Unit 2 Bio Ev

Ch 8

When researchers find that the genotype at one locus is nonrandomly associated with the genotype at another locus, they say that the two loci are

in linkage disequilibrium

Out of the following factors, which one(s) reduce(s) linkage disequilibrium by disrupting overrepresented haplotypes and by generating new ones?

A. sexual reproduction

B. crossing over

C. genetic recombination

D. all of the above

D. all of the above

If a locus is in linkage disequilibrium with neutral genetic markers nearby on the chromosome, it is likely that a new mutation occurred at this locus. If this new allele is also found at high frequency, we can assume that it has likely been favored by ...

 recent positive natural selection

The figure below shows that ...

 

A. the decline in linkage disequilibrium is inversely proportional to the rate of recombination between them

B. the decline in disequilibrium occurs more slowly with a lower rate of recombination

C. the decline in disequilibrium occurs more quickly with a lower rate of recombination

D. none of these is an accurate statement

B. the decline in disequilibrium occurs more slowly with a lower rate of recombination

Out of the following statements, which one gives an accurate representation of the ideas of Muller's ratchet?

A. Sexual reproduction is selected because it reintroduces no-mutation genotypes that have been lost from the population.

B. Linkage disequilibrium increases in populations by genetic drift because no-mutation multilocus genotypes are lost by chance.

C. Deleterious mutations accumulate in asexual populations, resulting in a significant genetic load.

D. All of the above accurately represent the conditions of Muller's ratchet.

 

D. All of the above accurately represent the conditions of Muller's ratchet.

The generation of new allele combinations as a consequence of sexual reproduction and meiosis, is called

genetic recombination

When there are loci in linkage disequilibrium with certain alleles of interest, they can be used as markers to reconstruct the evolutionary history of those alleles in the population. The chapter describes a marker/allele combination in humans where the allele in question has an insertion that makes the enzyme GBA that it codes for nonfunctional. The figure below shows the decay curve for linkage disequilibrium between the mutated GBA allele and the marker (named D1S305). The orange lines show the current level of linkage disequilibrium and the inferred number of generations that have passed since the most recent common ancestor. If we assume the present level of linkage disequilibrium to be 0.35 (orange line with arrow), and the average generation time to be 25 years, how many years total has it taken for the linkage disequilibrium to reach that value?

. about 1375 years total

An important advantage of sexual reproduction is that it

A. helps to recreate genotypes that are either rare or missing in a population, but are favored by selection 

B. reduces linkage disequilibrium

C. recreates adaptive genotypes in the evolutionary "arms race" between parasites and hosts

D. does all of the above

D. does all of the above

Whenever there is an evolutionary arms race between hosts and parasites or other biological antagonists, sex will be favored because it regenerates genotypes that are missing or rare in the population due to prior selection imposed by the other antagonist. This hypothesis is known as the _______ hypothesis.

Red Queen

The L503F allele of the humane ergothioneine transporter protein is statistically associated with higher incidence of Crohn's disease. The allele makes the transporter more effective at taking up ergothionine, which is an antioxidant. What did Huff et al. suggest as a cause for the association between the allele and the disease?

E. B. and C.

Lec 9 genetic drift

What is migration?

Individuals moving between breeding population

What do migration do on the population?

• Homogenizes allele frequencies across populations

• introduces new genetic variation from other populations

What is genetic drift?

A random changes in allele frequencies due to finite(small) population size

Random change are not adaptations why?

Natural selection leads to adaptations through non-random changes while genetic drift(random changes) also leads to evolution because allele frequencies change

What are some genetic drift observations?

• allele frequencies in small populations change due to chance

• changes are faster and larger in smaller populations

• One of the alleles will eventually fix (= reach 100% frequency) the other allele(s) will go extinct

Which of the two alleles is more likely to reach fixation? What determines which allele is more likely to reach fixation?

• Probability of fixation depends on initial allele frequency (note it’s a probability, not a guaranteed outcome in a specific case)

• Reduction of genetic variation (but random fluctuations occur until fixation, genetic variation is reduced when one allele goes extinct)

What is the expected heterozygosity?

A measure of genetic variation

• highest for intermediate allele frequency (p=q=0.5)

• frequency of heterozygotes [=2 (p)(1-p)]

What is the founder effect?

