Chapter 6 - Drift and Selection

ZIMMER and EMLEN FREEMAN and HERRON

6.1 The Genetics of Populations p. 161

  •  Although individual organisms can change over their lifetime, evolution occurs only when the frequencies of alleles within a population change from one generation to the next.
  1. The ways of change
  2. Population genetics
    1. Study of the distribution of alleles in populations and causes of allele frequency changes
  3. Key Concepts
    1. Diploid individuals carry two alleles at every locus
      1. Homozygous: alleles are the same
      2. Heterozygous: alleles are different
    2. Evolution: change in allele frequencies from one generation to the next
 
 6.2 Change over Time-or Not p. 162
  • Hardy-Weinberg equilibrium is an outcome of a mathematical model that demonstrates the relationship between allele frequencies and genotype frequencies.
  • The model reaches equilibrium when genotype frequencies no longer change between iterations.
  • An introduction to Hardy-Weinberg from Kimball's Biology Place
  1. Assumptions for Hardy-Weinberg equilibrium:
    1. No selection on any genotype (Genotypes do not differ in fitness)
    2. No mutation
    3. No migration
    4. No random events affecting population
    5. Mating within population at random (panmixis)
    6. In other words, no evolution.
  2. Population allele frequencies do not change if:
    1. Population is infinitely large
    2. Hardy-Weinberg assumptions are valid
  • Key points:
    1. Conclusion 1: At equilibrium, allele frequencies do not change from generation to generation
    2. Conclusion 2: allele frequencies predict genotype frequencies (p2 + 2pq + q2)
    3. if population displaced from equilibrium, return to equilibrium in one generation
  •  
    INTRODUCTION
    1. An introduction to Hardy-Weinberg from Kimball's Biology Place
    2. Population genetics follows allele and genotypic frequencies across generations.
    3. population: a group of interbreeding organisms and their offspring
    4. gene pool: the collection of alleles present within a population 
    5. allele frequency: the proportion of an individual allele within the gene pool 
    6. genotype frequency: the proportion of a genotype within the population 
    7. Hardy-Weinberg equilibrium: null model for gene frequencies in the absence of evolution.
      1. The null hypothesis is that the observed and expected values are not significantly different from one another for either allele frequencies or genotype frequencies
      2. Null hypothesis and HW.

    6.3 Evolution’s "Null Hypothesis" p. 163

    • The Hardy-Weinberg model begins with several assumptions that may not hold in natural populations, including no mutation, migration, selection, or drift, and that mating is entirely random.
    1. Populations evolve through a variety of mechanisms  (Fig. 6.3)
      1. Drift
      2. Natural selection
      3. Migration (gene flow)
      4. Mutation
    2. Key Concept
      1. Hardy-Weinberg serves as the fundamental null model in population genetics
      2. Box 6.2 The Relationship between Allele and Genotype Frequencies

    Adding migration to the H-W analysis: Migration as an evolutionary force

    • migration: movement of alleles between populations = gene flow
    • One-island model

    Box 6.2 The Relationship between Allele and Genotype Frequencies p. 164
    1. Allele frequencies predict genotype frequencies
    2. The General Case

      1. fr(A1) = p
      2. fr(A2) = q
      3. p + q = 1
      4. the frequency of genotypes is [Figs. 6.6 - 6.9]:
        1. homozygote A1: fr(A1A1) = p2
        2. heterozygote A1A2: fr(A1A2) = pq + pq = 2pq
        3. homozygote A2: fr(A2A2) = q2
      5. p = p2 + ½ (2pq) = p2 + pq
      6. q = q2 + ½ (2pq) = q2 + pq
      7. p + q = 1
      8. (p + q)2 = 1
      9. p2 + 2pq + q2 = 1 (the Hardy-Weinberg Principle)
      10. Same trick works with multiple loci: e.g., 3 alleles 
        1. p + q + r = 1 
        2. p2 + q2 + r2 + 2pq + 2pr + 2qr = 1
    3. Key Concepts
      1. Hardy-Weinberg theorem proves that allele frequencies do not change in the absence of drift, selection, mutation, and migration
      2. Mechanisms of evolution are forces that change allele frequencies

      THE HARDY-WEINBERG EQUILIBRIUM PRINCIPLE

    • Does the gene pool predict the distribution of genotypes within a population?

