BIO120 course flashcards
Lecture 1. Introduction to Evolutionary biology
Nothing in Biology makes sense except in the light of evolution...
1973, Theodosius Dobzhansky
What is evolutionary biology?
How is evolution studied?
Why is it relevant?
The Theory of Evolution
The two core tenets of evolution:
1. Living things change over time.
2. Adaptations
Evolution challenges the view of special creation, which is direct creation of all living things in
effectively their present form.
Important conclusions about evolution verified by scientific study:
• Organisms on Earth have changed through time.
• The changes are gradual not instantaneous.
• Lineages split by speciation, resulting in generation of biodiversity.
• All species have common ancestor.
• Adaptations result from natural selection.
So, biodiversity and adaptation are therefore products if evolution.
Biodiversity is:
• The diversity of life on Earth.
• The number and kinds of living organisms in given area.
Adaptation is:
• Any trait makes an organism better able to survive or reproduce in a given environment.
• The evolutionary process that leads the origin and maintenance of such traits.
Microevolution: Evolutionary patterns and processes observed withing species.
Macroevolution: Evolutionary patterns and processes observed among species.
Two Major areas of evolutionary study are 1. evolutionary history and 2. evolutionary
mechanisms.
Evolutionary History
Goals are patterns:
• Determine the evolutionary relationships of organisms in terms of common ancestry.
• Identify and understand long-term patterns in evolution.
In Practice:
• Uses comparative data from sub-disciplines of systematics, biogeography, paleontology,
morphology, development, and molecular biology.
Evolutionary tree = a phylogenetic tree = a phylogeny.
Split points in phylogenetic trees are called nodes. We can do a rotation at any node (rotation at an
internal branch) without changing the meaning of a diagram.
Evolutionary Mechanisms
Goals are processes:
• Determine the particular processes responsible for evolutionary change (e.g., natural
selection).
• Identify the major forces of evolution.
In Practice:
• Uses experimental and comparative studies of the genetics and ecology of populations.
• Focuses primarily on the population level.
How is Evolution studied?
A variety of approaches are used to address scientific questions:
• Observational – describe and quantify,
• Theoretical – develop models: verbal, graphical, mathematical, computational.,
• Comparative – obtain data from many species,
• Experimental – manipulate a system to address a scientific hypothesis; requires an
experimental design and statistical analysis.
Scientific theories have testable and falsifiable hypothesis.
The strongest studies us more than one source of evidence.
Why is Evolution relevant?
Reasons:
1. Curiosity: children’s questions,
2. Medicine: pathogens, viruses and etc.,
3. Agriculture: herbicide-resistant superweeds overpowering crops,
4. Environment: climate change,
5. Biology: example: mitochondria.
Lecture 2. Darwin’s Big Idea and How it Changed Biology
Biology before Darwin & Wallace
Darwin, Wallace and development of their idea
Darwinian Evolution: A revolutionary new model
Biology before Darwin & Wallace
Open questions in Darwin’s time:
• Where do species come from?
• How can we explain complex adaptations (i.e., traits with clear and elaborate function for the
survival and reproduction of organisms)?
In European society dominant view of those questions came from a branch of theology called
natural theology. A luminary in this field was William Paley with his idea of “The Argument from
Design”. You have an object (like watch) that has clearly designed to do a specific function,
therefore there must’ve been a designer. Another object (like rock) it does not have a specific
purpose. An organism (like a plant or mammal) has some features and adaptations that have distinct
functions (designed elements), therefore there is a divine designer (special creation).
Jean-Baptiste de Lamarck (1744-1829) he was the first to use the term evolution to refer to
biological change. Lamarck proposed a hypothesis called “The inheritance of acquired
characters”. A giraffe acquires a new characteristic, due to striving for it, and can pass that along
to its offspring. According to Lamarck’s theory, organisms can change their phenotype within a
generation through exercise, they can pass along that acquired phenotype to the offspring. So, this
theory assumed hierarchy of life and that organisms are organized in a chain - chain of being. Life
starts by a creator, yet it is simple. Those simple organisms evolve and get more complex.
