A study by the Ocean Wildlife Campaign urged states to undertake a num

This sentence has parallelism error. The list is not parallel. Since 3rd element of the list is not underlined, elements 1 and 2 should follow the structure of element 3. Thus, all elements should be verb-ing forms as follows:

1) establishing size limits for shark catches
2) closing state waters for shark fishing during pupping season
3) requiring commercial fishers to have federal shark permits
This sentence also has modifier error. The modifier “which includes…” modifies the closest noun or noun phrase. In this sentence, it does not make sense for the “which modifier” providing list of remedies to modify either the noun phrase “decline in shark population” or the noun “the shark population”.

In A and B, the singular verb includes implies that the pronoun which refers either to the singular noun decline or to the singular noun population, but neither the decline nor the population is including the list of remedies that follows. Eliminate A and B.
C and E lack parallelism: the establishment of (the + noun + preposition), the establishing of (the + gerund + preposition), and the closing of (the + gerund + preposition) are not parallel with requiring commercial fishers (gerund + direct object). Eliminate C and E.
The correct answer is D.
D is correct primarily because A, B, C and E each have a clear error.
In D, including and establishing are performing different functions.

Generally, when a present participle (such as including) is preceded by a comma, it refers to the subject of the previous clause. It could be argued that including refers to the study: the study is including -- among the remedies that it recommends -- establishing size limits, closing state waters, and requiring fishers to have permits.
Establishing is not a present participle but a gerund (a verb functioning as a noun). Establishing size limits is one of the remedies that the study is including.