evolution exam 2

evidence of natural selection 3

beautiful design

odd design

good design

natural selection has to explain

every adaptation

- In most cases, this adaptation is step-by-step

Examples

• Body form, size, & color

• How fishes evolved limbs & whales evolved flippers

• Behavior, including altruism & cooperation

• Our metabolic system

• Our immune system

• SEX!

• Why we don’t live forever (and probably why we get wrinkles and sore knees as we age)

• The human eye (which also includes some bad design)

artificial selection

natural selection definition

A difference, on average, between the survival and reproduction of individuals with certain phenotypes compared to individuals with other phenotypes

not survival of the fittest

It is difficult to define natural selection in a succinct manner, because natural selection is not a “force” like Newtonian

mechanics: it is a multi-step process

natural selection steps? 3

1. individuals vary in phenotype

2. some of this phenotype variation is heritable

3. the variable heritable genetic traits affect an individuals probability of leaving offspring (“selected” by nature)

natural selection - struggle for existence leads to __?

Not all individuals survive to reproduce, or reproduce maximally

There is a struggle for existence, leading to variability in reproductive output

industrial melanism

Before 1850: light form at nearly 100%

Coal pollution darkened the tree trunks and killed the lichens

1848: 1st dark morph in Manchester, England

Within about 50 years, the dark morph increased to nearly 100%

Clear air legislation passed in 1950

today: light form >70%

outcome of natural selection: genetic composition of the population changes across generations

natural selection nuances 12

only impacts …

operates on what

can operate even if …

composed of _

every generation reflects ___

does not lead to ___

what can evolve?

what must each adaptation do?

what determines which genes make it to the next generation?

is it random?

what does it never do?

can only improve what

1. Traits under natural selection only impact the probability of survival and reproduction

2. Natural selection operates on the phenotypes of individuals within a population, while populations evolve across generations (the gene pool is changed)

3. Natural selection can operate even if the characters under selection are not heritable – but in this case, the population will not change in its genetic composition across generations

4. Natural Selection is a process composed of testable components

5. Natural Selection cannot predict the future. Every generation reflects the impacts of natural selection on the previous generation. (Avoid teleology)

6. Natural Selection is not progressive, and does not lead to perfection. It can only filter variation according to fitness in the current population

7. New traits can evolve by natural seelection

8. an adaptation must evolve by increasing the reproductive success of its possessor

   • Reproduction, not survival, determines which genes make it to the next generation

   • A gene that benefits reproduction at a young age, yet leads to wrinkles, grey hair, stiff joints, beer guts, and disease in old age, can be favored by natural selection

   • Another definition of natural selection = the non-random survival and reproduction of variants randomly generated with respect to need

9. Natural Selection is not random: with knowledge about ecology and heritability, evolution by natural selection can be predicted accurately.

10. Natural selection never favors a trait “for the good of the species,” as it can only act on individuals and proceeds without foresight (no teleology!)

11. Natural Selection can only improve the mean fitness of a population. It can never operate to lower mean population fitness, even if that is a good idea from a design perspective

12. An appropriate metaphor, developed by the great French geneticist Francois Jacob, is to think of evolution as a “tinkerer” rather than an engineer

    • Tinkering proceeds step-by-step, including complex structures such as the vertebrate eye

    • This imposes important limitations, or “evolutionary constraints,” on evolutionary change

    • Evolution cannot select on variation that does not exist, and biases in the production of variation can influence the evolutionary path taken by a population

variations of individual phenotypes can be due to 3

could be due to genetic factors, environmental factors, or their interaction

finches

beak depth is hertiable

big drought = 84% finches died, struggle for existence, seed abundance dropped dramatically = struggle for existence of seed eaters

characteristics of the average seed also change

direction of selection depends on ecology (droughts etc)

bad design by evolution

Bad Design: An engineer or biologist could do better, but the oddities are tell-tail marks of evolutionary tinkering by natural selection

fitness

the extent to which an individual contributes genes to future generations.

A good measure of fitness is the number of offspring produced by an individual in its lifetime.

