Measures of genetic distance
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Measures of Genetic Distance. M.B. McEachern, W. Savage, S. Hooper, S. Kanthaswamy. Genetic Distance ( D ). Quantitative measure of genetic divergence between two sequences, individuals, or taxa

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Measures of genetic distance

Measures of Genetic Distance

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

Genetic distance d
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.)

3 most commonly used distance measures
3 Most Commonly used Distance Measures

  • Nei’s genetic distance (Nei, 1972)

  • Cavalli-Sforza chord measure (Cavalli-Sforza and Edwards, 1967)

  • Reynolds, Weir, and Cockerham’s genetic distance (1983)

  • Nei’s assumes that differences arise due to mutation and genetic drift, C-S and RWC assume genetic drift only

Nei s genetic distance
Nei’s Genetic Distance

  • D = -ln I

    where I = Σxiyi / (Σxi2Σyi2)0.5

  • For multiple loci, use the arithmetic means across all loci

  • Interpreted as mean number of codon substitutions per locus

Assumptions for nei s distance
Assumptions for Nei’s Distance

  • IAM

  • All loci have same rate of neutral mutation

  • Mutation-genetic drift equilibrium

  • Stable effective population size

Cavalli sforza chord distance
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

Reynold s distance
Reynold’s 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, θ

    D = -ln(1-θ)

What is coancestry
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

Testing significance of distance measures
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


  • Computes Nei’s, C-S, and Reynold’s genetic distances using GENDIST (we will do this in lab today)

  • Uses Bootstrap to generate confidence intervals (but we don’t know how to view that output)

  • Other programs that estimate distance: TFPGA, GDA, Popgene, DISPAN

Lots of other distance measures
Lots of other Distance Measures!

  • Euclidean distance

  • Shared allele distance

  • Roger’s distance

  • Goldstein distance (for microsatellites)

In lab today
In Lab Today:

  • Use Phylip to estimate genetic distance for Bear data

  • AMOVA using Arlequin