Measures of Genetic Distance

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Measures of Genetic Distance

• M.B. McEachern, W. Savage, S. Hooper, S.
  Kanthaswamy

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Genetic Distance (D)

• Quantitative measure of genetic divergence
  between two sequences, individuals, or taxa
• Relative estimate of the time that has past since
  two populations existed as a single, panmictic
  population
• Units of D depend on the kind of molecular data
  collected (allozymes, nucleotide sequences, etc.)

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3 Most Commonly used Distance Measures

• Neis genetic distance (Nei, 1972)
• Cavalli-Sforza chord measure (Cavalli-Sforza and
  Edwards, 1967)
• Reynolds, Weir, and Cockerhams genetic distance
  (1983)
• Neis assumes that differences arise due to
  mutation and genetic drift, C-S and RWC assume
  genetic drift only

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Neis Genetic Distance

• D -ln I
• where I Sxiyi / (Sxi2 Syi2)0.5
• For multiple loci, use the arithmetic means
  across all loci
• Interpreted as mean number of codon substitutions
  per locus

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Assumptions for Neis Distance

• IAM
• All loci have same rate of neutral mutation
• Mutation-genetic drift equilibrium
• Stable effective population size

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Cavalli-Sforza Chord Distance

• populations are conceptualised as existing as
  points in a m-dimensional Euclidean space which
  are specified by m allele frequencies (i.e. m
  equals the total number of alleles in both
  populations). The distance is the angle between
  these points
• xi and yi are the frequencies of the ith allele
  in populations x and y
• Assumes genetic drift only (no mutation)
• Geometric distance b/w points in
  multi-dimensional space

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Reynolds Distance

• Assumes IAM
• Developed for allozyme data on small populations
  and assumes genetic drift is only force operating
  on allelic frequencies (i.e. no mutation)
• Based on the coancestry coefficient, ?
• D -ln(1-?)

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What is Coancestry?

• Degree of relationship by descent between two
  individuals
• Probability that a randomly picked allele from
  one individual is IBD to a randomly picked allele
  in another individual

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Testing Significance of Distance Measures

• Bootstrap generation of many new data sets by
  resampling original data with replacement
• For each bootstrap data set, obtain estimates of
  parameters of interest and their variances
• Generates confidences intervals of parameter
  estimates

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Phylip

• Computes Neis, C-S, and Reynolds genetic
  distances using GENDIST (we will do this in lab
  today)
• Uses Bootstrap to generate confidence intervals
  (but we dont know how to view that output)
• Other programs that estimate distance TFPGA,
  GDA, Popgene, DISPAN

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Lots of other Distance Measures!

• Euclidean distance
• Shared allele distance
• Rogers distance
• Goldstein distance (for microsatellites)

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In Lab Today

• Use Phylip to estimate genetic distance for Bear
  data
• AMOVA using Arlequin