BIOB51 Notes

Chapter 1
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A phylogeny is a hypothesis about how a feature arose

Universal molecular homology: genetic code

Chapter 2
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All life forms are related

Homology: the study of likeness, specifically the fundamental similarities underlying obvious physical differences
among species
o DIVERGENT EVOLUTION HOMOLOGOUS STRUCTURES
STRUCTURAL
o The underlying vertebrate forelimb design is the same (pretty much) even though they are functionally
and superficially different
o Streamlined shape in sharks and dolphins does NOT fit this because they have similar features for the
same purpose (nonhomologous similarities)
MOLECULAR
o A good example is a genetic flaw/mutation
o Shared flaws in organisms suggest common ancestry
o Example: chromosome 17 has a gene for PMP-22 flanked by identical sequences called CMT1A repeats
Humans share this genetic flaw with chimpanzees
Proximal repeat
o Processed pseudogenes: non-functional copies of normal genes that originate when processed mRNAs
are accidentally reverse transcribed to DNA by reverse transcriptase, then inserted back into the genome
at a new location
Most genes in human genome have coding bits (Introns) separated by non-coding bits (exons)
Also called retrotransposed
Lack upstream promoters, so are DOA, non-functional
No function means it acquires mutations, older = more mutations
o If species are related by descent from a common ancestor, then
o Genetic code is universal molecular homology
Most organism have the same triplet code
If alternative genetic codes are possible and advantageous, why dont we use them?
All organism inherited fundamental internal machinery from a common ancestor
Yeast lovastatin angiogenesis

Chapter 3 (pgs. 77-97)

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To increase frequency of desirable traits in their livestock and crops, plant/animal breeders employ artificial
selection
o Example: domesticated tomatoes are way bigger than wild tomatoes
A process similar to artificial selection occurs automatically in nature natural selection
Darwins postulates
o Individuals within a population different from one another
o The differences are (partially) passed from parents to offspring
o Some individuals are more successful at surviving and reproducing than others
o Successful individuals arent just lucky succeed because of the variant traits they have inherited
If all of the postulates are true, then the composition of the population will change from generation to generation
Natural selection results in evolution
Individuals who are better at surviving and reproducing are physically better fit (Darwinian fitness)
o NOT NECESSARILY PHYSICALLY FIT
o This type of fitness is relative to other members in a population
o Traits that increase and organisms fitness (adaptation/adaptive traits)
Natural selection acts on phenotypes, but evolution consists of changes in allele frequencies
Exaptation: a trait that is used in a novel way
o Happenstance
o Enhances individuals fitness
o The trait may form a completely new structure

Additional modifications are called secondary adaptations

Chapter 4 (pgs. 109-131, 134, 138-142)

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Evolutionary/phylogenetic tress and how to read them

o Depicts genealogical relationship between a group of organisms
o The root of the tree is the common ancestor (left)
o Time proceeds L R
o Nodes represent most recent common ancestor
Divergent vs convergent evolution (both are forms of macroevolution)
o Divergent: 2 separate species evolve differently from a common ancestor
Convergent: when unrelated species evolve similarities when adapting to similar environments, live in relatively
same way as each other (i.e. ostriches and emus)
o Reversal: lost of derived traits, return to ancestral condition
o Homoplasy: similarty in character traits due to convergenece or reversal
Character shared by a set of species not present in their common ancestor (i.e. evolution of the
eye)
Monophyletic group = clade
o An ancestor and ALL of its descendants
Outgroups/outgroup analysis: an outgroup serves as a reference when studying the relationship between 3+
monophyletic groups
o Ingroups are species whose relationship you wish to infer
o Must not be in the ingroup but closely related enough that you can make a meaningful comparison
Parsimony analysis: preference given to hypothesis that requires fewest evolutionary changes (simplest
scenario)
What is a synapomorphy?
o Synapomorphy is a shared derived characteristic present in ancestral species
o Derived trait shared by two or more members of a group
o Apomorphy derived or special trait/character
o Plesiomorphy ancient/ancestral trait
What is homoplasy? Why does homoplasy make it more challenging to estimate evolutionary history?
o Homoplasy is a similarity in characters traits due to convergence or reversalbasically, characteristics in
a set of species are present which were not present in their common ancestor (and thus, not inherited)
o It can be misleading because it makes species that are not closely related appear as if they are closely
related

