This document summarizes key concepts in population genetics, including: - Detecting genetic variation such as SNPs and microsatellites using DNA sequencing and PCR - Haplotypes, which are combinations of alleles on the same chromosome, and how they can be used to trace human origins - The Hardy-Weinberg law and how it relates allele and genotype frequencies in a population - Factors that modulate genetic variation, such as mutation, migration, genetic drift, and natural selection - Examples of how these concepts are applied, such as in conservation genetics, calculating disease risks, DNA forensics, and ancestry tracing.

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