This presentation was originally prepared by C. William Birky, Jr. Department of Ecology and Evolutionary Biology The University of Arizona It may be used with or without modification for educational purposes but not commercially or for profit. The author does not guarantee accuracy and will not update the lectures, which were written when the course was given during the Spring 2007 semester.
Population and Evolutionary Genetics The Nature and Origin of Biological Diversity
Now look at the DNA sequence: The bp difference at site 74, C vs. A, is the one that causes the difference between threonine and lysine at amino acid 25. This is a change in the second codon position. There are a number of other differences between the three Adh genes from D. melanogaster, and also between the three species. Most of these are synonymous differences = differences that change from one codon to a synonymous codon and hence don’t change an amino acid. E.g. site 15: codon difference ATC vs. ATT, both code for isoleucine. Change in third codon position, where most changes are synonymous/silent.
Hypothetical example: • Population of Drosophila melanogaster is examined for genetic variation at the Adh locus. • Sample of 100 flies subjected to electrophoresis. • Calculate genotype and gene frequencies: • Numbers of genotypes 40 FF 40 FS 20 SS total 100 • Genotype frequencies 0.40 0.40 0.20 1 • Numbers of genes 80 F 40 F • 40S 40S 200 • Allele frequencies 0.4F 0.2F 0.6 F • 0.2S 0.2S 0.4 S • 1
Inbreeding Produces Homozygotes e.g. selfing Aa 1/4 1/2 1/4 1/4 AA 1/2 Aa 1/4 aa ?
all Aa 1/4 1/2 1/4 1/4 AA 1/2 Aa 1/4 aa 1/4 1/2 1/4 3/8 AA 1/4 Aa 3/8 aa 1/4 1/2 1/4 7/16 AA 1/8 Aa 7/16 aa How many heterozygotes after n generations?
all Aa 1/4 1/2 1/4 1/4 AA 1/2 Aa 1/4 aa 1/4 1/2 1/4 3/8 AA 1/4 Aa 3/8 aa 1/4 1/2 1/4 7/16 AA 1/8 Aa 7/16 aa How many heterozygotes after n generations? (1/2)n
Calculation of p is tedious by hand for large samples. Best to use calculator with statistical functions or use Excel spreadsheet. Example of data from small sample of freshwater invertebrate Keratella cochlearis. This is the nucleotide diversity of 590 bp of the mitochondrial cox1 gene.