Usually fitness is applied to phenotypes. For example, what is the average fitness of green vs. red beetles?

fitness landscape

fitness v trait value

fitness v trait value

can go from a peak to valley, or vice versa, but never straight from peak to peak/valley to valley

convergent evolution of camera like eye

how does a camera like eye evolve?

vertebrate eye: the axons, nerve fibers, of the retinal cells run over the retina and converge into the optic nerve forming a blind spot

octopus eye: in cephalopods, the axons run directly from the base of the retinal cells into the optic ganglion

hardy weiberg equation

p2+2pq+q2 = 1

AA Aa aa

assumptions for HW principle to be true 8

1. Diploid organism

2. Sexual reproduction

3. Non-overlapping generations

4. Infinite population size

5. No migration (no gene flow)

6. No mutation

7. No natural selection

8. Mating is random

bolded in evolution

how HW can change with the assumptions ¾

allele frequencies, genotype frequencies, reestablished by ?

1. If the allele frequencies in a population are given by p and q, then genotype frequencies will be given by p2, 2pq, and q2 when the population is in Hardy-Weinberg equilibrium

2. Within a population, allele frequencies will not change from generation to generation unless one of assumptions 4 – 7 is violated. Violation of assumption 8 (random mating) changes genotype frequencies, but not allele frequencies

3. Only one round of random mating is required to re-establish H-W equilibrium

simplified

1. allele frequencies are p and q, then genotype frequencies are p2, 2pq, q2

2. allele frequencies will not change unless assumption(s) 4-7 are violated

3. genotype frequencies (not allele) will change when 8 is violated

4. random mating reestablishes HW

how to calculate frequency of allele A vs a

A = A2 + ½ 2Aa

A = p2 + ½ 2pq

sub q for 1-p

A = p2 + p(1-p)

A = p

p = AA + ½ Aa / # individuals total = %

q = 1-p = aa + ½ Aa / # individuals total = %

calculate expected number of individuals with a genotype given allele frequencies

p = X allele frequency

q = Y allele frequency

p2 = X2 * total individuals

2pq = 2 * X * Y * total individuals

q2 = Y2 * total individuals

steps to a statistical test 6

1.Have a hypothesis

2.Define the expectation under the null  hypothesis of no effect

3.Collect data

4.Compute a test statistic

5.Find the probability of your test statistic  under the null hypothesis

6.Interpret your results

chi-square test

X2 = SUM ( observed - expected )² / expected

draw X2 distribution and what is the critical value

fitness: absolute, relative, component, natural selection,

Absolute Fitness: The fitness of a phenotype is the average lifetime reproductive success of individuals with that phenotype (alternatively, the per capita growth rate of a phenotype)

Fitness component: an individual’s score on a measure of performance expected to correlate strongly with the genetic contribution to the next generation (e.g., survival, fecundity, etc.)

Natural Selection: A consequence of differences in fitness between individuals that differ in phenotype

Relative Fitness (W): The fitness of a phenotype compared with others in the population. Usually, the maximum relative fitness = 1. To calculate relative fitness, divide all absolute fitness values by the maximum absolute fitness.

calculate expected number of individuals at time t1

calculate absolute fitness

absolute fitness equation

how to calculate relative + equation

how to solve if there was evolution?

what is fitness 3

description? explanation?

how does a trait contribute to the reproductive success

how is fitness context dependent?

1. fitness is a description, not an explanation

   • herbert spenser - survival of the fittest

   • tautology: who survives? the fittest. who is the fittest? those that survive - explains fitness

2. an advantageous trait causally contributes to the organisms survival and reproductive success

   • doesn’t tell us why

   • may be genetically correlated

3. the phenotype of an organism in relation to the environment it inhabits determines how fit that organism is

   • fitness is context dependent

   • finches - example?

the general selection model

and /\q

genetic variance pq and frequency of p - graph and location

general selection model equation

and what it can solve for

The greater the difference between the relative fitnesses, the …

This quantifies the relationship between allele frequency and fitness. The greater the difference between the relative fitnesses, the greater the rate of evolution

selection with dominance /\q = ?

relative fitness, frequency before selection, contribution to next generation, after selection, frequency after selection

where s = selection coefficient

directional selection

Directional selection will always __ mean population fitness

a mode of natural selection in which a phenotype is consistently favored, causing allele frequencies to shift over time in the direction of that phenotype.

