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15
Mechanisms of Evolution
Chapter 15 Mechanisms of Evolution
Key Concepts
• 15.1 Evolution Is Both Factual and the Basis of
Broader Theory
• 15.2 Mutation, Selection, Gene Flow, Genetic
Drift, and Nonrandom Mating Result in
Evolution
• 15.3 Evolution Can Be Measured by Changes
in Allele Frequencies
• 15.4 Selection Can Be Stabilizing, Directional,
or Disruptive
Chapter 15 Mechanisms of Evolution
Key Concepts
• 15.5 Genomes Reveal Both Neutral and
Selective Processes of Evolution
• 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New
Features
• 15.7 Evolutionary Theory Has Practical
Applications
Chapter 15 Opening Question
How do biologists use evolutionary theory
to develop better flu vaccines?
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
Biological populations change over time, or
evolve.
Evolutionary change is observed in laboratory
experiments, in natural populations, and in the
fossil record.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
Evolutionary theory—understanding the
mechanisms of evolutionary change.
It has many applications: study and treatment of
diseases, development of crops and industrial
processes, understanding the diversification of
life, and how species interact.
It also allows us to make predictions about the
biological world.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
Theory—In everyday speech, an untested
hypothesis or a guess.
Evolutionary theory is not a single hypothesis,
but refers to our understanding of the
mechanisms that result in genetic changes in
populations over time and to our use of that
understanding to interpret changes in and
interactions among living organisms.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
Even before Darwin, biologists had suggested
that species had changed over time, but no one
had proposed a convincing mechanism for
evolution.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
Charles Darwin was
interested in geology
and natural history.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
In 1831, Darwin
began a 5-year
voyage around the
world on a Navy
survey vessel, the
HMS Beagle.
Figure 15.1 The Voyage of the Beagle
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
From the observations and insights made on the
voyage, and new ideas from geologists on the
age of the Earth, Darwin developed an
explanatory theory for evolutionary change:
• Species change over time.
• Divergent species share a common ancestor.
• The mechanism that produces change is
natural selection.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
In 1858, Darwin received a paper from Alfred
Russel Wallace with an explanation of natural
selection nearly identical to Darwin’s.
Both men are credited for the idea of natural
selection.
Darwin’s book, The Origin of Species, was
published in 1859.
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
By 1900, the fact of evolution was established,
but the genetic basis of evolution was not yet
understood.
Then the work of Gregor Mendel was
rediscovered, and during the 20th century, work
continued on the genetic basis of evolution.
A “modern synthesis” of genetics and evolution
took place 1936–1947.
Figure 15.2 Milestones in the Development of Evolutionary Theory
Concept 15.1 Evolution Is Both Factual and the Basis of Broader
Theory
The structure of DNA was established by 1953
by Watson and Crick.
In the 1970s, technology developed for
sequencing long stretches of DNA and amino
acid sequences in proteins.
Evolutionary biologists now study gene structure
and evolutionary change using molecular
techniques.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Biological evolution refers to changes in the
genetic makeup of populations over time.
Population—a group of individuals of a single
species that live and interbreed in a particular
geographic area at the same time.
Individuals do not evolve; populations do.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
The origin of genetic variation is mutation.
Mutation—any change in nucleotide sequences.
Mutations occur randomly with respect to an
organism’s needs; natural selection acts on this
random variation and results in adaptation.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Mutations can be deleterious, beneficial, or have
no effect (neutral).
Mutation both creates and helps maintain
genetic variation in populations.
Mutation rates vary, but even low rates create
considerable variation.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Because of mutation, different forms of a gene,
or alleles, may exist at a locus.
Gene pool—sum of all copies of all alleles at all
loci in a population.
Allele frequency—proportion of each allele in
the gene pool.
Genotype frequency—proportion of each
genotype among individuals in the population.
Figure 15.3 A Gene Pool
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Many of Darwin’s observations came from
artificial selection of domesticated plants and
animals.
Selection on different characters in a single
species of wild mustard produced many crop
plants.
Figure 15.4 Many Vegetables from One Species
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Darwin bred pigeons and recognized similarities
between selection by breeders and selection in
nature.
Figure 15.5 Artificial Selection
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Laboratory experiments also show genetic
variation in populations.
Selection for certain traits in the fruit fly
Drosophila melanogaster resulted in new
combinations of genes that were not present in
the original population.
Figure 15.6 Artificial Selection Reveals Genetic Variation
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Natural selection:
• Far more individuals are born than survive to
reproduce.
• Offspring tend to resemble their parents, but
are not identical to their parents or to one
another.
• Differences among individuals affect their
chances to survive and reproduce, which will
increase frequency of favored traits in the next
generation.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Adaptation—a favored trait that evolves through
natural selection.
Adaptation also describes the process that
produces the trait.
Individuals with deleterious mutations are less
likely to survive and reproduce and to pass
their alleles on to the next generation.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Migration of individuals between populations
results in gene flow, which can change allele
frequencies.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Genetic drift—random changes in allele
frequencies from one generation to the next.
In small populations, it can change allele
frequencies. Harmful alleles may increase in
frequency, or rare advantageous alleles may
be lost.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
A population bottleneck—an environmental
event results in survival of only a few
individuals.
Genetic drift can change allele frequencies.
Populations that go through bottlenecks loose
much of their genetic variation.
Figure 15.7 A Population Bottleneck
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Founder effect—genetic drift changes allele
frequencies when a few individuals colonize a
new area.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Nonrandom mating:
Selfing, or self-fertilization is common in plants.
Homozygous genotypes will increase in
frequency and heterozygous genotypes will
decrease.
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Sexual selection—mates are chosen based on
phenotype, e.g., bright-colored feathers of male
birds.
There may be a trade-off between attracting
mates (more likely to reproduce) and attracting
predators (less likely to survive).
Concept 15.2 Mutation, Selection, Gene Flow,
Genetic Drift, and Nonrandom Mating Result in Evolution
Or, phenotype may indicate a successful
genotype, e.g., female frogs are attracted to
males with low-frequency calls, which are
larger and older (hence successful).
Studies of African long-tailed widowbirds showed
that females preferred males with longer tails,
which may indicate greater health and vigor.
Figure 15.8 What Is the Advantage?
Figure 15.9 Sexual Selection in Action (Part 1)
Figure 15.9 Sexual Selection in Action (Part 2)
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
Evolution can be measured by change in allele
frequencies.
Allele frequency =
number of copies of allele in population
total number of copies of all alleles in population
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
For two alleles at a locus, A and a, three
genotypes are possible: AA, Aa, and aa.
p = frequency of A; q = frequency of a
2 N AA  N Aa
p
2N
2 N aa  N Aa
q
2N
Figure 15.10 Calculating Allele and Genotype Frequencies
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
For each population, p + q = 1, and q = 1 – p.
Monomorphic: only one allele at a locus,
frequency = 1. The allele is fixed.
Polymorphic: more than one allele at a locus.
Genetic structure—frequency of alleles and
genotypes of a population.
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
Hardy–Weinberg equilibrium—allele
frequencies do not change across generations;
genotype frequencies can be calculated from
allele frequencies.
If a population is at Hardy-Weinberg equilibrium,
there must be no mutation, no gene flow, no
selection of genotypes, infinite population size,
and random mating.
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
At Hardy-Weinberg equilibrium, allele
frequencies don’t change.
Genotypes frequencies:
Genotype AA Aa aa
Frequency p2 2pq q2
Figure 15.11 One Generation of Random Mating Restores Hardy–Weinberg Equilibrium (Part 1)
Figure 15.11 One Generation of Random Mating Restores Hardy–Weinberg Equilibrium (Part 2)
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
Probability of 2 A-gametes coming together:
p  p  p 2  (0.55) 2  0.3025
Probability of 2 a-gametes coming together:
q  q  q 2  (0.45) 2  0.2025
Overall probability of obtaining a heterozygote:
2 pq  0.495
Concept 15.3 Evolution Can Be Measured by Changes in Allele
Frequencies
Populations in nature never meet the conditions
of Hardy–Weinberg equilibrium—all biological
populations evolve.
The model is useful for predicting approximate
genotype frequencies of a population.
Specific patterns of deviation from Hardy–
Weinberg equilibrium help identify mechanisms
of evolutionary change.
Concept 15.4 Selection Can Be Stabilizing, Directional, or
Disruptive
Qualitative traits—influenced by alleles at one
locus; often discrete qualities (black versus
white).
Quantitative traits—influenced by alleles at more
than one locus; likely to show continuous
variation (body size of individuals).
Concept 15.4 Selection Can Be Stabilizing, Directional, or
Disruptive
Natural selection can act on quantitative traits in
three ways:
• Stabilizing selection favors average
individuals.
• Directional selection favors individuals that
vary in one direction from the mean.
• Disruptive selection favors individuals that
vary in both directions from the mean.
Figure 15.12 Natural Selection Can Operate in Several Ways (Part 1)
Figure 15.12 Natural Selection Can Operate in Several Ways (Part 2)
Figure 15.12 Natural Selection Can Operate in Several Ways (Part 3)
Concept 15.4 Selection Can Be Stabilizing, Directional, or
Disruptive
Stabilizing selection reduces variation in
populations, but does not change the mean.
