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The 4th Deep Time Meeting and Workshop
February 22-23, 2003

University of Florida
Gainesville, Florida


Meeting agenda

The 4th Deep Time meeting participants

Student Travel Awards

Dr. Vincent Savolainen's lecture notes and links to other speakers' homes

Meeting summary

Images from the workshop

Meeting announcement


Meeting Agenda
Saturday, February 22 (8am - 5pm): Workshop on Estimating Divergence Times

Morning: Seminars by invited speakers (Frazier-Rogers Hall Conference Room 122, next to Dickinson Hall-FLMNH)

8:00-8:20am
Introduction to Deep Time Project and student travel awardees – Doug Soltis
Logistics: lunch, dinner, reimbursement, etc. – Pam Soltis
8:20-9:10am
PHYLOGENETIC DATING WITH CONFIDENCE INTERVALS USING MEAN PATH-LENGTHS
Kare Bremer
Department of Systematic Botany
Evolutionary Biology Centre
Uppsala University, Sweden
9:10-10:00am
DATING PHYLOGENIES: NON-PARAMETRIC RATE SMOOTHING USING
TREEEDIT AND PAUP
Vincent Savolainen
Jodrell Laboratory, Molecular Systematics Section
Royal Botanic Gardens, Kew, UK
10:00-10:20am
Coffee Break
10:20-11:10am
IS ESTIMATING DIVERGENCE TIMES FROM SEQUENCE DATA IMPOSSIBLE, OR JUST REALLY HARD?
Mike Sanderson
Section of Evolution and Ecology
University of California, Davis
11:10-12:00
INTRODUCTION TO BAYESIAN DIVERGENCE TIME ESTIMATION
Jeff Thorne
Department of Statistics
North Carolina State University
12:00-1:00pm
Lunch break (Box lunch from Heavenly Ham).

Afternoon: Hands-on computer workshop (Carr Hall 611)

1:00-2:40pm
Vincent Savolainen
2:40-3:00pm
Coffee Break
3:00-3:50pm
Jeff Thorne
3:50-4:40pm
Discussion
6:00pm
Group dinner in the Museum lobby (BBQ)

Sunday, February 23 (8:30am - 5pm): Deep Time Reports, Discussion, and Presentations (Frazier-Rogers Hall Conference Room 122)

Morning: Reports and discussion

8:30-10:00am Reports
Student Travel and Training Awards and Advertisement of post-doc position – Pam
Plan for Mobile meeting (short business meeting and dinner) – Pam
Symposium proposal announcement – Pat
Report from Pam on databasing – Pam
Update on web site and Fossil Database – Hallie Sims and Hongshan Wang
Goals for the next 6 months and next year – Doug
10:00-10:30am
coffee break
10:30-12:00
Discussion, Goals for next 6 months and next year
12:00-1:00pm
Lunch break (Box lunch from Heavenly Ham)

Afternoon: Presentations

1:00-1:40pm
Paul Manos

1. AN UPDATE ON INTEGRATING FOSSIL AND LIVING JUGLANDACEAE
2. DEEP AND NAGGING ISSUES WITH MODERN PLATANACEAE
1:40-2:00pm
(Jenny) Q.-Y. Xiang, Tae-Kun Seo, and Jeffery Thorne

INTERCONTINENTAL DISJUNCT BIOGEOGRAPHIC PATTERNS IN CORNUS (CORNACEAE): DIVERGENCE TIMES AND EVOLUTIONARY RATES
2:00-2:20pm
James A. Doyle

INTEGRATING FOSSILS INTO PHYLOGENIES OF CHLORANTHACEAE - AN UPDATE
2:20-2:40pm
Kathleen A. Kron

SUMMARY ON THE RESEARCH PLAN FOR ERICALES
2:40-3:10pm
Coffee break
3:10-3:30pm
David Springate

CORRELATION OF MOLECULAR AND MORPHOLOGICAL RATES IN PHYLOGENIES
3:30-3:50pm
Hongzhi Kong

DIVERSIFICATION AND EVOLUTION OF BISEXUAL FLOWERS IN THE CHLORANTHACEAE
3:50pm
Final wrap-up – David Dilcher
6:00pm
Group dinner at Steve’s Café Americain, 12 West University Ave

