“covered by” vs. “covered with”

I found this sentence in some book:

Imagine a young child who already knows that creatures that live in water are fish, they have gills, and their skin is covered by scales.

Saying “their skin is covered by scales” sounds so strange to me. Why isn’t it “their skin is covered with scales”? Which version is better, and why?

Solution 1:

with: characterized or distinguished by; having as a possession, attribute, accouterment; a person with brown hair.

by: I can find nothing comparable. Over the surface of, through the medium of, along, or using as a route: He came by the highway. She arrived by air.

This surprises me as much as it does you.

Covered by/with was helpful.

When referring to a substance that sticks to another, use in or with: covered with blood

Use covered with to indicate an unusual amount of something on top of something else; use covered by to connote a covering so dense that the object being covered is completely obscured from view:

• The mountain was covered with fog.
• The mountain was covered by fog.

It appears that both by and with can be used in your sentence, the favorite being with by a margin.

Solution 2:

In that sentence, I would prefer covered with scales. However, I believe both are technically correct.

It may be only a stylistic preference, but here's the semantic difference as I see it:

covered by seems more suitable when there is something over top of another thing - a bed covered by a blanket, saucepans covered by lids.

covered with seems more suitable when there is something making up an attribute that is less readily removable, such as a ring covered with diamonds or a bird covered with feathers.

The distinguishing factor is that 'covered with' implies that the covering object is part of the covered object.

Solution 3:

"Covered with" vs. "covered in" vs. "covered by".
"Covered by"is more apt than "covered with"in this context.
"Covered by" highlights that the scales are more readily removable in comparison to other species covered with scales. Furthermore.. In Wikipedia,articles relating to scales of snake,reptiles;there is usage of 'with scales' but article on fish scales uses 'by scales'.

I have a conjecture, this is related to biology(more specifically ichthyology i.e study of fishes) and sometimes taking only the English point of view is not correct approach.