OEB 53 R EADING NOTES
 200 EARS OF DARWIN : A THEORY ’S O RIGINS
CHAPTER 1: HE VIRUS AND THE W HALE (HOW SCIENTISTS STUDY EVOLUTION )
1.1 W HALES: M AMMALS GONE TO SEA
Natural selection is a mechanism that can lead to evolution, whereby differential survival or
reproduction of individuals causes some genetic types to outcompete others.
Convergent evolution: the independent origin of similar traits in separate lineages
Homologous characteristics are similar in two or more species because they are inherited from a common
A synapomorphy is a derived form of a trait that is shared by a group of related species (i.e., one that
evolved in the immediate common ancestor of the group and was inherited by all its descendants).
Phylogeny: a visual representation of the evolutionary history of populations, genes, or species.
1.2 VIRUSES: THE DEADLY ESCAPE ARTISTS
A mutation is any change to the genomic sequence of an organism.
Viral reassortment occurs when genetic material from different strains gets mixed into new combinations
within a single individual.
1.3 EVOLUTION : A TAPESTRY OF CONCEPTS
Genetic drift is evolution arising from random changes in the genetic composition of a population from
one generation to the next.
Phenotypes are measurable aspects of organisms, such as morphology (structure), physiology, and
behavior. Genes interact with other genes and with the environment during the development of the
1.4 COMMON M ISCONCEPTIONS ABOUT EVOLUTION
1. Evolution is “just” a theory
2. Evolutionary biology has a complete explanation for everything that happened in the history of
3. The theory of evolution is about the origin of life.
4. The study of evolution is the search for direct ancestors and missing links.
5. Evolution violates the second law of thermodynamics.
6. Evolution is natural selection.
7. Evolution is entirely random. OEB 53 R EADING NOTES
8. Evolution provides secies with the adaptations they “need.”
9. Evolution is a march of progress.
10. Evolution always goes from simple to comllex.
11. Evolution is the result of individuals adapting to their environment.
12. Evolution has made living things perfectly adapted to their environment.
13. Evolution happens for the good of the species.
14. Evolution promotes selfishness and cruelty.
15. Evolution seeks a peaceful harmony in nature.
16. Some forms of life are higher on the ladder of life, and some are lower.
17. Evolution has produced a stable diversity of life. OEB 53 R EADING N OTES
 ECONCILING DARWIN & M ENDEL : THE M ODERN SYNTHESIS
CHAPTER 2: IOLOGY (FROM N ATURAL PHILOSOPHY TO D ARWIN )
2.1 NATURE BEFORE DARWIN
Taxon (plural, taxa): a group of organisms that a taxonomist judges to be a taxonomic unit, such as a
species or order.
Taxonomy is the science of describing, naming, and classifying species of living or fossil organisms.
2.2 EVOLUTION BEFORE DARWIN
Paleontology is the study of prehistoric life.
Extinction is the permanent loss of a population or species, arising with the death or failure to breed of
the last individual.
2.3 THE U NOFFICIAL NATURALIST
Uniformitarianism was the idea that the natural laws observable around us now are also responsible for
events in the past. One part of this view, for example, was the idea that the Earth had been shaped by the
cumulative action of gradual processes like sediment deposition and erosion.
Fact 1: All species have such great potential fertility that their population size would increase
exponentially if all individuals that were born reproduced successfully.
Fact 2: Except for minor annual fluctuations and occasional major fluctuations, populations
normally display stability.
Fact 3: Natural resources are limited. In a stable environment they remain relatively constant.
>> Inference 1: Since more individuals are produced than can be supported by the available
resources but population size remains stable, it means that there must be a fierce struggle for
existence among the individuals of a population, resulting in the survival of only a part, often a
very small part, of the progeny of each generation.
>> Inference 2: Survival in the struggle for existence is not random but depends in part on the
hereditary constitution of the surviving individuals. This unequal survival constitutes the process
of natural selection.
Fact 4: No two individuals are exactly the same; rather, every population displays enormous
Fact 5: Much of this variation is heritable. OEB 53 R EADING N OTES
>> Inference 3: Over the generations this process of natural selection will lead to a continuing
gradual change of populations, that is, to evolution and to the production of new species.