August Weismann (1834-1914) proved that Lamarck was wrong in his “Germplasm Theory”
(1889). It stated that inheritance works though germ cells (gametes) only; somatic cells do not
function as agents of heredity. Thus, genetic information cannot pass from soma to gametes and
onto next generation. He conducted an experiment, where he chopped off mice’s tails, yet new
generation mice had tails. Modern interpretation in molecular terms is: Genetic information flows in
one direction only, from DNA to protein but never in reverse.
Darwin, Wallace and development of their idea
Charles Darwin (1809-1882) was sent to Medical School at University of Edinburgh by his father.
He hated Medical School and dissections of human cadavers; he threw up during those processes
and graduated with mediocre grades. He got lucky with a job as ship’s naturalist on Voyage on
H.M.S. Beagle around the world (1931-1836) and was intellectual companion to Capt. Robert
FitzRoy. H.M.S. Beagle was originally ought to map coast of South America. During the trip he made
numerous observations and spent the rest of his life in seclusion at Down House (Darwin family
house in Kent, England) developing his ideas, conduction experiments, and writing 25 books.
Darwin read Charles Lyell’s (1797-1875) book “Principles of geology” (1830), where Lyell argued
for uniformitarianism – the forces and processes that shape the Earth’s surface are uniform through
time and forces we see are the same as previous eons. Darwin got two implications:
1. Notion of a dynamic rather than a static world,
2. Changes build up gradually by the same mechanisms today as in the past.
During the trip Darwin saw hat species vary. In Galapagos Islands he saw 4 similar species of
mockingbird endemic to the islands that descended from a Soth American mainland ancestor. So,
Darwin starts to doubt fixity of species (March, 1837).
After voyage of Beagle, in September 1838, Darwin reads Tomas Malthus’s “An Essay on the
Principle of Population” (1798) and things started to click here. In his work Malthus points out the
fact that biological organisms, including human, if completely unchecked by any sort of mortality or
limits, grow exponentially, yet resources never grow exponentially, they are finite and, in best of
circumstances, grow geometrically. These two facts necessitate there being a constant struggle for
existence, so that in every generation there must be some that succeed and some that do not.
After all of this he developed first comprehensive theory of evolution.
Alfred Russel Wallace (1823-1913) after reading Malthus as well, independently comes to the
same conclusion as Darwin: the chief mechanism of evolution is natural selection.
Two major theses of Darwin’s (and Wallace’s) Theory of Evolution:
• All organisms have descended with modification from a common ancestor (thus, living
things change over time),
• The process leading to evolution is natural selection operation on variation among
individuals.
Darwinian Evolution: A revolutionary new model
Darwin’s Mechanism of Natural Selection has 3 major components:
• Variation: Individual variation in a population,
• Heredity: progeny resemble their parents more than unrelated individuals,
• Differential fitness: some forms are more successful at surviving and reproducing than
other in a given environment (i.e. some forms are more fit than others).
Natural selection is heritable variation in fitness.
According to Lamark there is a transformational evolution, but according to Darwin there is a
variational evolution, thus there is a differential fitness.
Important Elements of Darwin’s Theory:
1. Evolution occurs at level of populations (individuals do not evolve),
2. Variation is not directed by environment (individuals do not induce adaptive variation when
needed),
3. Most fit type depends on the environment,
4. “Survival of the fitter”: Evolution works with available variation, and will nor necessarily
achieve perfection.
Implications of Darwin’s Theory of Evolution:
• Concept of changing universe, which replaced the view of static world,
• A phenomenon with no purpose, natural selection revealed how complex adaptations with
important “functions” can arise through an unplanned process.
With Darwin’s idea, we recognize that largely all populations of any organism are going to have
some sort of intrinsic variation. For example, in bacteria-antibiotic battle, even before we have any
antibiotics, there are going to be naturally some forms in this population of bacteria that are more
resistant to antibiotics and some are less (even before we applied any antibiotic) – it is just natural
variation. Introduction of the antibiotic leads to favoring of resistant bacteria, that have an allele for
antibiotic resistance. The one that are susceptible have very low fitness.
Differential fitness leads to proliferation of some variants more than others, and that the
change is occurring between generations not within them.
Lecture 3. The Evidence for Evolution
Evidence from Geology
Evidence from Homology
Evidence Biogeography
Evidence Domestication
Evidence from Geology
Discoveries of Transitional Fossils
Tiktaalik roseae, discovered 2006
• Age: 375 million years,
• Origin: Ellesmere Island, Nunavut, Canada,
• Number of individuals found: 10,
• Nickname: “fishapod”.
Evolution of Whales
Lessons from geology:
• Earth is very old - this allows for immense amount of time for biological evolution,
• Intermediate forms – evidence for transitional fossils linking features of seemingly dissimilar
relatives (e.g., ungulates and whales, or tetrapods and fish),
• Fossils in younger strata increasingly resemble modern species in same region (older strata
show increasing differences).
Evidence from Homology
Homology – similarity of traits in two or more species that is due to inheritance from a common
ancestor.
Vestigial (rudimental) structures – features inherited from an ancestor, but reduced in morphology
and function, which are homologous to functional structures in related species.
Galapagos flightless cormorant vs. mainland cormorants (which can fly)
Surface-dwelling (gray) and cave-dwelling (pink) morphs of Astynax mexicanus fish. Cave-
dwelling fish have vestigial eyes and cannot see.
Vestigial structures in Humans: ear muscles, appendix, tailbone, goosebumps.
Organismal features are consistent with modification of pre-existing structures, which wouldn’t be
expected if each organism was individually optimally designed.
Approximately 500 genes are shared across all forms of life.
Lessons from homology:
• Vestigial traits – can only be explained by the presence of functional traits in ancestors,
followed by evolutionary degradation,
• Homologous structures are ubiquitous (found everywhere) across organisms –
fundamental structural similarity reflects common ancestry and homologous structures have
evolved to serve very different structures.
Evidence from Biogeology
Galapagos Islands are 15 main islands of volcanic origin (formed 0.7-4.2 million years ago), so
flora and fauna colonized from mainland South America. Forms in different islands were slightly
different. Darwin saw cacti that were similar to mainland cacti. Cacti have freshly bird-dispersed
fruits, which explain how cacti got there.
Tortoises on different islands have different shell shapes.
Beak diversity among Galapagos Finch species.
Australia is isolated, has distinct biota (flora and fauna) with high endemism and many unique
adaptations. An example of uniqueness is mammal-pollinated Banksia.
Biogeography since Darwin:
• Geographically close organisms resemble each other,
• Different groups of organisms adapt to similar environments in different parts of the world,
• Geographically isolated regions have unusual organisms.
Lessons from biogeography:
• Remote island biotas are dominated by good colonists, have continental affinities and
locally-differentiated species,
• Biogeographically isolated regions have species adapted to niches unusual for their
group and harbor endemic radiations of species that convergent with radiations elsewhere.
Evidence from Domestication
Artificial selection is causing evolutionary change.
Domesticated Pigeon Diversity – some domestic races of pigeons differ fully as much from each
other in external characters as do the most distinct natural genera.
Lessons from domestication:
• Vast amount of heritable variation,
• This variation can be selected on, leading to dramatic changes over generations,
• Aritificial selection is the human imposed analog to natural selection in wild.
Lecture 4. Evolutionary Significance of Genetic Variation
Where does genetic variation come from?
How is it inherited?
How does it influence trait variation?
Some definitions
Genotype – genetic construction of an organism, usually defined in relation to a particular gene or
gene combination
Phenotype – feature of the organism as observes, often used when discussing a trait of an organism
that varies (e.g. size, color, enzyme activity, mRNA expression level)
Genome – the entirety of an organism’s DNA including genes and non-coding regions
Where does genetic variation come from?
Sources of Genetic Variation
1. Mutation – a stable (not fixed by DNA reparation) change in the DNA sequence,
• Occur at a low rate,
• Different possible effects on fitness: neutral, deleterious (weakly detrimental up to lethal),
beneficial,
• Is inevitable phenomenon,
• NOT directed toward an outcome by the organism or by environment – it is random
with respect to effects on fitness,
• Rate depends on the type of mutation – can also vary among genes,
• Environment can affect mutation rate (e.g. mutagens, heavy metals, high temperature)
4 major types of mutations:
1. Point mutations – ATGCAGT → ATCCAGT,
2. Insertion/deletions (“indels”) – ATGCAGT → ATGGCAGT,
3. Changes in repeat number – ATGATGATG → ATGATGATGATGATG,
4. Chromosomal rearrangements – ATGCAGT → TGACGTA
How to Identify mutation?
• Trio study – deep sequencing of the entire genome.
What is the rare of mutation in human?
• Per base pair of DNA – 16×10-9
.
• Per individual genome (×2 of 3 billion base pair genome) – 96 new mutations.
• For entire human population (8.2 billion) – every base pair in genome mutated ≈131
times over per generation
Silent mutation/substitution
Number of mutations that affect fitness (per diploid genome each generation) are quite high
in humans in comparison to rats. Yet, in total, mutation rate that don’t affect fitness are of
times higher than the fitness-affecting rate of mutation. Thus, most mutations are silent.
G6PD Deficiency in Humans is due to two amino acid substitutions.
• Allele B (no anemia, malaria susceptibility) – Val-Asn-Le – GTG-AAT-CTA
• Allele A- (anemia, malaria resistance) – Met-Asp-Leu – ATG-GAT-CTG
Beneficial mutations are very rare!
2. Independent assortment of chromosomes during meiosis,
• 2
n
(n = number of sets of chromosomes),
• Humans have 2
23 ≈ 8.4 million gamete combinations.
3. Recombination / cross-over of sister chromatids during meiosis.
• 2
n
(n = number of sets of chromosomes),
• Humans have 2
23 ≈ 8.4 million gamete combinations,
How is genetic variation inherited and how it influences trait variation?
Before Mendel:
Preformationism (1700s) – only one parent contributes to inheritance
Theory of blending inheritance (1800s) – problem: there is no way for beneficial mutation to increase
in frequency without being lost.
Mendel: Understanding Variation
Gregor Mendel (1822-1884) conducted experiment and came to following key conclusions:
1. Inheritance is determined by discrete particles – genes,
2. Each diploid organism carries two alleles of each gene,
3. Gametes fuse to make offspring – sperm / pollen fuses with egg / ovule,
4. Offspring inherit one gamete from each parent at random.
Phenotypic polymorphisms with simple Mendelian genetic causes
• Common in nature,
• Direct correspondence between traits and its genetic basis,
• Easy to track selection & evolution.
Yet, most traits vary continuously, not with discrete categories.
Partial inheritance
Discrete / Discontinuous variation: Simple Mendelian genetics
• Genes of major effect,
• We can measure dominance and recessiveness, spread of alleles; changes in allele
frequency.
Continuous / Complex / Quantitative variation: Quantitative genetics
• Many genes with alleles of small effect, important environmental effects,
• We can measure response as change in average trait value.
Lecture 5. Genetic variation: Models & measurement
What forces act on genetic variation?
How can we measure genetic variation?
How much genetic variation exists in natural populations?
Foundations of Population Genetics
1920s-1950s: Mathematical evolutionary theory for population genetic change
• Initiated by R.A. Fisher (1890-1960), J.B.S. Haldane (1882-1964), S. Wright (1889-1988),
• Provided the foundations for "Neo-Darwinism" and the "New Synthesis"
• Continuous variation and Darwinian natural selection - 100% consistent with Mendel's Laws,
• Demonstrated the evolutionary significance of genetic variation and led to several key
questions and development of the fields of ecological & evolutionary genetics.
Forces acting on genetic variation (alleles) and evolution
I) Mutation
• Ultimate source of genetic variation,
• Caused by errors during replication (not directed),
• Increases genetic variation in populations.
II) Recombination
• Creates new combinations of mutations,
• Increases genetic variation in populations.
III) Genetic drift – change in the frequency of an existing allele due to random change (unrelated
to fitness of an organism)
• Random sampling affects every generation,
• More important for smaller populations,
• Decreases genetic variation in populations.
IV) Natural selection
a) Negative / purifying selection
• Mutations that reduce fitness are removed by natural selection,
• Decreases genetic variation in populations.
b) Positive / directional selection (adaptation)
• Mutations that increase fitness will eventually become fixed in population – occurs when
polymorphic locus becomes monomorphic due to the loss of all but one allele (can occur
due to natural selection or genetic drift),
• Decreases genetic variation in populations.
c) Balancing selection favoring diversity
• Natural selection can act to maintain diversity over the long term (e.g., heterozygote
advantage),
• Increases (or retains) genetic variation in populations.
V) Migration (gene flow – movement of genetic material from one population to another)
• Influences the structuring of diversity over a large spatial scale,
• Decreases differences between populations,
• Increases genetic variation in populations.
Metrics of Genetic Variation
Heterozygosity (H) – having both copies of the allele in the same individual
• Fraction of individuals that are heterozygous, averaged across gene loci.
Polymorphism (P)
• Proportion of gene loci that have 2 or more alleles (are not fixed) in the population,
• A locus can be polymorphic without being heterozygous.
How much genetic variation exists in natural populations?
What maintains genetic variation? – Two schools of thought
1. Mutation-selection balance model / classical school (mutations are bad)
• T.H. Morgan (1866-1945) and H.J. Muller (1890-1967)
• Low heterozygosity,
• Low polymorphism,
• Wild type is “normal” genotype,
• Negative natural selection,
• Less fit types reintroduced by mutation,
• Followed by selection acting to remove them.
2. Selection maintaining variation / balance school
• E.B. Ford (1901-1988) and T. Dobzhansky (1900-1975)
• High heterozygosity due to heterozygote advantage,
• High polymorphism,
• Frequency-dependent selection,
• Balancing natural selection - favours diversity,
• Fitness varies in space or time,
• Umbrella term “balancing selection”,
Two schools differed in their predictions on how much genetic variation occurs in natural
populations.
Approach 1:
Study genetic diversity with morphological and cytological markers with discretely mendelian traits.
Approach 2:
Rather than focus on Mendelian discrete traits, focus on continuous polygenic traits by applying
artificial selection.
Evolutionary responses of continuous traits
• Demonstrate existence of heritable variation in fitness-related phenotypes,
• Due to many underlying genes.
Are these responses due to:
A) Balance school - many alleles previously at intermediate frequency that change in
frequency?
B) Classical school - many initially rare & deleterious alleles that increase in frequency?
Everything changed with Richard Lewontin and the Electrophoresis revolution
• Allozyme (different allelic forms of the same protein) gel electrophoresis provided a way to
ask “What proportion of genes are variable (P&H)?”, and answer to that resolves dispute
between the classical and balance school,
• Initiated large scale surveys of electrophoretic variation in enzymes & proteins in diverse
organisms.
This became a revolutionary way to measure diversity at genes that encode enzymes & proteins.
Advantages of studies of enzyme polymorphism
• Mani loci can be examined,
• Can be used in nearly any organism,
• Loci co-dominant, heterozygotes can be identified,
• Variation examined close to DNA level,
• Provides genetic marker loci for other studies.
After applying this technique to pretty much everything scientists found that genetic variation seems
to be very high. Polymorphism [0.25-0.5] and heterozygosity is pretty appreciable. It seemed that
balance school was right, right?
3. The Neutral Theory: Selectively neutral variation
• Having genetic diversity is often neutral – it doesn’t have any phenotypic effect or it
has a phenotypical effect that is not selected upon,
• Negative selection rapidly eliminates detrimental mutations,
• Positive selection rapidly fixes beneficial mutations,
• The only mutations left to create genetic variation are selectively neutral,
• New mutations neither eliminated nor retained by selection.
Nowadays, genetic variation is studied at DNA level with DNA sequencing.
Example. When we domesticated corn, corn reduced genetic diversity compared to its wild ancestor
teosinte. Yet, selection on some genes reduced diversity further than expected by genetic drift from
the founder event.
Humas show loss of genetic variation with increasing distance from East Africa.
AA Aa aa Aa aa AA AA AA aa Aa
Fast * * * * * *
Slow * * * * * * *
No. 1 2 3 4 5 6 7 8 9 10
FF FF FF FF FF FF FF FF
* * * * * * * *
Monomorphic gene
FF FS SS MM FM MS FF FS
* * * * *
* * *
* * * *
1 2 3 4 5 6 7 8
Polymorphic gene
Lecture 6. Sex, Reproductive systems, and Evolution
The costs & benefits of sex
The causes & consequences of the evolution of sex
The causes & consequences of inbreeding & outbreeding
Reproductive models
All genetic diversity arises during the process of reproduction.
Sexual reproduction:
• 2 parents contribute to genetic material to offspring,
• Meiotic, reductive division to form gametes,
• Fusion of gametes.
Asexual reproduction:
• 1 parent contributes to genetic material,
• No meiotic reductive division,
• Offspring are genetic replicas / clones of parents.
Parthenogenesis – asexual reproduction in which embryo develops from an egg without
fertilization.
Clonal propagation – asexual reproduction not involving an egg.
Water fleas (Daphnia) are facultatively sexual. Asexually – parthenogenesis and sexually – by
mating. Whether they are asexual or sexual depends on environment.
The Costs and Benefits of Sex
Costs of sexual reproduction:
• The Two-fold cost if Meiosis – compared to an asexual female, a sexual female contributes
only 50% of her gene copies to the next generation. This transmission bias flavours asexual
in competition with sexual females,
• Can continually recreate unfavourable combinations of alleles (Ex. AA – adapted to dry,
aa – adapted to wet habitat, Aa – adapted no neither and has very little fitness),
• Time and energy to find and attract mates,
• Increased energetic costs of mating,
• Risk of predation and infection,
• Costs of producing males.
Benefits of sexual reproduction:
• Favourable combinations of mutations brought together more rapidly,
• Elimination of harmful mutations,
• “Lottery models” – benefits if genetic variation in variable/unpredictable environments,
1. “Tangled Bank hypothesis” – spatially heterogenous environment – maybe
environment is not uniform and you are not sure where your offspring will land – having
genetic diversity ensures more fitness,
Reproductive
system Asexual Sexual
Sexual system Dioecious Hermaphrodite
Mating system Cross-fertilization Self-fertilization
2. “Red Queen hypothesis” – temporally heterogenous environment – what’s good in
one decade can be good might be bad for another decade.
Many theoretical models, but only limited experimental evidence.
Macroevolutionary History of Asexuality:
Asexuality by parthenogenesis:
• Sporadically distributed across animal kingdom,
• More common in invertebrates, rare in vertebrates.
Asexuality by clonal propagation:
• Much more common in plants,
• Few species (if any) are exclusively asexual.
Asexual species are usually at the tip of phylogenies
• Macroevolutionary pattern indicates higher extinction rate,
• Low chance of long-term evolutionary persistence,
• Probably due to extremely low genetic variation & accumulation of deleterious mutations.
Males in Bdelloid Rotifer are unknown, which are rare case of ancient obligately asexuality.
The causes & consequences of inbreeding & outbreeding
Outbreeding: Mates are less closely related than random.
Inbreeding: Mates are more closely related than random.
Outcrossing: Mating with someone else either by outbreeding or inbreeding. Fusion of gametes
(from meiotic division) from 2 parents.
Selfing (self-fertilization): Mating with yourself. It is the most extreme form of inbreeding, but it is
NOT asexual reproduction. Fusion of gametes (from meiotic division) from 1 parent.
In nature there is a continuum between outbreeding and inbreeding.
Terms outcrossing and selfing are used to talk about hermaphrodites, those who have potential to
mate with themselves.
Potential for Inbreeding:
• Local population substructure enhances mating among relatives,
• Hermaphroditic organisms (most plants, many animals) have potential for self-fertilize,
• In small populations, even random mating can lead to mating with relatives.
Inbreeding Avoidance Traits in Flowering Plants:
• Timing offset between male and female reproduction – within a flower pollen and ovule
maturation times are different, as well as male and female flowers open at different times,
• Morphological and physiological mechanisms to avoid selfing – self-incompatibility.
Inbreeding Avoidance Traits in Animals:
• Dispersal by one sex (males readily disperse, in comparison to females),
• Delayed maturation,
• Extra pair copulation (biological term for “cheating”),
• Kin recognition and avoidance.
Population genetic effects of inbreeding:
• Changes genotype frequencies – homozygosity↑, and heter/ozygosity (H)↓,
• Does not directly change allele frequencies – does not change polymorphism (P).
Inbreeding depression – reduction of fitness (viability / survival↓, fertility↓) of inbred offspring
compared to outcrossed offspring. Strong inbreeding depression disfavors inbred offspring, thus
favouring outcrossed mating systems. Fitness gets reduced due to homozygosity of recessive
deleterious alleles. Recessive alleles can be seen by selection.
Genetic Consequences of Inbreeding:
• Heterozygosity (H)↓ by 50% per generation with self-fertilization,
• Competition between homozygous genotypes (selection) and genetic drift of small
populations can reduce polymorphism (P).
Homozygosity for deleterious recessive alleles results in inbreeding depression.
Inbreeding depression CAN change allele frequencies.
Inbreeding depression causes reduced fitness... yet selfing has evolved many times!
• It is one of the most common evolutionary transitions,
• It is associated with extensive phenotypic evolution,
• Roughly 20% of plants and hermaphroditic animals are highly selfing.
So... why is that?
Automatic selection of selfing gene (R.A. Fisher, 1941)
Over short term:
• If conditions are favourable selfing can spread via natural selection,
1. Lack of “reproductive assurance” due to rarity of pollinators or mates,
2. Transmission advantage from self + exported pollen,
3. Low inbreeding depression.
• BUT harmful effects of inbreeding depression encourage outcrossing.
Over long term:
• Selfing leads to low diversity and inefficient selection,
• Can drive higher extinction rates in selfing species,
• Macroevolutionary pattern of greater prevalence of outcrossing.
Outcrosser Selfer
Seed 1 2
Pollen 1 1
Total Gene copies 2 3
Lecture 7. Natural Selection and Adaptation
Types of selection – Models of selection on phenotypes
Studying Selection and Adaptation
Definitions
Fitness: Genetic contribution of individuals to next generation, relative to other individuals, as a
result of differences in viability and fertility (= Darwinian fitness)
• A relative quantity; not absolute survival or offspring number.
Selective advantage: The amount by which some individuals of a given genotype are better
adapted to a given environment
• Reflects relative differences in fitness.
Adaptation: (for a GIVEN environment)
[noun] A trait that contributes to fitness by making an organism better able to survive or reproduce
in a given environment
• Compared to the prior ancestral state, this link between trait and environment makes it
adaptive.
[verb] Evolutionary process that leads to the origin and maintenance of such traits
• Natural selection.
Artificial Selection: Selection by humans towards a goal.
Natural Selection: Selection by abiotic and biotic environment, which has no “goal” and affects all
organisms including humans.
Models of natural selection
Natural selection on alleles:
1. Positive / directional selection (i.e., adaptation) – even minor advantages can spread
through populations with enough time and reach fixation as frequency approaches 1,
2. Negative / purifying selection,
3. Balancing selection to maintain variation
For mendelian traits natural selection works the same way and alleles can be simply substituted by
discrete mendelian traits. Yet, for most polygenic continuous traits this will not work. Most continuous
traits have normal distribution and can be described as normal distribution diagrams. So how is
selection going to act on these individuals from different parts of the distribution.
Natural selection on quantitative traits:
1. Stabilizing selection – favours individuals with average phenotypic traits,
2. Directional selection – favours one extreme, shift in the mean not the variance,
3. Disruptive selection – favours both extremes and leads to trait divergence. In some cases,
may lead to speciation if trait divergence causes reduction in gene flow.
Studying adaptation
1. Analyzing genomic diversity - testing correlation of alleles or traits with environment over
space and time,
2. Genes targeted by selection ought to show distinctive patterns,
3. Experimental manipulations in field and lab.
Examples of evolution due to pollution:
• The Peppered Moth (Biston betularia) and industrial melanism in England,
• Heavy metal tolerance in plants in Ontario.
DNA Variation at G6PD
A selective sweep occurs when selection causes a new mutation to increase in frequency so
quickly that nearby alleles “hitchhike” and also increase in frequency.
Setting up E. coli LTEE experiment
Lecture 8. Population Structure: Genes & Phenotypes
Genetic differentiation of populations
Phenotypic differentiation of populations
Definitions
Population: A group of individuals of a single species occupying a given area at the same time.
Migration: The movement of individuals from one population to another.
Gene flow: The movement of alleles from one population to another
Genetic drift: Stochastic changes in allele frequency due to random variation in fecundity and
mortality. Most important when populations are small
Population Bottlenecks (special case of genetic drift): A single sharp reduction in abundance,
usually followed by rebound. This causes loss of diversity.
Founder Event (special case of genetic drift): Colonization by a few individuals that start a new
population. Colonizing group contains only limited diversity compared to the source population.
Key questions:
What forces influence genetic differentiation of populations?
• How is diversity distributed within vs. between populations.
What forces influence the phenotypic differentiation of populations?
• Can we distinguish genetic from environmental effects on phenotypes?
Genetic differentiation of populations
If the environment is different for two populations of same species, a divergent selection will occur
pulling these populations apart. Another factor that will push populations apart is genetic drift. Yet,
populations are going to be held together with gene flow. Gene flow is going to reduce differences
between populations.
Measuring gene flow:
• Difficult to observe and measure,
• Use experimental approaches,
• Use neutral genetic markers like polymorphic genetic variants that are not direct targets of
selection. Rule out selection on particular alleles “after the fact” of migration. Let us infer non-
selective processes affecting genetic diversity of populations.
Question: How much gene flow occurs between geographically separated populations?
Experiment:
• Establish two populations, fixed for alternative alleles, separated by given distance,
• Take neutral genetic marker that will go flow fast in gel (F) and the other allele slow (S),
• Frequency of heterozygotes = estimate of gene flow.
Stochastic (unpredictable or random) evolutionary forces are mutation, recombination and genetic
drift. Deterministic (predictable or non-random) evolutionary force is natural selection.
Genetic drift is more pronounced in small populations
• More drastic fluctuations each generation,
• More rapid loss of genetic diversity (i.e., faster time to allele fixation or loss),
• Less consistency across replicate populations.
Human population differentiation from East Africa: lower gene flow with increasing distance.
Isolation by distance: Accumulation of local genetic variation due to geographically limited
dispersal.
Sometimes distance alone could be enough barrier to slow down gene flow.
Phenotypic differentiation of populations
Phenotypic differentiation may be:
• adaptive (local adaptation),
• due to genetic drift,
• phenotypic plasticity.
Testing for local adaptations and plasticity:
• Reciprocal transplant studies,
• Genomic analysis.
Phenotypic plasticity: The ability of a genotype to modify its phenotype in response to a particular
environment
• Occurs through modifications to development, growth, and/or behavior (under genetic
control),
• Common in sedentary organisms (also in animal behavior),
• Phenotypic plasticity often is an adaptation to unpredictable environments (but not all
phenotypic plasticity results from adaptation).
So, how to tease apart phenotypic plasticity from local adaptation? The best way is Reciprocal
Transplant Studies - introducing organisms from each of two environments into the other.
• Differences between populations due to BOTH plasticity and genetics,
• Evidence for widespread local adaptation – local populations had highest fitness.
No single “best” phenotype across the globe due to trade-offs.