Phenetic Analysis

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Phenetic Analysis

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

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Principles of Phenetic (Distance) Analysis

• Use overall similarity among taxa (populations,
  species, etc.)all characters boiled down a
  matrix of pairwise similarities
• Collapse multidimensional patterns of variation
  into very few artificial dimensions, to permit
  interpretation

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Principles of Phenetic (Distance) Methods

• Sometimes the only valid approach for some kinds
  of datae.g., continuous morphological variables,
  population-level molecular markers
• Very successful for distinguishing recognizable
  taxa in a group of closely related plants
  (especially below genus level)

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Principles of Phenetic (Distance) Methods

• Sometimes the only valid approach for some kinds
  of datae.g., continuous morphological variables,
  population-level molecular markers
• Very successful for distinguishing recognizable
  taxa in a group of closely related plants
  (especially below genus level)

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Characters

• Variables ideally continuous (permits greatest
  flexibility of analysis) can include binary,
  multistate qualitative traits but this severely
  limits analytical methods
• Very useful to do initial (even preliminary)
  group assignments for samples

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Analytical Approaches

• Four main types
• Cluster analysisuses similarity matrix
• Principal components analysisuses original data
  set
• Principal coordinates analysisuses dissimilarity
  matrix from Gowers coefficient (allows mixed
  data types)
• Canonical variates analysisuses original data
  set
• CVA alone requires samples assigned to groups,
  but most powerful of all methods

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ExampleMesoamerican Hybanthus elatus complex
What the Hell are these!?
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ExampleMesoamerican Hybanthus elatus complex
potosinus
verbenaceus
el X verb??
elatus
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ExampleMesoamerican Hybanthus elatus complex
Leaf shape, margin and petiole traits
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ExampleMesoamerican Hybanthus elatus complex
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ExampleMesoamerican Hybanthus elatus complex
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ExampleMesoamerican Hybanthus elatus complex

• Pollen stainability data

elatus
??
poto
verb
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ExampleMesoamerican Hybanthus elatus complex

• Weird Hybanthus largely distinct from relatives
  but intermediate between H. elatus and H.
  verbenaceus
• Distributed between them geographically and
  altitudinally, ecologically distinct from both
• Pollen stainability?partially sterile
• Produces normal fruits and seeds!
• Recent hybrid derivative, now partly stabilized?

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ExampleCentral and Marginal Populations of
Froelichia floridana

• Study began with ecological investigations of
  Ohios only (endangered) population of Froelichia
  floridana (Snake Cotton, Amaranthaceae)
• McCauley needed genetic data to interpret
  diversity and affinities to other source areas
• Used Inter-Simple Sequence Repeat (ISSR)
  fingerprinting method

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ExampleCentral and Marginal Populations of
Froelichia floridana
Ohio pop

• Ohio population not known in early 1900s
• Found in 1954 along Ohio River near Marietta
• Currently state endangered

McCauley and Ballard (2002)
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ExampleCentral and Marginal Populations of
Froelichia floridana

• Genetic data analyzed using Neighbor-joining
  (related to Cluster Analysis)
• All state samples coherent units
• Ohio groups w/Midwestern pops

McCauley and Ballard (2002)
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ExampleCentral and Marginal Populations of
Froelichia floridana

• Analysis of Molecular Variance compared ISSR
  diversity of central (old) vs. marginal
  (recent) populations
• Genetic diversity of central populations gtgt
  marginal ones
• ?Marginal pops (incl. OH) recent migrants

McCauley and Ballard (2002)
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References