Random changes in allele frequency and reduced genetic variation, associated with founding of new population by a few individuals

Could a founder events cause a reduced variation?

Yes, the decreasing genetic variation with increasing distance away

A new mutation has a frequency of what and what do you expect how it would look?

A frequency of 1/2N (N= populations)

• will be a low but non zero probability of fixation of neutral mutations due to genetic drift

• this probability is larger in smaller population

How does selection will also influence fixation probability?

Random force of genetic drift acts at the same time as the non- random force of natural selection

Why is genetic drift is strong in small populations and weak in large ones?

In small population

• genetic drift might overpower natural selection

• randomness may dominate in small populations

• changes in frequency changes occur faster and one allele to fixation(100%) and others to extinction, reducing genetic variation

In large population

• natural selection less likely to be overpowered by genetic drift

• genes that affect fitness are more likely to behave as predicted by selection coefficient in large populations

Lec 9 .2 Genetic Drift

What is the "Rule of Thumb" equation determining whether genetic drift or natural selection dominates an allele's path?

if |s| < 1/2Ne

s=selection coefficient

Ne= effective population size

N= census population size

When this condition is met, the allele behaves as if it is completely neutral, allowing even deleterious mutations to randomly increase in frequency.

What does the value 1/2N mathematically represent in population genetics?

It is the probability of fixation for a brand-new, completely neutral mutation in a diploid population of size N

Categorize the five violations of Hardy-Weinberg equilibrium and their general effects on genetic variation.

• Selection: Nonrandom /Deterministic force; usually decreases genetic variation; generates adaptations.

• Mutation: Random force; generates genetic variation; alters allele frequencies very slowly.

• Migration: Homogenizes allele frequencies across populations; introduces variation to local populations.

• Genetic Drift: Random chance in allele frequencies; dominates in small populations; decreases genetic variation over time.

• Nonrandom Mating: Changes genotype frequencies but not allele frequencies; not an evolutionary force by itself.

what is inbreeding and what is inbreeding depression

Inbreeding is the reproduction among related individuals

inbreeding depression is reduced fitness due to inbreeding

Universal Cause: Both are driven by increased homozygosity and decreased heterozygosity across genes.

What are the three distinct forms of inbreeding depression discussed in the lecture?

1. Among Populations: Reduced average fitness of an entire population due to chronically small population sizes and fixed deleterious alleles.

2. Within Populations via Nonrandom Mating: Individuals preferentially select relatives or practice self-fertilization (selfing), reduce fitness due to decreasing individual heterozygosity inbred individuals.

3. Within Populations via Random Mating: In small populations, individuals mate randomly but run a high statistical chance of pairing with relatives due to limited options, reduce fitness due to decreasing individual heterozygosity inbred individuals

What single genetic hallmark is common to all three types of inbreeding depression?

They are all fundamentally caused by increased homozygosity and decreased heterozygosity across the genome.

Define Heterozygosity and Inbreeding Coefficient (F).

• Heterozygosity: The proportion of genetic loci that bear two different alleles (Aa) instead of two identical ones (AA or aa).

• Inbreeding Coefficient (F): A measure of the level of inbreeding, typically ranging from 0 (completely outbred) to 1. For example, offspring resulting from full-sibling mating have an F = 0.25.

What genetic pattern is observed in Island Foxes (Urocyon littoralis) compared to mainland Gray Foxes?

Island foxes demonstrate drastically lower heterozygosity across autosomal, neutral, coding, and conserved non-coding DNA sites. This is driven by centuries of small, isolated island populations (ranging from ~326 to 1968 individuals per island) magnifying genetic drift.

How does the Florida Panther exemplify population-level inbreeding depression, and how was it resolved?

A tiny, isolated population suffered severe genetic defects and low average fitness because genetic drift drove deleterious alleles to high frequencies. Conservationists reversed this by promoting gene flow/migration via the translocation of panthers from outside populations.

What absolute lifespan cost is observed due to inbreeding depression in purebred dogs?

On average, purebred dogs have a lifespan that is ~1.2 years shorter than size-matched mixed-breed dogs due to population-level inbreeding and closed studbooks.

What baseline biological impact does an inbreeding coefficient of F = 0.25 have on wild vertebrates generally?

According to a 2019 multi-species study, wild vertebrate offspring born to full siblings (F = 0.25) experience a massive survival reduction, keeping only 42% of the survival rate observed in outbred individuals.

