Should my citation style exactly match the original title?
All-caps are just a typographical decoration or emphasis of the whole title. You do not need to keep them for the same reason you do not need to use the same font and font size (as used for the original paper title) when citing. Something similar holds for title case (i.e., capitalising the first letter of all words except of, the an similar) – it’s just a typographical choice and does not affect the content.

Italics (unless they apply to the whole title) on the other hand serve some non-decorative purpose. In your examples, they allow you to directly see where a potentially complicated species name starts and ends. In other cases they may signal that a word is standing for the word itself, such as:


  On the evolution of the in Old English


In those cases, keeping the italics may really ease reading and thus I would personally opt for it in general. Keep in mind that the italics of italics are upright if you choose to italicise titles in general in your style, and you would e.g. get¹:


  Aaron A. Aaronson, On the evolution of the in Old English, Journal of Definite Articles (2015)


Finally note that you may have no choice regarding this anyway, as your supervisor or the journal you are submitting to prescribe some citation style.




¹ LaTeX does this for you automatically if you use \emph instead of \textit or similar to italicise.