The Botanical Review 64(1)
Interpreting Botanical Progress
January-March 1998

Phylogenetics and Character Evolution in the Grass Family (Poaceae): Simultaneous Analysis of
Morphological and Chloroplast DNA Restriction Site Character Sets


ROBERT J. SORENG 1
AND
JERROLD I. DAVIS

L.H. Bailey Hortorium
462 Mann Library
Cornell University
Ithaca, NY 14853


1 Present address:  Botany Department, National Museum of Natural History,
                    Smithsonian Institution, Washington, DC 20560-0001



   I. Abstract....................................................................  2
  II. Introduction................................................................  3
 III. Methods.....................................................................  7
      A. Taxon Sample.............................................................  7
      B. Chloroplast DNA Restriction Site Characters..............................  7
      C. Structural Characters.................................................... 11
      D. Data Analysis............................................................ 12
  IV. Results..................................................................... 14
      A. Colinearity of the Chloroplast Genomes................................... 14
      B. Characteristics of the Data Matrix....................................... 14
      C. Cladistic Analyses....................................................... 15
         1. Chloroplast DNA Restriction Site Data................................. 15
         2. Structural Character Data............................................. 20
         3. Simultaneous Analysis of Restriction Site and
              Structural Characters............................................... 21
         4. Topological Similarities among Unweighted Analyses.................... 25
         5. Incongruence among Unweighted Analyses................................ 31
         6. Implied Weighting..................................................... 32
   V. Discussion.................................................................. 34
      A. Scoring of Structural Characters and Use of Exemplar Taxa................ 34
      B. Analyses of Molecular Data Sets.......................................... 35
      C. Phylogenetic Structure of the Grasses.................................... 36
         1. Support for Groups Identified by the Present Analysis................. 36
         2. Comparison of Results of Simultaneous Analysis with Previous
              Classifications and Hypotheses of Phylogeny of the Grasses.......... 36
      D. Structural Character Evolution in the Grasses............................ 43
         1. Spikelets............................................................. 43
         2. Lodicules............................................................. 46
         3. Stamen Number......................................................... 47
         4. Stigmatic Branching................................................... 47
         5. Fruit Characteristics................................................. 48
        6. First Seedling Leaf.................................................... 49
        7. Cross-Venation......................................................... 50
        8. Microhairs............................................................. 50
        9. Arm Cells.............................................................. 51
       10. Fusoid Cells........................................................... 51
       11. Photosynthetic Pathway................................................. 51
       12. Chromosome Numbers..................................................... 52
     E. Synapomorphies of Various Groupings of Ehrhartoideae, Pooideae, 
          Brachyelytrum, and the PACC Clade....................................... 52
     F. Placement of Five Problematic Taxa within Pooideae........................ 53
     G. Taxonomic Conclusions..................................................... 54
     H. Breeding Systems in Grasses............................................... 55
        1. Evolution of Wind Pollination in Grasses............................... 55
        2. Evolution of Self-Incompatibility in Grasses........................... 56
     I. Biogeography.............................................................. 57
  VI. Acknowledgments............................................................. 59
 VII. Literature Cited............................................................ 59
VIII. Appendix 1:  Restriction Site Character Data................................ 67
  IX. Appendix 2:  Structural Characters and States............................... 74
   X. Appendix 3:  Structural Character Data...................................... 84

 
New Books Received................................................................ 89










