Sarah Mathews Lead PI, Jianhua Li CoPI, Harvard University

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• Sarah Mathews (Lead PI), Jianhua Li (Co-PI),
  Harvard University
• Reed S. Beaman (PI), Nico Cellinese (Co-PI),
  University of Florida
• Christopher S. Campbell (PI), University of Maine
• Richard C. Cronn (Collaborator), USDA Forest
  Service
• Sean W. Graham (Co-PI), University of British
  Columbia
• Stefanie M. Ickert-Bond (PI), University of
  Alaska
• Dean G. Kelch (PI), University of
  California-Berkeley California State Herbarium
• Aaron I. Liston (PI), Oregon State University
• Linda A. Raubeson (PI), Central Washington
  University
• Gar W. Rothwell (PI), Gene Mapes (Co-PI), Ohio
  University
• Andrea E. Schwarzbach (PI), University of
  Texas-Brownsville
• Dennis W. Stevenson (PI), Damon Little
  (Collaborator), New York Botanical Garden
• Ruth A. Stockey (Co-PI), University of Alberta

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Project overview, 7 March 2008

• Rationale
• Approach
• Progress report

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Extant land plants
charophytes
angiosperms
liverworts
lycophytes
hornworts
Gnetales
conifers
mosses
Ginkgo
cycads
ferns
1,200
100
8,500
700
90
1
300
300,000
12,000
10,000
seed plants
vascular plants
land plants
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Problems in the inference of seed plant phylogeny

• extinctions
• saturation at nucleotide sides
• extreme rate variation
• conflicting signal within single loci
• incongruent trees from single locus data sets
• error and bias in phylogenetic reconstruction

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80 of seed plant lines are extinct
Burleigh and Mathews 2004. Amer J Bot 91
1599-1613

• Doyle, J. A. 1998. Annu Rev Ecol Syst 9 448-462.

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Problems in the inference of seed plant phylogeny

• extinctions
• saturation at many nucleotide sides
• extreme rate variation among sites
• heterotachy
• conflicting signal within single loci
• incongruent trees from single locus data sets
• error and bias in phylogenetic reconstruction

Gnetales
Welwitschia mirabilis (1 species)
Gnetum (40 species)
Ephedra (50 species)
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THE GNEPINE HYPOTHESIS The most radical,
shocking, and controversial placement of any
group of plants concerns the Gnetales - JD
Palmer, DE Soltis, MW Chase 2004
Burleigh and Mathews 2004 Amer J Bot 91 1599-1613
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Gnepine Gnetales-sister
Burleigh and Mathews 2007a. Int J Plant Sci 168
125-135.
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Among-Locus Variation in the Inference of Seed
Plant Phylogeny
Gnetifer
Gnepine
Burleigh and Mathews 2007a. Int J Plant Sci 168
125-135.
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Gnepine vs Gnetales-sister
Gnepine vs Gnetifer (conifers monophyletic)
Burleigh and Mathews 2004. AJB 91 1599-1613
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Assessing Systematic Error in the Inference of
Seed Plant Phylogeny
Rates of erroneous reconstruction from parsimony
analysis of data simulated on a 12-locus data set
Burleigh and Mathews 2007b. Int J Plant Sci 168
111-124. See also Sanderson et al. 2000. Mol
Biol Evol 17 782-797.
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Our approach

• Gymnosperm AToL Research Objectives
• Assemble molecular matrices that represent every
  living species of gymnosperm (1070 species)
• - Previous molecular data sets had included
  few gymnosperms 10-69 species 10-33 genera out
  of 85
• 2. Assemble morphological matrices that include
  200 extant and 80 extinct gymnosperms
• - Substantially increase the number of extant
  taxa scored for morphological data

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Our approach, graphically
characters
taxa

• Characters from fossils (80 taxa, 250 char)
• Morphological characters from living taxa (200
  taxa, 250 char)
• Nucleotide data from 200 core taxa
• Nucleotide data from 870 additional taxa

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Or perhaps,
characters
taxa

• Characters from fossils (80 taxa, 250 char)
• Morphological characters from living taxa (200
  taxa, 250 char)
• Nucleotide data from 200 core taxa
• Nucleotide data from 870 additional taxa

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Expected outcomes

• Rigorous tests of current phylogenetic hypotheses
• Better resolution of tip phylogenies
• Implications
• Deeper understanding of the pattern of seed plant
  evolution
• Context in which to examine the origin of
  innovations that fueled their radiation (e.g.,
  seeds, flowers)

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Progress

• Draft of morphological matrix in circulation
• Sequencing of nuclear genes underway in all
  relevant labs
• Sampling lists, distributions, responsibility
  assignments entered into TOLKIN
• Pilot workshop held (outreach program)
• Pilot plastid genome sequencing effort nearly
  complete

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At the poster session, check out
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At the poster session, check out
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At the poster session, check out