    A Numerical Example

    1. hypothetical population through one cycle from gametes in generation 1 to gametes in generation 2 (Fig. 6.1)
    2. Figure 6.2: A gene pool with allele frequencies of 0.6 for allele A and 0.4 for allele a.
    3. simulation showing allele frequencies change across generations as a result of chance for 100 sperm and 100 eggs (Fig. 6.3)
      1. For example, 34 AA, 57 Aa, and 9 aa adults
      2. The 34 AA adults produce 340 A gametes; the 57 Aa adults produce 285 A gametes and 285 a gametes; and the 9 aa adults produce 90 a gametes.
    4. Punnett square [Fig. 6.4]
    5. F1 gene pool with fr(A) = 0.6 and fr(a) = 0.4 (fig. 6.2) yields zygotes with AA = 0.36, Aa = 0.48, and aa = 0.16 [Fig. 6.5, Box 6.1 in Freeman and Herron]
    6. F2 gene pool has gametes with fr(A) = 0.6 and fr(a) = 0.4 (Figs. 6.6, 6.7)

     Box Figure 6..3.1 in Zimmer and Emlen: Testing Hardy-Weinberg Predictions
    Genotypes AA AS SS  
    Observed no. among adults 9,365 2,993 29 Total: 12,387
    Observed freq. among adults 0.756  0.242 0.002  
    Expected no. among adults (H-W) 9,523  2,676 188 Total: 12,387
    Expected freq. among adults (H-W)  0.769   0.216 0.015  
    • The population is not in Hardy-Weinberg equilibrium.  Observed values differ significantly from expected.

     sickle cell anemia:

    •  Individuals with sickle cell trait (AS heterozygotes) are more resistant to malaria. 
    • In regions with malaria, AS individuals have greater fitness, and are present in higher numbers than predicted by H-W (heterozygote advantage)

    6.4 A Random Sample p.165

    • Like natural selection, genetic drift is a mechanism of evolution
    • drift describes the changes in allelic frequencies that arise by chance because the number of individual alleles that can be passed on in diploid organisms is limited.
    1. Genetic drift causes evolution in finite populations
      1. Results of experiments by Buri on genetic drift in laboratory populations of Drosphila. (Fig. 6.4 from Hartl)
    2. Figure 6.4 is a three dimensional representation of Fig. 7.16 in F&H 4th ed
      1. The figure shows  bw75  allele frequencies in all 107 populations over 19 generations (Y axis).
      2. the X axis represents the frequency of the  bw75  allele, and the vertical (Z) axis represents the number of populations showing each frequency.
      3. The frequency of  bw75  was 0.5 in all populations in generation zero (box in lower left of figure).
      4. By the end of the experiment, 30 populations had become fixed at a frequency of 0, and 28 had become fixed at a frequency of 1 (box in lower right of figure).
    3. Genetic drift results from random sampling error(Fig. 6.5)

      • In this simulation from Wikipedia, there is fixation in the blue "allele" within five generations.

    4. Drift reduces genetic variation in a population 
      1. Alleles are lost at a faster rate in small populations
        1. Alternative allele is fixed
      2. Fig. 6.6, same as Figure 7.15 in F&H, 4th ed.
        1. Plots of the frequency of allele A1 over 50 generations.
        2. Initial frequency of A1 was 0.5
        3. Eight populations are tracked in each, with one highlighted in red.
        4. Genetic drift leads to random fixation of alleles
        5. Drift is a more powerful force of evolution in small populations

    Allele frequencies and Drift

    Image from Wikipedia Simulation of genetic drift of 20 unlinked alleles in populations of 10 (top) and 100 (bottom). Drift to fixation is more rapid in the smaller population.

    1. Key Concepts
      1. Genetic drift causes allele frequencies to change in populations
      2. Alleles are lost more rapidly in small populations 

    6.2     GENETIC DRIFT

    • A Model of Genetic Drift
    1. bag-of-beans analogy
    2. start with 100 beans: A1 = 0.6, A2 = 0.4
    3. pick 20 at random to produce 10 individuals of the next generation 
    4. A1 = 0.7, A2 = 0.3 [Fig. 6.10]
    5. Range of possible outcome for 10 zygotes produced at random [Fig. 6.11]
  • Genetic Drift and Sample Size
    1. Random fluctuations in gene frequency due to sampling error in finite populations.
      1. probability of bias decreases as sample size increases
      2. Random biases are expected when sample sizes are small.
      3. A1 = 0.6, A2 = 0.4: initially allele frequencies fluctuate wildly, but approach Hardy-Weinberg value for a large number of zygotes [Fig. 6.12]
    2. sampling error does not lead to adaptation, but leads to changes in allele frequency 
      • genetic drift: deviation of a population from Hardy-Weinberg expectations due to sampling error
      • Biases due to sampling error are purely random
    3.  Several processes in natural populations result in sampling error
      1. genetic drift: during random mating (of small populations), alleles are "sampled" to form progeny
      2. founder events: sampling small number of genotypes from a source population
      3. population bottlenecks: population crashes to low numbers then regrows. 
    4. Random Fixation of Alleles

    5. Variation in small populations is reduced by genetic drift
    6. alleles can be lost or fixed [Fig. 6.13]
      1. rate of loss or fixation depends on sample size
      2. even for larger sample sizes, substantial variation in allele frequency between populations can be created [Fig. 6.13c]
      3. If genetic drift is the only evolutionary force at work, eventually one allele will drift to a frequency of 1.
    7. Probability of an allele being lost through drift is inversely proportional to its initial frequency.
      1. experiment with fruit flies shows that nonselected allele initially present at 0.5 has an equal probability of being lost or fixed [Fig. 6.14
      2. drift reduces heterozygosity [Fig. 6.15].
    8. Drift in Ozark collared lizards (Tempelton et al., 1990)
      1. Collared lizards populations are currently limited to scattered, small exposed rocky outcrops
      2. populations on glades are small, therefore they should show evidence of drift [fig. 6.16]
        1. single genotype within populations (because drift fixes one allele at each locus)
        2. variation in genotypes among populations (because which allele is fixed is random)
      1. Population size and genetic diversity in four plant taxa [Fig. 6.17]
        1. Genetic diversity increases with population size

      The Rate of Evolution by Genetic Drift

      When mutation, genetic drift, and selection interact, three processes occur

      1. Deleterious alleles appear and are eliminated by selection
      2. Neutral mutations appear and are fixed or lost by chance
      3. Advantageous alleles are swept to fixation by selection

    9. Neutral theory: 2 is more important

    10. Selectionist theory: 3 is more important

  • 6.5 Bottlenecks and Founder Effects p. 169

    • Genetic bottlenecks and founder effects are population phenomena
    • when population sizes are drastically reduced, not only is genetic variation lost, but the effects of drift become increasingly important.
    1. Bottlenecks reduce genetic variation (Fig. 6.8)
      1. Northern elephant seal populations were reduced to about 30 individuals in the 1800’s
      2. Many mitochondria loci became monomorphic
    2. Rare alleles are likely to be lost during a bottleneck (Fig 6.9)
    3. Founder effect (Figs. 6.10-11)
      1. Founder effects cause genetic drift
      2. 28 mutineers from the HMS Bounty settled on Pitcairn Island with 6 Tahitian men and 12 women
    4. Norfolk Island
      1.  ]Identification of X-Linked Genes in Migraine (Figs. 6.12)
    5. Key Concept
      1. Even brief bottlenecks can lead to a drastic reduction in genetic diversity that can persist for generations

    Founder effect

    Simple illustration of founder effect. The original population is on the left with three possible founder populations on the right.

