consortium of
paleontologists, including focus group member Charles Marshall (Harvard)
and includes collection-based occurrence and taxonomic data for marine
and terrestrial animals and plants. Sudhir Kumar and Blair Hedges are
developing (with support from NSF) a database of molecular and fossil
times of divergence, to be released later this year. The initial focus
of that database has been on vertebrates, where information is most
extensive, but other organisms are being included in future development
of the database.

We propose to continue development of databases of interest to the
astrobiological community. The importance of these activities was
highlighted at the Executive Council Retreat in Wyoming (2003), where
members of several NAI focus groups met and discussed the need to
organize and develop database activities within NAI. Ideas were
presented that proposed collaborations, especially between Evolutionary
Genomics and Mission to Early Earth. One of the co-chairs of this focus
group (Hedges) is part of the NAI database "consortium" that resulted
from those discussions and will help to bring together interested
parties.