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What are the overall relationships of these populations? How is the variation partitioned? Is there genetic structure? PowerPoint Presentation
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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?. Uses of AMOVA. Quantifying genetic structure Hypothesis testing Is there genetic structure?

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slide1

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

uses of amova
Uses of AMOVA
  • Quantifying genetic structure
  • Hypothesis testing
    • Is there genetic structure?
    • What factors explain the most among group variance?
slide3
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

slide4

Lack of genetic and plumage differentiation in the red-billed quelea across a migratory divide in southern Africa.Dallimer et al. 2003 Molec. Ecol 12:345-353

disadvantages of amova
Disadvantages of AMOVA
  • testing of groups limited to the user’s imagination and persistence (usually not all possible groupings are tested)
  • assume sampling sites = populations
  • biological vs. statistical significance
programs used for amova
Programs used for AMOVA
  • Arlequin (most commonly used)
  • GDA
  • TFPGA
  • GenAlEx
amovas in arlequin
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
arlequin
ARLEQUIN
  • advantages
    • Accepts several types of data
    • Phi (Φ) – analog of FST for haplotypic data
    • Minimum spanning networks and trees
arlequin9
ARLEQUIN
  • disadvantages
    • The manual !!!
    • Finicky with input file format
    • SEE HANDOUT
today in lab
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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