ABSTRACTS FOR PROJECT UPDATES

David Springate
Jodrell Laboratory, Molecular Systematics Section
Royal Botanic Gardens, Kew
Richmond Surrey TW9 3DS London UK
CORRELATION OF MOLECULAR AND MORPHOLOGICAL RATES IN PHYLOGENIES

James A. Doyle
Section of Evolution and Ecology
University of California, Davis, CA 95616
INTEGRATING FOSSILS INTO PHYLOGENIES OF CHLORANTHACEAE - AN UPDATE
ABSTRACT: A morphological cladistic analysis of living and fossil Chloranthaceae (Eklund, Doyle & Herendeen, in press and in prep.) illustrates problems of integrating fossils into phylogenies of modern groups, effects of fossils on topology and scenarios for character evolution, and the use of fossils in calibrating molecular dating studies. Improved morphological data give trees more consistent with molecular phylogenies than those in previous studies, with Hedyosmum basal and Ascarina sister to Sarcandra and Chloranthus, and with some of the same clades in Hedyosmum and Chloranthus. Cenomanian Couperites fruits with anatropous ovules and Clavatipollenites pollen, which has been compared with Ascarina but is actually plesiomorphic for the family, may represent either an extinct line within Chloranthaceae or an extinct sister group. Barremian-Aptian fruits attach near or below the base of crown-group Hedyosmum, providing a minimum age for the family. The arrangement of living species of Sarcandra and Chloranthus suggests that the bizarre trilobed androecium of Chloranthus arose by subdivision of a single stamen, but Late Cretaceous androecia with free stamen lobes attach below the crown group, favoring instead the hypothesis that the trilobed androecium arose by fusion of three stamens. The basal position of the fossils is indirectly supported by a molecular dating analysis of Zhang & Renner (in press), which indicates that the crown group of Chloranthus is much younger than the Cretaceous (Miocene). Addition of the fossils also causes a shift in ingroup topology toward that found by Kong et al. (2002) with molecular data, suggesting that morphological cladistic analyses that incorporate fossil taxa may perform better than morphological analyses of Recent taxa alone.

Hongzhi Kong
Department of Biology and Life Science Consortium
Penn State University
University Park, PA 16802, USA
DIVERSIFICATION AND EVOLUTION OF BISEXUAL FLOWERS IN THE CHLORANTHACEAE

Jenny Xiang
Intercontinental Disjunct Biogeographic Patterns in Cornus (Cornaceae): Divergence Times and Evolutionary Rates.
(Jenny) Q.-Y. Xiang*1, Tae-Kun Seo2, and Jeffery Thorne2
1 Department of Botany, North Carolina State University
2 Department of Statistics, North Carolina State University
ABSTRACT: The dogwood genus Cornus consists of approximately 55 species widely distributed in the Northern Hemisphere, with one species extending to South America and one species isolated in tropical Africa. The genus traditionally figures several historically important biogeographic patterns, with the Pagoda dogwoods (Subg. Mesomora) exhibiting an eastern Asian- eastern North American disjunction, the Big-bracted dogwoods (including Subg. Cynoxylon and Subg. Syncarpea) displaying an eastern Asia, eastern and western North American disjunction, and the Cornelian cherries (Subg. Cornus, Subg. Sinocornus, Subg.Afrocrania) having an eastern Asian, western North American, European, and African disjunction. With the discovery of a new intercontinental disjunct pattern displayed by Cornus oblonga and C. peruviana in eastern Asia and South America by our recent phylogenetic study, there are a total of four lineages of the genus exhibiting discontinuous distributions, each representing a different biogeographic pattern. To understand the origin and evolution of these biogeographic patterns, we estimated divergence times of the disjunct taxa using DNA sequence data from three genes (26S rDNA, rbcL, and matK) on a phylogenetic framework. Divergence times and evolutionary rates were inferred via a Bayesian approach
that combines fossil and molecular sequence data but that does not assume a molecular clock. The divergence times and evolutionary rates will be compared between sister disjunct taxa to determine if a general relationship among age, rate, and area of endemism exists.

