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Population and evolutionary genetics 1
This document provides an overview of population and evolutionary genetics. It defines population genetics as the study of genetic variation within and between populations, examining how allele frequencies change over time due to various factors. Evolutionary genetics studies how evolutionary forces lead to speciation and diversification of organisms. The document notes that nothing in biology makes sense except in light of evolution, and discusses how human genetics has been shaped by both evolution and human population movements. It also clarifies terminology and discusses concepts like Hardy-Weinberg equilibrium, genetic drift, and how violations of Hardy-Weinberg assumptions like non-random mating can occur.
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Overview of the presentation and inclusion of key information about the presenter.
Population genetics studies genetic variation and evolutionary genetics examines forces that lead to speciation.
Quote by Dobzhansky highlighting evolution's critical role in understanding biology.
Human genetics shaped by billions of years of evolution and population movements.
Definitions of genetic variation, polymorphism, and mutation along with their significance.
Key factors affecting allele frequency: population size, selective pressure, mutation, and migration.
Introduction to Hardy-Weinberg equilibrium, factors that keep allele frequencies constant.
Discussion on Hardy-Weinberg Equation relating allele and genotype frequencies.
Calculating carrier frequencies in populations for recessive disorders like PKU and color blindness.
How deviations from Hardy-Weinberg apply to populations, including stratification and mating.
Explains how assortative mating and consanguinity affect genetic diversity and recessive disorders.
Factors violating Hardy-Weinberg: mutation, gene flow, and their effects on allele frequencies.
Examples of gene flow, including ancient human admixture and its implications for genetics.
Discussion on genetic drift, population bottlenecks, and founder effects reducing genetic diversity.
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Population and evolutionary genetics 1
- 1. Population and Evolutionary Genetics 1 Dr.Daniel Gaston [email protected] March 2018 https://goo.gl/E9LatX https://www.slideshare.net/dangaston
- 2. What are Populationand Evolutionary Genetics? “Population genetics is the study of genetic variation within and between populations. It involves the examination and modelling of changes in the frequencies of alleles in populations over space and time. Concerned with genetic, environmental, and societal factors.” “Evolutionary genetics is the study of how evolutionary forces and population genetics lead to speciation and diversification of organisms over time. Evolutionary genetics also studies the evolution of genome architecture and other aspects of genetic change.”
- 3. "Nothing in BiologyMakes Sense Except in the Light of Evolution" -- Theodosius Dobzhansky
- 4. Human Genetics isProfoundly Shaped by Billions of Years of Evolution We are here
- 5. Human Genetics isProfoundly Shaped by Human Population Movements
- 6. Mutation vs Polymorphismvs Variant â—Ź Genetic variant/variation is the broadest term â—Ź Polymorphism refers to variants present in a population â—‹ Generally common, minor allele > 1% in population â—‹ May or may not be associated with disease â—Ź Mutation has variable meaning depending on field of genetics â—‹ Synonymous with variant in evolutionary genetics â—‹ Often reserved for deleterious variation in medical/disease genetics
- 7. Population and EvolutionaryGenetics: A Brief Interlude About Terminology â—Ź Common and Rare: Are statistical properties of alleles â—Ź Dominant and Recessive: Are genotypic properties of alleles â—Ź Advantageous and Deleterious: Are phenotypic properties of alleles Any combination of these is possible!
- 8. What is PopulationGenetics? â—Ź Inheritance of individual genes is typically governed by Mendelian principles â—Ź What factors influence the frequency of alleles in a population? â—‹ Population size â—‹ Selective pressure â—‹ Reproductive forces â—‹ Mutation â—‹ Migration â—Ź What is a population? â—‹ A community of reproducing individuals inhabiting a geographic area â—‹ Sexually reproducing populations = Mendelian populations
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- 10. Hardy-Weinberg Equilibrium â—Ź Independentlydescribed by WH Hardy (British Statistician) and Wilhelm Weinberg (German Physician) in 1908 â—Ź The genetic variation within a population will remain the same from one generation to the next in the absence of disturbing factors
- 11. Hardy-Weinberg Equilibrium andthe Hardy-Weinberg Equation To the Editor of Science: I am reluctant to intrude in a discussion concerning matters of which I have no expert knowledge, and I should have expected the very simple point which I wish to make to have been familiar to biologists. However, some remarks of Mr. Udny Yule, to which Mr. R. C. Punnett has called my attention, suggest that it may still be worth making...
