Question 1

The counterpart to use of mtDNA to reconstruct maternal lineages is the use of chloroplast DNA to reconstruct paternal lineages.

Accepted Answer

Chloroplast DNA is typically inherited maternally in most plants, similar to mitochondrial DNA in animals, and is not used to reconstruct paternal lineages.

Question 2

Maximum confidence is a procedure for reconstructing phylogenetic trees invoking the fewest number of steps or mutations.

Accepted Answer

Maximum confidence is a procedure for reconstructing phylogenetic trees that maximizes the probability that the observed data is consistent with the proposed tree. It does not necessarily invoke the fewest number of steps or mutations.

Question 3

Nuclear DNA sequence is more abundant than mtDNA and is therefore preferable for use in reconstructing events like domestication or human migration.

Accepted Answer

The answer of Nuclear DNA sequence is more abundant than...

Question 4

The five-kingdom taxonomic system is not especially old; for a long time, three kingdoms were recognized, then four, then (as of 1959) five. In light of Carl Woese's discovery of deep genetic divergence within the Kingdom Monera, why do you think he did not simply suggest adding a sixth kingdom rather than the supra-kingdom classification of domains?

Accepted Answer

The answer of The five-kingdom taxonomic system is not especially...

Question 5

Pseudogenes tend to have lower average substitution rates than functional genes.

Accepted Answer

Pseudogenes, which are non-functional segments of DNA that resemble functional genes, tend to have higher average substitution rates than functional genes because they are not subject to natural selection to maintain their sequence, allowing mutations to accumulate more rapidly.

Question 6

Many viruses are helped along in generating antibody-evading capsid protein variations by replication error.

Accepted Answer

Replication errors can result in mutations that lead to changes in the capsid protein of a virus, which can help the virus evade antibodies.

Question 7

In a molecular-evolutionary analysis, you estimate the number of base substitutions per site (K) at 0.82. Given an estimated divergence time (T) of 10 million years based on the fossil record, what is the substitution rate (r)?

Accepted Answer

The answer of In a molecular-evolutionary analysis, you estimate the...

Question 8

Distinguish between a gene tree and a species tree.

Accepted Answer

The answer of Distinguish between a gene tree and a...

Question 9

The "three domain" classification advocated by Carl Woese and his colleagues is based on molecular-evolutionary data. What are the domains and the arguments for formally recognizing them in classification?

Accepted Answer

The answer of The "three domain" classification advocated by Carl...

Question 10

Define codon bias. If synonymous substitutions give the same amino acid, why should there be a bias in which codons are used to encode that amino acid?

Accepted Answer

The answer of Define codon bias. If synonymous substitutions give...

Question 11

High molecular similarity reflects evolutionary relatedness.

Accepted Answer

The answer of High molecular similarity reflects evolutionary relatedness....

Question 12

The McDonald-Kreitman test is an important tool in molecular evolutionary analysis. What is this test, and what kinds of insights can it provide?

Accepted Answer

The answer of The McDonald-Kreitman test is an important tool...

Question 13

What is the rationale behind the bootstrap procedure, where trees are repeatedly reconstructed following resampling with replacement of the original data?

Accepted Answer

The answer of What is the rationale behind the bootstrap...

Question 14

Of the six codons that encode the amino acid leucine in yeast, approximately 80 percent of them are UUG. This is an example of codon bias.

Accepted Answer

Codon bias refers to the preference for certain codons over others that encode the same amino acid. In yeast, if UUG is used 80% of the time for leucine, it indicates a bias towards this codon.

Question 15

It is not unusual for a phylogeny reconstruction to result in more than one equally robust phylogenetic trees that differ in their branching patterns. How can this be the case if evolution only took one true pathway?

Accepted Answer

The answer of It is not unusual for a phylogeny...

Question 16

One problem commonly experienced in phylogeny reconstruction arises when two or more of the groups being compared have accumulated far more genetic changes (mutations) than the others in the comparison. This situation often results in a phenomenon known as "long branch attraction," where the highly mutated lineages end up grouping together in a phylogenetic analysis even if in fact they are distantly related. What do you think causes long branch attraction? How might it be compensated for?

Accepted Answer

The answer of One problem commonly experienced in phylogeny reconstruction...

Question 17

In the following alignment of 12 base pairs, which sites are phylogenetically informative? Sequence 1 ATTGGTATAAAA Sequence 2 ATTAGTATAAAA Sequence 3 ATTGGTATCAAA Sequence 4 ATTAGTATCAAA

Accepted Answer

The answer of In the following alignment of 12 base...

Question 18

What are some weaknesses of (1) parsimony methods, and (2) distance matrix methods of phylogeny reconstruction.

Accepted Answer

The answer of What are some weaknesses of (1) parsimony...

Question 19

Genetic distance refers to the proportion of dissimilar nucleotides between two homologous sequences.

Accepted Answer

Genetic distance is indeed the proportion of dissimilar nucleotides between two homologous sequences.

Question 20

The noncoding 5' flanking region of genes is more constrained by selection than the noncoding 3' flanking region.

Accepted Answer

The 5' flanking region contains important regulatory sequences such as the promoter, enhancers, and silencers, which are crucial for the initiation of transcription. These sequences are highly conserved and essential for proper gene expression. In contrast, the 3' flanking region contains elements that affect mRNA stability and processing, but they are generally less conserved than the 5' flanking region. Therefore, the 5' flanking region is more constrained by selection than the 3' flanking region.

Quiz 2: Variations in Chromosome Structure and Number