Lecture 8 From Inheritance to Population Genetics

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Lecture 8From Inheritance to Population Genetics

• Dominance and co-dominance
• Mendelian inheritance
• Hardy-Weinberg equilibrium
• Population differentiation

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Direct vs indirect sequence detection

• Direct
• Code of life
• Basis of inheritance
• Obtain lots of characters
• Independent
• 800-1000 characters
• Can distinguish mutations
• Synonymous vs. non-synonymous
• Transitions vs. transversions
• Relatively short section
• Inherited as one unit
• Biased sample
• Need primers
• Heterologous primers

• Indirect
• Only part of variation detected
• Important part?
• Mutation rate may be v. high
• Mini-, microsatellites
• Several (many) loci surveyed
• Or longer fragment
• Recombination
• Creation of variability
• Good coverage of genome
• Selected loci
• Genome mapping
• Independent gene lineages
• Primers
• Varies between markers

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RAPDRandom Amplified Fragment Polymorphism

• Arbitrary primers
• 8-10 bp long
• V. little development
• PCR
• Amplification where primers on opposite strands
  are close
• Variability
• Point mutations
• Insertions / deletions
• Low stringency
• Annealing temp 35-45oC

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Dominant and co-dominant
AA
AB
BB

• Estimation of allele frequencies ?
• Analysis of 1 / 0
• Phenotypic trait

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Dominant Minisatellites
Single Locus
Multilocus
Ind. 1
Ind. 2
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Review of key concepts

• Types of mutations
• Substitutions
• Synonymous / non-synonymous
• Codon position
• Transition / transversion
• Mutation rates
• Accumulation of mutations
• Multiple hits
• Transitions
• 3rd codon positions
• Direct sequencing

• Indirect sequence detection
• Lots of methods
• Different parts of sequence diversity
• RAPD
• Reproducibility
• dominance
• Direct vs. indirect sequence detection

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Mendelian inheritance

• If patterns of inheritance follow Mendelian laws
• Mendelian inheritance

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Mendelian inheritance The Hardy Weinberg Law
male

• Punnett Square
• Add frequencies
• f(A)0.3
• f(B)0.7

female
males
females
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Mendelian inheritance The Hardy Weinberg Law

• Punnett Square
• Add frequencies
• p2 2pq q2
• Hardy Weinberg Law

male
female

• Assumptions ideal population
• Diploidy
• Sexual reproduction
• Random mating
• No selection
• No mutation
• Large populations size
• No inbreeding

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Why is this important?

• Calculation of heterozygosity
• Observed heterozygosity (Ho)
• Frequency of heterozygotes
• Expected heterozygosity (He)
• Frequency of heterozygotes expected under HW
• He1-Spi2

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Why is this important?

• What about dominant markers?

AA
AB
BB
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Why is this important?

• Test
• Data
• Mis-scoring
• Non-genetic variation
• Locus under selection
• Biology of the population
• Mixture or panmictic
• Inbreeding
• Sexual reproduction
• Selection

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Deviations from HWexample

• Population mixture (N50)
• Pop 1
• p(105)0.8, q(107)0.2

• Pop 2
• p(105)0.2, q(107)0.8

• Mixture
• p(105)0.5, q(107)0.5

x27.445 P0.006

• Wahlund effect
• Can we go further than that?