Homologous traits are similar because they are inherited from a common ancestor.
Analogous traits are similar because they have converged on a shared form. They are not derived from a
Natural selection is a mechanism that can lead to evolution, whereby differential reproduction of
individuals causes some genetic types to replace (outcompete) others.
Adaptations are inherited aspects of an individual that allow it to outcompete other members of a
population that lack the trait (or that have a slightly different version of that trait). Adaptations are traits
that have evolved through the mechanism of natural selection.
2.4 DARWIN IN THE TWENTY FIRSTCENTURY
Sexual selection arises when individuals of one sex (usually males) compete with each other over access
to individuals of the other sex. It can lead to the evolution of traits like showy ornaments or weapons that
improve an individual’s chance of mating.
Genetic drift is a change in the frequency of traits or genetic variants that arises across generations due to
random events. Drift is most pronounced in small populations. OEB 53 R EADING NOTES
 ENETIC VARIATION & H ARDY W EINBERG
CHAPTER 5: AW M ATERIAL (HERITABLE VARIATION AMONG INDIVIDUALS )
5.1 EVOLUTION ’S MOLECULES : ROTEINS , DNA, AND RNA
Amino acids: the structural units that, among other functions, link together to form proteins.
Nucleotides: the structural units that link together to form DNA (and RNA). Each nucleotide includes a
Nucleobase (base): one of four nitrogenbased molecules in DNA
Mutation: any change to the genomic sequence of an organism
RNA: the third macromolecule essential for all known forms of life (along with DNA and proteins). It
differs structurally from DNA in having the sugar ribose instead of deoxyribose and in having the base
uracil instead of thymine.
Genes: segments of DNA whose nucleotide sequences code for proteins, or RNA, or regulate the
expression of other genes.
Gene expression: the process by which information from a gene is transformed into a product.
Sexual chromosome: chromosomes tat pair during meiosis but differ in copy number between males and
females. For organisms such as humans with XY sex determination, X and Y are the sex chromosomes.
Females are the homogametic (XX) and males are the heterogametic sex (XY).
Autosomes: chromosomes that do not differ between the sexes.
Ploidy: the number of copies of unique chromosomes in a cell (n). Normal human somatic cells are
diploid, with two copies of 23 chromosomes.
Transcription: the process that takes place when RNA polymerase reads a coding sequence of DNA and
produces a complementary strand of RNA, called mRNA.
Translation: the process that takes place when a strand of mRNA is decoded by a ribosome to produce a
strand of amino acids.
Transcription factors: proteins that bind to specific DNA sequences and act, in essence, like a light
switch by turning all the sequences on or off simultaneously
Hormone: a molecular signal that flows from cells in one part of the body to cells in other parts of the
body. Hormones act directly or indirectly to alter expression of target genes.
RNA splicing: the process of modifying RNA after transcription but before translation, during which
introns are removed and exons are joined together into a contiguous strand.
Alternative splicing: the process of combining different subsets of exons together, yielding different
mRNA transcripts from a single gene. OEB 53 R EADING N OTES
Genome: all of the hereditary information of an organism. The genome comprises the totality of the
DNA, including the coding and noncoding regions.
MicroRNA: one group of RNAs that act as posttranscriptional regulators of gene expression.
MicroRNAs bind to complementary sequences on specific mRNAs and can enhance or silence the
translation of genes. The human genome encodes more than 1000 of these tiny RNAs.
Pseudogenes: DNA sequences that resemble functional genes but have lost their proteincoding ability or
are no longer expressed. Pseudogenes often form after a gene has been duplicated, when one or more of
the redundant copies subsequently lose their function.
Mobile genetic elements: types of DNA that can move around in the genome. Common examples
include transposons (“jumping genes”) and plasmids.
