COMPUTING HETEROZYGOSTIY
Observed heterozygosity (Ho) is a proportion.
Ho = number of heterozygous loci (in an individual) divided by the total number of loci
Ho = number of heterozygous loci (in an individual) divided by the total number of loci
So the natural range is:
0 < Ho < 1
So why do you see data with 0.5 as the maximum?
1. Biallelic loci (most SNP datasets)
For a locus with two alleles (A and a):
Maximum heterozygosity (Ho) occurs when
Expected heterozygosity (He):
If the population is near Hardy-Weinberg equilibrium, then:
Ho = (approx) He < 0.5.
So in biallelic systems, heterozygosity cannot exceed 0.5. Many SNP-based population genetics papers implicitly assume this, so figures get scaled 0-0.5.
2. Multiallelic loci (e.g., microsatellites)
With 3 or more alleles, heterozygosity can exceed 0.5.
Example: 4 alleles at equal frequency (0.25 each):
0 < Ho < 1
So why do you see data with 0.5 as the maximum?
1. Biallelic loci (most SNP datasets)
For a locus with two alleles (A and a):
Maximum heterozygosity (Ho) occurs when
- p = q = 0.5
Expected heterozygosity (He):
- He = 2pq = 2(0.5)(0.5) = 0.5
If the population is near Hardy-Weinberg equilibrium, then:
Ho = (approx) He < 0.5.
So in biallelic systems, heterozygosity cannot exceed 0.5. Many SNP-based population genetics papers implicitly assume this, so figures get scaled 0-0.5.
2. Multiallelic loci (e.g., microsatellites)
With 3 or more alleles, heterozygosity can exceed 0.5.
Example: 4 alleles at equal frequency (0.25 each):
In the theoretical limit (many alleles, equal frequency):
He→1
So for microsatellites or highly polymorphic loci, a 0-1 scale is appropriate.
In the theoretical limit (many alleles, equal frequency):
He→1
So for microsatellites or highly polymorphic loci, a 0-1 scale is appropriate.