    Sampling Processes and the Founder Effect/h4>

    Founder effect depends on allele frequencies in source population and number of founders (Nf)

    • three males and two females of large ground finches remained on Daphne Major in 1982 and bred there. The population established there by 1993 had larger and wider bills than nonbreeding visitors
    • High frequencies of disease alleles in some isolated human populations.
      • Ellis-van Creveld Syndrome (dwarfism) in Amish populations (F&H p 168)

    Random Fixation of Alleles

    1. Variation in small populations is reduced by genetic drift
      1. alleles can be lost or fixed [Fig. 6.13]
        1. rate of loss or fixation depends on sample size
        2. even for larger sample sizes, substantial variation in allele frequency between populations can be created [Fig. 6.13c]
        3. If genetic drift is the only evolutionary force at work, eventually one allele will drift to a frequency of 1.
      2. Probability of an allele being lost through drift is inversely proportional to its initial frequency.
        1. experiment with fruit flies shows that nonselected allele initially present at 0.5 has an equal probability of being lost or fixed [Fig. 6.14]
        2. drift reduces heterozygosity [Fig. 6.15].
    2. Drift in Ozark collared lizards (Tempelton et al., 1990)
      1. Collared lizards populations are currently limited to scattered, small exposed rocky outcrops (glades), that are islands in the forested habitat
      2. populations on glades are small, therefore they should show evidence of drift [fig. 6.16]
        1. single genotype within populations (because drift fixes one allele at each locus)
        2. variation in genotypes among populations (because which allele is fixed is random)
    3. Population size and genetic diversity in four plant taxa [Fig. 6.17]
      1. Genetic diversity increases with population size

    6.6 Selection: Winning and Losing p. 172

    • Natural selection arises whenever individuals vary in the expression of their phenotypes, and this variation causes some individuals to perform better than others.
    1. The concept of fitness
    2. Fitness: the reproductive success of an individual with a particular phenotype
    3. Components of fitness:
      1. Survival to reproductive age
      2. Mating success
      3. Fecundity
    4. Relative fitness: fitness of a genotype standardized by comparison to other genotypes
      1. wxy = relative fitness of genotype AxAy 
      2. Relative fitness can be measured in two ways
        1.  wxy = Number of offspring for a particular genotype/average number of offspring for all genotypes
          1. If a genotype produces more offspring than average  wxy  > 1
          2. If a genotype produces fewer offspring than average  wxy  < 1
        2.  wxy = 1 - s
          1. s is the selection coefficient:
          2. 0<s<1;
          3. The genotype that produces the largest number of  fertile progeny has s = 0
          4. s = 1 indicates complete lethality.
          5. as s 1, relative fitness of wxy
    5. Contribution of alleles to fitness
      1. Average excess of fitness: difference between average fitness of individuals with allele vs. those without
      2. delta p = (p / w) / aA   (you do not have to know how to use this formula)
        1. where delta (p) = change in allele frequency due to selection
        2. p is the frequency of allele Ai
        3. w is the average fitness of the population
        4.  aA is average excess of fitness of the Ai allele
        5. If aA is positive, allele Ai will increase in frequency in the next generation
        6. If aA is negative, allele Ai will decrease in frequency in the next generation
    1. Key Concepts
      1. Selection occurs when genotypes differ in fitness
      2. Outcome of selection depends on frequency of allele and effects on fitness
      3. Population size influences power of drift and selection
        1. Drift more powerful in small population
        2. Selection more powerful in large population

    Adding selection to the H-W analysis: Changes in allele frequencies

    • Fitness of a genotype depends on relationship between genotype and phenotype
    • Selection can cause allele frequencies to change across generations when individuals with some genotypes survive at higher rates than individuals with other genotypes [Fig. 6.11]
    •  Alleles that confer reproductive success are selected for and can become fixed in populations [Fig. 6.12].

    SSmall Differences, Big Results 176

    • Selection and drift are powerful forces that can rapidly shape the relative distributions of allele frequencies within a population./li>
    1. NNatural selection more powerful in large populations (Fig. 6.13)
      1. allele that increase fitness 5% starts with em>frequency = 0.1
      2. in population of 10,000 individuals, allele becomes more common in all computer simulations
      3. drift is more important in small populations, more fit allele can be lost
    2. Drift weaker in large populations
    3. Small advantages in fitness can lead to large changes over the long term

     

     
    PPatterns of Selection in Time and Space 177
    • Selection is not a uniform process. It can vary over time, and geographical factors can produce spatial variation./li>
    1. Pleiotropy
      1.  mutation in a single gene that affects many phenotypic traits
      2. Net effect on fitness determines outcome of selection
    2. Antagonistic Pleiotropy
      1.  alleles can have negative effects on one aspect of fitness, but positive effects on another trait A.can lead to evolutionary “trade-offs” in fitness (e.g. between fertility and survival)
      2. can maintain genetic variation within populations
    3. Pleiotropy may constrain evolution
      1. Net effect on fitness determines outcome of selection
    4. Pesticide resistance and pleiotropy (Fig. 6.2)
      1. Ester1 allele for resistance arouse by mutation
      2. Increased frequency of pesticide resistance allele (from 0 to >50%) on coast by 1973.
      3. SSelected against inland
    5. Pesticide resistance and pleiotropy (Fig. 6.14)
      1. Ester4 allele provides slightly less protection, but spread and replaced Ester1 allele because it did not have costs for inland population and therefore spread /ol>
      2.  Key Concepts
        1. Alleles may have pleiotropic effects
          1. When fitness effects oppose each other, environment determines direction of selection
           
    Fifty Thousand Generations of Selection: Experimental Evolution 178
    • Scientists can closely observe selection in carefully designed experiments on rapidly reproducing organisms such as bacteria./li>
    1. Experimental evolution provides important insights about selection
    2. Natural selection in action  (Lenski's experiment) (FFig. 6.15-6.16)
      1. Alleles that lower fitness experience strong>negative selection
      2. Alleles that increase fitness experience positive selection

    Growth in cell size of bacteria in the Lenski experiment

    1. Key Concepts
      1. Laboratory evolution studies reveal how alleles rise and spread through populations

     

     

    Mutation and Selection

    • mutation provides variation that can be strongly acted on by selection
    • changes over time in cell size on E. coli grown on a limiting medium (Lenski's lab) [Fig. 66.25
    Dominance: Allele versus Allele 180
    • The interaction of alleles at the same locus can produce its own dynamics of selection./li>
    1. Relationships among alleles at a locus
      1. Additive: allele yields twice the phenotypic effect when two copies present
      2. Dominance: dominant allele masks presence of recessive in heterozygote
    2. Effects of selection on different types of alleles  (Fig. 6.17)
      1. Additive
      2. Dominant
      3. Recessive
    3.  Key Concepts
      1. Rare alleles almost always carried in a heterozygous state
        1. Recessive alleles invisible to selection
        2. Selection cannot drive dominant to fixation

    6.3    PATTERNS OF SELECTION

    Selection on Dominant and Recessive Alleles

    • selection in Tribolium (flour) beetles [Fig. 6.16]
      • when a recessive allele is common (and a dominant is rare), evolution by natural selection is rapid
      • when the recessive allele is rare, most copies will be hidden in heterozygotes and natural selection will be unable to change frequencies and fix alleles even if selection is very strong
    • An algebraic treatment of selection on recessive and dominant alleles [Box 6.7]
      • if selection favors a recessive allele it will increase slowly at first.  As the recessives increases the rate of evolution will accelerate until the recessive is fixed [Fig. 6.17]
      • sselection against lethal dominants can eliminate them in one generation
    Mutation-Selection Balance 182
    • The origin of new mutations and the purging action of selectionbr>produce equilibrium.
     Mutation generates variation
    1. Mutation rates for any given gene are low
      1. A.In humans: 1.1 x 10-8 per position  per haploid genome
    2. But, considering genome size and population size many new mutations arise each generation
      1. Estimate in humans: 9.8 billion new mutations
    3. Mutation is the source of variation for selection and drift to act
    4. Mutations are the source of new genetic variation in populations   
      1. Can be many mutations in a large population

    Box 6.6 Mutation-selection balance for a Recessive Allele

    1. Mutation-selection balance
      1. Equilibrium frequency reached through tug-of-war between negative selection and new mutation
    2. Explains persistence of rare deleterious mutations in populations
      1. as selection removes deleterious alleles, mutation resupplies them.
      2. A balance between the two may explain the persistence of deleterious alleles in populations
      3. μ = rate at which A1   A2
      4. wxy = relative fitness of AxAy  = 1 - s
      5. s is the selection coefficient: 0<s<1; as s 1, relative fitness of wxy
      6. equilibrium frequency of q = (μ/s)1/2 [see Box 6.10 for derivation]
      7. if A2 is a lethal dominant, then = μ/s = μ [see Box 6.10 for derivation]
      8. spinal muscular atrophy
        1. a loss of function allele with q = .01 in Caucasian populations
        2. s is estimated to be 0.9
        3. μ = s* 2 = 0.9 x 10-4 per allele per generation
        4. this agrees with the observation that 7 of 340 affected individuals carried a new mutation not present in either parent.
        5. This is a mutation rate of 1.1 x 10-4 per allele per generation

     

    Mutation-Selection Balance

    Example: Cystic Fibrosis

    1. CF is caused by recessive loss-of-function mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene
    2. gene plays a role in allowing cells of lung lining to ingest and destroy Pseudomonas aeruginosa bacteria
    3. inability to destroy bacteria means individuals homozygous for mutant CFTRs have chronic P. aeruginosa lung infections [Fig. 6.26]
    4. ultimately leads to severe lung damage and early death
    5. homozygous recessive (cc) lethal
    6. 1/2000 (0.0005) people in northern Europe have CF
      1.  if in H-W equilibrium, then q2 = 0.0005 and q = 0.0224 
      2. if c is maintained by mutation selection balance, and cc has 0 fitness, s = 1, then
      3. q = 0.0224 = (μ/1)0.5
      4. μ = 0.0005 = 5 x 10-4, an unusually high mutation rate, suggesting incorrect assumptions
    7. actual mutation rate is 6.7 x 10-7
    8. perhaps c is maintained by heterozygote superiority
    9. cells heterozygous for CF have a substantial resistance to the bacteria that cause typhoid [Fig. 66.27]
    • Selecting Diversity 184
      • Although natural selection often leads to a loss of genetic varia-br>tion, it can favor multiple alleles within a population.
    1. Balancing selection
      1. Some forms of selection maintain diversity in populations:
        1. Negative frequency-dependent selection
        2. Heterozygote advantage
    2. Negative frequency-dependent selection
      1. Elderflower orchids [Fig 6.17]
        1. Negative frequency-dependent selection maintains a dramatic flower color polymorphism (2 colors)
        2. Both provide no nectar reward to pollinators (bees)
    3. Heterozygote advantage and sickle-cell anemia
    Key Concepts
    1. Balancing selection maintains multiple alleles in populations
      1. Negative frequency-dependent
      2. Heterozygote advantage

     

    Frequency-Dependent Selection

    1. selection can maintain two different alleles in a population if each allele is advantageous when it is rare
      1. Third edition: frequency of left-handed scale-eating fish [Fig. 5.19] over time [Fig. 5.20].
        1. as left handed increase, prey become wary of being bit on the left
        2. left decrease and right increase leading to an increase of left.
        3. fluctuation around equilibrium value
      2. Elderflower orchids [Fig 6.21]

    Selection on Heterozygotes and Homozygotes

    • the heterozygote can have a fitness between both homozygotes [Box 6.8]
    • heterozygote superiority = heterosis = overdominance
      1. Drosophila: equilibrium frequency for viable and lethal alleles [Fig.6.18].
      2. sickle cell anemia and malaria.
    • heterozygote inferiority or underdominance
      1. compound chromosomes in fruit flies [Fig. 6.19] 
        1. are either fixed if the frequency of C(2) > 0.8 
        2. eliminated if C(2) < 0.8
        3. in equilibrium only if C(2) = 0.8. 
        4. Heterozygotes are inviable
    1. selection can promote increased heterozygosity [Fig.6.11]
    2. selection can promote reduced variability [Figs.6.11, 6.12, 6.13]
    3. &  many other patterns such as
       

    6.7 Inbreeding: The Collapse of a Dynasty p. 187

    • Inbreeding is not a mechanism of evolution, but it can reduce the relative fitness of individuals, specifically when individuals become homozygous for rare, recessive alleles that detrimentally affect performance.
    1. Inbreeding and the Hapsburg dynasty /a>
    2. Inbreeding coefficient
      1. Probability that two alleles are identical by descent
    3. Inbreeding depression results in reduced fitness
      1. Rare deleterious alleles more likely to combine in homozygotes
    4. Key Concepts
      1. Alleles are identical by descent if they both descended from a single mutational event
      2. Inbreeding increases percentage of loci that are homozygous for alleles identical by descent
        1. Recessive alleles exposed to selection
    5. Genetic bottlenecks often go hand in hand with inbreeding and selection

    6.3     NONRANDOM MATING

    1. does not by itself cause evolution
    2. causes genotype frequencies to change, altering proportions of phenotypes, and therefore affects natural selection
    3. inbreeding, mating among genetic relatives, increases the frequency of homozygotes, decreases the frequency of heterozygotes.  Reduced heterozygosity is most dramatic with selfing.  [Fig. 7.25]--- frequency of A1A2 = 2pq/2n, where n is the generation
    4. genotype frequencies change, but allele frequencies do not [Table 7.4]

    General Analysis of Inbreeding

    • panmixia = random mating
    • F: inbreeding coefficient, the probability that the two alleles within an individual are identical by descent (autozygous)
    • F provides a measure of the extent to which inbreeding has increased the frequency of homozygotes and decreased the frequency of heterozygotes relative to Hardy-Weinberg.
    • " F = 0 for no inbreeding; F = 0.5 for selfing (the probability that the offspring of a self fertilizing plant will inherit two copies of its parents genes is 50%)

    Computing F

    • Estimating inbreeding from pedigrees [Fig. 7.27]
    • must know pedigree (humans, captive populations, long-term studies)
    • siblings share 50% of their genes by descent with each other and with parents; (identical twins share 100% of their genes)

    Inbreeding Depression Is A Consequence of Being Diploid

    • inbreeding depression = inbred offspring are inferior to outbred offspring in survival & reproduction. By increasing the frequency of homozygotes, inbreeding can expose deleterious recessive alleles to selection [Figs. 7.28-30]
    • IInbreeding depression widespread in plants and animals. Evolution has selected for various mechanisms of inbreeding avoidance

    6.8 Landscape Genetics p. 192

    1. Landscape Genetics
      1. Combines population genetics, landscape ecology, and spatial statistics
    2. Population Structure
      1. populations that are subdivided by geography, behavior, or other influences that prevent individuals from mixing completely.
      2. Population subdivision leads to deviations from Hardy-Weinberg predictions.
    3. Population subdivision (Fig. 6.25)
    4. Many organisms occupy ranges that are discontinuous (Fig. 6.24)
    5. Genetic Distance (FST)
      1. measures how different populations are from each other genetically.
    6. Isolated populations become genetically distinct as a result of genetic drift  (Fig. 6.26)
    7. Subdivided populations show distinct genetic structure  (Fig. 6.27)
    8. Gene flow homogenizes allele frequencies  (Fig. 6.29)
      1. In natural populations there is a tension between drift and migration.
      2. Drift causes populations to diverge.
      3. Gene flow: movement, or migration, of alleles from one population to another.
      4. Counteracts gene loss; prevents divergence
    9. Amount of gene flow varies with the biology of the organism (Fig. 6.30)
    10. Loci that have diverged faster than predicted by drift may be under selection (Fig. 6.28)
    11. Humans can alter population structure of other organisms (Fig. 6.31)
    12. Key Concepts
      1. Population subdivision enhances the effects of genetic drift
      2. Divergence in allele frequencies
      3. Gene flow counteractions subdivision by homogenizing allele frequencies
     
       
    1. 5.4  Measuring Genetic Variation in Natural Populations/b>

      • The traditional view (pre 1960's) was that allelic variation in populations would be limited
      • most populations have extensive allelic variation

      Determining Genotypes

      1. gel electrophoresis
      2.  Determining CCR5 genotypes by electrophoresis of DNA [Fig. 5.12, Table 5.3]
        1. 32 base pair deletion (Δ32) on CCR5 co-receptor reduces susceptibility to AIDS
        2. Both alleles yield two fragments because they are cut once by the restriction enzyme:
        3. three genotypes
          1. Δ32/ Δ32 are highly resistant;
          2. +/Δ32 progress to AIDS more slowly than +/+.

      Calculating Allele Frequencies

      • genetic variation is computed from the frequency of each allele present
      • documenting allele frequencies can reveal interesting patterns [Table 5.3]

      How Much Genetic Diversity Exists in a Typical Population?

      1. Electrophoresis of proteins reveals most populations harbor considerable genetic diversity
        1. In typical populations, protein variations indicate between a third and a half of all coding loci are polymorphic or individuals are heterozygous at 4 to 15% of loci   [Fig. 5.13]
        2. about 7% of all plant species have a heterozygosity between 0.10 and 0.12. [Fig. 5.13]
        3. DNA sequence variation suggests even greater variation [Fig. 5.14]

      Why are Populations Genetically Diverse?

      • balance theory: genetic diversity is maintained by natural selection
      • neutral theory: mutations are equivalent and not eliminated by selection

      6.2    SELECTION

      Empirical Research on Allele Frequency Change by Selection

      • Frequency change in the Alcohol Dehydrogenase (ADH) gene alleles in laboratory populations of Drosophila exposed to ethyl alcohol
      • ADHS decreases, ADHF increases, no change in controls [Fig. 6.13]

      Adding Selection to Hardy-Weinberg Analysis: Calculation of Genotype Frequencies

      The Fitness Effects of Mutation

      1.  replacement substitutions:
        1. highly deleterious to beneficial
        2. Most have very small effects on fitness.
        3. Most are slightly deleterious or neutral (silent).

      The Fitness Effects of Mutations

      1. Fig. 5.5a How do most mutations affect fitness?
        1. Individuals in the control populations (under natural selection) had higher fitness than those in experimental populations
        2. Selection acted more strongly on individuals in the control population
        3. Most mutations result in new alleles that have slightly deleterious effects.

      5.4  Measuring Genetic Variation in Natural Populations

      Determining Genotypes

      1. gel electrophoresis
      2.  Determining CCR5 genotypes by electrophoresis of DNA [Fig. 5.12, Table 5.3]
        1. 32 base pair deletion (Δ32) on CCR5 co-receptor reduces susceptibility to AIDS
        2. Both alleles yield two fragments because they are cut once by the restriction enzyme:
        3. three genotypes
          1. Δ32/ Δ32 are highly resistant;
          2. +/Δ32 progress to AIDS more slowly than +/+.

      Calculating Allele Frequencies

      How Much Genetic Diversity Exists in a Typical Population?

      1. Electrophoresis of proteins reveals most populations harbor considerable genetic diversity
        1. In typical populations, protein variations indicate between a third and a half of all coding loci are polymorphic or individuals are heterozygous at 4 to 15% of loci   [Fig. 5.13]

        2. about 7% of all plant species have a heterozygosity between 0.10 and 0.12. [Fig. 5.13]

        3. DNA sequence variation suggests even greater variation [Fig. 5.14]

      Why are Populations Genetically Diverse?

       

       

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