Biology Departement

Lecture 9:
Quantitative and
Population Genetics
Outline
• Quantitative Inheritance.
• Population Genetics  The Hardy-Weinberg Equilibrium and Mating
Systems.
• Population Genetics  Processes That Change Allelic Frequencies.
Traits Controlled by Many Loci
Comparison of continuous variation (ear length in corn) with
discontinuous variation (height in peas).
Comparison of continuous variation (ear length in corn) with
discontinuous variation (height in peas).
Comparison of continuous variation (ear length in corn) with
discontinuous variation (height in peas).
 Peas Corn
P1 Dwarf x Tall Short x Long

F1 Tall x Self Intermediate x Self

F2 ¼ Dwarf; 3/4 Tall No discrete catagories
One-Locus Control
Cross involving the grain color of wheat in which one locus is segregating.
Two-Locus Control
Cross involving wheat grain color in which two loci are segregating
Three-Locus Control
Crosses involving three loci controlling
wheat grain color.
Multilocus Control

• Phenotypes determined by
multiple loci with alleles that
contribute dosages to the
phenotype will approach a
continuous distribution.
Measuring Quantitative Variation
Types of traits and inheritance (1)
• Qualitative or discontinuous or categorical traits  posses only a
few distinct phenotypes; often exhibit simple inheritance; only one or
two genes are involved and the environment has little or no effect on
the phenotype.
• Quantitative or continuous or metrical traits  phenotype must be
described by a quantitative measurement; arise from 2 phenomena,
polygenic and environmental factors (multifactorial); complex
inheritance.
Types of traits and inheritance (2)
• Threshold traits  some categorical traits do not show simple
inheritance but have complex inheritance.
• Meristic trait or counting trait  quantitative but restricted to
certain discrete values; usually exhibit complex inheritance.
• Threshold characteristics exhibits only two phenotypes, but
determined by multiple genetic and environmental factors.
• The expression of the characteristics depends on and underlying
suspectibility (liability or risk) that varies continuously.
Genetic and Environmental Factors Influence
Quantitative Traits
• Edward M. East extended
Nilsson-Ehle’s studies to a trait
that did not show simple
Mendelian ratios in the F2. East
studied the length of the corolla in
tobacco flowers.
Influence of environment on phenotypic distributions
Population Statistics
Mean
Variance and Standard Deviation
Covariance and Correlation (1)
Covariance and Correlation (2)
Population Genetics
What is population genetics?
• Analyzes the amount and distribution of genetic variation in
populations and the forces that control this variation.
• Mathematically based principles for changes in genotypes through
time—individuals, populations, etc.
• Examine mutation, migration, breeding system, among-population
interactions, stochastic forces and selection on allele frequencies.
• Developed to bridge gap between “genes” and “species evolution”-
microevolution.
• “alleles” may be any kind of heritable mutation.
Detecting Genetic Variation
• Single nucleotide polymorphisms (SNPs)
• Microsatellites (repeating sequences)
• Haplotypes (and the Human Hap Map)
• Other detection methods possible
Single nucleotide polymorphisms (SNPs)
• SNPs are the most prevalent types of polymorphism in most
genomes.
• Most SNPs have just two alleles—for example, A and C.
• SNPs are usually considered common SNPs in a population if the less
common allele occurs at a frequency of about 5 percent or greater.
SNPs for which the less common allele occurs at a frequency below 5
percent are considered rare SNPs.
• For humans, there is a common SNP about every 300 to 1000 bp in
the genome. Of course, there are a far greater number of rare SNPs.
Microsatellites
• Microsatellites are powerful loci for population genetic analysis for
several reasons:
1. unlike SNPs, which typically have only two alleles per locus and
can never have more than four alleles, the number of alleles at a
microsatellite is often very large (20 or more).
2. they have a high mutation rate, typically in the range of 10−3 to
10−4 mutations per locus per generation as compared to 10−8
to10−9 mutations per site per generation for SNPs.
Haplotypes
• Geneticists use the term haplotype to refer to the combination of
alleles at multiple loci on the same chromosomal homolog.
• Two homologous chromosomes that share the same allele at each of
the loci under consideration have the same haplotype.
The HapMap Project
• A consortium of scientists around the world genotyped thousands of
people representing the diversity of our species for hundreds of
thousands of SNPs and microsatellites.
The haplotype network for human mtDNA haplotype groups drawn onto
a world map. The ancestral L haplotype group appears in Africa, and the
derived groups (A, B, and so on) are dispersed throughout the world.
The Gene-Pool Concept and the
Hardy–Weinberg Law
The Gene Pool
• The sum total of all alleles in the breeding members of a population
at a given time.
• We can describe the variation in a population in terms of genotype
and allele frequencies.
Hardy-Weinberg Equilibrium
1. The allelic frequencies at an autosomal locus in a population will
not change from one generation to the next (allelic-frequency
equilibrium).
2. The genotypic frequencies of the population are determined in a
predictable way by the allelic frequencies (genotypic-frequency
equilibrium).
3. The equilibrium is neutral. That is, if it is perturbed, it will be
reestablished within one generation of random mating at the new
allelic frequencies (if all the other requirements are maintained).
Mating is often not random; three common
mating systems
• Assortative mating (positive and negative)
• Isolation by distance (leds to subpopulations and perhaps new
species)
• Inbreeding (increases homozygosity and can result in a reduction in
vigor and reproductive success, i.e., inbreeding depression)
Assortative mating
• Positive assortative mating occurs when similar types mate; for
example, if tall individuals preferentially mate with other tall
individuals and short individuals mate with other short individuals.
• Negative assortative or disassortative mating occurs when unlike
individuals mate—that is, when opposites attract. One example of
negative assortative mating the major histocompatibility complex
(MHC), which is known to influence mate choice in vertebrates. MHC
affects body odor in mice and rats, providing a basis for mate choice.
Women preferred the scent of men whose MHC haplotypes were
different from their own.
Isolation by distance
• Individuals are more apt to mate with a neighbor than another
member of their species on the opposite side of the continent.
a) Allele frequency variation across Kansas for a hypothetical
species of wild sunflower.
(b) Frequency variation for the FYnull allele of the Duffy blood
group locus in Africa.
Inbreeding
• Progeny of inbreeding are more likely to be homozygous at any locus
than progeny of non-inbred matings.
• Inbreeding can lead to a reduction in vigor and reproductive success
called inbreeding depression.
(a) Pedigree for a half-sib mating drawn in the standard format. Small colored balls represent a
single copy of a gene. Within individual A, the pink and blue copies represent the copies of the
gene that she inherited from her mother and father, respectively.
(b) Pedigree for a half-sib mating drawn in the simplified format used for the
analysis of inbreeding. Only lines connecting parent to offspring are drawn, and
only individuals in the “closed inbreeding loop” are included. w, x, y and z are
symbols for the allele transmitted from parent to offspring.
Migration
• Individuals move from one territory to another  carry their genes
with them.
• The introduction of genes by recent migrants can alter allele and
genotype frequencies within a population and disrupt the state of
Hardy–Weinberg equilibrium.
End of this topic