Are mutations a source of genetic variation?

Question

Here is a question from the book SAT II Success Biology E/M (where the SAT is the exam taken by the American high school students):

Which of the following statements is true about mutations?
(A) Rates tend to be very high in most populations.
(B) generally lethal
(C) irreversible
(D) Only certain gene locations are affected.
(E) source of genetic variation

In my opinion, we can definitely eliminate A, B, and D.
Then, I struggle between C and E since I think mutations are definitely a source of genetic variation but are as well generally irreversible (I've found evidence on different websites, including this http://hawaiireedlab.com/wpress/?p=154 where the author writes that only some mutations are reversible).
In the end, I think I should have probably gone with E because C can be seen as having some exceptions.
Then, here is the book explanation for this question:

The correct answer is (C). These recent conclusions about mutations—recall that Darwin did not know of mutations—are all the reverse of those listed in the choices, with the exception of choice (C), the correct answer. Rates, in fact, tend to be below in populations, mutations are generally not lethal, any gene location can be affected, and they are felt to be the source of genetic variation. Darwin felt over-production of offspring was the source of potential variation.

The answer is C here. However, I didn't particularly understand why E wasn't considered a correct answer.
Could you please explain why C, and not E, is correct?

Answer 1

Going through the possible answers

(A) Rates tend to be very high in most populations.

This is a very unclear statement. What does "high" mean? In humans, the average mutation rate per reproduction per nucleotide is of the order of $10^{-8}$ (Rahbari et al., 2016) (hence of the order of 10 - 100 mutations for the whole genome). Whether someone wants to call that high or low is up to this person original intuition.

(B) generally lethal

No, that's wrong (Robert et al., 2018)

(C) irreversible

It is a little unclear. By "irreversible", do they mean that the function of the gene (or of any other functional element in the genome) cannot be restored or do they mean that a specific mutation cannot be exactly undone by a future mutation. In both cases, however, it would be wrong!

Mutations that restore the function of a gene (or any other genomic functional element) are called reverse mutations (aka. suppressor mutations; I personally don't know of any difference between the concepts of reverse mutation and suppressor mutation). Most reverse mutations are likely to act via a second mutation that restores the function of the gene rather than undoing the previous mutation. It does not mean however that it is impossible a mutation that perfectly undoes a previous mutation. Consider a substitution inverting A into T. A reverse mutation could do just the opposite.

(D) Only certain gene locations are affected.

Mutation rate varies throughout the genome but all of the genome is subject to some non-zero mutation rate.

(E) source of genetic variation

Yes, mutations are the ultimate source of genetic variation in populations, while genetic drift and directional selection removes variation.

As other users have highlighted in their answers, many mutations (incl. synonymous mutations but not only and soma mutations) do not bring up any the underlying genetic variance of phenotypic traits. These details are however mainly irrelevant; what matters is that it still remain true that (some) mutations increase genetic variance.

We could also add the complication as to wonder whether by "genetic variance", they meant "genetic variance underlying phenotypic variance" (which is its standard usage) or "genetic variance where one allele is given an arbitrary value and another (problem arising for loci with more than 2 alleles segregating). More information about the terminology and the math when it comes to quantifying genetic variance in the post Why is a heritability coefficient not an index of how “genetic” something is?

What I would have answered

The correct answer is (C). These recent conclusions about mutations—recall that Darwin did not know of mutations—are all the reverse of those listed in the choices, with the exception of choice (C), the correct answer. Rates, in fact, tend to be below in populations, mutations are generally not lethal, any gene location can be affected, and they are felt to be the source of genetic variation. Darwin felt over-production of offspring was the source of potential variation.

I disagree. To me, B and D are wrong, A is unclear, C is slightly unclear but wrong in both interpretations I can think of and E is correct. I would have answered E.

About the justification given

Rates, in fact, tend to be below in populations [..]

This piece of the sentence is not even grammatically correct. Below what? It highlights that A is unclear.

they are felt to be the source of genetic variation

The term "felt" is poorly chosen here IMO, but this piece of the sentence seems to rather give credit to answer E. I think, whoever wrote this answer mistakenly wrote C instead of E

Darwin felt over-production of offspring was the source of potential variation.

Really, who cares about Darwin thoughts on the subject here?! But in any case, this sounds like a misrepresentation of Darwin's ideas. More info can be found in Charlesworth and Charlesworth (2009) and also maybe this post

Answer 2

Mutations are one of multiple reasons for genetic variation, hence phenotypic variation. By definition, mutations are alterations of genetic code and unpredictable changes in nucleotide sequences {in nucleic acids(level)}.

So yes, mutations are responsible for variation, but not all the time, and not all mutations actually result in variation. Silent mutations are neither harmful nor beneficial. They do not improve organisms by any means. On the other hand, nonsense mutations are readily harmful and can result in death.

Other sources of variation include:

1. Independent assortment of chromosomes (meiotic division), as per Mendel's first law of independent assortment.

2. crossing over of bivalents

3. environmental changes, which subsequently lead to beneficial mutations.

Answer 3

It depends. A mutation in somatic cells is not a source of genetic variation because they are not inherited by offspring. But mutations in the sex cells are a source of variation. Your answer key does not appear to be sure of the correct answer because it says the reverse of every answer but C is true of mutations but then agrees with answer E. Also unless part of the question is missing, what Darwin thought is not really relevant. Also, more offspring means more chances of offspring carrying a mutation.

Answer 4

That question was graded incorrectly.

(A) Rates tend to be very high in most populations.

That's a badly designed answer. What populations are they discussing? In lower-order life forms (viruses and bacteria for instance), mutations are the main source of genetic variation and occur often, which they thrive on (often to our detriment). Complex life forms, especially those with long life-cycles, tend to have much lower rates of mutations.

(B) generally lethal

No debate here, obviously wrong.

(C) irreversible

Wrong wrong wrong. No idea what the grader was thinking when this was picked as the "correct" answer. There's always the possibility that a base could change in a species, and later be flipped back to the wild-type in a distant descendant - by random chance alone.

(D) Only certain gene locations are affected.

No debate here, obviously wrong. Mutations can happen anywhere in the genome.

(E) source of genetic variation

This should be the correct answer. If you start with a bunch of bacteria (same species, no plasmid transfer or other shenanigans allowed), obviously they can only gain new alleles and functionality via mutations.

Now if you consider the recombination and meiosis approach: you still need mutations to produce varying alleles that can be mixed and matched. If every human had the exact same* genome (for purposes of simplicity assume there's only 1 possible X chromosome and 1 possible Y chromosome across the species, females get 2 copies of the exact same X chromosome while males get 1 each of X and Y), you can recombine all you like at each generation and everyone ends up being a genetic carbon copy of each other (all differences at adulthood would be purely chalked up to nurture as opposed to nature).