Chapter 5
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There are 3 kinds of variations amongst individuals

o Genetic variation
o Environmental variation
o Genotype-by-environment interaction

Chapter 6 (up to 217)

Chapter 10 (pgs. 369-378)

MENDEL AND POPULATIONS (6.4, 7)

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Clines and Adh in fruit flies*

Non-random mating
Consanguinity, inbreeding depression
Heterozygosity
Neutral theory of molecular evolution
Null model: if selection is not acting and
o No mutations
o No migration
o No chance events that limit genetic transmission
o Individuals mate at random
o THEN,
Population is at Hardy-Weinberg equilibrium HWE)
Allele frequencies in a population will remain constant from one generation to the next
Cystic fibrosis (CF) is autosomal recessive and lethal, CTFR mutation (cystic fibrosis transmembrane
conductance regulator)
o Protein expressed in the mucus membrane lining the lungs/intestines
Allows the cells to destroy bacterium P. aeruginosa
In individuals with CF, P. aeruginosa causes chronic lung infections and severe lung damage
Selection against alleles causing CF seems to be strong
o Fitness cost vs. fitness advantage
CF heterozygotes may be resistant to typhoid fever (from salmonella typhi)
The bacteria cross the epithelial layer by exploiting CTFR receptor
Heterozygotes that have fewer copies of the receptor will be less vulnerable to infiltration
o If its lethal, how has it remained so common
Heterozygote superiority?
Mutations introduced to populations
Source of all new genes and alleles
o Delta F508 mutation deletion mutation
Deletion in DNA sequence at position 508
Results in absence of Phe (TTT)
o Pier et al
Constructed murine cells with delta F508 mutations
Homozygous WT, heterozygote, and homozygous recessive
Exposed cells to Salmonella typhi
Measured number of bacteria that got inside the cells
Results
Homozygous recessive totally resistant to infection
Heterozygotes partially resistant
Homozygous WT totally susceptible
Conclusion: CF disease alleles are maintained in populations because
Mutation is not a rapid mechanism of evolution
o Shown by Hard-Weinberg equilibrium
Mutation and Selection
o Zhang et al. inbreeded Drosophila populations to induce rapid loss of genetic diversity
Flies had to evolve to adapt to salty conditions
o Some mutations can be deleterious
Selection comes in to eliminate these types of mutations from the population
This doesn't always happen and deleterious alleles continue to be introduced because
theyre continuously made
o Mutation-selection balance: when the rate of deleterious alleles being created is equal to the rate being
eliminated by selection (kind of equilibrium)
Frequency of the allele at equilibrium where the allele is recessive:

Where q^ = equilibrium frequency

U = mutations rate
S= selection coefficient
A number between 0 and 1, strength of selection against the allele
Relative fitness of a phenotype (compares it to another favoured phenotype)
o In this case, it measures if its LESS FIT
o So s = 0 selectively neutral, lower number is better
o S=1 completely lethal compared to favoured phenotype
o If there are 100 offspring produced by favoured phenotype and only 90 by the
phenotype against it, s = 0.1
CF example:
Mutation rate of CF is 2 of every 30,000, s=1 (effectively lethal)
U = 6.7 x 10-7

CLINES and SELECTION

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Cline: A regular change in the frequency of an allele or an inversion over a geographic area
Flies and ADH
o Natural selection can cause allele frequencies to change
Flies given ethanol spiked food
o Violated HWE principle of no selection
ADHf have higher fitness than flies carrying ADHs when given ethanol spiked food
F allele has higher fitness than S allele because it can break down ethanol faster
o Gets rid of toxic products way faster

How does non-random mating and inbreeding affect a population?