It is often called purifying selection—selection
against any deleterious mutations to the usual
gene sequence.
Figure 15.13 Human Birth Weight Is Influenced by Stabilizing Selection
Concept 15.4 Selection Can Be Stabilizing, Directional, or
Disruptive
Directional selection—individuals at one extreme
of a character distribution contribute more
offspring to the next generation.
An evolutionary trend may result.
Example: Texas Longhorn cattle.
Figure 15.14 Long Horns Are the Result of Directional Selection
Concept 15.4 Selection Can Be Stabilizing, Directional, or
Disruptive
Disruptive selection—individuals at opposite
extremes of a character distribution contribute
more offspring to the next generation.
Increases variation in the population; can result
in a bimodal distribution of traits.
Figure 15.15 Disruptive Selection Results in a Bimodal Character Distribution
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Types of mutations:
• Nucleotide substitution—change in one
nucleotide in a DNA sequence (a point
mutation).
• Synonymous substitution—most don’t affect
phenotype because most amino acids are
specified by more than one codon.
• Nonsynonymous substitution—deleterious
or selectively neutral.
Figure 15.16 When One Nucleotide Changes (Part 1)
Figure 15.16 When One Nucleotide Changes (Part 2)
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Substitution rates are highest at positions that do
not change the amino acid being expressed.
Substitution is even higher in pseudogenes,
copies of genes that are no longer functional.
Figure 15.17 Rates of Substitution Differ
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Types of mutations: Insertions, deletions, and
rearrangements
Can have larger effect than point mutations.
Can change the reading frame of protein-coding
sequences.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Neutral theory—at the molecular level, the
majority of variants in most populations are
selectively neutral.
Neutral variants must accumulate through
genetic drift rather than positive selection.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Rate of fixation of neutral mutations by genetic
drift is independent of population size.
1
2 N

2N
N = population size
μ = neutral mutation rate
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
The rate of evolution of particular genes and
proteins is often relatively constant over time,
and can be used as a “molecular clock” to
calculate evolutionary divergence times
between species.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Fitness of genotypes:
Genotypes of higher fitness increase in
frequency over time; those of lower fitness
decrease over time.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Relative rates of substitution types differ as a
function of selection:
• If similar, the corresponding amino acid is likely
drifting neutrally among states.
• If nonsynonymous substitution exceeds
synonymous, positive selection results in
change in the corresponding amino acid.
• If synonymous substitution exceeds
nonsynonymous, purifying selection resists
change in the corresponding amino acid.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Evolution of lysozyme:
Lysozyme digests bacteria cell walls; found in
almost all animals as a defense mechanism.
Some mammals are foregut fermenters, which
has evolved twice—in ruminants and leafeating monkeys (langurs). Lysozyme in these
lineages has been modified to rupture some
bacteria in the foregut to release nutrients.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Lysozyme-coding sequences were compared in
foregut fermenters and their non-fermenting
relatives, and rates of substitutions were
determined.
The rate of synonymous substitution in the
lysozyme gene was much higher than
nonsynonymous, indicating that many of the
amino acids are evolving under purifying
selection.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Replacements in lysozyme happened at a much
higher rate in langur lineage.
Lysozyme went through a period of rapid change
in adapting to the stomachs of langurs.
Lysozymes of langurs and cattle share five
convergent amino acid replacements, which
make the protein more resistant to degradation
by the stomach enzyme pepsin.
Figure 15.18 Convergent Molecular Evolution of Lysozyme (Part 1)
Figure 15.18 Convergent Molecular Evolution of Lysozyme (Part 2)
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Lysozyme in the crop of the hoatzin, a foregutfermenting bird, has similar adaptations as
those of langurs and cattle.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Heterozygotes can be advantageous as
environmental conditions change, and
polymorphic loci are maintained.
Colias butterflies live in an environment with
temperature extremes. The population is
polymorphic for an enzyme that influences
flight at different temperatures.
Heterozygotes are favored because they can
fly over a larger temperature range.
Figure 15.19 A Heterozygote Mating Advantage (Part 1)
Figure 15.19 A Heterozygote Mating Advantage (Part 2)
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Genome size and organization also evolves.
Genome size varies greatly.
If only the protein and RNA coding portions of
genomes are considered, there is much less
variation in size.
Figure 15.20 Genome Size Varies Widely
Figure 15.21 A Large Proportion of DNA Is Noncoding
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
Much of the noncoding DNA does not appear to
have a function.
Some noncoding DNA can alter the expression
of surrounding genes.
Some noncoding DNA consists of pseudogenes.