The rate of change in allele frequency is a function of the allele frequencies, the relative fitness values, and the mean population fitness in the population (as reflected in the General Selection Model)

Directional selection will always increase mean population fitness

Selection with dominance when the fitness of the homozygous recessive = 0

relative fitness, frequency before selection, contribution to next generation, after selection, frequency after selection

qn =?

eugenics

The study and practice of control over the evolution of human populations in an effort to decrease the frequency of undesirable traits (a largely ugly history)

cystic fibrosis

Cystic fibrosis transmembrane conductance regulator (CFTR)

Cell surface protein

Expressed in the mucus lining of the intestines and lungs

• CFTR enables cells to ingest and destroy the bacterium

• Pseudomonas aeruginosa

• Homozygotes for loss-of-function mutations suffer chronic infections with the bacterium, resulting in cystic fibrosis and severe lung damage

Homozygotes for loss of function mutations suffer chronic infections with severe lung damage (s = 1)

30,000 disease-causing alleles sequenced

• 500 different loss of function mutations found!

• estimated rate, mu = 6.7 × 10^-7

• known rate? mu = 0.0004

• how does it compare to estimated rate? lower than predicted?? im so lost

eugenics + cystic fibrosis: selection when the homozygous recessive fitness = 0

given q0 = 0.01, qn = 0.005

does eugenics work? (how long will it take)

overdominance find p and q

balancing selection

where Aa are dominant

Forms of natural selection that maintain variation within a population

sickle cell anemia

HbA: normal allele in hemoglobin

HbS: sickle cell allele in hemoglobin

Homozygotes for the HbA allele are susceptible to malaria in West Africa

• Malaria caused by the protozoan Plasmodium falciparum (Alveolata)

• Invades red blood cells and eats the hemoglobin

• Maria causes severe fevers

• Infected blood cells clump up and cause dangerous clots

Homozygotes for the HbS allele suffer from a severe anemia

• The red blood cells do not carry oxygen well and form a sickle shape when they do not have oxygen

• This blocks blood vessels and eventually leads to death

• When sickled cells pass through the spleen they are detected by white blood cells as defective and destroyed (not good when you are already short on with oxygen!)

overdominance + sickle cell anemia

HbAHbS heterozygotes are resistant to malaria but suffer mild anemia

estimated relative fitness in West Africa

AA: 0.88, Aa: 1.0, aa: 0.14

predicted equilibrium: HbA: 0.88, HbS: 0.12

observed frequency: HbA: 0.89, HbS: 0.11

underdominance

special?**

AA and aa homozygotes are dominant

s is negative

Underdominance

What are the stable equilibria?

Is underdominance an example of balancing selection?

What are the stable equilibria?

0, 1 – 0%, 100%,

Is underdominance an example of balancing selection? NO

mutation 6

Mutations the “raw material” of the evolutionary process

Mutation = fundamental to evolutionary theory

Mutation includes

• point mutations

• indels

• gene duplication

• transposable elements

• chromosomal mutations (e.g. inversions, translocations)

• genome-level mutations (e.g. polyploidy)

mutations caveats 3

environment, constraints?

Mutation has causes, but is random with respect to adaptive “needs” (avoid teleology!)

The environment does not induce adaptive mutations: no “inheritance of acquired characters”

• Lamarck (1744-1829): Philosophie Zoologique (1798)

• Epigenetic inheritance is not truly Lamarckian

Developmental constraints prevent many mutations from ever being expressed at the phenotypic level or biases the production of phenotypic variation in particular ways

purifying selection

removing dominant/co-dominant

removing recessive

Purifying selection = selection against deleterious mutations

Removed by selection if dominant or co-dominant

If recessive, mutation/selection balance

mutation-selection balance

selection w/o mutation

mutation w/o selection

µ = A → a (forward mutation rate)

ν = a → A (backward mutation rate)

How does mutation change the frequency of allele a?