Paul Manos
Department of Botany
Duke University
Durham, NC 27708-0338
1. AN UPDATE ON INTEGRATING FOSSIL AND LIVING JUGLANDACEAE
2. DEEP AND NAGGING ISSUES WITH MODERN PLATANACEAE


The 4th Deep Time meeting participants

James Albert, University of Florida
Monica Arakaki, University of Florida
Charles Bell, Yale University
Mario Blanco, University of Florida
Kare Bremer, Uppsala University, Sweden
Sam Brockington, University of Florida
Julie Broughton, University of California, Santa Barbara
Matyas Buzgo, University of Florida
Sarah Corbett, University of Florida
Charles Davis, University of Michigan
David Dilcher, University of Florida
James Doyle, University of California, Davis
Matt Gitzendanner, University of Florida
Mike Heaney, University of Florida
Pat Heredeen, The George Washington University
Khidir Hilu, Virginia Tech
Sara Hoot, University of Wisconsin-Milwaukee
Walter Judd, University of Florida
Sangtae Kim, University of Florida
Lisa Kirkendale, University of Florida
Hongzhi Kong, Penn State University
Kathleen Kron, Wake Forest University
Jiri Kvacek, National Museum, Czech Republic
Heather Loring, University of Florida
Terry Lott, University of Florida
Yi-bo Luo, Chinese Academy of Sciences, China
Susana Magallon, Universidad Nacional Autónoma de México
Maria Malay, University of Florida
Steve Manchester, University of Florida
Paul Manos, Duke University
Hilary McManus, University of Connecticut
Elvia Melendez-Ackerman, University of Florida
Christopher Meyer, University of Florida
Roger Moore, University of Tennessee Martin
Brian Moore, Yale University
Ashley Morris, University of Florida
Michael Nowak, Oklahoma University
Sang-Hun Oh, Duke University
Darin Penneys, University of Florida
Mihai Popa, University of Bucharest, Romania
Ann Powell, Wake Forest University
Mike Sanderson University of California, Davis
Vincent Savolainen, Royal Botanic Gardens, Kew, UK
Jurg Schonenberger, University of Wisconsin-Madison
Hallie Sims, National Museum of Natural History
Pam Soltis, Florida Museum of Natural History
Doug Soltis, University of Florida
David Springate, Royal Botanic Gardens, Kew, UK
Jennifer Tate, University of Florida
Jeff Thorne, North Carolina State University
Maria von Balthazar, University of Wisconsin-Madison
Hongshan Wang, Florida Museum of Natural History
Norris Williams, University of Florida
Richard Winkworth, Yale University
Jenny Xiang, North Carolina State University
Mi-Jeong Yoo, University of Florida
Wenheng Zhang, North Carolina State University


Deep Time Gainesville meeting (2003) student travel award

Chuck Bell, Yale Univ.
Julie Broughton, UC-Santa Barbara
Yi-bo Luo, Chinese Acad of Sciences
Hilary McManus, Univ. of Connecticut
Brian Moore, Yale Univ.
Michael Nowak, Oklahoma
Sang-Hun Oh, Duke
Mihai Popa, Romania
Ann Powell, Wake Forest
David Springate, Kew
Richard Winkworth, Yale
Wenheng Zhang, NC State


Dr. Vincent Savolainen's lecture notes (click to download in pdf format)

Pratical file (txt)

Questions with these two files? Please contact Dr. Vincent Savolainen.

Kåre Bremer

Michael J. Sanderson

Jeffrey L. Thorne


Meeting summary

Overview

The meeting started with a brief introduction of the Deep Time project to new participants by Doug Soltis. The total number of Deep Time participants since the project started in August 2001 is 94. Fifty-seven participants representing 24 institutions from 7 countries attended the 4th meeting (See the list of 4th meeting participants).

