They should all be periods
Poe, or more accurately the speaker, is posing that the bird is clumsy.
In general, it is "D. all of these" that should be considered when trying to discover the theme of a piece of literature, since pretty much any element can develop a theme.
The changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations, caused by the alteration of single base units in DNA, or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes.