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Chapter 17

Chapter 17. Population Genetics. 8 and 11 April, 2005. Genes in natural populations. Overview. Populations contain a great deal of genetic variation. If no forces act to change gene frequencies, equilibrium is reached in one generation of random mating.

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Chapter 17

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  1. Chapter 17 Population Genetics 8 and 11 April, 2005 Genes in natural populations

  2. Overview • Populations contain a great deal of genetic variation. • If no forces act to change gene frequencies, equilibrium is reached in one generation of random mating. • Mutation, selection, migration, and random sampling can change allele frequencies. • Changes in frequencies of phenotypes are consequence of changes in allele frequencies at several loci.

  3. Genes in populations • New alleles introduced by mutation • Migration changes population composition • Mating may be random or assortative and may involve inbreeding or outbreeding • Recombination produces new combinations of alleles • Random fluctuation in reproductive rates may result in genetic drift in allele frequencies • Differential reproduction by different genotypes may result in natural selection

  4. Gene frequencies • Gene frequency refers to proportion of • particular allelic form among all copies of gene in population • Usually estimated by sampling population • diploid: 2 copies of gene • homozygotes: 2 copies of allele • heterozygotes: 1copy of each allele • haploid: 1 copy of allele • For two alleles, p + q = 1, where p and q are frequencies of the two alleles

  5. Calculating gene frequencies • Consider a sample of genotypes with the following frequencies A/A 0.36 A/a 0.48 a/a 0.16 p = frequency of A = 0.36 + 0.48/2 = 0.6 q = frequency of a = 0.48/2 + 0.16 = 0.4 (note: calculations use all of the data)

  6. Heterozygosity • Total frequency of heterozygotes for gene in question • Greatest when there are many alleles at equal frequencies • Also measured from haplotypes • combinations of alleles at closely linked loci • greater than heterozygosity because two or more heterozygotes are considered

  7. Polymorphism • Genetic variation occurs both within and between populations • Basis for evolutionary change • Most common variant is wild-type • Protein polymorphism • immunologic: recognized by antibodies • amino acid sequence • deduced from DNA sequence • differences in electrophoretic mobility

  8. DNA polymorphism • Chromosome polymorphism • karyotype differences • supernumerary chromosomes • translocation and inversion heterozygotes • Restriction fragment length polymorphism (RFLP) • mutation creates or abolishes restriction sites, resulting in different size fragments • Variable number tandem repeats (VNTR) • Complete sequence variation • SNP: single-nucleotide polymorphism • variation in both coding and noncoding regions • At DNA level, some variation may have no visible effect

  9. Hardy-Weinberg equilibrium • In large randomly mating populations with no mutation, no migration, and no selection, allele frequencies will be in equilibrium • At equilibrium, genotype and phenotype frequencies are function of allele frequencies • A/A A/a a/a • p2 2pq q2 • Allele frequencies are constant over time

  10. Consequences of H-W equilibrium • Most copies of rare alleles are present in heterozygotes, not homozygotes (2pq >> q2) • Does not apply to sex-linked genes if males and females have unequal gene frequencies • Based on random mating • random with respect to genes that have no influence over mate choice • mating may be random within subgroup (endogamy) but not in population as whole

  11. Sources of variation (1) • Mutation • source of genetic variation • mutation rate too low to drive evolutionary change • Recombination • linkage disequilibrium • nonrandom association of alleles • occurs with each new mutation • repeated recombination randomizes combinations of alleles (haplotypes) • linkage equilibrium

  12. Sources of variation (2) • Migration • immigration: migration into population • emigration: migration from population • if populations differ in gene frequencies, migration will alter frequencies • Nonrandom mating • inbreeding: mating between relatives • increased homozygosity • outbreeding: mating between non-relatives • positive assortative mating: mating between like individuals • negative assortative mating: mating between unalike individuals

  13. Homozygosity • May result from • systematic inbreeding • continued positive assortative mating • Allele may become fixed (p = 1, q = 0) in local population • Same consequence may occur when new population is founded by a few individuals

  14. Selection (1) • Natural selection: differential rates of reproduction and survival among different genotypes • term used by Darwin by analogy with artificial selection • Darwinian fitness: relative probability of survival and rate of reproduction • consequence of relationship between phenotype and environment • same genotype may have different fitness in different environments

  15. Selection (2) • Frequency-independent selection • fitness of phenotype is independent of frequency of phenotypes • fixed property of individual’s genotype • Frequency-dependent selection • fitness of phenotype changes depending upon frequency of phenotype in population • Fitness often measured as viability, the probability of survival to reproductive age

  16. How selection works (1) Differential reproduction of different genotypes, e.g., a/a lethal at maturity genotype A/A A/a a/a q born 0.81 0.18 0.01 0.1 mature 0.81 0.18 0.00 - corrected 0.818 0.182 0.00 0.091 q = 0.091 – 0.100 = – 0.019

  17. How selection works (2) • Genotype a/a may not be lethal, but have reduced fitness • not all offspring reach reproductive age • mature genotype leaves fewer offspring • Each allele may have associated fitness, W • WA/A WA/a Wa/a • allele with highest mean fitness relative to mean of other alleles increases in frequency, others decrease

  18. Well modeled behavior of a population where W(A/A) = 1, W(A/a) = 0.75 and W(a/a) = 0.4.

  19. Balanced polymorphism • Difficult for selection to remove already rare allele (masked in heterozygotes) • When fitness of heterozygote is greater than fitnesses of homozygotes, then stable equilibrium is possible where p and q have significant frequencies • balanced polymorphism a result of overdominance • Balanced polymorphism may also result from • equal fitnesses of all genotypes (selective neutrality) • introduction of new alleles by mutation and their removal by selection

  20. W(ST/ST) = .89, W(ST/CH) = 1.0 and W(CH/CH) = 0.41.

  21. Artificial selection • Truncation selection • for continuously varying character, only individuals above or below given phenotypic value are chosen for reproduction • when repeated, called constant truncation • Fitness may be reduced with increased selection

  22. Random events • Genetic drift • change in gene frequency as a result of chance events from generation to generation • most effective in small populations • may result in fixation of allele (p = 1) • Founder effect • small group breaks off from larger population • founding group contains sample of alleles not necessarily in same frequency as parent population • May result in establishing new mutation in population even though it is selected against

  23. Assignment: Concept map, Solved Problems 1-4, All Basic and Challenging Problems.

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