If ∆qm is the per generation change in q due to mutation, then:

∆qm = pµ – qν

If pµ > qν, then ∆qm is positive

Mutation without selection will increase the frequency of the a allele

Selection without mutation will decrease the frequency of the a allele

When there is selection against the aa genotype, the frequency of the a allele declines

final q of mutation-selection balance

spinal muscular atrophy

Neurodegenerative disease – degeneration of the muscles that control voluntary movement

Deletions at one locus cause the disease

One of the most common lethal autosomal recessive diseases in Caucasians

Frequency of loss-of-function alleles = 0.01

Fitness of homozygotes for loss of function alleles = 0.1 (s = 0.9)

Direct Estimate of mutation rate: Sequenced 340 patients with SMA, as well as their parents

Estimated mutation rate: 1.1 x 10

Mutation/Selection Balance may maintain the disease

genetic drift definition

leads to the loss of __?

amount of possible change in allele frequency is proportional to __?

the probability of fixation of an allele =

what does it create

how does genetic drift affect mean allele frequency?=

how does it affect heterozygosity

can produce what? (special name)

A change in allele frequencies across generations due to random error in the sampling of gametes

populations are not infinite

1. genetic drift leads to the loss of genetic variation within a population

2. The amount of possible change in allele frequency per generation is proportional to the population size

3. The probably of fixation of an allele is equal to the initial frequency of the allele

4. Genetic drift creates differences among populations

5. Genetic does not change the mean allele frequency among populations

6. Genetic drift lowers heterozygosity

7. Genetic Drift can produce “Founder Effects”

binomial distribution + equation

The discrete probability distribution of the number of successes in a sequence of N independent yes/no experiments (e.g., drawing an A allele or not), each of which yields success with probability p (freq. of the A allele) or failure with probability q (freq. of the a allele)

The number of ways of drawing i A alleles out of 2N draws

graphically how is the amount of possible change in allele frequency per generation is proportional to the population size shown?

The probability of fixation of a novel mutation =

genetic drift is more likely to remove ___

variance among population _ across generations

genetic diversity is __ within populations

genetic diversity ____ between populations

increases

diversity is lost within pops

diversity increases between pops

Missouri Ozark Mts

8000-4000 years ago: Desert!

4000- present: Savanna

Lizards live on rocky outcrops (“glades”) in the savanna (mixed woodland & grassland)

1950’s: Fire suppression

• Red cedars invade the glades

• Dense understory between glades

Result: populations small & isolated (no gene flow between them)

8 multi-locus genotypes

Most populations fixed for a single multi-locus genotype.

2/3rds of glades now contain no lizards

genetic drift and heterozygosity equation

genetic drift __ heterozygosity

Genetic drift lowers heterozygosity

The loss of heterozygosity is more pronounced in smaller populations

founder effect

Genetic Drift can produce “Founder Effects”

Founder effect: Change in allele frequencies that occurs during the establishment of a new population due to sampling error in drawing founders from the source population.

= a population bottleneck that results from colonization

= a form of genetic drift

Genetic Drift can produce “Founder Effects”

example of eye problems?

Pingelapese people of eastern Caroline Islands, ~2700 SW of Hawaii

Descended from 20 people in 1775, originally on Pingelap Atoll

1 individual heterozygous for loss-of-function allele for CNBG3 gene

When homozygous, this gene causes achromatopsia:

color blindness, extreme sensitivity to light, poor visual acuity

Among the Pingelapese, 1/20 have achromatopsia

Worldwide: 1/20,000 have achromatopsia

summary of genetic drift and what it leads to, affects, changes, creates 7

1. Genetic drift leads to the loss of genetic variation within a population

2. The amount of possible change in the gene frequency per generation in the population due to genetic drift is proportional to population size

3. The probably of fixation of an allele is equal to the initial frequency of the allele

4. Genetic drift creates differences among populations

5. On average, genetic drift does not change the mean allele frequency among populations

6. Genetic Drift lowers heterozygosity

7. Genetic Drift can produce “Founder Effects”

effective population size

Ne

The size of an idealized population in which the rate of genetic drift is the same as in the actual population

Ne is usually less than the census N

effective population size 3 main parts?

1. variation in the number of progeny

2. unequal number of males and females

3. variation in population size

effective population size equation for unequal males and females

effective population size is highest when the Nm = Nf

effective population size equation with variation in population size

Ne is the harmonic mean of the census population size through time

nonrandom mating

Nonrandom mating occurs when individuals mate assortatively, for instance, if large females are more likely to mate with large males and vice versa. Nonrandom mating is a violation of HW

inbreeding

a form of what? ___ homozygosity

the mating among genetic relatives, which is a form a nonrandom mating. Inbreeding is a problem in small populations and is a serious concern in conservation biology

increases homozygosity

Inbreeding & Nonrandom mating

related to gene + allele frequencies, the difference, homozygosity?

Genotype frequencies change, allele frequencies do not

With nonrandom mating, cannot predict genotype frequencies from allele frequencies (violates HW)

All nonrandom mating increases homozygosity

The difference: inbreeding impacts the entire genome, whereas mate choice only impacts the loci that influence mate choice (and loci genetically linked to them)

California Sea Otters - Enhydra lutris

wahlund effect?

Distributed from Alaska to Baja California

Over-hunted for their amazing fur: about 50 individuals left in 1911

Now >1500

There is an excess of homozygosity. This is consistent with inbreeding

Other violations of HW could be responsible; more studies needed for a definitive statement

What if two distinct populations are mixed into a single sample? You get the same signature as inbreeding: a deficit of heterozygotes, and an excess of homozygotes. This is called the Wahlund Effect

coefficient of inbreeding

F = Coefficient of Inbreeding = the probability that two alleles are Identical by Descent (IBD): both copies descended from the same ancestral allele in an earlier generation. Alleles that are IBD are called autozygous

Inbreeding can be quantified as the reduction in heterozygosity

coefficient of inbreeding equation

when F>0, F=0,F=?

1 – F = The probability that two alleles are not IBD. These individuals are called allozygous, and can be either heterozygotes or homozygotes

when F>0, homozygosity increases

F = probability that 2 alleles in an individual are IBD

When F = 0, you have the normal HW equation

Homozygous vs. Heterozygous

Autozygous vs. Allozygous

calculating F from a pedigree

Genotype frequencies given inbreeding

AA,Aa,aa given p2+2pq+q2

inbreeding depression

By increasing the frequency of homozygotes, inbreeding increases the probability of homozygous deleterious, recessive alleles. For example, inbreeding increases the incidence of Cystic Fibrosis in humans

In captive populations (zoos), inbreeding is a serious problem.

In wild populations, inbreeding lowers the fitness of individuals and populations

Inbreeding is a big topic in conservation, because endangered populations are often small, which results in inbreeding. As if endangered species didn’t have enough problems...

inbreeding avoidance 4

Mate Choice

Dispersal from natal site

Self-incompatibility loci in plants

Management: move individuals between populations (=gene flow) to combat the decline in heterozygosity

migration = aka

gene flow

the movement of alleles between populations

gene flow violates HW

When will migration not change allele frequencies in a population? When the following equation = ??

how does migration change the allele frequencies

Thus: migration does not change the allele frequencies when m = 0 and when the frequency of the A allele is the same in both populations

impacts of gene flow on (1) populations (2) between populations (3) within populations

Gene flow homogenizes populations genetically

Gene flow decreases genetic variance between populations

Gene flow increases genetic variance within populations

difference between migration and genetic drift

The effect of Migration is opposite Genetic Drift

Gene flow and selection can work in opposite directions, as shown by the water snake example

GOOGLE:

Natural selection and genetic drift tend to enhance genetic differences among populations; migration tends to homogenize genetic difference, decreasing the differences among populations.

population structure def

due to 5

Population Structure: The presence of allele frequency differences among populations

Population structure is due to several evolutionary processes:

1. Natural Selection

2. Genetic Drift

3. Founder Effects

4. Gene Flow (migration)

5. Mutation

The most important consequence of population structure:

A reduction in the average heterozygosity relative to that expected if all the subpopulations were a single, randomly-mating population

Thus, population structure, like inbreeding, leads to a loss of heterozygosity (however, the loss is hypothetical in the case of population structure, and real in the case of inbreeding!)

FST

FST is the proportion of the total genetic variance contained in a subpopulation (the S subscript) relative to the total genetic variance (the T subscript)

interpreting FST

0.00 - 0.05 = Little

0.05 - 0.15 = Moderate

0.15 – 0.25 = Great

0.25 – 1 = Very Great

genetic drift and population structure and Fst

Genetic Drift increases divergence among populations over time

Increase in Fst over time among populations as a consequence of genetic drift

migration (gene flow) and population structure

Migration (= gene flow) makes populations more similar to one another. In the absence of any other evolutionary processes, gene flow will completely homogenize subpopulations

Changes in allele frequency between two populations that are exchanging 10% of their individuals each generation (m = 0.10)

What is the balance between gene flow and genetic drift on population structure?

bro idk

Fst and Ne and m equation

bro im lost on W7L1 slide 15

drift migration equilibrium

small amounts of migration between populations will minimize the loss of polymorphism and heterozygosity within subpopulations due to genetic drift, while allowing for divergence in allele frequencies among subpopulations

Quantitative Genetics

the investigation of continuously variable traits that are influenced by the combined effects of many loci as well as environmental factors

Two Schools of thought on variation

Late 1800’s to 1918

Biometrical School

• Initiated by Darwin’s cousin, Francis Galton

• Saw heritable variation as continuous

• Existed before 1900

• Maintained that Darwin’s idea of slight differences among individuals was the essence of evolution

• Most naturalists and systematists belonged to this school

Mendelian School

• Mostly laboratory geneticists

• Viewed variation as discrete and sudden, not continuous

• Most laboratory geneticists did not believe in evolution by natural selection: too slow & required too subtle variation

• Some even dismissed continuous variation as heritable at all

Both schools right, both schools wrong

BbSs x BbSs

Fisher (1918) – Published a paper showing mathematically that many genes of small effect could produce biometrical variation. Landmark paper, as it united the Biometricians and the Mendelians.

Assume loci are additive:

• capital letters (B, S) contribute +1

• lower case letters (b, s) contribute 0

many loci =?

continuous variation

Logic: if continuous variation is composed of discrete units, then ..

the original phenotype should be recoverable

variance

normal distribution is described by 2 parameters - mean and standard deviation

Variance is a measure of how data points differ from the mean

phenotypic variance Vp

Vp=Vg+Ve

Vg=Va+Vd+Vi

additive genetic variance, dominant, epistatic variance Vi, environmental variance Ve, genetic variance Vg

Additive Genetic Variance, Va

is due to what? almost completely responsible for ?

When the Phenotypic Value for a heterozygote is exactly intermediate between both homozygotes, the characters are said to be “additive”.

VA is due to the independent effects of alleles on a phenotype.

Additive genetic variance is almost completely responsible for heritable genetic variation

Dominance Variance, Vd

due to what? is it hertiable? why/why not

When Phenotypic Value deviates from additivity, this is called Dominance Variance, and it is due to interactions among alleles at a locus

Dominance effects are not transmitted directly from parent to offspring because only one allele is contributed by each parent

Epistatic Variance, Vi

due to? hertiability?

Epistatic variance is genetic variation due to interactions among loci.

Epistatic variance is not heritable variance because interactions among loci can’t be passed on to offspring due to independent assortment

Epistasis: The effect of the interaction between two or more loci on the phenotype whereby their joint effects differ from the sum of the loci taken separately

Epistasis is common...

epistasis

The effect of the interaction between two or more loci on the phenotype whereby their joint effects differ from the sum of the loci taken separately

Environmental variance

Differences among individuals in a population that are due to differences in the environments they have experienced