5.2 M UTATIONS: CREATING VARIATION
Vertical gene transfer: the process of receiving genetic material from an ancestor
Horizontal gene transfer: any process in which genetic material is transferred to another organism
Plasmids: molecules of DNA, found most often in bacteria, that can replicate independently of
Cisacting elements: stretches of DNA located near a gene—either immediately upstream (adjacent to
the promoter region), downstream, or inside an intron—that influence expression of that gene. Cis regions
often code for binding sites for one or more transposable factors.
Transacting elements: sequences of DNA that are located away from the focal gene (e.g., on another
chromosome). These stretches of DNA generally code for a protein, microRNA, or other diffusible
molecule that then influences expression of the focal gene.
Somatic mutations: mutations that affect cells in the body (“soma”) of an organism. These mutations
affect all the daughter cells produced by the affected cell and can affect the phenotype of the individual.
In animals, somatic mutations are not passed down to offspring. In plants, somatic mutations can be
passed down during vegetative reproduction.
Germline mutation: mutations that affect the gametes (eggs, sperm) of an individual and can be
transmitted from parents to offspring. Because they can be passed on, germline mutations create the
heritable genetic variation that is relevant to evolution.
Allele: one of several alternative forms of the DNA sequence of the same locus.
Meioisis: a form of cell division that occurs only in eukaryotes, in which the number of chromosomes is
cut in half. Meiosis gives rise to gametes or spores and is essential for sexual reproduction. OEB 53 R EADING N OTES
Genetic recombination: the exchange of genetic material between paired chromosomes during meiosis.
Recombination can form new combinations of alleles and is an important source of heritable variation.
5.4 THE LINK BETWEEN MOST PHENOTYPES AND GENOTYPES S C OMPLEX
Genotype: the genetic makeup of an individual. Although a genotype includes all the alleles of all the
genes in that individual, the term is often used to refer to the specific alleles carried by an individual for
any particular gene.
Phenotype: an observable, measurable characteristic of an organism. A phenotype may be a
morphological structure, developmental process, a physiological process or performance trait, or a
behavior. Phenotypes can even be the molecules produced by genes.
Genetic polymorphism: the simultaneous occurrence of two or more discrete phenotypes within a
population. In the simplest case, each phenotype results form a different allele or combination of alleles of
a single gene. In more complex cases, the phenotypes result from complex interactions between many
different genes and the environment.
Polyphenic trait: a trait for which multiple, discrete phenotypes can arise from a single genotype
depending on potential circumstances.
Dominant allele: alleles that produce the same phenotype whether they are paired with an identical
allele or a different allele (i.e., a heterozygotic state).
Recessive allele: alleles that produce their characteristic phenotypes only when paired with an identical
allele (i.e., a homozygotic state).
Quantitative traits: measurable phenotypes that vary among individuals over a given range to produce a
continuous distribution of phenotypes. Quantitative traits are sometimes called complex traits; they’re
also sometimes called polygenic traits because their variation can be attributed to polygenic effects (i.e.,
the cumulative action of many genes).
5.5 HOW D O GENES RESPOND TO THE ENVIRONMENT ?
Morphogen: a signaling molecule that flows between nearby cells and acts directly to alter expression of
Phenotypic plasticity: changes in the phenotype produced by a single genotype in different
environments. OEB 53 R EADING N OTES
CHAPTER 6: HE W AYS OF C HANGE (DRIFTAND SELECTION ), 6.1 – 6.3
6.1 THE GENETICS OF POPULATIONS
Genetic locus (plural, loci): the specific location of a gene or piece of DNA sequence on a chromosome.
When mutations modify the sequence at a locus, they generate new alleles—variants of a particular gene
or DNA region. Alleles are mutually exclusive alternative states for a genetic locus.
Population genetics: the study of the distribution of alleles within populations and the mechanisms that
can cause allele frequencies to change over time.
6.2 CHANGE OVER TIME— OR NOT
Theorem: a mathematical statement that has been proven based on previously established theorems and
axioms. Theorems use deductive reasoning and show that a statement necessarily follows from a series of
statements or hypotheses—the proof. Theorems are not the same as theories. Theories are explanations
supported by substantial empirical evidence—the explanations are necessarily tentative but weighted by
the quantity of evidence that supports them.