Some consists of parasitic transposable
elements.
Concept 15.5 Genomes Reveal Both Neutral
and Selective Processes of Evolution
The amount of nonconding DNA may be related
to population size.
Noncoding sequences that are only slightly
deleterious are likely to be purged by selection
most efficiently in species with large population
sizes.
In small populations genetic drift may overwhelm
selection against these sequences.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Sexual reproduction results in new combinations
of genes and produces genetic variety that
increases evolutionary potential.
But in the short term, it has disadvantages:
• Recombination can break up adaptive
combinations of genes
• Reduces rate at which females pass genes to
offspring
• Dividing offspring into genders reduces the
overall reproductive rate
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Why did sexual reproduction evolve? Possible
advantages:
• It facilitates repair of damaged DNA. Damage
on one chromosome can be repaired by
copying intact sequences on the other
chromosome.
• Elimination of deleterious mutations through
recombination followed by selection.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
• In asexually reproducing species, deleterious
mutations can accumulate; only death of the
lineage can eliminate them
Muller called this the genetic ratchet—
mutations accumulate or “ratchet up” at each
replication; Muller’s ratchet.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
• The variety of genetic combinations in each
generation can be advantageous (e.g., as
defense against pathogens and parasites).
Sexual recombination does not directly influence
the frequencies of alleles. Rather, it generates
new combinations of alleles on which natural
selection can act.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Lateral gene transfer—individual genes,
organelles, or genome fragments move
horizontally from one lineage to another.
• Species may pick up DNA fragments directly
from the environment.
• Genes may be transferred to a new host in a
viral genome.
• Hybridization results in the transfer of many
genes.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Lateral gene transfer can be advantageous to a
species that incorporates novel genes.
Genes that confer antibiotic resistance are often
transferred among bacteria species.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Gene duplication—genomes can gain new
functions.
Gene copies may have different fates:
1.Both copies retain original function (may
increase amount of gene product).
2.Gene expression may diverge in different
tissues or at different times in development.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
3. One copy may accumulate deleterious
mutations and become a functionless
pseudogene.
4. One copy retains original function, the other
changes and evolves a new function.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Sometimes entire genomes may be duplicated,
providing massive opportunities for new
functions to evolve.
In vertebrate evolution, genomes of the jawed
vertebrates have 4 diploid sets of many genes.
Two genome-wide duplication events occurred
in the ancestor of these species. This allowed
specialization of individual vertebrate genes.
Concept 15.6 Recombination, Lateral Gene Transfer,
and Gene Duplication Can Result in New Features
Successive rounds of duplication and sequence
evolution may result in a gene family, a group
of homologous genes with related functions.
The globin gene family probably arose via gene
duplications.
Figure 15.22 A Globin Family Gene Tree
Concept 15.7 Evolutionary Theory Has Practical Applications
Molecular evolutionary principles are used to
understand protein structure and function.
Puffer fish have a toxin (TTX) that blocks sodium
ion channels and prevents nerve and muscle
function.
Genes for sodium channel proteins in puffer fish
have substitutions that prevent TTX from
binding.
Study of these gene substitutions aid in
understanding how sodium channels function.
Concept 15.7 Evolutionary Theory Has Practical Applications
Living organisms produce many compounds
useful to humans. The search for such
compounds is called bioprospecting.
These molecules result from millions of years of
evolution.
But biologists can imagine molecules that have
not yet evolved. In vitro evolution—new
molecules are produced in the laboratory to
perform novel and functions.
Figure 15.23 In Vitro Evolution (Part 1)
Figure 15.23 In Vitro Evolution (Part 2)
Concept 15.7 Evolutionary Theory Has Practical Applications
In agriculture, breeding programs have benefited
from evolutionary principles, including
incorporation of beneficial genes from wild
species.
An understanding of how pest species evolve
resistance to pesticides has resulted in more
effective pesticide application and rotation
schemes.
Concept 15.7 Evolutionary Theory Has Practical Applications
Molecular evolution is also used to study disease
organisms.
All new viral diseases have been identified by
evolutionary comparison of their genomes with
those of known viruses.
Answer to Opening Question
Changes in surface proteins make influenza
virus strains undetectable to the host’s immune
system (positive selection for changes in
surface proteins).
By comparing ratios of synonymous to
nonsynonymous substitutions, biologists can
detect which mutations are under positive
selection.
Answer to Opening Question
They then assess which current flu strains show
the greatest number of changes in these
positively selected codons.
These flu strains are most likely to survive and
lead to flu epidemics of the future, so they are
the best targets for new vaccines.
Figure 15.24 Evolutionary Analysis of Surface Proteins Leads to Improved Flu Vaccines