The first day was focused on an educational workshop emphasizing methods of phylogenetic analysis, integrating fossils into molecular phylogenetic analysis, molecular dating. Four invited speakers spent Saturday morning on lectures dealt with methods of dating divergences and the afternoon with hands-on computer workshops. Five research groups (see presentation section) presented the results of their efforts to integrate fossil and modern taxa into a single phylogenetic tree. At present, there are at least 11 active research groups have been sponsored or assisted by Deep Time: Basal Angiosperms; Betulaceae; Chloranthaceae; Cornales; Ericales; Fagales; Hamamelidaceae; Juglandaceae; Legumes; Palms, Platanaceae.

Deep Time will host a symposium dealing with Deep Time issues (dating, integrating fossils) during Botany 2003 at Mobile, Alabama. The Deep Time web site is growing and there is lots of useful information available there, still with much more to come. Deep Time is working with Hallie Sims (who is representing the Paleobiology Database) to consider folding our Deep Time database into their existing database.

Lectures

The first lecture on “Phylogenetic Dating With Confidence Intervals Using Mean Path-Lengths” was given by Kare Bremer from the Uppsala University, Sweden. The second lecture by Vincent Savolainen from the Royal Botanic Gardens, Kew, UK, was focused on “Dating Phylogenies: Non-Parametric Rate Smoothing Using Treeedit and Paup”. After coffer break, Mike Saderson from the University of California, Davis, gave a lecture on “Is Estimating Divergence Times From Sequence Data Impossible, Or Just Really Hard?” followed by the lecture on “Introduction To Bayesian Divergence Time Estimation”, given by Jeff Thorne from North Carolina State University. The afternoon session was moved to the computer lab for the lecturers to show meeting participants on how to run programs such as TreeEdit, Paup, PATH, McRobot, etc.

Reports and Discussions

Student Travel and Training Awards: Pam Soltis reported that a total of 13 student/postdoc travel grants (up to $1000 each) have been awarded to support students to travel to this Deep Time meeting/workshop.

Deep Time recommended APG II, proposed by the Angiosperm Phylogeny Working Group, to the Paleobiology Data Base for a classification scheme for Angiosperms. Copyright issues concerning images were also discussed during the meeting. Deep Time will draft form letters to ask for copyright to put images of published fossils on the Deep Time database. Difficulties on this issue were also discussed. Potential supplementary grant for hiring data enters was proposed.

“Help Desk” – a web page with phylogenetic experts’ names and email addresses was proposed by meeting participants.

Presentations

Six presentations (see meeting agenda and for the tiles and abstracts) were offered on the updates of current research projects on Juglandaceae and Platanaceae (Paul Manos), Cornales (Jenny Xiang), Chloranthaceae (James Doyle and Hongzhi Kong), Ericales (Kathleen Kron), and “Correlation Of Molecular And Morphological Rates In Phylogenies (David Springate).”

Goals for the next 6 months

Deep Time will host a symposium dealing with Deep Time issues (dating, integrating fossils) during Botany 2003 at Mobile, Alabama. A functional database (or a prototype) should be available before the next Deep Time meeting. PDB (Paleobiology Data Base) will set up a Deep Time working group and the Taxon Pages (with images, taxonomic and reference information, etc) proposed by Deep Time group will possibly be up by August 2003.


Dr. Jeff Thorne lecturing on “Introduction To Bayesian Divergence Time Estimation”.

Jeff Thorne

Lecture 1

Lecture 2

* Images courtesy of Jenny Xiang


Meeting announcement


The 4th Deep Time meeting will be held at the University of Florida, Gainesville, Florida on Feb. 22nd (Saturday) and 23rd (Sunday), 2003. This workshop and meeting will focus on methods for estimating divergence times from molecular data.

Travel Support

  • The Deep Time RCN will provide travel support to faculty participants attending the meeting, on a reimbursement basis requiring original receipts.
  • Students and Post-docs: The Deep Time RCN will offer travel awards of up to $1000 each (again on a reimbursement basis with original receipts) to attend the 4th meeting/workshop at Gainesville, Florida.
  • Undergraduates, graduate students, and postdocs are eligible to apply.
    To apply for student travel and research awards, please send 1-page narrative describing the proposed activity (including how it will benefit your research), CV, and a letter from your advisor to Pam Soltis psoltis@flmnh.ufl.edu by February 1, 2003.

