Download CHAPTER 24 Population Genetics

Peter J. Russell
A molecular Approach 2nd Edition
CHAPTER 24
Population Genetics
edited by Yue-Wen Wang Ph. D.
Dept. of Agronomy,台大農藝系
NTU
遺傳學 601 20000
Chapter 24 slide 1
Introduction
1. Population genetics is the field of genetics that studies heredity in groups of
individuals for traits that are determined by one, or only a few genes.
2. Both Population and Quantitative Genetics use Mendelian principles, and both
are amenable to mathematical treatment.
3. These areas of genetics have been important in the fusion of Mendelian theory
with Darwinian theory to create the neo-Darwinian synthesis that underlies
much of current biological thinking (Figure 24.1).
4. Population geneticists study the genetic structure of populations, and how they
change geographically and over time.
5. A Mendelian population is a group of interbreeding individuals who share a
common set of genes. The total of all alleles in the population constitutes the
gene pool.
6. Modern molecular biology techniques have allowed for rapid advancement in
population genetics.
7. Mathematical models are often developed in population genetics. The HardyWeinberg law is a major example.
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Chapter 24 slide 2
Fig. 24.1 The major architects of neo-Darwinian theory (a) Sir Ronald Fisher (b)
Sewall Wright (c) J. B. S. Haldane
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Chapter 24 slide 3
Genetic Structure of Populations
Genotypic Frequencies
1. Genotypic frequencies are a way to study the genes
in a particular gene pool by quantifying the
genotypes (pairs of alleles) at a given locus.
2. To calculate genotypic frequency, count individuals
with one genotype, and divide by total individuals in
the population. Repeat for each genotype in the
population.
3. A frequency is a proportion with a range of 0–1. If
43% of population has a trait, the frequency of that
trait is 0.43. For any given trait, the sum of the
genotypic frequencies in a population should be 1.
Spot patterns on the moth Panaxia dominula are an
example (Figure 24.2).
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Chapter 24 slide 4
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Chapter 24 slide 5
Allelic Frequencies
1.
Allelic frequencies give more information about the structure of
the population than genotypic frequencies.
Allelic Frequency= No. of copies of a given allele / Sum of counts of all alleles in the population
2.
May be calculated in two different ways:
a. From observed number of different genotypes at a particular locus.
p=f(A)= ((2 x Count of AA) +(1 x count of Aa)+(0 x count of aa)) / (2 x total number of individuals)
b. From genotypic proportions.
p= f(A)=(Frequency of the AA homozygote) + (1/2)(frequency of the Aa heterozygote)
p= f(a)=(Frequency of the aa homozygote) + (1/2)(frequency of the Aa heterozygote)
3.
Allelic frequencies at an X-linked locus are more complex because
one sex will have only one X-linked allele while the other has two.
p=f(XA)=((2 x XAXA females) + (1 x XAXa female) + (1 x XAY male)) / ((2 x number of females)+ (1 x number of males))
p=f(Xa)=((2 x XaXa females) + (1 x XAXa female) + (1 x XaY male)) / ((2 x number of females)+ (1 x number of males))
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Chapter 24 slide 6
The Hardy-Weinberg Law
1. This is a simple explanation showing how Mendelian
segregation influences allelic and genotypic frequencies
in a population.
2. There are three parts to the law: one set of assumptions
and two major results.
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Chapter 24 slide 7
Assumptions of the Hardy-Weinberg Law
1. This law is a simplification of complex events. There are
certain assumptions that must be present for the law to
apply:
a. The population is infinitely large, to avoid genetic drift. (Since
this is impossible, large populations are studied when possible
since they are mathematically similar to infinite ones.)
b. Mating is random with regard to the trait(s) under study.
c. There is no natural selection of the trait(s) under study.
d. No mutations occur.
e. No migration occurs.
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Chapter 24 slide 8
Predictions of the Hardy-Weinberg Law
1. If the conditions are met, the population will be in genetic
equilibrium, with two expected results:
a. Allele frequencies do not change over generations, so the gene
pool is not evolving at the locus under study.
b. After one generation of random mating, genotypic frequencies
will be p2, 2pq and q2, and will stay constant in these proportions
as long as the conditions above are met. This is Hardy-Weinberg
equilibrium, which allows predictions to be made about
genotypic frequencies.
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Chapter 24 slide 9
Derivation of the Hardy-Weinberg Law
1. Zygotes are formed by random combinations of alleles, in
proportion to the abundance of that allele in the population. (Figure
24.3)
2. When a population is in equilibrium, genotypic frequencies will be
in the proportions p2, 2pq and q2. This results from the expansion of
the square of the allelic frequencies: (p + q)2 = p2 + 2pq + q2.
3. Mendelian principles acting on a population in equilibrium will
work to maintain that equilibrium (Table 24.1 and 24.2). Albinism is
an example.
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Chapter 24 slide 10
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Chapter 24 slide 11
Fig. 24.3 Relationship of the frequencies of the genotypes AA, Aa, and aa to the
frequencies of alleles A and a in populations in Hardy-Weinberg equilibrium
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Chapter 24 slide 12
Extensions of the Hardy-Weinberg Law
to Loci with More than Two Alleles
1.
2.
Often more than two alleles are possible at a given locus, and the
frequencies of possible genotypes are still given by the square of
the allelic frequencies.
If three alleles are present (e.g., alleles A, B and C) with
frequencies p, q, and r, the frequencies of the genotypes at
equilibrium will be:
(p + q + r)2 = p2(AA) + 2pq(AB) + q2(BB) + 2pr(AC) + 2qr(BC) + r2(CC)
3.
Blue mussel population of Long Island Sound (Figure 24.6) is an
example.
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Chapter 24 slide 13
Extensions of the Hardy-Weinberg Law to SexLinked Alleles
1. In species where sex is chromosomally determined, humans or
Drosophila for example, females have two X chromosomes while
males have only one. In females, Hardy-Weinberg frequencies are the
same as for any other locus. In males, frequencies of the genotypes are
the same as frequencies of the alleles in the population.
2. Because males receive their X chromosome from their mothers, the
frequency of an X-linked allele will be the same as the frequency of
that allele in their mothers. For females the frequency will be the
average of both parents.
3. With random mating, the difference in allelic frequency between the
sexes will be reduced by half in each generation (Figure 24.4). One
generation after allelic frequencies become equal in males and females,
the genotypes will be in Hardy-Weinberg proportions.
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Chapter 24 slide 14
Fig. 24.4 Representation of the gradual approach
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Chapter 24 slide 15
Testing for Hardy-Weinberg Proportions
1. Data from real populations rarely match Hardy-Weinberg
proportions. Use a chi-square test to check whether
deviation is larger than expected by chance.
2. If the deviation is larger than expected, researchers begin
to study which of the Hardy-Weinberg assumptions is
being violated.
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Chapter 24 slide 16
Using the Hardy-Weinberg Law to Estimate
Allelic Frequencies
1. If one or more of the alleles is recessive, one can’t distinguish
between heterozygous and homozygous dominant individuals. Can
use Hardy-Weinberg law to calculate the allele frequency based on
information about the number of homozygous recessive individuals.
26/6000=0.0043=q2
q=√0.0043=0.065
p=1-q=1-0.065=0.935
Heterozygote (Carrier)=2pq
=2(0.935)(0.065)
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Chapter 24 slide 17
Genetic Variation in Space and Time
1. The genetic structure of populations can vary in space (Figure 24.6)
and time.
2. An allele frequency cline is a clear pattern of variation across a
geographic transect, usually correlated with a physical feature like
temperature or rainfall. (Figure 24.7)
3. Statistical tools are used to quantify spatial patterns of genetic
variation. These are important in conservation biology.
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Chapter 24 slide 18
Fig. 24.6 Geographic variation in frequencies of three alleles of the locus coding for
the enzyme leucine amino peptidase (LAP) in the blue mussel
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Chapter 24 slide 19
Fig. 24.7 Temporal variation in the locus coding for the enzyme esterase 4F in the
prairie vole, Microtus ochrogaster
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Chapter 24 slide 20
Genetic Variation in Natural Populations
1. Genetic variation is important in natural populations:
a. It determines the potential for evolutionary change and
adaptation.
b. It provides clues about roles of various evolutionary processes.
c. It allows predictions about a population’s chances for long-term
survival.
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Chapter 24 slide 21
Measuring Genetic Variation at the Protein Level
1. Understanding genetic variation in a population (Figure 24.8) was difficult before
molecular biology because most phenotypes are the result of multiple genes, and there
was no technique available to determine allele frequencies.
2. Protein electrophoresis (Lewontin and Hubby, 1966) separates proteins on the basis of
size, charge and conformation, and so often can separate the gene products of different
alleles.
3. The amount of genetic variation within a population is usually measured by two
parameters:
a. Proportion of polymorphic loci (those with more than one allele within a population).
Proportion is calculated by dividing total of loci with more than one allele by total number of
loci examined.
b. Heterozygosity (the proportion of an individual’s loci that are heterozygous). Determine for
individuals, and then average to obtain estimate of heterozygosity of the population.
4. Proteins with similar sizes and charges will conform in gel electrophoresis, and so allele
differences are likely to be underestimated. Even so, much more variation (Table 24.3) is
seen at most loci than would be predicted by the classical model.
5. Kimura proposed the neutral-mutation model, saying that the combination of random
mutations and chance fixation of alleles is responsible for some variations that are not
functionally different and so are not acted upon by natural selection. However, DNA
sequencing has undermined this model.
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Chapter 24 slide 22
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Chapter 24 slide 23
Measuring Genetic Variation at the DNA Level
1. PCR (polymerase chain reaction) allows amplification of DNA regions from
many individuals. Fragments may be analyzed for size, restriction sites and
DNA sequence (Figure 24.9).
2. Restriction fragment length polymorphisms (RFLPs) are a quick way to map
genes and gain an idea of how many DNA differences occur within a
population (Figure 24.10). Limitation of RFLP analysis is that it only assesses
variation in sites for particular restriction enzymes.
3. DNA sequence analysis shows that there is more variation and therefore many
more alleles of most genes than previously believed. Different regions will
have different levels of variation. Exons are less likely to vary than introns and
flanking sequences, and changes within exons are often synonymous.
4. DNA length polymorphisms result from deletions and insertions of short
stretches of nucleotides, especially in noncoding regions. Microsatellites or
STRPs (short tandem repeat polymorphisms) are very simple repetitive
sequences that occur different numbers of times in different individuals. Both
are useful in determining genetic variability within a population.(Table 24.4
and 24.5)
iActivity: Measuring Genetic Variation
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Chapter 24 slide 24
Fig. 24.9 DNA from individual 1 and individual 2 differ in one nucleotide, found
within the sequence recognized by the restriction enzyme BamHI
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Chapter 24 slide 25
Fig. 24.10 Restriction patterns from five mice
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Chapter 24 slide 26
Forces that Change Gene Frequencies in
Populations
1. Few populations are actually in Hardy-Weinberg equilibrium,
and so their allele frequencies do change, and evolution
occurs.
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Chapter 24 slide 27
Mutation
1. Usually a mutation converts one allelic form of a gene to another.
(Table 24.6)
2. Mutations may be neutral, detrimental or advantageous, depending on
the environment. Environmental changes may favor different alleles
than those previously favored.
3. The frequency of alleles in a population is determined by interaction of
mutation rates and natural selection.
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Chapter 24 slide 28
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Chapter 24 slide 29
Random Genetic Drift
1. Called “drift” for short. Results from random events in small
populations (sampling error).
2. Effective population size is the number of adults contributing
gametes to the next generation. Includes the number of breeding
females plus the number of breeding males. (Remember that if,
for example, one male contributes most of the gametes, his
alleles will be present at a higher frequency in the next
generation.)
3. The standard error of allelic frequency is a useful mathematical
analysis for understanding the limits of allelic frequency. (Figure
24.11)
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Chapter 24 slide 30
Fig. 24.11 Results of Buri’s study of genetic drift in 107 populations of Drosophila
melanogaster
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Chapter 24 slide 31
4.
Genetic bottlenecks and founder effects arise when
populations expand from a small number of ancestors. Even
though the population may become large, only the alleles that
were present in the ancestors (and those that have arisen by
mutation in the meantime) will be present in the population.
Examples include:
a. the islanders of Tristan da Cunha.
b. The Dunker sect in the U.S. (Table 24.7)
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Chapter 24 slide 32
5. Effects of genetic drift:
a. Allelic frequencies will change over time, and may reach values of 0.0
or 1.0. When this occurs, the remaining allele is “fixed” in the
population, and only mutation can change its frequency. This reduces
the heterozygosity of the population, resulting in reduced genetic
variation. (Figure 24.12 and 24.13)
b. Individual populations will not necessarily drift in the same direction,
and so genetic divergence can result. This may eventually result in
speciation. Experimental evidence (Table 24.8) confirms that there is
more variance in allelic frequency among small populations than
among large ones.
c. Neutral mutations are not subject to natural selection, and may be used
to estimate the time elapsed since two species shared a common
ancestor.
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Chapter 24 slide 33
Fig. 24.12 The effect of genetic drift in the frequency (q) of allele A2 in four populations
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Chapter 24 slide 34
Fig. 24.13 The average time to fixation or loss of an allele from population as a function
of population size and initial allele frequency as predicted by Kimura
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Chapter 24 slide 35
Balance between Mutation and Random Genetic
Drift
1. In a population, mutation adds variation, and random
genetic drift removes variation. When these forces are
combined, the infinite alleles model predicts that they will
balance with each other and a steady state of
heterozygosity will result. (Figure 24.14)
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Chapter 24 slide 36
Fig. 24.14 Relationship between the neutral parameter  = 4Ne and the expected
heterozygosity under the infinite alleles models
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Chapter 24 slide 37
Migration
1. While Hardy-Weinberg assumes no migration, many populations are
not isolated and will exchange genes with other populations. Genetic
migration is about gene movement, rather than actual movement of
organisms, and is referred to as gene flow.
2. Gene flow has two major effects on a population:
a. May introduce new alleles to a population.
b. When migrants have different allelic frequency than recipient
population, allelic frequencies will be altered in the recipient
population.
3. Gene flow is diagrammed in Figure 24.15. Note that if gene flow
continues, the differences in allelic frequencies between the
populations will decrease. (Figure 24.16)
4. The balance between drift and migration will determine whether two
populations remain similar to one another. This is important in
conservation biology, where fragmentation of habitats may prevent
gene flow.
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Chapter 24 slide 38
Fig. 24.15 Theoretical model illustrating the effect of migration on the gene pool of a
population
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Chapter 24 slide 39
Fig. 24.16 Extensive gene flow occurs among populations of monarch butterfly
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Chapter 24 slide 40
Natural Selection
Animation: Hardy-Weinberg and Natural Selection
1. Adaptation is the process by which traits evolve that increase the
organism’s chances of surviving to reproduce. Adaptation is mainly the
result of natural selection. (Figure 24.17 and 24.18)
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Chapter 24 slide 41
2. Natural selection is the differential survival of genotypes, and the
alleles that survive are more likely to be represented in the next
generation. Over time, this increases the adaptation of organisms to
their environment.
3. Darwinian fitness is the relative reproductive ability of a particular
genotype. It involves both the number of offspring, and their relative
fitness.
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Chapter 24 slide 42
4. Natural selection may result in increasing or decreasing
genetic variation, depending on environmental conditions.
It can be calculated using the “table method” (Table 24.9.
24.10 and 24.11). The premise is that the contribution of
each genotype to the next generation will be equal to the
initial frequency of the genotype multiplied by its fitness.
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Chapter 24 slide 43
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Chapter 24 slide 44
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Chapter 24 slide 45
5. Recessive traits often result in reduced fitness (Figure 24.20), and so
there will be selection against homozygous recessives, decreasing the
frequency of the recessive allele, but not eliminating it from the
population, because as the allele becomes less frequent it is more likely
to be found in a heterozygote, creating a protected polymorphism.
Effects of dominant traits are shown in Figure 24.21 and Table 24.12.
6. Some forms of selection result in maintaining genetic variation. If a
heterozygote has higher fitness than either of the homozygotes, allelic
frequencies will reach equilibrium and become stable. The relationship
between sickle-cell anemia and resistance to malaria is a famous
example. (Figure 24.22)
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Chapter 24 slide 46
Fig. 24.20 Effectiveness of selection against a recessive lethal genotype at different initial
allele frequencies
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Chapter 24 slide 47
Fig. 24.21 Fitnesses of the genotypes AA, Aa, and aa are 1, 0.5, and 0.5, for the dominant
case; 1, 0.75, and 0.5 for the additive case; and 1, 1, and 0.5 for the recessive case
Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
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Chapter 24 slide 48
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Chapter 24 slide 49
Fig. 24.22 The distribution of malaria caused by the parasite Plasmodium falciparum
coincides with distribution of the Hb-S allele for sickle-cell anemia
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台大農藝系 遺傳學 601 20000
Chapter 24 slide 50
Balance Between Mutation and Selection
1. The balance between mutations and natural selection results in
evolution.
2. When an allele becomes rare, its change in frequency with each
generation becomes very small. At the same time, mutations occur
which produce new alleles and increase the frequency. Eventually
equilibrium will be obtained.
3. Selection is continually acting on dominant alleles, but can only act on
a recessive ones in homozygotes. Therefore detrimental dominant
alleles are generally less common than recessive ones.
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Chapter 24 slide 51
Assortative Mating
1. Individuals do not always mate randomly. When a
particular phenotype is preferred in mates, allele
frequencies will be affected.
2. Positive assortative mating occurs when individuals with
similar phenotypes mate preferentially.
3. Negative assortative mating occurs when phenotypically
dissimilar individuals mate preferentially.
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Chapter 24 slide 52
Inbreeding
1. Inbreeding is the preferential mating between close relatives.
2. Small populations will show this effect even if there is no tendency
to select relatives, because even-chance matings are likely to involve
relatives.
3. Self-fertilization is an extreme case of inbreeding seen in many plants
and a few animals. Table 24.13 illustrates the effects.
4. Inbreeding has results similar to genetic drift in a small population.
Heterozygosity decreases and homozygosity increases. In large
populations, inbreeding will result in constant allele frequencies even
though homozygosity increases.
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Chapter 24 slide 53
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Chapter 24 slide 54
Effects of Evolutionary Forces on the Genetic
Structure of a Population
Changes in Allelic Frequency Within a Population
1. Factors with potential to change allelic frequencies are:
a. Mutation, although it occurs at a slow rate and creates a relatively small
change in allelic frequencies.
b. Migration, which may create major changes in allelic frequencies.
c. Genetic drift, which produces substantial changes in small
populations.
d. Selection, which alters frequencies and continues to act even when
equilibrium has been reached.
2. Non-random mating affects genotypic frequencies in a population.
Inbreeding increases homozygosity, and decreases fitness if deleterious
recessive alleles are present.
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Chapter 24 slide 55
Genetic Divergence Among Populations
1. Genetic drift can produce divergence among populations.
2. Migration will decrease divergence by encouraging gene flow between
populations.
3. Natural selection can either increase divergence by favoring different
alleles in different populations, or decrease divergence by selecting
against certain alleles.
4. Non-random mating may contribute to the effects of other processes by
altering the effective population size.
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Chapter 24 slide 56
Increases and Decreases in Genetic Variation Within
Populations
1. Effects are similar to those among populations (above):
a. Migration increases genetic variation.
b. Mutation also increases variation.
c. Genetic drift decreases variation due to loss of alleles.
d. Inbreeding decreases variation.
e. Natural selection may either increase or decrease genetic variation,
depending on the environment and other circumstances.
f. All of these effects combine within a population in complex ways to
determine an overall pattern of genetic variation.
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Chapter 24 slide 57
The Role of Genetics in Conservation Biology
1. Human activities are reducing the available habitat and altering the
environment for many species, resulting in declining numbers and
escalating rates of extinction. Intelligent conservation efforts must
consider survival of gene pools, as well as survival of individuals.
2. Population viability analysis is used to determine how large a
population needs to be to prevent extinction within a set period of time.
An adequate gene pool is needed to ensure the potential for the
population to evolve over time.
3. Inbreeding has occurred in zoos and game management programs, and
is now a recognized concern in developing conservation strategies.
4. Until habitat destruction is addressed, genetic conservation efforts can
only slow the depletion of gene pools and the loss of species that will
inevitably result.
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Chapter 24 slide 58
Speciation
1. When populations are subdivided to the point that they never
interbreed, different alleles will become fixed in the subpopulations
over time.
2. If the subpopulations are then reunited, they may fail to mate or may
produce hybrids of low fitness.
3. Understanding which genes are involved in reproductive isolation
requires an understanding of basic principles of speciation.
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Chapter 24 slide 59
Barriers to Gene Flow
1. Barriers to gene flow eventually arise between isolated populations, preventing
interbreeding. There are two major categories of barriers:
a. Post-zygotic barriers usually arise first, resulting in poor fitness of offspring (often
including infertility).
b. Pre-zygotic barriers that prevent mating result when alleles of individuals that
discriminate in mating become increasingly frequent in the population.
2. In this reinforcement model, post-zygotic isolation leads to pre-zygotic isolation.
The genes potentially involved include those for:
a. Temporal isolation, with different mating or activity periods preventing mating
between the populations.
b. Ecological isolation, with each population in a distinct niche and therefore spatially
isolated.
c. Behavioral incompatibility, allowing the two species to recognize and avoid each
other as mates.
d. Mechanical isolation, in which the genitalia of the two populations do not fit together.
e. Gametic isolation, in which gametes from different populations do not fuse correctly.
3. Pre-zygotic isolation accelerates the rate of divergence, with strong selection
against interspecies mating resulting in a complete barrier to gene flow.
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Chapter 24 slide 60
Genetic Basis for Speciation
1. In species that display post-zygotic isolation:
a. Hybrid males (the heterogametic sex) are usually sterile.
b. Hybrid females (the homogametic sex) are often fertile.
c. This is Haldane’s Rule (after J. B. S. Haldane).
2. Crosses between species of Drosophila are an example:
a. The F1 of a cross between D. simulans and D. mauritiana will include:
i. Females that are viable and fertile.
ii. Males that are sterile.
b. Backcrossing the F1 females to D. simulans males will produce some fertile
male offspring.
c. These types of experiments show that many genes are involved in the
fertility of male hybrids.
3. Abalone provide another example of prezygotic isolation.
a. Sperm and eggs of more than one species may co-occur.
b. Eggs allow penetration only by conspecific sperm due to specific molecular
interactions between the sperm protein lysin and the egg glycoprotein
VERL.
c. Lysin and VERL molecules in abalone display rapid adaptive evolution.
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Chapter 24 slide 61