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

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
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
Neis Genetic Distance
D = -ln I
where I = x
i
y
i
/ (x
i
2
y
i
2
)
0.5

For multiple loci, use the arithmetic means
across all loci
Interpreted as mean number of codon
substitutions per locus
Assumptions for Neis Distance
IAM
All loci have same rate of neutral mutation
Mutation-genetic drift equilibrium
Stable effective population size
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
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-)
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
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

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

Lots of other Distance Measures!
Euclidean distance
Shared allele distance
Rogers distance
Goldstein distance (for microsatellites)
In Lab Today:
Use Phylip to estimate genetic distance for
Bear data
AMOVA using Arlequin