Phylogenetic Analysis and Classification

1
Phylogenetic Analysis and Classification

• Plant Systematics (PBIO 309/509)
• Harvey Ballard

2
Fundamentals of Phylogenetic Analysis

• Contrary to phenetic approaches, phylogenetic
  algorithms retain individuality of each character
  (not boiled down to similarity coefficient
  across taxa)
• Each character has one or more states (only those
  with gt1 are informative)

3
Fundamentals of Phylogenetic Analysis

• Groupings of taxa (clades) are made based on
  shared derived character states
• Only monophyletic groups (a hypothetical ancestor
  and ALL descendants) is valid

4
Fundamentals of Phylogenetic Analysis
A monophyletic (a clade)
B paraphyletic (a grade)
AB polyphyletic
Judd et al. (2002)
5
Fundamentals of Phylogenetic Analysis

• Need to include character states for an ancestor
  (usually unavailable) or a near outgroup (close
  relative) to polarize the statesancestral?derived
  
• Synapomorphy shared derived state uniting 2 or
  more taxa
• Autapomorphy state found only in 1 taxon,
  represents divergence

6
Constituents of a Phylogeny
Wiley et al. (1991)
7
Fundamentals of Phylogenetic Analysis
autapomorphies
synapomorphies
Judd et al. (2002)
8
Which Tree is Correct?

• Taxa joined together in all possible
  combinations, to make multiple trees
• Number of steps (state changes) required in each
  character added up across all characters tree
  length
• Parsimony criterion for tree selection tree with
  shortest length wins

9
Which Tree is Correct?

• Several taxa and characters?astronomical number
  of possible treescomputer algorithms have
  heuristic tree-building strategies
• Often, multiple trees are shortest, with trees
  differing in certain taxon positions
• Consensus tree summarizes tree branching pattern
  with conservative relationships

10
Which Tree is Correct?
Circles polytomies, as incongruent branch
positions among trees
Stevens (2006)
11
Reading DNA Phylogenies

• Example Lyonia group in Ericaceae (heath family)

Circles indicate high bootstrap support and high
decay valuesstrong branches
Judd et al. (2002)
12
A Phylogenetics Nightmare from Hell

• Single genes can represent the evolutionary
  history of THAT GENE rather than the whole
  organism
• Recent aim is to evaluate results from multiple
  genes
• Sometimes results are still not fully congruent
  e.g., 18S often conflicts with phylogenies from
  other nuclear and chloroplast genes

13
A Phylogenetics Nightmare from Hell
Phylogenies of Poaceae using different genes,
morphology
Judd et al. (2002)
14
References

• Judd, W. S., C. S. Campbell, E. A. Kellogg, P. F.
  Stevens, and M. J. Donoghue. 2002. Plant
  systematicsA phylogenetic approach, 2nd ed.
  Sinauer Associates, Sunderland, MA. pp. 13-40.
• Stevens, P. F. 2006. Angiosperm phylogeny
  website. Version 6, May 2005. Accessed at
  http//www.mobot.org/MOBOT/research/APweb/.
• Wiley, E. O., D. Siegel-Causey, D. R. Brooks, and
  V. A. Funk. 1991. The compleat cladistA primer
  of phylogenetic procedures. Univ. Kansas Museum
  Nat. Hist. no. 19.