Bio3400 Chapter 25 Population Genetics
    25.1 Allele Frequencies in Population Gene Pools Vary in Space and Time
     
     
     
     
    A population is a group of individuals with a common set of genes that lives in the same geographic area and can or does interbreed. A population's gene pool is all of the alleles present in that population. Due to population dynamics, the gene pool can change over time.
     
     
     
     
  1. The Hardy-Weinberg Law describes the relationship between         frequencies and           frequencies in an ideal population.
    • Extremely large population size.
    • No gene flow due to migration.
    • No mutations .
    • Random mating.
    • No natural selection .
     
     
     
     
  2. Mendelian inheritance preserves allele frequencies in a population, resulting in constant genetic variation.
     
     
     
     
  3. At Hardy-Weinberg equilibrium, the distribution of 2 alleles p and q in a population can be modeled by these equations:
     
     
     
     
    • The allele frequencies are described by p + q = 1, where p is the dominant allele frequency and q is the recessive allele frequency.
       
       
       
       
    • The genotype frequencies are described by p2 + 2pq + q2 = 1, where p2 and q2 are frequencies of the homozygous genotype and 2pq is the frequency of the heterozygous genotype.
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
    The Hardy-Weinberg law makes two predictions:
     
     
     
     
    (1) the frequency of the alleles in the gene pool does not change over time; and
     
     
     
     
    (2) after one generation of random mating, the genotype frequencies for two alleles can be calculated as p2�+�2pq�+�q2 = 1 where p equals the frequency of allele A and q is the frequency of allele a
     
     
     
     
  4.            traits are polygenic and often multifactorial but have a small number of discrete phenotypic classes.

      For a population in Hardy-Weinberg equilibrium, genotype frequencies can be calculated from allele frequencies using Mendelian principles of segregation and simple probability. Here the frequency of the A allele is 0.7, and the frequency of the a allele is 0.3. The genotype frequencies in the next generation are:
    • AA: 0.49
    • aa: 0.09
    • Aa: 0.21 x 2 = 0.42 Under Hardy-Weinberg equilibrium, allele frequencies in the next generation should remain constant. For example, the A allele should be 0.49 + (0.5 x 0.42) = 0.7.


      The distribution of 2 alleles in Hardy-Weinberg equilibrium is p + q = 1, where p is frequency of allele A, and q is frequency of allele a. The three genotypes AA, Aa, and aa have the frequencies p^2, 2pq, and q^2, respectively, and these frequencies also add up to 1.
     
     
     
     
     
     
     
     
     
     
     
     
    25.3 The Hardy-Weinberg Law Can Be Applied to Human Populations
     
     
     
     
    An example of how the Hardy-Weinberg law can be applied to humans is analysis of susceptibility to HIV-1 infection based on the genotype for the CCR5 HIV-1 receptor gene Table 25.1 and Figure 25.3.

      A deletion in the human CCR5 gene makes the individual resistant to HIV-1 infection by altering the syrface receptor for the virus. The mutant (D32) allele can be distinguished from the normal (1) allele by RFLP analysis with a restriction enzyme. The 1 allele produces a 332-bp fragment and a 403-bp fragment; the D32 allele produces a 332-bp fragment and a 371-bp fragment. Heterozygotes produce three bands.
     
     
     
     
    25.4 The Hardy-Weinberg Law Can Be Used for Multiple Alleles, X-Linked Traits, and Estimating Heterozygote Frequencies
     
     
     
     
    Frequencies for multiple alleles can be calculated using the Hardy-Weinberg equation by adding more variables.
     
     
     
     
    For instance, in a situation involving three alleles (p�+�q�+�r = 1), the frequencies of the genotypes are given by (p�+�q�+�r)2 = p2�+�q2�+�r2 +�2pq�+�2pr�+�2qr = 1.
     
     
     
     
    An example of genotype frequency calculations for ABO blood type is given in Table 25.3.
     
     
     
     
    In using the Hardy-Weinberg equation to calculate allele and genotype frequencies for X-linked traits in mammals, the frequency of the X-linked allele in the gene pool will equal the frequency of males expressing the X-linked trait.
     
     
     
     
    For females, the frequency of having the allele in question will be q2 if the allele frequency is q.
     
     
     
     
    The Hardy-Weinberg law also allows the frequency of heterozygotes in a population to be estimated. In general, the frequencies of all three genotypes can be estimated once the frequency of either allele is known and Hardy-Weinberg assumptions are invoked (Figure 25.5).

      Under Hardy-Weinberg equilibrium, the frequencies of all three genotypes can be calculated once the frequency of either allele is known. Heterozygotes increase rapidly in a population as the values of p and q move from 0 or 1. Most genetic diseases are recessive traits with low frequencies in the population, and most individuals carrying the allele are heterozygotes.
     
     
     
     
    25.5 Natural Selection Is a Major Force Driving Allele Frequency Change
     
     
     
     
    If individuals of all genotypes are subject to natural selection and do not have equal rates of survival and reproductive success, allele frequencies may change from one generation to the next. Natural selection is the principal force that shifts allele frequencies within large populations.
     
     
     
     
    Hardy-Weinberg analysis allows fitness w to be examined for each genotype. For a homozygous recessive individual that dies before producing offspring, w = 0, and the frequency of the recessive allele will decrease in each generation (Figure 25.6).

      Natural selection reduces the frequency of a lethal recessive allele, a. This decline can be calculated as q[g] = q[0] / 1+gq[0]. The frequency of a is halved in 2 generations, and halved again by the 6th generation. Subsequent reductions occur slowly because the majority of a alleles are carried by heterozygotes.
     
     
     
     
    The rate at which the frequency of a deleterious allele declines depends on the strength of selection applied (Figure 25.7).

      A deleterious allele (a) is codominant and starts at a frequency of 0.99. The rate of decline depends on its fitness as measured by W. A strong selection pressure where 90% of the heterozygotes (WAa = 0.90) and 80% of the aa homozygotes survive (Waa = 0.80), the frequency of allele a drops from 0.99 to less than 0.01 in 85 generations. Under weak selection pressure where WAa = 0.998 and Waa = 0.996 it takes 1000 generations for the frequency of allele a to drop to 0.93.
     
     
     
     
    Selection in natural populations works as predicted to increase the frequency of the allele to which selective pressure is applied. No such increase is observed in populations not subjected to the selection (Figure 25.10).

      In the 4 locations where chlorpyrifos had been used to control mosquitoes for 22 years, the frequency of the Ace^R allele was higher than those locations chlorpyrifos was never used. Control


      As a control, the frequency of an allele for an enzyme unrelated to chlorpyrifos metabolism (aspartate amino transferase 1) shows no pattern in response to the pesticide. 25_10b-selection_alleles.jpg,812,492-->
     
     
     
     
    Selection acting on quantitative traits can be directional, stabilizing, or disruptive (Figure 25.12).

      Natural selection can affect quantitative traits in 3 ways:
    • Stabilizing selection favors intermediate types, with both extreme phenotypes being selected against.
    • Directional selection selects for one phenotypic extreme, and is widely practiced in plant and animal breeding.
    • Disruptive selection is selection against intermediates and for both phenotypic extremes.


      Stabilizing selection selects against extreme phenotypes, faboring average individuals. This reduces the population variance, but without shifting the mean. In humans, infant mortality increases on either side of the optimal birth weight of 7.5 pounds. 25_11-selection-stabilizing.jpg,800,512-->


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      Disruptive selection is the opposite of stabilizing selection because the intermediate types are selected against. In an experiment disruptive selection was applied to a population of Drosophila on the basis of bristle number. In each generation, only the flies with high- or low-bristle numbers are allowed to breed. After several generations, most of the flies could be easily placed in a low- or high-bristle category. In natural populations, such a situation might exist for a population in a heterogeneous HinT 25_13-selection-disruptive.jpg,340,568-->
     
     
     
     
    In directional selection, the genotype conferring one phenotypic extreme is selected, resulting in a change in the population mean over time.
     
     
     
     
    In stabilizing selection, intermediate types are favored, and both extreme phenotypes are selected against. This will reduce the population variance over time but not the mean.
     
     
     
     
    In disruptive selection, both phenotypic extremes are selected for, and the intermediates are selected against. This will result in a population with an increasingly bimodal distribution for the trait (Figure 25.13).

      Disruptive selection is the opposite of stabilizing selection because the intermediate types are selected against. In an experiment disruptive selection was applied to a population of Drosophila on the basis of bristle number. In each generation, only the flies with high- or low-bristle numbers are allowed to breed. After several generations, most of the flies could be easily placed in a low- or high-bristle category. In natural populations, such a situation might exist for a population in a heterogeneous HinT


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      13-14_disruptive_selec.jpg,502,450-->
     
     
     
     
    25.6 Mutation Creates New Alleles in a Gene Pool Mutation is the only process that creates new alleles in a gene pool. Because most mutations are recessive, indirect methods using probability and statistics are often employed to determine the mutation rate.
     
     
     
     
    If the mutation rate is known, the extent to which mutation can cause allele frequencies to change from one generation to the next can be estimated.
     
     
     
     
    In general, although mutation provides the raw material for evolution, mutation by itself plays a relatively insignificant role in changing allele frequencies (igure 25.14).

      With a mutation rate () of 1.0 x 10^-5, it takes 70,000 generations to reduce the frequency of allele A from 1.0 to 0.5. Thus mutation by itself plays a relatively insignificant role in changing allele frequencies.
     
     
     
     
    25.7 Migration and Gene Flow Can Alter Allele Frequencies When a species divides into populations that are separated geographically, the allele frequencies in these new populations may differ over time due to migration.
     
     
     
     
    Migration occurs when individuals move between the populations and may have a large effect on allele frequency if the rate of migration is large or if the allele frequency of the migrant population differs greatly from that of the population to which it is moving.
     
     
     
     
    25.8 Genetic Drift Causes Random Changes in Allele Frequency in Small Populations
     
     
     
     
    Genetic drift occurs when the number of reproducing individuals in a population is too small to ensure that all the alleles in the gene pool will be passed on to the next generation in their existing frequencies. Genetic drift may result in one allele becoming fixed and one allele disappearing in a population.
     
     
     
     
    25.9 Nonrandom Mating Changes Genotype Frequency but Not Allele Frequency
     
     
     
     
    Nonrandom mating can take the form of positive assortive mating in which similar genotypes are more likely to mate than dissimilar ones, negative assortive mating in which dissimilar genotypes are more likely to mate than similar ones, and inbreeding in which mating individuals are related.
     
     
     
     
    For a given allele, inbreeding increases the proportion of homozygotes in the population, and a completely inbred population theoretically will consist only of homozygotes.
     
     
     
     
    Self-fertilization is a form of inbreeding common in plants. The rate of homozygotes in a self-fertilizing population rapidly increases over a few generations, but the overall allele frequency does not change (Figure 25.17).

      Inbreeding among relatives reduces genetic variation by decreasing heterozygote frequency. In the extreme form of inbreeding, self-fertilization, for an individual heterozygous at one locus, 94% of its descendants are homozygous in 4 generations. Note, however, that the allele frequencies of A and a remain unchanged at 50%.
     
     
     
     
    A coefficient of inbreeding can be calculated to give the probability that two alleles of a given gene in an individual are identical because they are descended from the same single copy of the allele in an ancestor (Figure 25.18).

      The coefficient of inbreeding (F) is the probability that the two alleles of a gene in an individual are identical because they are descended from the same allele in an ancestor. In this example for the offspring between first cousins, first measure the probability that she will be homozygous for the recessive allele a inherited from her great-grandmother. Each generation has a 1/2 probability of inheriting the a allele. The probability that all 6 inheritances contain the a allele is (1/2)^6 = 1/64. Since she can also be homozygous for any of the other 3 alleles in her great-grandparents, F = 4 x (1/64) = 1/16.
     
     
     
     
    One consequence of inbreeding is an increased chance that an individual will be homozygous for a recessive deleterious allele. The significance of this fact is that inbred populations often have a lowered mean fitness, called inbreeding depression.
     
     
     
     
    If members of two inbred lines are mated, the offspring often display hybrid vigor. Hybrid vigor is highest in the F1 generation and generally declines thereafter.
     
     
     
     
    Inbreeding may increase the efficiency with which selection removes a deleterious allele from a population.