mechanisms of evolution - california state university ...dgray/evol322/chapter5.pdf · mechanisms...
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Mechanisms of Evolution
• Mutation and Genetic Variation
• Mendelian Population Genetics– Selection and mutation
• Mendelian Population Genetics– Migration, Drift, Non-random Mating
• Evolution at Multiple Loci– Linkage, sex, and quantitative genetics
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Mutation and Genetic Variation
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Importance of Mutation
• Source of new genetic variation
• Without mutation– No new genes
– No new alleles
– Eventually no evolutionary change• Even if there is selection
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Two major questions
• What are the mechanisms generatinggenetic variation?
• How do biologist measure genetic variationin populations?
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Major classes of mutations
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DNA recap
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DNA
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DNA -> mRNA -> Protein
• DNA sequence read as triplets– Three bases encode 1 amino acid
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Point Mutation
• Single base substitution– Error in synthesis– Error in repair after damage
• Transition: purine for purine (A and G) orpyrimidine for pyrimidine (T or C)
• Transversion: purine for pyrimidine orpyrimidine for purine
• Transition:Transversion 2:1
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Synonymous and Non-synonymous point mutations
• Synonym: word that says the same thing
• Codon UAU = Tyrosine
• Codon UAC = Tyrosine
• CAC = Histidine
• CAA = Glutamine
• Third position mutations often silent (synonymous)
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Non-synonymous mutation
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Sickle-cell• Mutant hemoglobin crystalizes, pulling in wall
and deforming cell
• Sickled cells get stuck in capillaries
• Homozygous recessive usually die young
• Homozygous dominant susceptible to malaria
• Heterozygous individuals resistant to malaria
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Mutation rates - hard to measure
• Silent mutations, or mutations with littleeffect, not easily detected
• Easiest data to get are from appearance ofnon-functional (knockout) mutations– But there are a lot of ways to knock out a gene
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Ways to get cystic fibrosis:30,000 disease causing alleles
# mutants
Exons
Function
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Knockout mutations
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Mutation ratesMutations in corn
• Mutation rate low on a per gene basis
• Common considering the number of genes
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Mutation rates variable
• 500 times among different genes within aspecies
• Potentially 100,000 times across species
• Why?– Among individuals
– Among species
– Among genes
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Variation in mutation rate
• Among individuals– Allelic differences in DNA polymerase
• Making new errors
– Allelic differences in DNA repair• Fixing the errors
• Among species– Generation time likely important
• Among genes– Likely to depend on fitness effects
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New genes
• Gene duplications– Unequal crossover
• Overprinting
• cDNA insertion
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Unequal crossover
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Globin genes
• Hemoglobin molecule has 4 subunits
• Adult humans– 2 are from alpha cluster on chromosome 16
– 2 from beta cluster on chromosome 11
• Fetal humans in first trimester– two zeta and 2 epsilon chains
– Higher oxygen affinity than adult hemoglobin
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Homology of globin genes• Exon and intron positions and length
• Structure and function
• Sequence
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Other gene families
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Overprinting• mutation creating a new start codon (AUG) can
create a new gene• Two genes share a section in common• Tymoviruses have overprinted section
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cDNA insertion
• Adh gene in Drosophila usually onchromosome 2
• In D. teissieri and D. yakuba a similar genealso found on chromosome 3
• Both apparently functional
• The one on chromosome 3 may have arisenby insertion of reverse transcribed mRNA !
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Chromosome alterations
• Inversions
• Polyploidy
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Inversion
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Inversions and linkage
• Linkage: non-independent assortment atmeiosis
• Inversion prevents alignment
• Crossing over (recombination) very rarewithin an inversion– Genes within an inversion are linked
– Inherited together as a unit
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Advantage of inversion
• alleles that function well together staytogether– Not broken up by recombination
• If a linkage group is particularly adapted toan ecological circumstance, then individualswith linked genes may outreproduceindividuals with unlinked genes– Inverted linkage group increases in frequency
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Drosophila subobscura
• Has 6 chromosomes, each of which ispolymorphic for inverted linkage groups
• Frequency varies geographically withclimate: called a cline
• Semi-natural experiment: fly accidentallyintroduced to Chile and Washington state
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Inversion frequency selected
• Genes within inversion affect body size• Smaller flies favored in hot dry climates• Larger flies favored in cooler wetter
climates
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Polyploidy
• What is ploidy?
• Haploid
• Diploid
• So what could polyploid be?
• Common in plants, rare in animals– Self fertilization increases likelihood
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Tetraploidy
• Meiosis errorproduces diploidgametes
• With selffertilization, 4nindividual results
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Polyploidy and speciation
• 4n (or 8n or whatever) individual notcompatible with normal 2n
• Reproductively isolated• Estimated that 1/2 of all flowering plant
species are polyploid– Not all became species because of ploidy
• Polyploid formation may be as common as2 for each 10,000 offspring!
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Measuring genetic variation
• Classical view: there should be little geneticvariation– Selection should produce the ‘best’ type
– Called wild type
– Other variants eliminated
• Data show abundant genetic variation
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Phenotypic assay
• Mendel’ s peas– Red– White
• Works ok if phenotype directly revealsgenotype
• E.g. human resistance to parasitic flatwormSchistosoma mansoni– Brazil 60% homozygous resistant; 5%
homozygous susceptible; 35% heterozygous
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Electrophoresis
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Observinggenetic variation
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Recall the delta 32 mutation?
• That was the 32 base pair deletion in theCCR5 co-receptor
• HIV binds to the CD4 receptor and normalCCR5 co-receptor, gets into cell
• Delta 32 mutation stops HIV from bindingand getting into the cell
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CCR5 Delta32 geneticvariation
PCR increases quantity ofDNA
Restriction enzyme cuts of332 bp chunk
Remainder is one of twotypes:
403 bp wild type
371 bp delta 32
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Allele frequency
• Delta 32 allele of CCR5 prevents HIVinfection
• We’d like to know how frequent that alleleis
• We’d also like to know how the variation isdistributed
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Delta 32genotypes in
differentpopulations
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Calculating allele frequency fromgenotypic data
• +/+ = homozygous wild type• +/32 = heterozygous• 32/32 = homozygous recessive
• Suppose genotypic frequencies are+/+ = 25 people+/32 = 15 people32/32 = 10 people
50 people total; 100 alleles total
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Geographic genetic variation
Lactate dehydrogenase in mummichog(Fundulus heteroclitus)
LDH-Bb has higher catalytic activity atcolder temperatures
Lactate -> pyruvate
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Average (mean) heterozygosity
• To compare across studies we need a metric
• Mean heterozygosity is either– Average frequency of heterozygotes across loci
– Or
– Proportion of heterozygous loci in the ‘average’individual
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Populationheterozygosity
Generalization
1/3 to 1/2 of enzyme lociare polymorphic
Average individualheterozygous at 5 to15% of loci
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Summary• There is gobs of genetic variation
– Measured by electrophoresis of proteins or DNA– Summarized as heterozygosity or % polymorphic loci
• Genetic variation created by:– Mutation -> new alleles– Unequal crossover -> new genes– Insertion of rt transcribed mRNA -> new genes– Inversions -> linkage groups– Improper meiosis -> polyploidy
• Next 4 lectures cover ~100 pages and 2 chapters– Keep up with the reading