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 How does the inclusion of polyploids affect such tree building analyses? Baum et al. 2004

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.): character- state weighted parsimony analysis of chloroplast DNA restriction site data and its systematic and biogeographic implications. Systematic Botany 17:115-143.