 
I. Abstract

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character
sets, one representing variation in 364 mapped and cladistically informative restriction
sites from all regions of the chloroplast genome, the other representing variation in 42
informative "structural characters."  The structural character set includes morphological,
anatomical, chromosomal, and biochemical features, plus structural features of the
chloroplast genome.  The taxon sample comprises 75 exemplar taxa, including 72 
representatives of Poaceae and one representative of each of three related families
(Flagellariaceae, Restionaceae, and Joinvilleaceae); Flagellaria served as the out-
group for the purpose of cladogram rooting.  Among the grasses, 24 tribes and all
16 subfamilies of grasses recognized by various modern authors were sampled.  
Transformations of structural characters are mapped onto the phylogenetic hypotheses
generated by the analysis, and interpreted with respect to biogeography and the 
evolution of wind pollination in the grass family.  A major goal of the study was to
test the monophyly of several putatively natural groups, including Bambusoideae,
Pooideae, Arundinoideae, and the "PACC clade" (the latter comprising subfamilies
Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to
analyze the phylogenetic structure within these groups and others.  Several genera
of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, 
Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, and Streptochaeta)
also were included, with the goal of determining their phylogenetic affinities.  The two
character sets were analyzed separately, and a simultaneous analysis of the combined
matrices also was conducted.  The combined data set also was analyzed using homoplasy-
implied weights.  Among major results of the combined unweighted analysis were resolution
of a sister-group relationship between Joinvillea and Poaceae; resolution of a clade
comprising Anomochloa and Streptochaeta as the sister of all other grasses, with Pharus
the next group to diverge from the lineage that includes all remaining grasses; and
resolution of other taxa often assigned to Bambusoideae s.l. (including Ehrharta and
Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within
which is nested a clade that consists of Brachyelytrum, the PACC clade (including
Amphipogon), and Pooideae (including Brachypodieae, Stipeae, Anisopogon, Diarrhena,
Lygeum, and Nardus).  Within the PACC clade, Aristida is identified as the sister of all
other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each
resolved as monophyletic, the latter two being sister groups; and the remaining Arundinoid
elements constitute a paraphyletic group within which are nested these three subfamilies.
Within the Pooideae, four "core tribes" (Bromeae, Hordeeae [syn. Triticeae], Agrostideae
[syn. Aveneae], and Poeae, the latter including Sesleria) are resolved as a monophyletic 
group that is nested among the remaining elements of the subfamily (Brachypodieae,
Meliceae, Stipeae, Anisopogon, Diarrhena, Lygeum, and Nardus).  A second principal goal
of the analysis was to identify structural synapomorphies of clades.  Among the
synapomorphies identified for some of the major clades are: gain of a 6.4˙kb inversion 
in the chloroplast genome in Joinvillea and the grasses; reduction to 1 ovule per pistil, 
gain of a lateral "grass-type" embryo, and gain of an inversion around the gene trnT in 
the chloroplast genome in the grasses; loss of arm cells in the clade that consists of
Brachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an
elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets
in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain of
Panicum-type endosperm starch grains in the clade that comprises Centothecoideae
and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two
alternative placements of Pooideae among other groups).  These findings are consistent
with an origin and early diversification of grasses as forest understory herbs, followed
by one or more radiations into open habitats, concomitant with multiple origins of C4
photosynthesis and specialization for wind pollination.
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Cowling, R. M., D. M. Richardson, and S. M. Pierce. 1997.  Vegetation of Southern 
  Africa.  ISBN 0521-57142-1.  Cambridge University Press (40 W. 20th St., New York, 
  NY 10011-4211).  Price: $225.00 cloth.

Gómez, Pedro Sánchez, Juan Guerra Montes, Ernesto Coy Gómez, Antonio Hernández González, 
  Santiago Fernández Jiménez, and Antonio Felix Carrillo López. 1997.  Flora de Murcia-
  Claves de identificación de plantas vasculares.  ISBN 84-8958-20-2.  Promociones y 
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Hartl, Daniel L., and Andrew G. Clark. 1997.  Principles of Population Genetics.  
  ISBN 0-87893-306-9. Sinauer Associates (c/o Publishers Storage and Shipping, 46 
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Kececioglu, Dimitri, and Feng-Bin Sun. 1997.  Environmental Stress Screening: Its 
  Quantification, Optimization, and Management.  ISBN 0-13-324229-3.  Princeton Hall 
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Lumsden, Peter. 1997.  Plants and UV-B: Responses to Environmental Change.  ISBN 
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Nayar, N. M., and T. A. More. 1998.  Cucurbits.  ISBN 1-57808-003-7.  Science 
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Page, C. N. 1997.  The Ferns of Britain and Ireland. 2nd ed.  ISBN 0-521-58380-2 cloth; 
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Pushpangadan, P., K. Ravi, and V Santhosh. 1998.  Conservation and Economic Evaluation 
  of Biodiversity.  Volumes I & 2. ISBN 1-57808-002-9.  Science Publishers.  
  Price: $110.00 cloth.

Raghavendra, A. S. 1997.  Photosynthesis: A Comprehensive Treatise.  ISBN 0-521-57000-X.  
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Raschi, A., F. Miglietta, R. Tognetti, and P. R. van Gardingen. 1997.  Plant Responses 
  to Elevated C02 from Natural Springs.  ISBN 0-521-58203-2.  Cambridge University 
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Sierra, A. Mercado, V. Holubova-Jechova, and J. Mena Portales. 1997.  Monografla XXIII 
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Silvertown, Jonathan, Miguel Franco, and John L. Harper. 1997.  Plant Life Histories: 
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