Analysis of Molecular Variance AMOVA

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Analysis of Molecular Variance (AMOVA)
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Among groups (FCT)
Max
Among populationswithin groups (FSC)
0
Within populations (FST)
0
3
Among groups (FCT)
0
Among populationswithin groups (FSC)
0
Within populations (FST)
Max
4
A
B
Among groups
Max
Max
Among populationswithin groups
0
0
Within populations
0
0
A
B
5
A
B
A
B
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Analysis of Molecular Variance
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Relationship to F-statistics

• (1 FST) (1 FSC) (1 FCT)
• (1 FIT) (1 FIS) (1 FST)

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Nucleotide diversity

• p S xi xj dij
• xi frequency of ith haplotype
• xj frequency of jth haplotype
• dij proportion of sites at which ith and jth
  haplotypes differ

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Example

• Haplotype i 65
• ACGTTGTGCAACAATTGCATTTCTATTCGC
• Haplotype j 35
• ACGTCGTGCAACAGTTGCGTTTCTATTCGC
• dij 3/30 0.1
• p (0.65)(0.35)(0.1) 0.002275

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Example

• Haplotype i 50
• ACGTTGTGCAACAATTGCATTTCTATTCGC
• Haplotype j 35
• ACGTCGTGCAACAGTTGCGTTTCTATTCGC
• Haplotype k 15
• ACGTCGCGCAACAGTTGCGTTTTTATTCGC
• dij 3/30 0.1
• dik 5/30 0.167
• djk 2/30 0.067
• p (0.50)(0.35)(0.1) (0.50)(0.15)(0.167)
  (0.50)(0.15)(0.067) 0.0305

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pt nucleotide diversity across all
populations ps mean nucleotide diversity within
populations Fst (pt - ps)/ pt Fst (Ht
Hs)/Ht
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• pt nucleotide diversity across all populations
• ps mean nucleotide diversity within populations
• Fst (pt - ps)/ pt
• Fst (Ht Hs)/Ht

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Relationship to F-statistics

• (1 FST) (1 FSC) (1 FCT)
• (1 FIT) (1 FIS) (1 FST)
• FIT among all individuals
• FIS among individuals within populations
• FST among all populations
• FST among all populations
• FSC among populations within regions
• FCT among regions

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Relating to time

• Fst (t t0)/t (when mutations are rare)
• t mean time to coalescence for two alleles
  drawn at random from all individuals
• t0 time to coalescence for two alleles drawn at
  random from the same population
• when dij is linearly proportional to time since
  divergence, Fst Fst
• thus, combination of haplotype frequency
  differences among populations and evolutionary
  distances provides insight into evolutionary
  relationships among populations

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• Diploid system FST 1/1 4Ne(m µ)
• Uniparental haploid system
• FST 1/1 Ne(m µ)

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More on the coalescent

• Traditional (FST) approach to population genetics
  uses allele frequencies
• Coalescent uses genealogical information
• Evolutionary relationships among alleles
• Trees

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Gene trees vs species trees
Take-home messageuse multiple loci toinfer a
phylogeny