Issues When Dealing with
Polyploids
Inferring Freakish Phylogenies
Discussion Format
• Assumptions of Phylogenetics
• Phylogenetic Incongruence
Assumptions of Phylogenetics
• Phylogenetics assumes a strictly bifurcating
topology involving sister taxa/lineages
Baum et al. 2004
• How does the inclusion of polyploids affect such
tree building analyses?
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
McDade 1990
Incongruence
• Data can tell very different stories
• Morphology vs. Molecular
•
Molecular vs. Molecular
Poe 1996
Baum et al. 1998
Sources of Incongruence
• Technical
• Organism-level Processes
• Gene and Genome-level Processes
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
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
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
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
Species Trees vs. Gene
Trees
• Species have histories, but genes can have
histories of their own
Sang and Zhang 1999
Polyploids at the Gene and
Genome Level
• Issues to Consider
• Orthology vs. Paralogy
• Intragenic or Interallelic Recombination
• Interlocus Interactions
• Subfunctionalization
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...
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)
Interlocus Interactions
• “exon shuffling”
• “gene conversion”
• “concerted evolution”
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
Adams & Wendel 2005
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 44:1685-1700.
•
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.): characterstate weighted parsimony analysis of chloroplast DNA restriction site data and its systematic and
biogeographic implications. Systematic Botany 17:115-143.