Issues When Dealing with Polyploids

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Issues When Dealing with Polyploids

• Inferring Freakish Phylogenies

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Discussion Format

• Assumptions of Phylogenetics
• Phylogenetic Incongruence

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Assumptions of Phylogenetics

• Phylogenetics assumes a strictly bifurcating
  topology involving sister taxa/lineages
• How does the inclusion of polyploids affect such
  tree building analyses?

Baum et al. 2004
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Assumptions of Allopolyploids

• McDade 1990
• on average, will share more derived features with
  its parent that has the most derived characters
  therefore, placement nearest that parent
• basal clade placement to the lineage that
  includes the most derived parent
• inclusion will have limited effect on homoplasy

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McDade 1990
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Incongruence

• Data can tell very different stories
• Morphology vs. Molecular
• Molecular vs. Molecular

Baum et al. 1998
Poe 1996
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Sources of Incongruence

• Technical
• Organism-level Processes
• Gene and Genome-level Processes

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Morphological Continuum

• Polyploidy has the potential for producing plants
  with morphological intermediates.

Dupontia fisheri R. Br. s.l.
Aiken et al. 1995
2n 42, 44, 88, and 132
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Genomes

• cpDNA
• Maternal vs. Paternal
• nuclear DNA
• Biparental

http//www.gsst.kumamoto-u.ac.jp/en/org_res_act/dc
_dept_mat_lif_sci.html
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cpDNA
Wendel and Albert 1992
61 accessions from 40 species of
Gossypium resulted in 4 MP topologies differing
only in the placement of G. longicalyx and G.
anomalum
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Gen(om)e Choice

• When dealing with polyploids, which gen(om)e are
  you dealing with, does it possess a unique
  history and does it answer the question you are
  after?

Doyle et al. 1990
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Species Trees vs. Gene Trees

• Species have histories, but genes can have
  histories of their own

Sang and Zhang 1999
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Polyploids at the Gene and Genome Level

• Issues to Consider
• Orthology vs. Paralogy
• Intragenic or Interallelic Recombination
• Interlocus Interactions
• Subfunctionalization

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Orthology vs. Paralogy
A and B represent loci on the same chromosome
A1 - A2 and B1 - B2 represent orthologues
A1 - B2, B1 - A2, A1 - B1 and A2 - B2 all
represent paralogues
Inferring true history gets even stickier with
polyploids...
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Intragenic or Interallelic Recombination

• Composite molecules are produced possessing
  characteristics of both parental alleles/genomes
• Alleles do not arise via normal mutational
  processes and their relationships cannot be
  depicted in a hierarchical fashion
• Maize Adh1 Adh2 (Gaut and Clegg, 1993a Hanson
  et al. 1996)
• Arabidobsis Adh (Innan et al. 1996)

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Interlocus Interactions

• exon shuffling
• gene conversion
• concerted evolution

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Subfunctionalization

• Silencing and relative expression levels of
  genes duplicated by polyploidy can be variable in
  different parts of the plant, indicating
  differential regulation of the two homoelogs
  during plant development. -Adams and Wendel
  (2005)
• eg. cotton, Tragopogon, Arabidopsis

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Adams Wendel 2005
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Literature Cited

• Adams, K.L. and J.F. Wendel. 2005. Novel Pattern
  of Gene Expression in Polyploid Plants. TRENDS
  in Genetics 21(10)539-543.
• Baum, D.A., R.L. Small and J.F. Wendel. 1998.
  Biogeography and Floral Evolution of Baobobs
  (Adansonia, Bombacaceae) as Inferred from
  Multiple Data Sets. Systematic Biology
  47(2)181-207.
• Doyle, J.J., J.L. Doyle, J.P. Grace and A.H.D.
  Brown. 1990. Reproductively Isolated Polyploid
  Races of Glycine tacina (Leguminosae) had
  Different Chloroplast Genome Donors. Systematic
  Botany 15(2)173-181.
• McDade, L.A. 1990. Hybrids and phylogenetic
  systematics I. Patterns of character expression
  in hybrids and their implications for cladistic
  analysis. Evolution 441685-1700.
• Poe, S. 1996. Data Set Incongruence and the
  Phylogeny of Crocodilians. Systematic Biology
  45(4)393-414.
• Sang, T. and D. Zhang. 1999. Reconstructing
  Hybrid Speciation Using Sequences of Low Copy
  Nuclear Genes Hybrid Origins of five Paeonia
  Species Based on Adh Gene Phylogenies.
  Systematic Botany 24(2) 148-163.
• Soltis, P.S., J.J. Doyle and D.E. Soltis. 1992.
  Molecular Data and Polyploid Evolution in Plants.
  In Molecular Systematics of Plants pp. 177-201.
  Chapman and Hall New York and London.
• Wendel, J.F., and V.A. Albert. 1992.
  Phylogenetics of the cotton genus (Gossypium L.)
  character-state weighted parsimony analysis of
  chloroplast DNA restriction site data and its
  systematic and biogeographic implications.
  Systematic Botany 17115-143.