What are the overall relationships of these populations How is the variation partitioned Is there ge

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What are the overall relationships of these
populations?How is the variation partitioned?
Is there genetic structure?What is the genetic
structure?
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Uses of AMOVA

• Quantifying genetic structure
• Hypothesis testing
• Is there genetic structure?
• What factors explain the most among group
  variance?

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• Percentage of variation at three levels of
  population hierarchy in four distinct clusters of
  54 communities in India.
• Kashyap et al. 2003 Current Science
  85(4)464-473

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Lack of genetic and plumage differentiation in
the red-billed quelea across a migratory divide
in southern Africa.Dallimer et al. 2003 Molec.
Ecol 12345-353
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Disadvantages of AMOVA

• testing of groups limited to the users
  imagination and persistence (usually not all
  possible groupings are tested)
• assume sampling sites populations
• biological vs. statistical significance

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Programs used for AMOVA

• Arlequin (most commonly used)
• GDA
• TFPGA
• GenAlEx

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AMOVAS in Arlequin

• distance matrix is created within Arlequin or is
  included within the input file
• sum of squared deviations (from the distance
  matrix) is partitioned into hierarchical variance
  components
• variance components are tested for significance
  using permutation tests

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ARLEQUIN

• advantages
• Accepts several types of data
• Phi (F) analog of FST for haplotypic data
• Minimum spanning networks and trees

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ARLEQUIN

• disadvantages
• The manual !!!
• Finicky with input file format
• SEE HANDOUT

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Today in lab

• Review how to run an AMOVA
• How to group Sacramento bears?
• Maximize among group variance
• How to edit input files within Arlequin

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