Question 1

Which of the following best explains why gene trees may not always match species trees, as illustrated in the coalescence diagrams?

Accepted Answer

Incomplete lineage sorting can cause gene trees to differ from species trees.

Question 2

According to the Hasegawa model of nucleotide transition, which type of nucleotide substitution is more likely?

Accepted Answer

Transitions (purine to purine or pyrimidine to pyrimidine) are more likely than transversions.

Question 3

Which of the following is a purine base found in DNA?

Accepted Answer

Adenine

Question 4

What is a major biological insight gained from reconstructing evolutionary trees using Maximum Likelihood and Bayesian Inference?

Accepted Answer

They provide more accurate reconstructions by accounting for nucleotide transition probabilities.

Question 5

Based on the genome size and protein-coding gene number plots, which statement best describes the difference between bacteria and eukaryotes?

Accepted Answer

Bacteria have a linear relationship between genome size and number of protein-coding genes, while eukaryotes do not.

Question 6

Which of the following best describes the evolutionary significance of non-coding DNA in eukaryotes?

Accepted Answer

Eukaryotes tend to accumulate more non-coding sequences, which can play regulatory and structural roles.

Question 7

A researcher is comparing the BRCA1 gene tree to the mammalian species tree. What might she conclude if the gene tree does not match the species tree?

Accepted Answer

Incomplete lineage sorting or gene duplication/loss events may have occurred.

Question 8

Which of the following is a pyrimidine base found in both DNA and RNA?

Accepted Answer

Cytosine

Question 9

If a mutation changes a thymine (T) to a cytosine (C) in a DNA sequence, what type of mutation has occurred?

Accepted Answer

A transition

Question 10

Which of the following best explains why phylogenetic trees are important in clinical research, such as tracking the origins of HIV?

Accepted Answer

They can reveal the evolutionary relationships and transmission pathways of pathogens.

Question 11

Given the following scenario: A gene tree shows that a human gene is more closely related to a gorilla gene than to a chimpanzee gene, even though humans and chimpanzees are more closely related species. What is the most likely explanation?

Accepted Answer

Incomplete lineage sorting.

Question 12

Which equation best represents the probability of a nucleotide transition according to the Hasegawa model?

Accepted Answer

$P_{transition} > P_{transversion}$

Question 13

Why is Maximum Likelihood preferred over simple parsimony in reconstructing evolutionary trees?

Accepted Answer

It incorporates models of sequence evolution, such as transition/transversion rates.

Question 14

Which of the following statements about the accumulation of non-coding DNA is correct?

Accepted Answer

Eukaryotes tend to accumulate more non-coding DNA, leading to larger genome sizes.

Question 15

A scientist is using Bayesian inference to reconstruct a phylogenetic tree. What is a key advantage of this method?

Accepted Answer

It allows the incorporation of prior knowledge and provides probabilities for different trees.

Question 16

Which of the following best describes a transition mutation?

Accepted Answer

A change from one purine to another purine, or one pyrimidine to another pyrimidine.

Question 17

Which of the following is NOT a pyrimidine base?

Accepted Answer

Adenine

Question 18

If a eukaryotic organism has a genome size of 3,000 Mb but only 25,000 protein-coding genes, what does this suggest about its genome?

Accepted Answer

It contains a large amount of non-coding DNA.

Question 19

Which of the following scenarios would most likely result in a gene tree that does NOT match the species tree?

Accepted Answer

A recent gene duplication event followed by differential gene loss.

Gene Evolution and Phylogenetic Inference in Biological Evolution

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