- 12. Assumptions of Hardy-Weinberg ImageCredit: https://evieiraapbio.blogspot.ca/
- 13. Large Population Large populationbuffers against allele changes due to random events. Think of the impact of an earthquake on a large versus a small population
- 14. The Hardy-Weinberg Equation: LinkingAllele and Genotype Frequencies â—Ź In a population at Hardy-Weinberg Equilibrium we can relate allele frequencies to genotype frequencies. Alleles pair randomly â—‹ Frequency of A allele is p â—‹ Frequency of a allele is q â—‹ p + q = 1 â—‹ The genotype frequencies become (p + q)2 A (p) A (q) A (p) AA (p2 ) Aa (qp) a (q) Aa (qp) Aa (q2 )p2 + 2pq + q2 = 1
- 15. The Hardy-Weinberg Equation: LinkingAllele and Genotype Frequencies p2 + 2pq + q2 = 1
- 16. Generalizing Hardy-Weinberg to3 Alleles â—Ź For three alleles, instead of the binomial expansion of (p + q)2 it is the trinomial expansion of (p + q + r)2 : â—‹ p2 + q2 + r2 + 2pq + 2pr + 2qr
- 17. Hardy-Weinberg in Autosomal RecessiveDisorders ● Using Hardy-Weinberg to calculate carrier frequencies from population samples of recessive phenotype ● Group all disease-causing alleles together as if they were really only one disease-associated allele (q) ● Determine the frequency of the disease in the specified population, this is q2 ● This allows us to calculate the allele frequency (q) and the carrier frequency (2pq) ● Example: ○ The frequency of the disease PKU in a specific population is 1/4500 (q2 = 1/4500 = 0.000222…) ○ q = 0.015, 2pq = 0.029 (Carrier frequency in population is ~3%)
- 18. Hardy-Weinberg in X-LinkedDisorders: Red-Green Colour Blindness â—Ź Three possible female genotypes and 2 possible male genotypes for genes on the X chromosome (outside pseudo-autosomal region) Sex Genotype Phenotype Incidence (Approx) Male X+ Normal p = 0.92 Xcb Colour blind q = 0.08 Female X+ /X+ Normal (homozygote) p2 = (0.92)2 = 0.8464 X+ /Xcb Normal (heterozygote) 2pq = 2(0.92)(0.08) = 0.1472 Normal (combined) p2 + 2pq = 0.9936 Xcb /Xcb Colour blind q2 = (0.08)2 = 0.0064
- 19. If it appliesmainly to ideal populations, how else is it useful? Deviations from Hardy-Weinberg Equilibria
- 20. Assumptions of Hardy-Weinberg ImageCredit: https://evieiraapbio.blogspot.ca/
- 21. Chi-Squared Significance forDeviation from Hardy-Weinberg Phenotype White-spotted (AA) Intermediate (Aa) Little spotting (aa) Total Number 1469 138 5 1612 Assuming Hardy-Weinberg:
- 22. p = 0.954,q = 0.046, Exp(AA) = 1467.4, Exp(Aa) = 141.2, Exp(aa) = 3.4 Pearson’s chi-squared test (1 degree of freedom, 5% significance level 3.84): Null Hypothesis: Not Rejected Chi-Squared Significance for Deviation from Hardy-Weinberg Phenotype White-spotted (AA) Intermediate (Aa) Little spotting (aa) Total Number 1469 138 5 1612
- 23. Nonrandom Mating Violates Hardy-Weinberg Populationstratification Assortative mating Consanguinity
- 24. Population Stratification â—Ź Subgroupswith limited genetic mixing for historical, cultural, religious, or geographic reasons â—Ź Can mislead case-control studies when not accounted for â—Ź Hardy-Weinberg, when naively applied, will incorrectly estimate disease frequencies from genotype frequencies
- 25. Population Stratification Example â—ŹMinority population (10% of total population) â—Ź Allele frequency for mutant allele that causes a recessive disease in the minority population (qmin ) is 0.05. Therefore pmin is 0.95 â—Ź In the majority population (90%), mutant allele is essentially absent (qmaj ~ 0, pmaj ~ 1) â—Ź qpop = 0.1 x 0.05 = 0.005 â—Ź Naive application of Hardy-Weinberg to estimate disease frequency: â—‹ q2 pop = (0.005)2 = 2.5 x 10-5 â—Ź If stratification: q2 min = (0.05)2 = 0.0025 â—‹ q2 pop = 0.0025/10 = 2.5 x 10-4
- 26. Assortative Mating â—Ź Non-randommating based on traits â—Ź People tend to choose mates similar to themselves â—‹ IQ (some evidence) â—‹ Educational attainment â—‹ Congenital conditions â– Blindness â– Deafness â– Extreme short -stature â—Ź Results in an increase in homozygous genotypes â—Ź Disassortative mating for MHC
- 27. Consanguinity and Inbreeding â—ŹAlso increases the incidence of recessive disease by increasing the frequency of mating between carriers of recessive traits â—Ź Unlike assortative mating, resulting recessive disorders may be extremely rare and unusual compared to the population â—Ź Similar to founder effects
- 28. Non-Constant Allele Frequencies ViolateHardy-Weinberg Mutation Gene Flow Selection Genetic Drift
- 29. Mutation Adds NewAlleles â—Ź Much slower process than nonrandom mating â—Ź Less deviation from Hardy-Weinberg (at least for recessive mutations) â—Ź Rate of new mutation is typically << frequency of recessive disease causing alleles â—Ź Most deleterious mutations initially hidden in asymptomatic heterozygotes, not subject to selection â—‹ Not the case for X-linked or dominant
- 30. Gene Flow/Migration IntroducesNew Alleles â—Ź Conceptually similar to mutation, introduction of new alleles to a population â—Ź Migration in the broad sense: overcoming reproductive barriers of any kind (geographic, cultural, ethnic)
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- 33. Gene Flow: ArchaicHuman Admixture (Introgression)
- 35. Population Size andRandom Events: Genetic Drift
- 36. Population Size andRandom Events: Genetic Drift Small Population Larger Population
- 37. Population Bottlenecks Reduce Diversity:Founder Effects