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Less genetic variation

o Mendel
CF
Clines and Adh in fruit flies
Heterozygosity: the frequency of heterozygotes in the population
o H at the next generation = H at the present generation
o H(g)[1- 1/2N] where N= number of individuals in the population
Where H(g) is heterozygosity
o If the frequency of heterozygotes panthers= 0.440 and theres only 200 in the present generation
H (g+1) = H(g) [1-1/(2x200)]
= 0.439
If there are only 50 breeding adults panthers
o = 0.440[1-(1/2x50)]
= 0.436
o Fixation index/FST varies between 0 and 1
FST= (heterozygosity expected under HWE- heterozygosity over populations)/ HWE
heterozygosity
If q= 0.440 in all populations, then heterozygosity under HWE
HEW = 2pq = 2(1-q)q
o =(2)(0.56)(0.44) = 0.49
A population of 200 panthers with H= 0.439
o FST= (0.49-0.439)/0.49 = 0.104

Inbreeding
Floridian state animal (panther) on the verge of extinction
o Reasons (not including habitat loss and hunting)
Migration
Movement of alleles between populations; gene flow
Gene flow is a mechanism of evolution
Consider continental vs island populations
Migration alters genotype frequencies
o Violated HWE
o Example: snakes in lake Ontario islands
Prevents populations from diverging
FST value group of populations, variation of allele frequencies amongst members in
the population
Genetic drift
Example: Hawaiian crickets
Variation in the relative frequency of different genotypes in a small population
o Inidviduals by chance leave behind a few more descendants, not necessary
better genes, juts happen to survive
Mechanism of evolution

Non-random mating
Selfing
Most common type: inbreeding

o When a population has no selection, migration, mutation, an infinite # of individuals, and random mating
Genotype frequencies can be calculated by multiplying allele frequencies
MK Test of Positive Selection
o If there is positive selection on a gene locus
Variation at SILENT and REPLACEMENT sites of neutral alleles will have the same number of
synonymous and non-synonymous polymorphisms between related species as within a species
Polymorphism: locus at which different individuals in a population carry different alleles
Linkage disequilibrium: measures the degree to which two alleles at a loci are associated
o Based on expectations relative to allele frequencies
o To measure, compare observed and expected frequency of one haplotype
o Effects smaller populations more than larger ones
o Decay of linkage disequlibrium delayed in selfing populations
o If two genes are in linkage EQUILIBRIUM, they are inherited completely independently in each generation
o Disequilibrium inherited together more often than what would be expected
Neutral theory: explains observed patterns of amino acid sequence divergence (accumulation of independent
genetic mutations over time)
o Neutral mutations that rise to fixation by drift outnumber beneficial mutations
o Genetic drift and not selection mechanism form most molecular evolution
Migrating bears
If there is positive selection
o MK Test
o LD exists

Social Behaviour, etc.

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Inclusive fitness: the ability of an individual organism to pass on its genes to the next generation BUT takes into
account the shared genes passed on by the organisms close relatives

Hamilton
Example of how an allele causing altruistic behaviour can spread
Idea: the behaviour of an individual towards others can influence the success of the actors genes
Your grandparents genes are given to you, if they impose conditions on you conducive to your
reproductive success, its technically ensuring their genes are passed on as well
o Important on the relatedness of the actor and recipient
Genetic similarity between individuals
Hamiltons Rule: condition where altruism will increase in frequency (spreading)

Br C > 0 where B = benefit, C = cost, r = relatedness

o Point: altruism is likely to occur when benefits to the recipient are great, costs to actor are low, and the
individuals are closely related
Kin selection: type of natural selection where there is propagation of alleles that increase indirect fitness
Eusociality: highest level of organization in animal sociality defined by the following characteristics
o Overlapping generations
o Non-reproductive workers care for the young of 1+ reproductive workers
Division of labour
o Cooperative breeding: similar to aboveoffspring are taken care of by their parents as well as helpers
o How did it possibly come about?
Inbreeding
o
o
o

Parallel vs Convergent Evolution

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Parallel:
o Different species start with similar ancestral origins
o Evolve similar traits over time
o Experience similar kinds of environmental pressures
Survive only by undergoing similar types of adaptations
Convergent:
o Species that are not closely related to each other evolve similar kinds of traits
Dragonflies, hawks, and bats all have wings
Independent evolution of analogous structure

Pleiotropy and Developmental Trade-Offs

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Pleiotropy multiple functions of the same gene within a single organism

Beetles
o A