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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 Poe 1996 Baum et al. 1998
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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
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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 Novel Pattern of Gene Expression in Polyploid Plants. TRENDS in Genetics 21(10): Baum, D.A., R.L. Small and J.F. Wendel Biogeography and Floral Evolution of Baobobs (Adansonia, Bombacaceae) as Inferred from Multiple Data Sets. Systematic Biology 47(2): Doyle, J.J., J.L. Doyle, J.P. Grace and A.H.D. Brown Reproductively Isolated Polyploid Races of Glycine tacina (Leguminosae) had Different Chloroplast Genome Donors. Systematic Botany 15(2): McDade, L.A Hybrids and phylogenetic systematics I. Patterns of character expression in hybrids and their implications for cladistic analysis. Evolution 44: Poe, S Data Set Incongruence and the Phylogeny of Crocodilians. Systematic Biology 45(4): Sang, T. and D. Zhang 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) Soltis, P.S., J.J. Doyle and D.E. Soltis Molecular Data and Polyploid Evolution in Plants. In: Molecular Systematics of Plants: pp Chapman and Hall: New York and London. Wendel, J.F., and V.A. Albert 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 17:
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