Measuring genetic diversity in natural populations

Protein electrophoresis, or allozyme electrophoresis: the earliest widely-used method for screening population genetic diversity

* * * * *** * Heterozygotes Heterozygosity (H) = 8/20 = 0.40 Allozyme Electrophoresis: Each enzyme protein (this is phosphoglucomutase) is the product of a single genetic locus Different genetic forms of the enzyme at this locus appear as bands on the gel; these are called allozymes Allozymes are inherited as Mendelian codominant alleles at each locus

DNA fragments that are used to detect variation are also separated and analyzed using gel electrophoresis. This gel shows the DNA fragments from an assay for Restriction Fragment Length Polymorphism (RFLP). RFLPs, like all DNA-based assays for genetic variation, reveal much more diversity than seen when screening allozymes.

This gel shows three possible genotypes at the CCR5 coreceptor locus DNA fragments from this locus are produced by PCR amplification, followed by restriction enzyme digestion

Restriction enzyme digestion of the “wild type” allele (no deletion) produces a 403 bp and a 332 bp fragment The  32 allele contains a 32 bp deletion, transforming the 403 to a 371 bp fragment

Calculating allele frequencies at the CCR5 locus

Patterns of genetic diversity clinal variation

from Volpe and Rosenbaum (2000), p. 110

Allozyme variation at the alcohol dehydrogenase (Adh) locus in D. melanogaster Nearly all populations are polymorphic for the slow Adh S and fast Adh F alleles In Australia (and 2 other continents) the locus shows a cline—increase in frequency of Adh S towards the equator

The mummichog Fundulus heteroclitus shows clinal variation at lactate dehydrogenase-B: Ldh-B b increases towards the north This allozyme has a higher catalytic efficiency at lower temperatures

Allozyme surveys show that variation is nearly universal in humans and natural populations of animals and plants The average individual is heterozygous at 4-15% of its allozyme loci

DNA sequence surveys reveal even more genetic variation

In 15,000 cystic fibrosis patients (homozygous at CFTR): 30,000 different chromosomes 500 loss-of-function alleles