Exam 3

Question 1

What does it mean that SARS-CoV-2 is evolving to be a better human pathogen?

Answer 1

It’s increasing its transmissibility, measured by R₀.

Question 2

What pattern have we seen in SARS-CoV-2 variants over time?

Answer 2

New variants increase in frequency while older ones disappear.

Question 3

What is competition in ecology?

Answer 3

The struggle between organisms or genotypes for limited resources.

Question 4

How do SARS-CoV-2 variants compete?

Answer 4

Variants with higher transmissibility outcompete others, increasing in frequency.

Question 5

How do mutations drive diversification in viruses?

Answer 5

They enable specialization on new hosts or new serotypes, preventing cross-competition.

Question 6

Why don’t R₀-increasing mutations in one Dengue serotype outcompete others?

Answer 6

Because different serotypes are immunologically distinct and do not compete directly.

Question 7

What are the three assumptions of a phylogenetic tree?

Answer 7

Common ancestry, changes within lineages, and splitting of lineages.

Question 8

What is the continuity of life between any two extant organisms?

Answer 8

It traces through generations back to a common ancestor.

Question 9

How can you determine the order of trait evolution without fossils?

Answer 9

Use phylogenetic trees and compare with outgroups.

Question 10

What gene is used to build a universal tree of life?

Answer 10

A universal gene found across all organisms (e.g., rRNA genes).

Question 11

What are the three domains of life?

Answer 11

Bacteria, Archaea, and Eukarya.

Question 12

What evidence shows West Nile Virus came to the New World from the Middle East?

Answer 12

Phylogenetic similarity between Middle Eastern and New World strains

This indicates a close genetic relationship suggesting a common origin.

Question 13

How many times did HIV-1 spill over from chimpanzees?

Answer 13

Three or four times, all in southeastern Cameroon

This spillover is crucial for understanding the origins of the HIV epidemic in humans.

Question 14

What shows African wild primates harbor diverse SIVs?

Answer 14

Genetic diversity of SIVs found in different primates

This diversity highlights the evolutionary adaptations of SIVs in various primate species.

Question 15

What is the root-to-tip approach to dating viral origins?

Answer 15

Plotting genetic distance from the root against sampling time to estimate rate and time.

Question 16

What is needed for the genealogical approach to date viruses?

Answer 16

A well-sampled phylogeny and accurate branch lengths.

Question 17

How do we identify convergent evolution on a tree?

Answer 17

Similar traits evolve independently in different lineages.

Question 18

Why is DNA data better for phylogeny than morphology?

Answer 18

DNA has a universal scale and is less influenced by convergent evolution.

Question 19

What does the Neutral Theory say about DNA convergence?

Answer 19

Neutral mutations vastly outnumber adaptive ones, so convergence has minimal effect.

Question 20

What’s the bacterial origin of photosynthesis in plants?

Answer 20

Endosymbiosis of cyanobacteria-like ancestors.

Question 21

What bacterial roles are vital in ecosystems?

Answer 21

Nitrogen fixation, mineral cycling, and primary production.

Question 22

How do we interpret ‘when you were a tadpole and I was a fish…’?

Answer 22

Most of life’s history is bacterial; that poem misrepresents evolutionary timescales.

Question 23

What is homology?

Answer 23

Similarity due to shared ancestry.

Question 24

How do homologous structures support common ancestry?

Answer 24

They show underlying similarity despite different functions.

Question 25

What’s an example of evolutionary transition from fossils?

Answer 25

Tiktaalik linking fish to tetrapods; whales from artiodactyls.

Question 26

What three conditions are required for natural selection?

Answer 26

Variation, heritability, and differential fitness.

Question 27

What is fitness?

Answer 27

An organism’s reproductive success.

Question 28

What does the equation R = h²S predict?

Answer 28

The response to selection in a trait.

Question 29

What is self-starting evolution?

Answer 29

Evolution driven by internal changes, not environment. ## Footnote This concept highlights the role of intrinsic factors in the evolutionary process.

Question 30

How could early flight have evolved?

Answer 30

Incremental fitness advantages in gliding/leaping. ## Footnote This suggests that small adaptations over time can lead to significant evolutionary developments.

Question 31

What are the five forces of evolution?

Answer 31

Natural selection, genetic drift, mutation, migration, non-random mating. ## Footnote These forces interact to shape the genetic structure of populations over time.

Question 32

What is genetic drift?

Answer 32

Random changes in allele frequencies, especially in small populations. ## Footnote Genetic drift can lead to the loss of genetic variation and can cause populations to diverge.

Question 33

How does mutation affect evolution?

Answer 33

It provides new variation, the raw material for selection. ## Footnote Mutations can be beneficial, neutral, or harmful; beneficial mutations are more likely to be preserved through natural selection.

Question 34

How can migration help or hinder adaptation?

Answer 34

It can introduce beneficial alleles or swamp local adaptation. ## Footnote Migration can enhance genetic diversity but may also disrupt local adaptations.

Question 35

Fill in the blank: _______ is a force of evolution that results from random changes in allele frequencies.

Answer 35

Genetic drift ## Footnote Genetic drift is particularly significant in small populations.

Question 36

True or False: Mutation is the only source of new genetic variation in a population.

Answer 36

False ## Footnote Migration also contributes to genetic variation by introducing new alleles.

Question 37

What role does natural selection play in evolution?

Answer 37

It favors individuals with advantageous traits, leading to their increased representation in the population over time. ## Footnote Natural selection is a key mechanism that drives adaptation to the environment.

Question 38

List the five forces of evolution.

Answer 38

* Natural selection * Genetic drift * Mutation * Migration * Non-random mating ## Footnote Each force has a unique impact on the evolutionary process.

Question 39

What are the Hardy-Weinberg assumptions?

Answer 39

No mutation, migration, selection, or drift; random mating.

Question 40

How do you calculate allele frequencies from genotype frequencies?

Answer 40

Use p = freq(AA) + ½ freq(Aa), q = 1 - p.

Question 41

Are viruses alive?

Answer 41

If life is defined by the ability to evolve by natural selection, then yes. ## Footnote This definition of life is debated among scientists.

Question 42

Why is eradicating SARS-CoV-2 difficult?

Answer 42

Asymptomatic spread, vaccine hesitancy, and possible spillbacks from animals. ## Footnote These factors contribute to the ongoing transmission of the virus.

Question 43

What is Rt and why is it key to eradication?

Answer 43

Rt is the effective reproduction number; keeping it <1 leads to eradication. ## Footnote This indicates that each infected person must infect less than one other person on average.