Evolution exam 2 Manual

Is high fecundity associated with low or high survival?

Low survival

Is low fecundity associated with low or high survival?

High survival

What are two examples of hypothetical adaptation axes?

Spatial axis, seasonal axis

In an adaptive landscape, how does natural selection move a population?

Always up peaks

In an adaptive landscape, how does drift move a population?

Any direction; randomly; random direction

True or False: sometimes drift does not happen

False (drift always happens)

If the black dot represents a Massachusetts population of Drosophila, is it likely that these flies can adapt to winter in Vermont (reach the tallest peak)? Why? (Answer 1; Answer 2)

Yes; natural selection drives it upwards and there are no fitness valleys

If the red dot represents a Florida population of Drosophila, is it likely that these flies can adapt to winter in Vermont (reach the tallest peak)? Why? (Answer 1; Answer 2)

No; as it moves along the axes of metabolic capacity and cold tolerance, it reaches peaks which are not the optimum

Why can a population become “stuck” on peaks of lower fitness rather than progressing towards the optimum for an environment?

Natural selection is myopic; to move past a local maximum would mean temporarily decreasing fitness

What might allow the red population to leave the global maximum?

Drift

What does the process of local adaptation represent?

The journey of a population to maximize its fitness in an environment

In a static fitness landscape, where does the population end up?

Trapped on one peak (local or global maximum)

What is CCR5-Δ32?

A rare allele common in northern latitudes that confers resistance to HIV, but weakens the overall immune system. 

Is selection on the Δ32 allele in the north strong or weak? Why? (Answer 1; Answer 2)

Weak; because HIV/AIDS is rare

Is selection on the Δ32 allele in the south strong or weak? Why? (Answer 1; Answer 2)

Strong; because HIV/AIDS is common

Selection on the Δ32 allele in the south is strong, but the allele is rare (p = 0.01). What does this mean?

Response is weak

Why is response weak for the Δ32 allele in the south, where HIV/AIDS is common?

Because the Δ32 is infrequent (p = 0.01)

What does it mean to say that evolution is myopic?

Selection in an adaptive landscape may trap a population on a local peak

How can a population escape from being trapped on a local peak?

Drift may allow a population to acquire new allele frequencies and combinations that enable selection towards the highest peak; drift can allow populations to approach the domain of attraction of another peak

Sewell Wright’s hypothesis

Adaptive evolution may proceed most quickly when a population divides into subpopulations with restricted gene flow

What are the four components of Sewell Wright’s hypothesis?

Drift in local populations, intrademic selection (mass selection), interdemic selection, all demes acquire allele frequencies of “best” global peak

Why is the C allele described as being "TRAPPED" in the AC and SC genotypes (malaria)?

Because these heterozygotes have lower fitness (0.9 and 0.7) than the established AS genotype (1.0), making it difficult for the C allele to increase in frequency.

What mathematical term is used to explain why the CC genotype is almost non-existent when the C allele frequency is low?

Rare squared

Intrademic selection (mass selection)

When a population climbs a local peak

Interdemic selection

Emigrants proportional to relative fitness among demes

If deme A has much higher relative fitness than deme B, which will produce more migrants?

Deme A

Deme

A subdivision of a population consisting of closely related plants, animals, or people, typically breeding mainly within the group.

If f(A)>>f(S)>f(C) and CC is the most fit, but AS > AC > SC, what fact of adaptive landscapes prevents selection from making the CC genotype most common?

Selection has to go down hill to get CC homozygotes by getting C heterozygotes, which are the least fit

This “dynamic” landscape would lead to what kind of selection?

Directional selection

What would best describe the red population (provide the most accurate and prce4ise answer in the context of adaptive landscapes)?

Locally adapted

What forces are depicted here, in order (a, b, c)?

Selection, drift, selection

What does the evolutionary direction indicated by the arrows imply?

Drift

Polymorphism

When there are two or more possibilities for a trait on a gene

How are polymorphisms introduced?

Mutation

When a mutation reaches fixation as a result of selection, what does this result in?

Substitution

Substitution

“when the wild-type allele in a population changes from a previous one to a new one. [This is] The product of a mutation leading to a polymorphism and fixation.”

The “classical” school on new mutations

New mutations are bad

The “classical” school on the wild type allele

The wild type allele is always the best allele

The “classical” school on the effect of selection on variation

Selection removes variation

The “classical” school on new mutations and old wild-types

New mutations can enter populations to replace old wild-types

The “balance” school on new alleles

Most alleles can be beneficial

The “balance” school on fitness of mutations

Mutations can have varying fitness depending on the environment

The “balance” school on selection

Selection may “want” to preserve multiple alleles to deal with several challenges

A researcher studies a plant species distribution across a wide climate gradient. Whole genome sequencing reveals that most loci show an excess of rare young variants, but a small subset of loci show long term intermediate frequency haplotypes shared across related species. Field experiments show that these balanced loci shift fitness effects across environments, with heterozygotes favored only in drought years.

Assuming these results are true, which interpretation best integrates these results into the classic versus balance school debate?

The pattern suggests that while classic forces like purifying selection dominate genome wide, the presence of environment conditional balancing selection at specific loci reveals that both schools capture important but incomplete aspects of natural variation

What percentage of the genome codes for functional loci, and what percentage is regulatory? (functional %; regulatory %). The percentages to choose from are: 1.5-2.0%, 0.5-1.5%, 5.0-2.0%, 1.5-2.5%

1.5%-2.0%; 5.0-2.0%; 1.5-2.0; 5.0-2.0

According to Kimura, at what level do the great majority of evolutionary changes occur?