What metric measures genetic differentiation among distinct subpopulations, and what is its scale?

Genetic differentiation is measured using F_ST, which quantifies how much allele frequencies differ among distinct populations. Its value ranges from 0 (no differentiation; completely identical allele distributions) to 1 (complete differentiation; populations fixed for alternative alleles).

Using least-squares linear regression to determine the slope of the line of best fit for a data set of midparent and midoffspring values generates an estimate of heritability known as the ...

narrow-sense heritability

A general description of heritability would be to say that it measures

the portion of the total phenotypic variation in a trait that is due to variation in genes

Traits that are determined by a single locus are best termed ...

qualitative traits

By looking at associations between a marker locus genotype and a phenotype, researchers can learn the location of and the quantitative impact that QTLs have on phenotypes of quantitative traits. Examples of traits addressed in QTL mapping studies include ...

A. human diseases such as Crohn's disease

 

B. human personality traits

 

C. the speed of thoroughbred race horses

 

D. all of the above

D. all of the above

Using twin studies to estimate heritability has been a useful method for certain human traits, such as general cognitive abilities. How can twin studies be useful, and how are they performed?

They can indicate how much of the variation among individuals is due to variation in genes. They mostly compare identical and fraternal twins that live with their parents.

The overall variation in a trait that is found in a population is known as the ...

phenotypic variation

When genetically identical yarrow plants were grown at different elevations, the results are shown in the figure below. This finding documents that ...

the environment has a large effect on the phenotype of this yarrow genotype

Characteristics that are affected by many loci and whose phenotypes are continuously variable and affected by both genotypic and environmental influences are best termed ...

 

B. quantitative traits

When looking at IQ scores in humans, some people would argue that heritability can tell us something about the causes of differences between ethnic groups. Why is this perspective erroneous?

A. Heritability values are affected by the exact conditions of the experiment or the population from which the values were obtained and thus cannot be generalized across populations.

B. To assess the cause of differences between groups, members of the different groups have to be reared in identical environments. In humans, this experiment cannot be done.

C. Ethnic groups originate in different continents and thus necessarily differ in their genetic makeup, so heritability studies are not required. 

D. A. and B.

D. A. and B.

Take a look at the figures below. If A is a measurable trait in a population at a certain time, and B is the same trait several generations later, we would conclude that a type of selection called ................   selection has been at work.

Figure A                                                   Figure B

stabilizing

Lec 10: Heritability

What are qualitative traits, and what are their typical genetic mechanisms?

Traits characterized by discrete phenotypic categories (such as color, shape, or disease presence/absence and so on)

They are typically controlled by one or a few genes

What are quantitative traits, and what causes their variation?

Traits that dispaly continuous variations and must be measured numerically(such as height, weight, width, or speed). They are controlled by many genes (polygenic) and or influenced by envirnomental variation

What are quantitative trait loci (QTLs))

Genes that affect quantitative traits. their individual contributions combine to generate continuous phenotypic distributions across a population

What are phenotype and how is it determined?

It is the observed characteristics and it is determined by genotype and environment

What is the fundamental formula for phenotypic variation(Vp)?

V_P=V_E+V_G+V_GE

• \(V_{P}\) = Total Phenotypic Variation

• \(V_{E}\) = Environmental Variation

• \(V_{G}\) = Genetic Variation

• \(V_{GE}\) = Genotype-Environment Interaction Variation

• 
  

What are the sub-components that make up total Genetic Variation (V_G)?

V_G=V_A+V_D+V_I

• \(V_{A}\) = Additive Genetic Variation

• \(V_{D}\) = Dominance Genetic Variation

• \(V_{I}\) = Epistatic / Genetic Interaction Variation

Why is Additive Genetic Variation (\(V_{A}\)) uniquely important in evolutionary biology?

Because individuals only pass on half of their genes (single alleles) to their offspring rather than their intact multi-locus genotypes. \(V_{A}\) determines the resemblance between parents and offspring, and directly dictates the rate of evolutionary change in response to selection.

What is Broad-Sense Heritability (\(H^{2}\)) and its formula?

• The proportion of total phenotypic variation in a population that is attributable to all genetic differences (\(V_{G}\)).
  \(H^{2}=\frac{V_{G}}{V_{P}}\)

• 
  

• What is Narrow-Sense Heritability (\(h^{2}\)) and its formula?

