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Population genetics
- 1. Population Genetics Analysis of the amount and distribution of genetic variation in populations and the forces that control this variation.
- 2. Detecting Genetic Variation Over the past two decades, DNA sequencing and PCR have allowed geneticists to observe directly differences in DNA sequences. - locus – a location in the genome - SNPs (single nucleotide polymorphisms) - microsatellites – a short sequence motif, 2 to 6 bp long, that is repeated multiple times with different alleles having different numbers of repeats
- 3. Variation among homologous DNA sequences SNPs – most prevalent type of polymorphism in genomes rare SNPs = frequencies of <5% in a population within protein coding regions – can be either synonymous, nonsynonomous, or nonsense Indels, microsatellites
- 4. A microarray is used to detect variation in SNPs Allows rapid identification of all common SNPs that are present in either the homozygous or heterozygous condition across the entire genome
- 5. Detecting variation in microsatellites Very valuable for analysis of populations – many alleles are possible, located at many sites in genome, and there is a high mutation rate at microsatellite sequences PCR
- 6. A haplotype network shows the relationship among haplotypes Haplotypes – combination of alleles at multiple loci on the same chromosome
- 7. A prevalent Y-chromosome haplotype among Asian men may trace back to Genghis Khan
- 8. Mitochondrial haplotypes can be used to trace human origins to Africa
- 9. HapMap/1000 Genomes Projects – creation of a genome-wide haplotype map for humans, generated from the analysis of thousands of genomes representing the diversity of our species - gives a highly detailed picture of our species (www.hapmap.org http://www.1000genomes.org) - identify all SNPs that occur at a frequency of ≥1% - have now been generated for Drosophila, mouse, Arabidopsis, rice, and maize
- 10. The Gene-Pool Concept and Hardy-Weinberg Law Gene pool = the sum total of all alleles in the breeding members of a population at a given time
- 11. The gene pool can be characterized by genotype frequencies
- 12. Calculation of allele frequencies (see Box 18-1): p = fA/A + 1/2fA/a = frequency of A q = fa/a + 1/2fA/a = frequency of a, p + q = 1 Hardy-Weinberg Law fA/A = p2 fa/a = q2 fA/a = 2pq p2 + 2pq + q2 = 1.0
- 13. Assumptions when using the Hardy-Weinberg law to calculate allele or genotype frequencies: 1. assume there is random mating 2. assume equal viability, if a genotype has reduced viability then the estimates of gene frequencies will be inaccurate 3. assume population being studied does not contain isolated subpopulations that are partially or fully isolated 4. strictly applies only to infinite populations. For finite populations, there will be deviations from the predicted frequencies due to change when sampling the gene pool
- 14. Hardy-Weinberg still holds when there are >2 alleles per locus
- 15. Mating Systems Assortative mating – occurs if individuals choose mates based on resemblance to themselves can be positive or negative (disassortative) Isolation by distance – bias in mate choice arising from the amount of geographical distance between individuals Inbreeding – mating between relatives inbreeding depression – the increase probability of being homozygous for deleterious recessive alleles
- 16. Self-incompatibility leads to disassortative mating in Brassica Disassortative mating
- 17. Allele frequency may vary along a gradient Isolation by distance Wild sunflowers Duffy blood group locus
- 18. Inbreeding effects The degree of risk for homozygous recessive offspring increases dramatically for rare alleles (e.g., 250-fold greater risk when q = 0.001 and have parent-offspring or brother- sister matings)
- 19. The Modulation of Genetic Variation New alleles enter the population: mutation and migration Recombination and linkage disequilibrium Genetic drift and population size Selection
- 20. Mutation rate – probability that an allele changes to some other allelic form in one generation
- 21. Migrants from around the world have contributed to the genomes of some South Africans Migration – the movement of individuals between populations 39 individuals of mixed ancestry
- 22. Linkage disequilibrium = the nonrandom association between two loci Note: will decay over time because of recombination
- 23. Random genetic drift is weakest in large populations p = q = 0.5 p = q = 0.5 p = 0.1, q = 0.9 Each line represents a different simulation
- 24. The founder effect reduces genetic diversity Founder effect = random sampling or an original population to create a new population Bottleneck – a period of one or several consecutive generations of contraction of population size
- 25. The Domestication Bottleneck Agricultural selection
- 26. Allele frequencies change under the force of natural selection Natural selection – the process by which individuals with certain heritable features are more likely to survive and reproduce than other individuals that lack these features
- 27. Forms of Selection: directional selection – moves the frequency of an allele in one direction until it reaches fixation or loss positive selection – directional selection that works to bring a new favorable allele to higher frequency purifying selection – directional selection that removes deleterious mutations from the population balancing selection – heterozygous individuals have highest fitness, will move population to an equilibrium point artificial selection – human imposed selection
- 28. Resistance to pathogens Adaptation to regions diets Physiological adaptation to climate
- 29. Balancing selection can lead to regions of unusually high genetic diversity MHC – major histocompatibility complex, involved in immune system recognition of pathogens
- 30. Biological and Social Applications Conservation genetics Calculating disease risks DNA forensics Googling your DNA mates