Deck 15: Phylogenomics and the Molecular Basis of Adaptation

Question 1

Why have gene families evolved? Choose the most accurate answer for gene families in general.

A) Although in some cases researchers have inferred that gene families are adaptive, gene families may also evolve due to genetic drift.
B) Having multiple copies of a gene can increase transcription and translation of the gene, so when increased transcription is adaptive, then natural selection favors genes duplicating into gene families.
C) Gene families are adaptive because each gene can produce a slightly different protein, which allows for diverse functions that are favored by natural selection.
D) Gene families evolve because of the activity of mobile genetic elements, which cause repeated gene duplication events.

Answer 1

A

Question 2

What is a key difference between prokaryote genomes and the genomes of multicellular eukaryotes?

A) Multicellular eukaryote genomes have a greater number of protein-coding genes than prokaryote genomes.
B) Prokaryote genomes have more introns than multicellular eukaryote genomes.
C) Multicellular eukaryote genomes have larger intergenic regions than prokaryote genomes.
D) There are more mobile genetic elements in prokaryote genomes than in multicellular eukaryote genomes.

Answer 2

C

Question 3

What processes have been hypothesized to influence the evolution of mutation rates?

A) natural selection only
B) genetic drift only
C) both natural selection and genetic drift, acting in the same direction to either increase or decrease mutation rates
D) both natural selection and genetic drift, acting in opposing directions: one process favors increasing mutation rates and the other favors decreasing mutation rates

Answer 3

D

Question 4

How does a gene tree differ from a species tree?

A) A gene tree shows the relationships among all the genes in a species genome, whereas a species tree shows the relationships among species.
B) A gene tree is based on gene sequences, whereas a species tree is based on morphological features of each species.
C) A gene tree is a phylogeny of individual genes, and can include multiple genes from a single species and/or samples of the same gene from multiple species; in a species tree, each species is represented by only a single branch.
D) A gene tree is a subcategory of species tree, in which the data used to create the tree comes from gene sequences.

Question 5

What are mobile genetic elements,and how do they affect host organisms?

Question 6

Laboratory experiments about bacterial mutation rates have demonstrated which of the following?

A) Bacterial mutation rates rarely evolve in short-term laboratory experiments; they are a relatively fixed feature of a species biology.
B) In short-term laboratory experiments, bacterial mutation rates often evolve to be higher because higher mutation rates result in higher fitness.
C) In short-term laboratory experiments, bacterial mutation rates often evolve to be lower because mutations are typically deleterious for organisms.
D) Depending on the experiment, bacterial mutation rates sometimes evolve to higher rates, and other times evolve to lower rates.

Question 7

Which of the following is the most accurate statement about the relationship between gene duplication and mobile genetic elements?

A) The most common way that genes are duplicated is by the activity of mobile genetic elements.
B) A duplicated gene is an example of one kind of mobile genetic element.
C) Mobile genetic elements can cause gene duplication, but most gene duplication events are caused by other mechanisms.
D) Gene duplication is one kind of genomic defense against the spread of mobile genetic elements.

Question 8

Briefly describe three key differences between prokaryote genomes and the genomes of multicellular eukaryotes.

Question 9

Under most models for the preservation of duplicated genes that eventually perform new functions,what is the proposed order of events and evolutionary reasoning behind them?

A) After a gene is duplicated, it must rise to high frequency in a population due to drift; only after it has risen to high frequency will it then be likely to evolve to perform a new function favored by natural selection.
B) After a gene is duplicated, one of the copies must evolve to perform a new function that increases an organism's fitness; only after the new function evolves will the duplicated gene rise in frequency within the population due to natural selection.
C) After a gene is duplicated, it will typically be favored by natural selection even before it evolves to perform a new function, because having duplicate gene copies provides beneficial redundancy within genomes. Therefore, duplicate copies rise to high frequency in a population due to natural selection, and later a new function can evolve that is also favored by natural selection.
D) Duplicated genes usually differ in function immediately after duplication, because gene duplication is an imperfect process and mutations are typically introduced during duplication. If the duplicate copy happens to perform a new function that benefits an organism, it rises in frequency in the population due to natural selection.

Question 10

What is the relationship between mobile genetic elements and DNA methylation?

A) DNA methylation is considered to be a defense against the spread of mobile genetic elements because it prevents transcription.
B) DNA methylation is reduced in regions of the genome associated with mobile genetic elements because methylation only targets protein-coding genes.
C) DNA methylation prevents RNA interference and therefore allows mobile genetic elements to spread.
D) DNA methylation is a form of post-transcriptional silencing of mobile genetic elements.

Question 11

Methylation and RNA interference are both involved in regulating mobile genetic elements.Which of the following statements is TRUE?

A) Methylation is a form of post-transcriptional silencing, whereas RNA interference is a form of pre-transcriptional silencing.
B) Both are examples of post-transcriptional silencing.
C) Both are examples of pre-transcriptional silencing.
D) RNA interference is a form of post-transcriptional silencing, whereas methylation is a form of pre-transcriptional silencing.

Question 12

Which statement accurately describes a relationship between mutation rate and genome size?

A) Larger genomes have higher mutation rates across all domains of life.
B) Larger genomes have lower mutation rates across all domains of life.
C) Mutation rate increases with genome size in multicellular organisms.
D) Mutation rate increases with genome size in unicellular organisms.