• 
  

What is the mathematical numerical range of heritability (H² or h²)

• It strictly ranges from 0 to 1.

  • 0 = No phenotypic variation is due to genetic variation.

  • 1 = All phenotypic variation is due to genetic variation.

• Flashcard 10

  • Front: How do you estimate narrow-sense heritability (\(h^{2}\)) using an offspring-midparent regression?

  • Back: Plot the average trait value of the offspring (Midoffspring) on the y-axis against the average trait value of both parents (Midparent) on the x-axis. The slope of the resulting regression line directly equals \(h^{2}\).

• Flashcard 11

  • Front: How do you calculate \(h^{2}\) if you only have phenotypic data for one parent instead of a midparent average?

  • Back: You plot the offspring trait values against that single parent's values, find the slope of the regression line, and multiply the slope by 2 (\(h^2 = 2 \times \text{slope}\)).

• Flashcard 12

  • Front: What visual profile does an offspring-parent regression show for \(h^2 \approx 0\), \(h^2 \approx 0.5\), and \(h^2 \approx 1\)?

  • Back:

    • \(h^2 \approx 0\): A flat line (slope = 0); scattering of points shows no predictive relationship.

    • \(h^2 \approx 0.5\): A moderate, upward-sloping line.

    • \(h^2 \approx 1\): A steep line approaching a 45-degree angle (slope = 1); data points tightly cluster along the line.

• 
  

What major complication arises when estimating heritability if shared environmental factors are ignored?

If families share a more similar environment with each other than they do with the rest of the population, heritability will be significantly overestimated because environmental similarities are mistaken for genetic inheritance.

Name three methodological tweaks used to correct for shared environmental biases in heritability studies.

1. Cross-fostering experiments: Swapping offspring at birth to compare biological vs. foster parents (e.g., Mandarte Island song sparrows).

2. Twin studies: Comparing the trait similarities of identical (monozygotic) vs. fraternal (dizygotic) twins.

3. Pedigree analysis with mixed models ("animal models"): Utilizing complex datasets that incorporate phenotypic values of distant relatives.

Ch 12

What is sexual dimorphism?

phenotypic difference between (average) males and females in a population such as the coloration, size, behavior and so on

Why sexual dimorphism?

Ecological reasons such as reduce competition for resources

Roles in reproduction such as adaptations to lay eggs

Sexual selection: maximizing reproductive success by finding and securing mates

What is anisogamy?

The asymmetry in gamete size where females produce larger gametes which are eggs and males produce smaller gametes which are sperm

• this structure causes higher initial energy expenditure by females

What is asymmetric parental investment?

Parental care

• (incubating, feeding, protecting offspring) The sex investing more energy is limited by the gametes they can produce or the parental care they can provide, while the sex investing less energy is limited by the number of matings they can acquire. Female typically

Which sex typically experiences stronger sexual selection?

The sex that invests less energy into reproduction and is limited by availability of mates. typically male

What behavioral traits are characteristic of the sex experiencing stronger sexual selection versus the sex experiencing weaker sexual selection?

The sex under stronger selection is more competitive; the sex under weaker selection is more choosy among available mates.

How does rough-skinned newts is an example of asymmetric parental investment?

They have no parental care but female investment in egg much higher than male investment in sperm. This means many males at a time compete for access to females

This mean the reproductive success more strongly limited by mating opportunities for males than for females

How does broad nosed pipefish is an example of asymmetric parental investment?

Male receives eggs from female and looks after them meaning male invests more energy in reproduction than female

• meaning reproductive success more strongly limited by mating opportunities for females than for males

Fill in the blanks

sex that hass reproductiv success limited more by ____________ , which equal the sex investing _____ energy into reproduction and experiences _________ sexual selection

Lec 13

What is mutualism and what is the social interactions?

When both the actor and the recipient benefit

Ex: communal breeding

What is selfishness and what is the social interactions?

When only the actor benefit while the recipient don’t.

ex: cannibalism

What is altruism and what is the social interactions?

When the recipient benefit while the actor doesn’t

ex: predator warning, slime mold amoebae

What is spite and what is the social interactions?

When both don’t benefit

ex: lethal bacteriocins

Why does altruism happen?

It happen because of Kin selection, reciprocity, and multilevel selection

What is kin selection?

It is based off relatedness

the genetic benefit of helping another individual reproduce depends on how closely related that individual is (r), how big the cost(c ) of helping is and how big the benefit (B) to the recipient’s reproduction is.

How will the genes of an individual will increase in the population if?

• the individual reproduces or

• it helps a relative reproduce

What is hamilton”s rule?

Helping is favored if : Br-C>0

B: benefit

r: related

C: cost

Direct fitness vs indirect fitness vs inclusive fitness

Direct fitness : own reproduction without help

Indirect fitness: additional reproduction because of help

Inclusive fitness: direct fitnee+ indirect fitness

Why is alarm calling in animals considered a potential example of altruism?

It benefits others by alerting them to danger, but it may expose the caller to a higher risk of predation. However, absolute proof varies by species.

What is the primary hypothesis for why black-tailed prairie dogs utter alarm calls?

The kin selection hypothesis, which suggests the behavior evolved because it benefits close genetic relatives.

How can scientists test the hypothesis that kin selection explains alarm calling in black-tailed prairie dogs?

By measuring and comparing the frequency of alarm calls when individuals are living with close relatives versus when they are living with unrelated individuals.

What key observation supports the kin selection hypothesis in black-tailed prairie dogs?

They alarm call significantly more often when living with relatives, which results in expected indirect fitness gains.

What is the fundamental cause of parent-offspring conflict regarding parental investment?

Parental investment in one offspring reduces the resources available for other current or future offspring. This creates different investment optima, leading offspring to beg for more food even if it harms their siblings.

How does sibling relatedness affect an offspring's begging behavior according to kin selection?

Offspring should beg less when surrounded by full siblings than when surrounded by half siblings. This happens because the inclusive fitness cost of depriving a full sibling of food is higher than depriving a half sibling.

What is the inclusive fitness cost to an offspring when its begging behavior results in a lost sibling?

• Lost Full Sibling: Cost is 0.5 of the cost to the parent.

• Lost Half Sibling: Cost is 0.25 of the cost to the parent.

What evolutionary correlation is observed between begging behavior and mating systems across species?

There is a positive correlation between begging loudness and extra-pair paternity. Species with higher rates of extra-pair paternity (more half-siblings in the nest) exhibit louder begging behavior.

Altruism: Reciprocity

Individuals help each other because its actor expects to be helped by the recipient in the future (e.g., grooming in Hamadryas baboons)

Two factors that facilitate reciprocal altruism

• Familiarity with other individuals

• Punishment of cheaters

How much bigger must the benefit (B) be than the cost (C) for altruism to be favored between identical twins?

The benefit must be greater than the cost (B/C > 1).

• r = 1.0

• Calculation: 1.0 x B > C → B/C > 1/1.0 → B/C > 1

How much bigger must the benefit (B) be than the cost (C) for altruism to be favored between full siblings?

The benefit must be more than 2 times greater than the cost (B/C > 2).

• r = 0.5

• Calculation: 0.5 x B > C → B/C > 1/0.5 → B/C > 2

How much bigger must the benefit (B) be than the cost (C) for altruism to be favored between half siblings?

The benefit must be more than \(4\) times greater than the cost (B/C > 4).

• r = 0.25

• Calculation: 0.25 x B > C → B/C > 1/0.25 → B/C > 4

How much bigger must the benefit (B) be than the cost (C) for altruism to be favored between first cousins?

The benefit must be more than 8 times greater than the cost (B/C > 8).

• r = 0.125 (or 1/8)

• Calculation: 0.125 x B > C → B/C > 1/0.125→ B/C > 8

In which of the following groups should conflicts between parents and offspring over parental investment be the most pronounced?

A. birds

B. amphibians

C. fish

D. reptiles

A. birds

When the evolutionary fitness of an individual considers only its own descendants, without including the effect of the help it provides for others, this is referred to as ________.

A. indirect fitness

B. inclusive fitness

C. kin selection

D. direct fitness

D. direct fitness

Natural selection can operate through an increase in the frequency of alleles which promote the fitness of genetic relatives. This is called ________.

A. indirect selection

B. inclusive selection

C. direct selection

D. kin selection

D. kin selection

When genetically unrelated individuals exchange favors, to the benefit of both, this is referred to as ...

A. reciprocal altruism

B. group selection

C. mutual cooperation

D. kin selection

A. reciprocal altruism