Program (proposed)

  • Saturday, February 22 (8am - 5pm): Workshop on Estimating Divergence Times.
    • Morning: Seminars by invited speakers (Frazier-Rogers Hall Conference Room 122; (next to Dickinson Hall-Florida Museum of Natural History). Speakers: Kare Bremer, Mike Sanderson, Vincent Savolainen, Jeff Thorne.
    • Afternoon: Hands-on computer workshop (Carr Hall 611); limited to ~20-respond to Hongshan soon!
    • Group dinner.
  • Sunday, February 23 (8am - 5pm): Deep Time Presentations, Discussions, and Business Meeting.
    • Morning: Brief presentations and updates.
    • Afternoon: reports, discussion, plans.
    • Group dinner.

Presentations

If you are interested in presenting a 15-minute talk on research relevant to the Deep Time goals (see web site), please let Hongshan Wang know by Feb. 10. Please also indicate whether you will need overhead projector, slide projector, or LCD projector. If the latter, will you use your own computer or need to have one provided? Also, please indicate whether you will use a Mac or PC.

Logistics

  • Housing:
    We recommend three hotels: the Reitz Union Hotel, University Centre Hotel, and Rush Lake Motel. The Reitz Union Hotel is 5-10 minutes walking distance to Frazier-Rogers Hall and Carr Hall, where our meeting/workshop will be held. The University Centre Hotel is approximately 15 minutes away. Rush Lake Motel (with lower rates) is about 20 minutes walking distance to Frazier-Rogers Hall and Carr Hall. Advance reservations are strongly recommended! Please call hotel directly to make your reservations. Rooms have been block-booked at the Rush Lake Motel and University Centre Hotel for the duration of the meeting. When making reservations, please refer to the Deep Time for block rates (see below).

    Reitz Union Hotel:
    Phone: 352-392-2151
    Fax: (352) 846.2199
    E-mail: ruhotel@union.ufl.edu

    Rates:
    Standard Room 1 Queen Bed or 2 Double Beds $53 (One-person) and $58 (Two).
    Deluxe Room 2 Queen Beds $63 (One-person) $68 (Two).
    · Additional persons $5 each; no charge for children under 12 years of age.
    · Continental breakfast.

    University Centre Hotel:
    Phone: 1-800-824-5637 or 352-371-3333
    Fax: 352-371-3712

    Rates: $62 per night plus tax for a room with two double-sized beds
    $62 plus tax for a room with one king-sized bed.
    Complimentary shuttle service to Gainesville Regional Airport and breakfast.

    Rush Lake Motel:
    Phone: 352-373-5000
    Toll-Free: 1-888-787-4525

    Rates: $38 per night plus tax for one bed for one person.
    $42 plus tax for a room with two double-sized beds for two persons, $4 for each additional person with a maximum of four.
    Restaurant for breakfast nearby (not included).

    Transportation: As you begin to think of travel plans to Gainesville, please check ticket prices into Orlando and Jacksonville, as well as the price into Gainesville. Prices are usually much cheaper to the former two cities. The Orlando Airport is about a 2-hour drive from Gainesville; Jacksonville Airport is about 1 hour 45 minutes. We can arrange rental cars through Avis at state-government rates, if needed. Alternatively, shuttle service is available, but it is expensive ($65+ each way) and requires advance booking. Taxi fare from the Gainesville Regional Airport to the three hotels is approximately $10-15; note that the University Centre has complimentary shuttle service to Gainesville Airport. We will help coordinate car rentals and pick-up when we have everyone's flight itinerary. Please send Hongshan (hwang@flmnh.ufl.edu) your travel schedule with the following information: arrival/departure airport, date and time, flight number, and if car rental or pickup is needed.

    Driving directions and map are available at our website: http://www.flmnh.ufl.edu/deeptime/drivingdirections2003.html

Student Training Awards

The Deep Time RCN will also provide 5 awards of $2,000 each for student (undergraduate, graduate, and post-doc) research training through August, 2003. These awards will support extended research in labs of other Deep Time participants, participation in phylogenetics training courses, etc. Awards will apply toward travel and living expenses. Application details available at http://www.flmnh.ufl.edu/deeptime.

*Click here to print this announcement in pdf format.


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