Nucleotide Substitutions in Human-Chimp DNA Sequences

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What is the main difference between a synonymous and a non-synonymous substitution in a protein-coding sequence?

Synonymous substitutions are more likely to be under positive selection than non-synonymous substitutions.

Synonymous substitutions do not change the amino acid sequence, while non-synonymous substitutions do. (correct)

Synonymous substitutions are more common than non-synonymous substitutions.

Synonymous substitutions change the amino acid sequence, while non-synonymous substitutions do not.

According to the neutral theory of molecular evolution, what explains the observation that molecular clocks are approximately linear?

The majority of substitutions at the molecular level are neutral and not subject to strong selection. (correct)

The elimination of old alleles and the substitution of new alleles requires lots of genetic deaths, leading to a linear rate of substitution.

Positive selection drives the rapid fixation of new alleles, leading to a linear rate of substitution.

Different proteins evolve at different rates due to varying levels of functional constraint.

How do synonymous substitutions relate to the use of molecular clocks?

Synonymous substitutions are not useful for molecular clocks because they do not alter the amino acid sequence.

Synonymous substitutions are too rare to be useful for molecular clocks, which rely on the accumulation of substitutions over time.

Synonymous substitutions are under strong positive selection and therefore do not provide a reliable molecular clock.

Synonymous substitutions are the best molecular clock to normalize rates of substitution, as they typically diverge at rates similar to non-functional sequences. (correct)

What is the main difference between measuring selection on protein-coding genes versus measuring selection on synonymous and non-synonymous substitutions?

Measuring selection on protein-coding genes provides information about selection 'for' particular amino acid changes, while synonymous and non-synonymous substitutions provide information about selection 'against' particular amino acid changes. Signup and view all the answers

Which of the following is an example of a 'living fossil' that exhibits slow rates of morphological change?

Horseshoe crab Signup and view all the answers

What is the proposed explanation for the slow rate of morphological change observed in the horseshoe crab, a 'living fossil'?

The horseshoe crab has lived in a relatively stable near-shore environment, which has allowed it to maintain its ancestral morphology over long periods of time. Signup and view all the answers

What is the formula for measuring DNA Evolution by determining the divergence between sequences?

Divergence = – (number of differences) / (length of sequence) Signup and view all the answers

Which type of substitution occurs when a nucleotide change does not result in an amino acid change in the protein product?

Synonymous substitution Signup and view all the answers

What does a substitution rate measure in terms of DNA evolution?

Divergence between sequences and common ancestor Signup and view all the answers

How is the rate of neutral evolution calculated?

Rate of neutral evolution = 2Nu x 1/2N = u Signup and view all the answers

When applying the molecular clock, what does a negative sequence divergence value indicate?

The sequences are very similar Signup and view all the answers

In measuring selection on genes, what does a higher ratio of non-synonymous substitutions to synonymous substitutions imply?

Stronger positive selection on genes Signup and view all the answers

What is the assumption made about nucleotide frequencies at equilibrium?

Nucleotides have equal frequency of 0.25 Signup and view all the answers

Which of the following is NOT an assumption of common nucleotide substitution models?

Sequence changes are influenced by selection pressures Signup and view all the answers

What is the process of gene conversion, as described in the text?

The process by which one DNA sequence replaces a homologous sequence, resulting in identical sequences Signup and view all the answers

Which of the following statements about molecular clocks is TRUE?

Deviations from a molecular clock indicate slowing or acceleration of evolutionary change Signup and view all the answers

What is the difference between synonymous and non-synonymous substitutions?

Synonymous substitutions do not change the amino acid sequence, while non-synonymous substitutions do Signup and view all the answers

What factors can influence the rate of evolution in different genes or genomic regions?

All of the above Signup and view all the answers