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Challenges of Phylogenetics in the Context of Polyploidy and Incongruence in Evolutionary Trees

This paper discusses the complexities of constructing phylogenetic trees affected by polyploid organisms. It delves into assumptions that phylogenetics typically makes, such as strictly bifurcating lineages between sister taxa, and how polyploids introduce additional layers of incongruence. The influence of allopolyploids on phylogenetic analyses is explored, highlighting data discrepancies from morphology and molecular studies. By comparing species trees with gene trees, we address the unique histories of genomes and the implications of orthology versus paralogy, ultimately clarifying the intricate relationships in polyploid systems.

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Challenges of Phylogenetics in the Context of Polyploidy and Incongruence in Evolutionary Trees

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  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 Baum et al. 1998 Poe 1996

  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 http://www.gsst.kumamoto-u.ac.jp/en/org_res_act/dc_dept_mat_lif_sci.html

  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) • ArabidobsisAdh (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. 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.

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