Molecular level

Kimura: what causes changes at the molecular level?

Random drift of selectively neutral or nearly neutral mutants

What view does the neutral theory of molecular evolution build on?

The “classical” school view of “purifying selection”

Rate at which new mutations appear in a diploid organism

2(Neu)

Ne (effective population size)

Number of individuals contributing to the gene pool

What is Ne multiplied by for diploid organisms?

2

The average frequency of new mutations entering populations and the probability that a new mutation will eventually become fixed in the absence of selection is

1/(2Ne)

Rate of neutral evolution (why is the rate equal to the mutation rate)

u (because 1/(2Ne) x 2Ne(u) almost entirely cancel, leaving just u)

Rate of neutral evolution is equal to what?

u

What is u (neutral evolution)?

The probability that a particular gene copy mutates to a new allele in one generation; mutation rate

Kimura’s proposition, the expression above (1/(2Ne) x 2Ne(u) = u), shows the rate of neutral evolution equals the mutation rate because the probability of fixation of a new neutral mutation is one divided by two times the effective population size, while the number of new neutral mutations entering the population each generation is two times the effective population size times the mutation rate.

Which inference best reflects the deeper evolutionary meaning of this result, according to Kimura’s theory?

Neutral substitution rates remain constant across species regardless of differences in effective population size, implying that mutation rate, not population size, determines long term molecular change

What are the three steps for measuring DNA evolution?

Align sequences, determine length of sequences, count the number of differences

What does “aa/y” stand for?

Amino acids per year

What step must be completed for calculating divergence for a single lineage?

Dividing the total divergence by two (each lineage experiences half)

According to the neutral theory of molecular evolution, what are the majority of substitutions at the molecular level?

Neutral

True or False: according to the neutral theory of evolution, amino acid differences increase linearly with divergence time

True

True or False: constraint and purifying selection are important components of the neutral theory

True

What do patterns of molecular evolution reveal (important)?

Functional constraints

What do patterns of molecular evolution cause?

Different rates of evolution

If genes have different rates of evolution (which they do), then what does this reveal that genes also have?

Different constraints

What does neutral evolution say about the rates of evolution for different genes?

They are different

What does neutral evolution say about the rates of evolution across different species?

The rate of evolution is constant

Synonymous sites

Nucleotide differences between alternative codons

Nonsynonymous sites

Amino acids replacements sites (affects phenotype)

dN

Non-synonymous changes per non-synonymous site

dS

Synonymous changes per synonymous site

A gene can be either neutral, under positive selection, or under purifying selection. If dN/dS = 1, what does this mean?

Neutral

A gene can be either neutral, under positive selection, or under purifying selection. If dN/dS > 1, what does this mean?

Positive selection

A gene can be either neutral, under positive selection, or under purifying selection. If dN/dS < 1, what does this mean?

Purifying selection

BRCA 1 role

Providing DNA repair instructions

Why is BRCA 1 inconsistent with neutral expectations?

It exhibits variation in its dN/dS ratios across a phylogeny

What is the neutral prediction (DNA tests of neutrality)

Amino acid (non-synonymous) substitution rate (dN) should be lower than silent (synonymous) substitution rate (dS)

What is one region where amino acid mutations are favored?

Antigen recognition region

Why is dN/dS > 1 for antigen recognition regions?

To promote diversity and better recognition of foreign peptides

On average, how many nonsynonymous and synonymous sites do codons have?

2 nonsynonymous sites, 1 nonsynonymous site

dN/dS = 1. What selection is this gene under?

Neutral evolution

How common are deleterious mutations? Do they fix?

Common, don’t fix

How common are positive mutations? Do they fix?

Rare, fix

How common are neutral mutations? Do they fix?

Common, fix

According to the neutral theory of evolution, what type of mutation drives DNA variation across species?

Neutral mutations

You examine a protein coding gene across ten related species. The rate of synonymous mutation substitutions is much higher than the rate of nonsynonymous substitutions, but a few specific codons show elevated nonsynonymous change relative to the background.

Which interpretation best explains these patterns in terms of functional constraints and rates of evolution?

The lower nonsynonymous rate across most of the gene reveals strong functional constraint on amino acid changes, while the few codons with elevated nonsynonymous change suggest either relaxed constraint at these positions or episodes of positive selection

What are the arrangements of nucleic acids on a protein-coding gene called?

Introns and exons

Gene

Regions that are translated into proteins (exons) and regions that are not (introns)

How are exons organized?

Into codons

Codon

Triplet code; sequence of three consecutive nucleotides

Synonymous mutation

When the nucleotide sequence is changed but they still code for the same nucleic acid

Nonsynonymous mutation

When the nucleotide sequence is changed and they code for a different nucleic acid

Synonymous mutations do not have the capacity to alter splicing efficiency, and on average, they behave neutrally. As far as selection is concerned, these mutations don’t happen. What does this mean for the rate of divergence for synonymous mutations?

The rate is 1 to 1

Does natural selection “see” synonymous or nonsynonymous mutations?

Nonsynonymous mutations

What prevents the accumulation of nonsynonymous mutations (the line is closer to 0)?

Selection

What types of selection target nonsynonymous mutations?

Purifying selection and (more rarely) positive selection

True or False: most genes tolerate many nonsynonymous mutations

False

Generally speaking, does a gene have more nonsynonymous or synonymous mutations?

Synonymous mutations

True or False: genetic response are the only tool in an organism’s toolbox for dealing with stressors

False

Predictability

Physiological tools that an organism has in order to sense future environmental change