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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