Question 13

Which of the following most accurately describes the preservation of duplicate genes via the subfunctionalization model?

A) The ancestral gene performs two different functions, and eventually the two duplicate copies evolve so that one copy performs one function, and the other copy performs the other function; both copies are therefore required for the organism to have optimal fitness.
B) In order to be favored by natural selection and therefore to increase in frequency, the duplicated copies must evolve so that together they perform the original gene's functions better than the original gene, giving organisms with subfunctionalized genes a fitness advantage.
C) Subfunctionalization is most commonly a defense against mobile genetic elements. Because subfunctionalized genes separate two functions from an ancestral gene into two separate genes, a mobile genetic element insertion can damage only one of the two functions, not both; therefore, subfunctionalization is favored by natural selection in genomes with a high load of mobile genetic elements.
D) All that matters for the subfunctionalization model is that together the duplicated genes perform the original gene's function(s) the same or better; even if one gene copy becomes nonfunctional, this still counts as subfunctionalization so long as the other copy performs the original function.

Question 14

Briefly describe the relationship between DNA methylation,small RNAs (also known as RNA interference),and mobile genetic elements.

Question 15

Which of the following is a TRUE statement about the relationship between RNA interference and mobile genetic elements?

A) RNA interference is a mechanism that allows mobile genetic elements to move to new locations in a genome.
B) RNA interference is a laboratory method that researchers use to study how mobile genetic elements function.
C) RNA interference is a mechanism for silencing mobile genetic elements that exist in many kinds of organisms.
D) RNA interference does not have a known relationship with mobile genetic elements.

Question 16

What is meant by adaptation from standing genetic variation in natural populations?

A) A population adapts to an environmental change by the occurrence of a beneficial mutation in an individual that introduces genetic variation, which rises to high frequency in the population because it is favored by natural selection following the environmental change.
B) A population adapts to an environmental change by the rise to high frequency of an existing genetic variant that was already present in the population at low frequency before the environmental change.
C) Individuals with more variation present in their genomes are favored by natural selection following an environmental change, and the population adapts via an overall increase in genetic variation in the population because the most genetically variable individuals have highest fitness.
D) Genetic variation becomes costly for individuals following an environmental change, and the result is that overall genetic variation in a population decreases as the population adapts to the environmental change.

Question 17

Describe the general relationship between total genome size and the proportion of the genome that encodes mobile genetic elements for plants and animals.

Question 18

Immediately following a gene duplication event,what is the most likely evolutionary outcome for a duplicated gene?

A) Duplicated genes usually evolve to perform new functions that differ from their original function (called neofunctionalization), or both duplicate copies evolve via subfunctionalization.
B) Most gene duplication events are selectively neutral and therefore the duplicated gene usually spreads through the population. It can later evolve a new function or keep its original function.
C) Most gene duplication events are deleterious to an organism and therefore are lost due to natural selection.
D) Most gene duplication events are selectively neutral and are therefore lost due to drift.

Question 19

Which statement BEST describes the role and importance of mobile genetic elements in genomes?

A) Mobile genetic elements almost always have either neutral or deleterious consequences for their host.
B) Mobile genetic elements are largely beneficial to hosts because they introduce new phenotypic variation into a population via transposition and/or duplication of important genes.
C) Mobile genetic elements can have deleterious, neutral, OR beneficial consequences for the host organism, and all three kinds of outcomes are common.
D) Mobile genetic elements are especially important for plant genomes such as the tomato, but they are not present in most animal genomes.

Question 20

First,briefly describe the relationship between mutation rate and genome size for viruses and prokaryotes.Second,briefly describe the relationship between mutation rate and genome size for multicellular eukaryotes,if different from the first.

Question 21

Imagine you are studying an expanded gene family in a group of closely related species,and you would like to know whether the gene family expanded long ago in the common ancestor of all the species,or whether the gene family has expanded independently,and more recently,within some or all of the species.How would you use DNA sequences from the gene family in each species to test this? (Hint: Evolutionary trees are required.)

Question 22

Briefly describe the difference between adaptation from new mutation and adaptation from standing genetic variation in natural populations.

Question 23

Can mutation rates evolve in laboratory experiments? Briefly describe an experiment that researchers performed to investigate this,and state whether the mutation rate did evolve,and if so,whether it evolved to become higher or lower.

Question 24

Briefly describe the three phases included in most evolutionary models for the preservation of duplicate genes,and the evolutionary processes involved.

Question 25

The biologist Michael Lynch has a hypothesis about the role of effective population size in influencing the evolution mutation rates.Describe this hypothesis,with particular attention to the roles of natural selection and genetic drift,and how it can explain the pattern shown in the accompanying figure.

Question 26

Describe four possible fates of duplicated genes,and provide detail regarding the evolutionary hypotheses for how the four possible fates come about.

Question 27

Describe how mobile genetic organisms function,how they affect host organisms,and the mechanisms that host organisms possess to interact with mobile genetic elements.

Question 28

Briefly describe the escape from adaptive conflict hypothesis for the preservation of duplicate genes.

Question 29

Describe four major patterns in genome structure and function across all groups of organisms as they relate to overall genome size.

Question 30

How do researchers use gene trees,species trees,and rates of nonsynonymous versus synonymous nucleotide substitution,to explore the evolutionary history of gene families?