1. Issues When Dealing with Polyploids
Inferring Freakish Phylogenies

2. Discussion Format Assumptions of Phylogenetics
Phylogenetic Incongruence

3. 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

4. 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

5. McDade 1990

6. Incongruence Data can tell very different stories
Morphology vs. Molecular
Molecular vs. Molecular
Poe 1996
Baum et al. 1998

7. Sources of Incongruence
Technical
Organism-level Processes
Gene and Genome-level Processes

8. 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

9. Genomes cpDNA Maternal vs. Paternal nuclear DNA Biparental

10. 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

11. 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

12. Species Trees vs. Gene Trees
Species have histories, but genes can have histories of their own
Sang and Zhang 1999

13. Polyploids at the Gene and Genome Level
Issues to Consider
Orthology vs. Paralogy
Intragenic or Interallelic Recombination
Interlocus Interactions
Subfunctionalization

14. 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...

15. 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)

16. Interlocus Interactions
“exon shuffling”
“gene conversion”
“concerted evolution”

17. 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

18. Adams & Wendel 2005

19. 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: