Genetics Slide 4

Chapter
25
Population and
Evolutionary
Genetics
Lecture Presentation by
Dr. Cindy Malone,
California State University Northridge
© 2017 Pearson Education, Ltd.

Chapter Contents
25.1 Genotypic Variation Is Present in Most Populations

and Species
25.2 The Hardy–Weinberg Law Describes Allele
Frequencies and Genotype Frequencies in
Populations
25.3 The Hardy–Weinberg Law Can Be Applied to Human
Populations
Continued

Chapter Contents
25.4 Natural Selection Is a Major Force Driving Allele

Frequency Change
25.5 Mutation Creates New Alleles in a Gene Pool
25.6 Migration and Gene Flow Can Alter Allele
Frequencies
25.7 Genetic Drift Causes Random Changes in Allele
Frequency in Small Populations
25.8 Nonrandom Mating Changes Genotype Frequency
but Not Allele Frequency
Continued

Chapter Contents
25.9 Reduced Gene Flow, Selection, and Genetic Drift

Can Lead to Speciation
25.10 Phylogeny Can Be Used to Analyze Evolutionary
History

25.1 Genetic Variation Is Present In Most
Populations and Species

Section 25.1: Micro- and Macroevolution
 Microevolution
– Evolutionary change within populations of a
species
 Macroevolution
– Evolutionary change leading to emergence of new
species and other taxonomic groups

Section 25.1: Population
 Population
– A group of individuals belonging to same species
– Live in same geographic area
– Actually or can potentially interbreed

Section 25.1: Gene Pool
 Population’s gene pool

– All alleles present in population
– Genetic information carried by members of
population
– Most populations contain high degree of
heterozygosity

Section 25.1: Detecting Genetic Variation
 Genetic variation
– Can be detected using artificial selection
– If genetic variation does exist, then phenotype will
change over generations
 Example: Domestic dog
– Genetic and archeological evidence indicates
domestication of dogs took place at least 15,000
years ago
– Selection of desired traits present in genetic
variation in wild wolves

Section 25.1: Variations in Nucleotide
Sequence
 Most direct way to estimate genetic variation
– Compare nucleotide sequences of genes
carried by individuals in population
– Example: Alcohol dehydrogenase

Section 25.1: Alcohol Dehydrogenase
 Alcohol dehydrogenase (Adh)

– Analyzed gene (Adh) in Drosophila melanogaster
– Gene has two alleles, Adh-f and Adh-s
– Encoded proteins differ by a single amino acid
(threonine versus lysine at codon 192)
– Adh genes from five natural populations were
cloned and sequenced
(Figure 25-1 and Figure 25-2)

© 2017 Pearson Education, Ltd. Figure 25-1
Section 25.1: Five Populations of Drosophila
 Adh genes from individuals representing five

natural populations of Drosophila were cloned
– Cloned genes contained total of 43 nucleotide
variations in Adh sequence of 2721 base pairs
– Out of 14 variations in coding regions, only one
leads to amino acid replacement

Section 25.1: CF Gene
 CF gene
– Encodes cystic fibrosis transmembrane
conductance regulator (CFTR)
– Recessive loss-of-function mutation causes
cystic fibrosis, which affects secretory glands
and lungs
– More than 1900 different mutations of the CFTR
gene have been identified
(Figure 25-3)

Section 25.1: Neutral Theory
 Neutral theory of molecular evolution

– Genetic variation due to mutation and drift
– Proposes mutations leading to amino acid
substitutions are detrimental; only a small fraction
is favorable
– Alternative explanation for high genetic variation
is natural selection
– Enzyme or protein variations maintained by
adaptation to certain environmental conditions
 Sickle-cell anemia

25.2 The Hardy–Weinberg Law Describes
Allele Frequencies and Genotype
Frequencies in Populations

Section 25.2: Hardy–Weinberg Law
 Hardy–Weinberg law
– Describes what happens to allele and genotype
frequencies in “ideal” populations
– “Ideal” population
 infinitely large with random mating; not subject to
evolutionary forces (mutation, migration, or selection)

Section 25.2: Hardy–Weinberg Predictions
 Hardy–Weinberg law makes two predictions:

– Frequency of alleles in gene pool does not
change over time
– After one generation of random mating, genotype
frequencies for two alleles calculated as p2  2pq 
q2  1
 p equals frequency of allele A
 q is frequency of allele a

Section 25.2: Two-Allele System
 Two-allele system
– Expected genotypic frequencies for population in
Hardy–Weinberg equilibrium
 Calculated based on allele frequencies in gametes and
random mating

Section 25.2: Hardy–Weinberg Model
 Hardy–Weinberg model assumes

– Equal rate of survival and reproduction (no
selection)
– No new alleles arise or created by mutation
– No migration into or out of population
– Infinitely large population
– Random mating occurs

Section 25.2: Hardy–Weinberg Law
 Hardy–Weinberg law – three additional

consequences
– Dominant traits do not necessarily increase from
one generation to next
– Genetic variability can be maintained
– By knowing frequency of one genotype,
frequencies of other genotypes can be calculated

25.3 The Hardy–Weinberg Law Can Be
Applied to Human Populations

Section 25.3: CCR5 Gene
 Hardy–Weinberg law applied to humans

– Analysis of susceptibility to HIV-1 infection
– Based on CCR5 gene
 Encodes protein CCR5, a receptor for strains of HIV-1
(Figure 25-6)

Section 25.3: HIV-1 Infection Resistance
 Resistance to HIV-1
– Homozygous individuals resistant to HIV-1
infection
– Heterozygotes susceptible to infection but
progress more slowly to AIDS
(Table 25.1)
 Genotypes determined by direct DNA analysis
using PCR and restriction-enzyme digest
analysis
(Figure 25-7)

© 2017 Pearson Education, Ltd. Table 25.1
Section 25.3: Computing frequencies
 Table 25.2
– Two methods for computing frequencies of alleles
in population surveyed
a) Counting alleles
b) From genotype frequencies

Section 25.3: Calculating Frequencies of
Alleles
 Frequencies for multiple alleles
– Calculated by adding additional variables to
Hardy–Weinberg equation
– Example: Situation involving three alleles
pqr1
 Frequencies of genotypes given by
(p  q  r)2 
p2  q2  r2  2pq  2pr  2qr  1

Section 25.3: ABO Blood Type
 Example of genotype frequency calculations for

multiple alleles
– ABO blood type (Table 25.3)

Section 25.3: Frequencies of X-Linked Traits
 Calculating frequencies of X-linked traits

using Hardy–Weinberg equation
– Calculate allele and genotype frequencies for
X-linked traits in mammals
– Frequency of X-linked allele in gene pool equals
frequency of males expressing X-linked trait
– Each male has only one X chromosome
– Female with an allele on both X chromosomes will
be q2

Section 25.3: Heterozygote Frequencies
 Hardy–Weinberg law allows estimation of

frequency of heterozygotes in population
– Frequency of recessive trait determined by
counting individuals in population sample
– Example: Cystic fibrosis

Section 25.3: Cystic Fibrosis
 Cystic fibrosis (autosomal recessive)

– Incidence of 1/2500  0.0004 in people of
northern European ancestry
 Frequency of recessive allele
Since p  q  1, p  1  q  1  0.02  0.98

2pq  2(0.98)(0.02)  0.04, or 4%

25.4 Natural Selection Is a Major Force
Driving Allele Frequency Change

Section 25.4: Natural Selection
 Natural selection
– Major force driving allele frequency change
– Chief mechanism for transforming populations
– Principal force that shifts allele frequencies
within large populations
– Discovered independently by Charles Darwin and
Alfred Russel Wallace

Section 25.4: Wallace-Darwin Concept
 Wallace-Darwin concept of natural selection:

– Individuals exhibit variations in phenotype
– Variations are heritable (passed on)
– Organisms tend to reproduce in exponential
fashion
 More offspring are produced than can survive
– Some phenotypes are more successful at survival
and reproduce at higher rates

Section 25.4: Fitness (w)
 Hardy–Weinberg analysis allows fitness (w) to

be examined for each genotype
– Fitness: Individual’s genetic contribution to the
future generations
– Homozygous recessive individual who dies
before producing offspring: w  0
 Frequency of recessive allele will decrease in each
generation
(Figure 25-8)

Section 25.4: Degrees of Selection
 Figure 25-9
– Outcome of different degrees of selection
against nonlethal recessive allele a
– Intensity of selection varies
 Strong (red curve) to weak (blue curve)
 Intermediate values (yellow, purple, and green curves)

Section 25.4: Types of Selection
 Selection for traits classified as

– Directional selection
– Stabilizing selection
– Disruptive selection
(Figure 25-10)

Section 25.4: Directional Selection
 Directional selection
– Phenotypes at one end of spectrum become
selected for or against
– Usually as result of changes in environment
– Example: Beak size in finches during dry years
increased due to strong selection

Section 25.4: Stabilizing Selection
 Stabilizing selection
– Intermediate types are favored
– both extreme phenotypes are selected against
– Reduces population variance over time but not
the mean
– Example: Human birth weight study over an 11-
year period
(Figure 25-11)

Section 25.4: Disruptive Selection
 Disruptive selection
– Both phenotypic extremes are selected for
– Intermediates are selected against
– Results in population with increasingly bimodal
distribution for trait
– Example: Applied selection for low and high
bristle number in Drosophila population
(Figure 25-12)

25.5 Mutation Creates New Alleles in a
Gene Pool

Section 25.5: Mutation
 Mutation
– Within a population, the gene pool is reshuffled
each generation
– Mutation is the only process that creates new
alleles in gene pool
– Most mutations are recessive
– Indirect methods using probability and statistics or
large-scale screening programs are often
employed to estimate mutation rates

Section 25.5: Mutation Rates
 Mutation rates
– Number of new mutant alleles per given number
of gametes
– If mutation rate is known, the extent of change to
allele frequency from one generation to next can
be estimated

Section 25.5: Achondroplasia (Dwarfism)
 Achondroplasia – dominant form of dwarfism in

humans
– Skeletal disorder
 Enlarged skull
 Short arms and legs
 Diagnosed with X-ray examination at birth
 Fulfills requirements for measuring mutation rates

25.6 Migration and Gene Flow Can Alter
Allele Frequencies

Section 25.6: Migration
 Migration
– Occurs when individuals move between
populations
 Species divides into populations that are
separated geographically
– Allele frequencies in new populations may differ
over time
(Figure 25-13)

25.7 Genetic Drift Causes Random
Changes in Allele Frequency in Small
Populations

Section 25.7: Genetic Drift
 Genetic drift
– Significant random fluctuations in allele
frequencies in small populations
– Possible by chance alone
– Degree of fluctuation increases as population size
decreases
– Can also occur as result of:
 Founder effect
 Genetic bottleneck

Section 25.7: Founder Effect
 Founder effect
– Genetic drift can also arise through founder
effect
 Occurs when population originates from small number
of individuals
 Gene pool may not reflect larger population from which
founders are drawn

Section 25.7: Genetic Bottleneck
 Genetic bottleneck
– Genetic drift can also occur as result of genetic
bottleneck
– Develops when large population undergoes
drastic but temporary reduction in numbers
– Populations may recover, but with greatly reduced
genetic diversity

Section 25.7: Founder Effect
 Example of founder effect in human

populations
– High frequency of oculocutaneous albinism
(OCA) in the Navajo
– OCA frequency
 1/1500–1/2000 in Navajo
 1/3600 in whites
 1/10,000 in African-Americans

Section 25.7: PCR and DNA Analysis of OCA
 PCR screening of DNA and analysis of OCA

frequency
– Indicate mutant allele may have arisen as founder
mutation about 400–1000 years ago

25.8 Nonrandom Mating Changes Genotype
Frequency but Not Allele Frequency

Section 25.8: Nonrandom Mating
 Nonrandom mating
– Can change frequencies of genotypes in
population
– Subsequent selection for or against certain
genotypes can affect overall allele frequencies
– But nonrandom mating itself does not directly
change allele frequencies

Section 25.8: Forms of Nonrandom Mating
Forms of nonrandom mating

 Positive assortive mating: Similar genotypes
more likely to mate than dissimilar ones
 Negative assortive mating: Dissimilar
genotypes are more likely to mate than similar
one
 Inbreeding: Mating individuals are related

Section 25.8: Inbreeding
 Inbreeding
– Mating among closely related individuals
 For a given allele
– Inbreeding increases proportion of
homozygotes in population
– Completely inbred population theoretically will
consist only of homozygotes

Section 25.8: Coefficient of Inbreeding (F)
 Coefficient of inbreeding (F)

– Quantifies probability that two alleles of given
individual are identical because they are
descended from single copy of allele in ancestor
– F  1: All individuals in population are
homozygous; both alleles come from same
ancestral copy
– F  0: No individual has two alleles derived from
common ancestral copy (Figure 25-17)

25.9 Reduced Gene Flow, Selection, and
Genetic Drift Can Lead to Speciation

Section 25.9: Species and Speciation
 Species
– Group of actually or potentially interbreeding
organisms that is reproductively isolated in nature
from all other such groups
 Speciation
– Associated with changes in genetic structure of
populations with genetic divergence
– Genetic divergence of populations can reflect
action of natural selection, genetic drift, or both

Section 25.9: Macroevolution
 Macroevolution
– Genetic changes that result in reproductive
isolation between or among populations
– Leads to formation of new species

Section 25.9: Reproductive Isolation
 Reproductive isolating mechanisms

– Biological barriers that prevent or reduce
interbreeding between populations
– Mechanisms may be
 Ecological
 Behavioral
 Seasonal
 Mechanical
 Physiological

Section 25.9: Isolating Mechanisms
 Prezygotic isolating mechanisms

– Prevent mating from taking place
 Postzygotic isolating mechanisms
– Create reproductive isolation even when
members of two population mate with each other

Section 25.9: Changes Lead to Speciation
 Geographic changes can lead to speciation

– Example: Ancestors of snapping shrimp
– Prior to formation of Isthmus of Panama,
members were of a single species
(Figure 25-17)
 When the isthmus closed, each of seven
ancestral species was divided into two separate
populations

Section 25.9: Rate of Macroevolution and
Speciation
 Rate of macroevolution and speciation
– Average time for speciation 100,000–10 million
years
– Rapid speciation events have occurred
 Fishes in East African lakes
 Marine salmon
 Palm trees on isolated islands
 Polyploid plants
 Brown algae in Baltic Sea

Section 25.9: Speciation
 Figure 25-18
– Lake Apoyo in Nicaragua
– Formed within past 23,000 years
– Home to two species of cichlid fish
– Midas cichlid: Common in region
– Arrow cichlid: Found ONLY in this lake

Section 25.9: Speciation and Evolutionary
Origin
 Evolutionary origin of Arrow cichlid
– Phylogenetic, morphological, and ecological
analyses by researchers
– Sequence analysis of mtDNA indicates two
species are from monophyletic group
– Concluded that Arrow cichlid evolved from
Midas cichlid
(Figure 25-18)

25.10 Phylogeny Can Be Used to Analyze
Evolutionary History

Section 25.10: Phylogenies
 Phylogeny (evolutionary history)

– Genetic differences among present-day species
can be used to reconstruct their evolutionary
histories (phylogenies)
 Phylogenetic trees: Figure 25-21
– Branches represent lineages over time
– Monophyletic groups consist of an ancestral
species and all its descendants

Section 25.10: Cytochrome c
 Cytochrome c is a eukaryotic mitochondrial

protein
– Phylogenetic reconstruction of amino acids of
cytochrome c indicated it has evolved very
slowly in variety of organisms
– Genetic equidistance: Differences in amino acid
sequence between species are proportional to
evolutionary distance

Section 25.10: Minimal Mutational Distances
 Minimal mutational distances (amino acid

differences in protein)
– Data on distances between cytochrome c genes
of 19 organisms was used to construct
phylogenetic tree showing relationship among
various species
(Figure 25-21)

Section 25.10: Molecular Clocks
 Molecular clocks
– Measure rate of evolutionary change
– Measured in terms of amino acid or nucleotide
sequences; evolutionary changes accumulate at
constant rate over time
 Figure 25-22
– Molecular clock showing divergence times for
humans and other vertebrates based on fossil
record

Section 25.10: Complex Origins of Our
Genome
 Complex origins of our genome
– Genetic diversity in mtDNA used to infer where
Homo sapiens originated
– Highest levels of diversity in African populations
– Non-African populations had origins 50,000 years
ago
– H. sapiens originated in Africa from earlier
species of Homo

Section 25.10: Neanderthals
 Neanderthals (Homo neanderthalensis)

– Lived in Europe and western Asia about 300,000
years ago
– Disappeared about 30,000 years ago
– Coexisted with anatomically modern humans
(Homo sapiens) for about 30,000 years in several
regions

Section 25.10: Divergence of Neanderthals
 Phylogenetic tree shows pattern and times of

divergence of Neanderthals and our species
 Conclusions from this study
– Neanderthals are not direct ancestors of our
species
– Neanderthals and members of our species
interbred
– Neanderthals contributed to our genome


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Chapter

© 2017 Pearson Education, Ltd.

25.1 Genotypic Variation Is Present in Most Populations

© 2017 Pearson Education, Ltd.

25.4 Natural Selection Is a Major Force Driving Allele

© 2017 Pearson Education, Ltd.

25.9 Reduced Gene Flow, Selection, and Genetic Drift

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Population’s gene pool

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Alcohol dehydrogenase (Adh)

© 2017 Pearson Education, Ltd.

 Adh genes from individuals representing five

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Neutral theory of molecular evolution

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg law makes two predictions:

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg model assumes

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg law – three additional

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg law applied to humans

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Example of genotype frequency calculations for

© 2017 Pearson Education, Ltd.

 Calculating frequencies of X-linked traits

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg law allows estimation of

© 2017 Pearson Education, Ltd.

 Cystic fibrosis (autosomal recessive)

Since p  q  1, p  1  q  1  0.02  0.98

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Wallace-Darwin concept of natural selection:

© 2017 Pearson Education, Ltd.

 Hardy–Weinberg analysis allows fitness (w) to

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Selection for traits classified as

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

 Achondroplasia – dominant form of dwarfism in

© 2017 Pearson Education, Ltd.