The HardyWeinberg theorem proves that in the absence of drift, selection, migration, and mutation, allele
frequencies at a genetic locus will not change from one generation to the next.
6.3 EVOLUTION S “N ULL M ODEL”
Because it describes the conditions in which evolution will not occur, the HardyWeinberg theorem serves
as the fundamental null model of population genetics. OEB 53 R EADING NOTES
 GENETICS OF NATURAL SELECTION
CHAPTER 6: THE W AYS OF CHANGE (DRIFT AND SELECTION ), 6.6
6.6 SELECTION : WINNING AND LOSING
Fitness: the success of an organism at surviving and reproducing, and thus contributing offspring to
Relative fitness (of a genotype): the success of the genotype at producing new individuals (its fitness)
standardized by the success of other genotypes in the population (for example, divided by the average
fitness of the population)
Average excess of fitness (of an allele): the difference between the average fitness of individuals bearing
the allele and the average fitness of the population as a whole
Pleiotropy: the condition when a mutation in a single gene affects the expression of many different
phenotypic traits. Pleiotropy is considered to be antagonistic if a mutation with beneficial effects for one
trait also causes detrimental effects on other traits.
Negative selection: selection that decreases the frequency of alleles within a population. Negative
selection occurs whenever the average excess for fitness of an allele is less than zero.
Positive selection: selection that increases the frequency of alleles within a population. Positive selection
occurs whenever the average excess for fitness of an allele is greater than zero.
Epistasis: occurs when the effects of an allele at one genetic locus are modified by alleles at one or more
Additive allele: an allele that yields twice the phenotypic effect when two copies are present at a given
locus than when only a single copy is present. Additive alleles are not influenced by the presence of other
alleles (e.g., there is no dominance).
Negative frequencydependent selection: rare genotypes have higher fitness than common genotypes.
This process can maintain genetic variation within populations.
>> Example: purple and yellow orchards that do not produce nectar, bees learn to avoid the color that is
Balancing selection: selection that favors more than one allele. It acts to maintain genetic diversity in a
population by keeping alleles at frequencies higher than would be expected by chance of mutation alone.
>> Example: heterozygotes for sicklecell disease OEB 53 R EADING NOTES
CHAPTER 7: EYOND ALLELES (QUANTITATIVE GENETICS AND THE EVOLUTION OF PHENOTYPES )
7.1 GENETICS OF QUANTITATIVE TRAITS
Quantitative genetics: the study of continuous phenotypic traits and their underlying evolutionary
Variance: a statistical measure of the dispersion of trait values about their mean.
V =V +V
P G E
>> Broad sense heritability (H ) is a useful way to measure relative importance of genetic and
environmental effects on trait expression
H = G= G
V P V GV E
>> However, not all genetic variation actually contributes to phenotypic resemblance between offspring
and their parents. Only a portion of genetic variance enables a population to evolve in response to
selection. Alleles at a single locus can have additive efAects (V ), and sometimes they have dominance
effects (D ). Epistatic effecIs (V ) result when the effect of an allele at one locus depends on which allele
is present at another locus.
V GV +VA+V D I
Narrow sense heritability (h ): the proportion of the total phenotypic variance of a trait attributable to
the additive effects of alleles (the additive genetic variance). This is the component of variance that causes
offspring to resemble their parents, and it causes populations to evolve predictably in response to
2 V A V A V A
h = V = V +V = V +V +V +V
P G E A D I E
7.2 THE EVOLUTIONARY RESPONSE TO SELECTION
Selection can act in different ways on a population:
Directional selection favors individuals at one end of a trait distribution (oil content in corn)
Stabilizing selection favors individuals with a trait near the population mean
Disruptive selection selects against the population mean, favoring individuals at either end of the
population OEB 53 R EADING N OTES
Selection differential (S): a measure of the strength of phenotypic selection. The selection differential
describes the difference between the mean of all members of a population and the mean of the individuals
that reproduce, contributing offspring to the next generation.
The speed of evolution is a product of the strength of selection (S) and the extent to which offspring
resemble their parents for that trait (the heritability of the trait, h ).
7.3 D ISSECTING C OMPLEX TRAITS: QUANTITATIVE TRAIT LOCUS ANALYSIS
Quantitative trait loci (QTLs): stretches of DNA that are correlated with variation in a phenotypic trait.
These regions contain genes, or are linked to genes, that contribute to population differences in a
1. Create two truebreeding populations for two extremes, such as large size in one and small size in
2. Cross parental generation to produce the F 1eneration, heterozygous across loci.
3. Breed heterozygotes to produce a second generation (F ),2with a wide range of phenotypes. Now
offspring will differ in whether or not they have alleles from the large or small parental lines.
4. Examine DNA, looking for loci that correlate with different body sizes:
a. Identify a large number of distinct, short segments of DNA (SNPs, simple sequence
repeats, or transposable elements). Alleles must be different depending on whether from
original maternal or paternal chromosome.
b. Examine F f2shes for these genetic markers and test whether genotype at particular
markers is associated with the phenotypic trait of interest
c. Association does not mean that marker itself has direct effect, but indicates that nearby
loci might explain part of the phenotypic variance
5. Markers that have a statistically significant association with the expression of a phenotypic trait
are called QTLs.
Ex. Coat color in mice
Identified three QTL regions >> allelic variation in Agouti, Mc1r, and Courin genes could explain
almost all variation in 2 mice
Corin only accounts for a small amount of variation, while Agouti and Mc1r produce proteins that
are critical elements of the pathway for synthesizing the dark pigment, melanin, in growing hair. OEB 53 R EADING N OTES
Lighter coat color a result of two mutations: 1) decreased activity of melanocortin1 receptor, 2)
increases expression of Agouti, which interferes with Mc1r expression
Agouti allele found in beach mice must be present for Mc1r gene to have an effect
Agouti alters coat color by laying down a “prepattern,” expression of Agouti delays maturation of
Regions of strong Agouti expression spread further up the dorsal side of the embryo for beach
mice than in mainland mice
>> Engineered mainland oldfield mice that were homozygous for lightcolor allele of Agouti,
resulted in mice with a higher boundary between light belly and dark dorsal coat color, similar to
the original beach mice
7.4 THE EVOLUTION OF PHENOTYPIC PLASTICITY
Reaction norm: the pattern of phenotypic expression of a single genotype across a range of
environments. In a sense, reaction norms depict how development maps the genotype into the phenotype
as a function of the environment.
>> Reaction norms can be studied by rearing genetically similar organisms under different environmental
If different genotypes respond differently to the same set of environmental conditions, this variance in
how genotypes interact with their environment is V G × E
Understanding the evolution of phenotypic plasticity can be difficult because the plastic change in a
particular phenotype is not evolution—a hare turns from brown to white in response to the environment.
A populationlevel change in the amount or nature of plasticity, however, is evolution—populations of
hares become more or less sensitive to day length as a cue for the color change.
CHAPTER 8: NATURAL SELECTION (EMPIRICAL STUDIES IN THE W ILD )
8.1 EVOLUTION INA BIRD’S BEAK
Artificial selection: similar to natural selection, except that it results from human activity. When breeders
nonrandomly choose individuals with economically favorable traits to use as breeding stock, they impose
strong artificial selection on those traits
During a severe drought in Daphne Major, subtle differences in beak thickness among medium ground
finches affected who lived and who died. Because beak depth is highly heritable, natural selection could
lead to rapid evolution of beak size.
Natural selection is directional if it favors increases, or decreases, in the size or dimensions of a trait. It is
stabilizing or balancing if it favors the current value for the trait.
Longterm studies of natural selection often show fluctuations in the direction and magnitude of selection. OEB 53 R EADING N OTES
8.2 M ICEIN B LACK AND W HITE
Evolution in response to natural selection is the inevitable outcome whenever three conditions are met:
individuals differ in their expression of a trait; this variation is at least partially heritable; and, because of
these differences, some individuals survive and reproduce more effectively than others.
Specific features of the environment can generate natural selection on a trait. These agents of selection
can be events, such as storms or droughts, or environmental factors like predators or diet.
Hoekstra and colleagues discovered multiple origins of light coloration.
8.3 THE GEOGRAPHY OF FITNESS
Gene flow: the transfer of alleles from one population to another. It occurs when organisms or their
gametes move from one location to another.
Aposematism: an antipredator strategy used by a potential prey item to signal danger or a lack of
palatability. The most commonly known form of aposematism is warning coloration, in which the bright
coloration of prey that are potentially dangerous can act as a deterrent to potential predators.
Natural selection can lead to variation in space—across habitats or environments—just as dramatically as
it can lead to variation in a single habitat over time.
Scarlet kingsnakes look less like coral snakes the further away they are from the overlap zone between
habitats: mimicking a coral snake provides protection only from predators that live in the range of the
coral snake. Otherwise, the warning coloration attracts the attention of predators.
8.4 PREDATORS VERSUS PARASITOIDS : W HEN A GENTS OF SELECTION ACT IN OPPOSING D IRECTIONS
Extended phenotypes: structures constructed by organisms that can influence their performance or
success. Although they are not part of the organism itself, their properties nevertheless reflect the
genotype of each individual. Animal examples include the nests constructed by birds and the galls of flies.
When agents of selection act in opposition, the net effect can be a balance: stabilizing selection for an
intermediate trait value.
Flies form galls in plants, with the size of galls produced being a heritable phenotype of the flies. Large
galls are more easily preyed upon by birds, while small galls are more easily preyed upon by wasps. Thus,
there is stabilizing selection for intermediatesized galls.
8.5 REPLICATED N ATURAL EXPERIMENTS
Sometimes multiple populations independently experience the same change in their selection
environment. These populations are ideal for evolutionary studies because they act like replicated natural
experiments. The nature of the evolutionary response can be observed for each population and compared
across the different populations. OEB 53 R EADING NOTES
Marine sticklebacks are heavily armored to protect against predators. In freshwater lakes, there are lower
concentrations of predatory fish and it is more advantageous to grow fast rather than pay the cost of
growing spines and plates.
8.6 DRINKING M ILK: A FINGERPRINT OF NATURAL SELECTION
Genetic linkage: the physical proximity of alleles at different loci. Genetic loci that are physically close
to one another on the same chromosome are less likely to be separated by recombination during meiosis,
and are thus said to be genetically linked.
Selective sweep: strong selection can “sweep” a favorable allele to fixation within a population so fast
that there is little opportunity for recombination. In the absence of recombination, large stretches of DNA
flanking the favorable allele will also reach high frequency.
Hypothesis—Originally, humans had an LCT allele that stopped producing lactase after nursing.
Sometimes mutations gave rise to LCT alleles conferring lactose tolerance in adults, but they did not raise
fitness because feeding on milk as adults was rare. In cattleherding cultures, however, milk was plentiful,
and the ability to digest milk brought huge benefits. People who could get protein and other nutrients
from milk were more likely to survive and pass on their mutant copy of LCT to their offspring.
8.7 HUMANS AS AGENTS OF SELECTION
The speed of evolution is a product of the amount of available genetic variation and the strength of
selection. Weed and pest populations can be highly variable, and herbicides and pesticides can impose
extremely strong selection. The result: rapid evolution of resistance.
Types of human impact:
Chemical warfare (antibiotic/pesticide resistance)
Altered environments and invasive species
Hunting and fishing as agents of selection OEB 53 R EADING N OTES
 RIFT AND INBREEDING (A ND OTHER M ATING HABITS )
CHAPTER SIX: HE W AYS OF CHANGE (DRIFT AND SELECTION ), 6.4 6.5, 6.7
6.4 A RANDOM AMPLE
Fixed allele: an allele becomes fixed in a population when all of the alternative alleles have disappeared.
No genetic variation exists at a fixed locus within a population, because all individuals are genetically
identical at that locus.
Genetic drift is a mechanism of evolution because it causes the allele composition of a population to
change from generation to generation.
Alleles are lost due to genetic drift much more rapidly in small populations than in large populations.
6.5 BOTTLENECKS AND FOUNDER EFFECTS
Genetic bottlenecks: events in which the number of individuals in a population is reduced drastically.
Even if this dip in numbers is temporary, it can have lasting effects on the genetic variation of a
Founder effect: a type of genetic drift describing the loss of allelic variation that accompanies founding
of a new population from a very small number of individuals (a small sample of a much larger source
population). This effect can cause the new population to differ considerably from the source population.
6.7 NBREEDING : HE COLLAPSE OF A DYNASTY
Inbreeding coefficient (F): the probability that the two alleles at any locus in an individual will be
identical by descent.
Inbreeding depression: a reduction in the average fitness of inbred individuals relative to that of outbred
individuals. It arises because rare, recessive alleles become expressed in a homozygous state where they
can detrimentally affect the performance of individuals. OEB 53 R EADING NOTES
 VOLUTION OF G ENETIC DIVERSITY
CHAPTER SIX: HE W AYS OF CHANGE (DRIFT AND ELECTION ), 6.6
See Lecture 4.
CHAPTER SEVEN : BEYOND ALLELES (QUANTITATIVE GENETICS AND THE EVOLUTION OF PHENOTYPES )
See Lecture 4. OEB 53 R EADING N OTES
 INDING DARWIN IN DNA: T ESTING NEUTRALITY
CHAPTER NINE : HE HISTORY IN OUR GENES , 9.6
9.6 NATURAL SELECTION VERSUS N EUTRAL EVOLUTION
Synonymous substitutions: mutations that do not alter the amino acid sequence of a protein. Because
these mutations do not affect the protein an organism produces, they are less prone to selection and often
free from selection completely.
Replacement (nonsynonymous) substitutions: mutations that alter the amino acid sequence of a
protein. These can affect the phenotype and are therefore more subject to selection.
Kimura’s theory of neutral evolution:
Much of the variation in genomes was the result of genetic drift
>> Neutral mutations would become fixed in populations at a roughly regular rate. When a
population split into two populations, each lineage would acquire its own unique set of neutral
mutations. The more time that passed after the lineages diverged, the more different mutations
would be fixed in each one.
Evidence: regular mutations in cytochrome c
The Molecular Clock
Molecular clock: a method used to determine time based on basepair substitutions. Molecular clocks use
the rates of molecular change to deduce the divergence time between two lineages in a phylogeny, for
example. They work best when they can be “calibrated” with other markers of time, such as fossils with
HIV: relaxed molecular clock (allowing mutation rate to vary from branch to branch, and even
from site to site within genes), supported conclusion that HIV had not been accidentally
introduced in vaccines in the 1950s
Darwin’s finches: tracing all finches back to a common ancestor that lived between 2 to 3 million
years ago, connecting with geological research to determine islands had been much different
during that time
Mammals: using mammalian fossils to calibrate the clock, discovering two peaks of diversity
Footprints of Selection
Linkage disequilibrium studies effective only for relatively recent cases of natural selection (past several
thousand years). OEB 53 R EADING N OTES
>> Use neutral evolution as null hypothesis, start with assumption that any variation in homologous DNA
segments are the result of neutral evolution.
1. Compare substitutions that occur in replacement sites to synonymous sites. If they occur equally,
implies neutral evolution. Positive selection would produce a gene in which there are more
replacement mutations than would be expected through neutral selection. If replacement
mutations fewer than expected, indicates purifying selection.
2. McDonaldKreitman Test: compare the alleles of a gene within that species and also to the
homologous gene in other species, if neutral evolution, then ratio of replacement to synonymous
across species should e same as within the species.
a. If positive selection, then adaptive mutations will have rapidly increased in the focal
species as compared to the other species.
b. Within the species, selection will lead to the fixation of replacement substitutions, so the
ratio of replacement to synonymous substitutions within the species should be lower. OEB 53 R EADING N OTES
 EX AND SEXUAL SELECTION
CHAPTER 11: SEX (CAUSES AND CONSEQUENCES )
11. 1 EVOLUTION OF SEX
Reproduction: the formation of new individual organisms (offspring).
Hermaphrodites: individuals that produce both female and male gametes
Twofold cost of sex: asexual lineages multiply faster than sexual lineages because all progeny are
capable of producing offspring. In sexual lineages, half of the offspring are males who cannot themselves
produce offspring. This effectively halves the rate of replication of sexual species.
Muller’s ratchet: the process by which the genomes of an asexual population accumulate deleterious
mutations in an irreversible manner
Genetic load: the burden imposed by the accumulation of deleterious mutations
CONSEQUENCES OF SEXUAL REPRODUCTION
Twofold Cost of Sex: Asexual lineages have Combining Beneficial Mutations: By
an intrinsic capacity to grow more rapidly in each combining alleles of genes from two different
generation, because all progeny can produce individuals, sexual reproduction can bring
offspring. In sexual populations, males cannot separate beneficial mutations together in a single
themselves produce offspring individual faster than would be expected if they
had to arise spontaneously in the same genome.
Search Cost: Males and females must locate
each other in order to mate. This can involve Generation of Novel Genotypes: Through
time, energy, and risk of predation. recombination, meiosis provides an opportunity
for paired chromosomes to cross over, creating
Reduced Relatedness: Sexually reproducing gametes with unique combinations of alleles.
organisms pass only half of their alleles to their
offspring, because meiosis generates gametes that Faster Evolution: Offspring of sexual parents
are haploid. This halves the relatedness between will be more genetically variable than offspring
parents and their progeny. of asexually reproducing parents. This can speed
the evolutionary response to selection of sexual
Risk of Sexually Transmitted Diseases: populations and is critical for maintaining
Mating between males and females provides an
resistance to parents (the Red Queen effect).
effective means of transmission for many
pathogens. Asexual populations do not mate and Clearance of Deleterious Mutations: Sexual
so avoid this risk. populations can purge themselves of harmful
mutations because recombination can generate
individuals with allelic combinations that
exclude deleterious mutations. Asexual
populations cannot do so and they steadily and
irreversibly accumulate mutations until a lineage OEB 53 R EADING N OTES
is driven extinct (Muller’s ratchet).
Red Queen effect: for coevolving populations, to maintain relative fitness, each population must
constantly adapt to the other. This term is used to describe biological arms races between hosts and
Ecological situations that require rapid and continuous evolution are likely to favor the evolution and
maintenance of sex. Asexual animal lineages may evolve adaptations enabling them to compensate for the
lack of sex.
11.2 SEXUAL SELECTION
Anisogamy: sexual reproduction involving the fusion of two dissimilar gametes; individuals producing
the larger gametes (eggs) are defined as female, and individuals producing the smaller gamete (sperm) as
Fecundity: the reproductive capacity of an individual, such as the number and quality of eggs or sperm.
As a measure of relative fitness, fecundity refers to the number of offspring produced by an organism
Certainty of paternity: the probability that a male is the genetic sire of the offspring his mate produces
Operational sex ratio: the ratio of male to female individuals who are available for reproducing at any
Sexual selection: differential reproductive success resulting from the competition for fertilization, which
can occur through competition among the same sex (intrasexual selection) or through attraction to the
opposite sex (intersexual selection)
Sexual dimorphism: a difference in form between males and females of a species, including color, body
size, and the presence or absence of structures used in courtship displays (elaborate tail plumes,
ornaments, pigmented skin patches) or in contests (antlers, tusks, spurs, horns)
Opportunity for selection: the variance in fitness within a population. When there is no variance in
fitness, there can be no selection; when there is large variance in fitness, there is a great opportunity for
selection. In this sense, the opportunity for selection constrains the intensity of selection that is possible
Direct benefits: benefits that affect a particular female directly, such as food, nest sites, or protection
Indirect benefits: benefits that affect the genetic quality of a particular female’s offspring, such as male
offspring that are more desirable to females
Leks: assemblages of rival males who cluster together to perform courtship displays in close proximity
D IRECT BENEFITS OF FEMALE CHOICE OEB 53 R EADING N OTES
Direct Benefit Examples
Protection: When a female risks being trampled or
injured by competing males, she may benefit by Protection from lethal injuries by other
preferentially mating with large (dominant) males males: elephant seals, dungflies
that guard her from harassment. F