1. Compensatory Mutations
    changes at other loci that do not reduce the degree of resistance, but do reduce or eliminate the fitness costs associated with the resistant phenotype
  2. Haploid
    one gene copy at each loci
  3. Population Genetics two main theories
    • a. Darwin: natural Selection
    • b. Mendel: genetic transmission
  4. Continuous vs. Discontinuous variation
    • Continuous: finely graded continuous characters essential for Darwin's theory of evolution
    • Discontinuous: substantive discrete variations as studied by Mendel
  5. Polygenic traits
    traits affected by many genes simultaneously--first step in reconciling Darwinian natural selection with Mendel's inheritance b/c they can exhibit nearly continuous variation
  6. Multifactorial Inheritance
    inheritance of a polygenic trait (more complicated than simple Mendelian inheritance, but still predictable in a Mendelian framework)
  7. Additive Genetic Effects
    • the phenotype can be calculated by summing the effects of each allele
    • Example: more alleles for a darker color will give a darker phenotype
  8. Latent Variation
    genetic reassortment draws out new phenotypes from preexisting variation (even in the absence of mutation)
  9. Epistasis
    alleles at two or more loci interact in a non-additive way to form a phenotype (the effect of one allele depends on which allele(s) are present at other loci)
  10. Context Dependent
    the phenotypic effects of alleles at one locus depend on the context set by alleles at another locus
  11. Haplotypes
    a defined set of alleles, one at each locus under consideration--set of gene copies along one particular chromosome (i.e. ABc or aBC, not AaBBCc)
  12. Physical Linkage
    alleles on the same chromosome--separate together unless recombination occurs (if they are closer together recombination is less likely to affect them)
  13. Assortative Mating
    choose mates that are similar
  14. Linkage Disequilibrium
    statistical linkage between alleles at two different loci (i.e. alleles at locus A and locus B)
  15. Coefficient of Linkage Disequilibrium (D)
    difference between the actual frequency of the AB haplotype (hAB) and the expected frequency ( fA fB) of the same haplotype if the loci are independent—that is, if there is no association between the allele at one locus and the allele at the other (D=hAB - fA fB should be zero if independent)
  16. Coupling
    when "like" alleles tend to couple in haplotypes (i.e. A with B and a with b)
  17. Repulsion
    when "opposite" alleles tend to occur together (i.e. A with b and a with B)--doesn't tend to happen
  18. Positive vs. Negative linkage disequilibrium
    • Positive: excess coupling haplotypes
    • Negative: excess repulsion haplotypes
  19. Causes of Linkage Disequilibrium
    • mutation (simplest source)
    • selection (only for epistatic interactions)
    • genetic drift (fluctuation and/or loss of haplotype)
    • migration (intro of haplotypes--coupling, +D)
  20. Recombination and Linkage Disequilibrium
    In the absence of evolutionary processes recombination will dissipate linkage disequilibrium (recombination usually occurs between haplotype pairs) -- deltaD= -rD
  21. Alternate expression for coefficient of linkage disequilibrium (D)
    D= hAB hab - haB hAb (one half of frequency of coupling dbl heterozygotes - one half of frequency of repulsion dbl heterozygotes)
  22. Association Mapping
    technique by which loci responsible for disease/other traits are located--rate at which disequilibrium breaks down between two loci is proportional to the distance between them along the chromosome (fundamental principle underlying association mapping)
  23. Genetic Hitchhiking
    allele frequencies at loci that are physically linked to the locus under selection may also change--an unselected or disadvantageous allele is able to "ride" along with a nearby favorable allele and increase in frequency (recombination will eventually decrease association between these alleles)
  24. Background Selection
    selection tends to eliminate genetic background on which deleterious alleles arise
  25. Selection and Physical Linkage
    • Alleles can increase in frequency due to selection either because they directly code for beneficial traits on their bearers, or because they are physically linked to other beneficial alleles at other loci
    • Natural selection, be it positive or negative, tends to cause a decrease in genetic variation at loci near the selected allele
  26. Periodic Selection
    Result of tight linkage across entire bacterial genome: 1. New beneficial allele arises 2. fixation and selective sweep 3. new beneficial mutation arises and process repeats
  27. Selective Sweep
    when a beneficial mutation in bacteria is fixed, alleles at most other loci are also fixed because loci on bacterial chromosome are tightly linked
  28. Periodic Selection and Genetic Diversity
    Periodic selection greatly reduces genetic diversity (before heterogeneity can build up by mutation, selective sweep eliminates it, occurs over and over, especially with bottlenecks)
  29. Clonal Interference
    slowing down of selection (beneficial mutations compete with each other for fixation)
  30. Adaptive Landscape (Fitness Landscape)
    Interactions among genes are important, generating a genotype to phenotype map--think about diff phenotypic or genotypic combinations as points on a map (consider fitness points as well)
  31. Pleiotropy
    a single gene affects multiple phenotypes
  32. Norms of Reaction
    genes and environment interact in complex ways to determine phenotype
  33. Complications in genotype-phenotype map
    • 1. Pleiotropy
    • 2. Epistasis
    • 3. Norms of Reaction
    • 4. Dominance
    • 5. Multiple Pathways
  34. Dominance
    one allele may cover up another allele at the same locus
  35. Multiple Pathways
    A common phenotype may have a different genetic basis in different individuals
  36. Phenotypic Space (map)
    x- and y- axes represent the values of phenotypic traits (i.e. the size of a tree's leaves and the size of its flowers)--aspects of phenotype under consideration
  37. Fitness Peaks
    combination of traits associated with the greatest fitness values
  38. Fitness Valleys
    regions of lower fitness on fitness/adaptive landscape
  39. Genotype Space
    genotypes that are mutational neighbors—namely, those separated by a single mutation—appear close together in the genotype space, whereas those that are separated by many mutations appear far apart (regardless of phenotypic differences)--not continuous because mutations are discrete
  40. Quantitative Genetics
    study of continuously varying traits--enables us to track not only the phenotypes of the individuals in the population, but also the variation that is present in the population, and whether or not this variation is heritable
  41. Developmental Noise
    Random chance events during development that give rise to considerable phenotypic differences (with the same genotypes)
  42. Phenotypic Value (P)
    • P is defined as the phenotypic value of the continuous trait being studied
    • P= G + E (where G is due to genotype and E is due to environmental influence)
  43. Genotypic Value (G)
    expected phenotypic value of the individuals with that genotype
  44. Environmental Deviation (E)
    deviation from P and G is attributed to environmental effects--expected E is zero because it is equally likely to be positive or negative
  45. Variance
    statistical measure of variation in a sample (larger variance means individuals differ more from each other and from the mean)
  46. Phenotypic Variance (Vp)
    Vp = VG + VE
  47. Broad-Sense Heritability (H2)
    fraction of variance that is potentially heritable: H2=VG / (VG + VE)
  48. Dominance Effects
    interactions between two alleles at the same locus
  49. P = G + E = A + D + I + E
    • A: additive component (sum of expected individual effects on each allele--independent of genetic background
    • D: dominance component (sum of effects of dominance interactions between allele pairs at each locus)--depend on genetic background
    • I: interaction/epistatic component: effects of epistatic interactions across loci--dependent on genetic background
    • E: environment
  50. Narrow-sense heritability (h2)
    fraction of total variation that is due to additive genetic variation (accessible to natural selection) : h2= VA / (VA+VD+VI+VE)
  51. Breeder's equation
    relates the narrow-sense heritability, the strength of selection measured as S, and the consequences of selection measured as R: R=h2S (predicts evolutionary change for quantitative traits)
  52. Realized heritability
    Heritabilities estimated from the selection differential and the selective response
Card Set
Genetic Diversity consequences/causes