"Although the cacao plant probably originated in the upper Amazon region, the first cultivation for its seeds and pulp appears to have begun (E) in Mexico and Central America."
The several elements you need to pay attention to in this sentence are:
- the meaning: the idea which must be conveyed is that cacao cultivation (for seeds & pulp) seems to have started in Central America, even though the plant itself is believed to come from further south.
- the syntax and grammar: "the first cultivation" is the subject of the verb "appears to have begun," that is why the verb is conjugated at the 3rd-person singular.