Variation – Chapter 9
Some terms
• Genotype
• Allele – form of a gene, distinguished by effect on phenotype
• Haplotype – form of a gene, distinguished by DNA sequence
• Gene copy – number of copies of a given gene, used without distinguishing
allele or sequence differences
– Allele copies
Variation in phenotype can be due to genes AND environment:
Is variation genetic, environmental, or both?
• Cross phenotypes and use Mendalian ratio predictions
• Greater resemblance among siblings than among related individuals points
towards genetic contribution
• Common garden experiment
– See if differences persist over two generations
•
Genotype frequency is proportion of a genotype
A population has a frequency of alleles
•
Allele frequency is the relative commonness or rarity of an allele
Hypothetical population
If…
• Individuals mate at random and each genotype is equally represented by
males and females then..
Hardy Weinberg Equilibrium
• After one generation of random mating, genotype frequencies and allele
frequencies in a population will remain constant from generation to generation
• Has a set of 5 assumptions
• H-W can be modified for sex-linked loci and segregation other than 1:1
H-W assumptions
• Random mating
• Large population
• No gene flow
• No mutation
• Each individual has an equal chance of survival and reproduction
– (No natural selection)
Genetic Evolution
• Asks what happens when one or more of the assumptions are relaxed
• Violations of H-W are the major factors the cause evolutionary change
Frequencies of alleles
• Frequency of heterozygotes are highest when p = q
• When an allele is rare, almost all its carriers are heterozygotes
– This can cause concealed genetic variation in a population
Inbreeding
• Inbreeding occurs when individuals are more likely to mate with relatives that
with non-relatives or when gene copies are more likely to be identical by
descent
– Genes are identical by descent if they have descended from a common
ancestor relative to other gene copies in the population
Inbreeding
• As inbreeding proceeds, the frequency of each homozygote increases
• Frequency of heterozygotes is H = H0 (1-F)
– H0 is frequency of heterozygotes under HW
– F is the inbreeding coefficient
• F increases as inbreeding continues
– F can be calculated by the deficiency of heterozygotes from HW equilibrium
Inbreeding
• Self-fertilization is the most extreme form of inbreeding
Polymorphism
• Polymorphism is the presence in a population of two or more variants, either
alleles or haplotypes
– vs. monomorphism
• Can be controlled by one to more than one locus
Two loci
Genetic variation in viability
• Can perform crosses in flies to determine recessive lethal alleles
• 10% of alleles on chromosome 2 in Drosophila pseudoobscura are lethal when
homozygous
• Average person carries 3-5 lethal recessive alleles in heterozygote form
• Confirms that there is a great deal of concealed genetic variation
Inbreeding depression
• Because of these recessive alleles, inbreeding, when increasing the number of
homozygotes, reduces survival and fecundity
Inbreeding
• Inbreeding with selection over many generations can purge deleterious alleles
• Many mechanisms for inbreeding avoidance: behavioral and genetic
Endangered species
Genetic variation in proteins
• Enzymes are run through electrophoresis
• Electrophoretically distinguishable forms of an enzyme are called allozymes
Heterozygosity in proteins
• Average heterozygosity was 12% in Drosophila pseudoobscura
• Average heterozygosity in humans was 7%
Variation in DNA
• Variation determined by DNA sequencing
• Nucleotide diversity per site (π)
• Drosophila melanogaster has 5% average diversity
• Humans have .08% average diversity
Linkage
• Genes are physically associated with other genes on the same chromosome
• Changes in allele frequencies at one allele can cause changes in a linked
allele
Linkage
• Two loci in a population are in linkage equilibrium when the genotype of a
chromosome at one locus is independent of its genotype at the other locus
• Two loci are in linkage disequilibrium when there is nonrandom association
between a chromosome’s genotype at one locus and its genotype at the other
locus
Recombination
• Recombination reduces the level of linkage disequilibrium
• Tighter linkages take longer to break down from recombination
• Linkage disequilibrium is common in asexual populations due to little
recombination
Determining linkage equilibrium
• Use modified HW
•
Frequency of A1B1/A1B1 in next population should be pA2pB2 if population is in
linkage equilibrium
Heterostyly in Primula
• pin phenotype and thrum phenotype
• In most crosses, thrum dominant over pin
Quantitative traits
• Continuous variation vary because of both polygenic control, as well as
environmental factors
Genotype x environment interaction
• Genotype norm of reaction
Causes of variation
Estimating variation
• Use variance, which measures the spread of values around the mean
• Vpheno. = VG + VE
• Heritability is the proportion of the phenotypic variance that is genetic
– h2 = VG /(VG + VE)
Heritability
• Two ways to measure
– parent-offspring regression
– selection experiments
Parent-offspring regression
• If variation among individuals due to genes, then offspring resemble parents
• Plot midparent value against midoffspring value
• Slope of line = heritability
Parent-offspring regression
Selection experiments
Selection experiments
• Only particular individuals allowed to breed
• Difference between mean phenotype of population and mean of selected
group = selection differential, S
Selection experiments
• The change in offspring phenotype between selected group and unselected
population is the response to selection, R
Heritability estimates