Finally, my Latin classes will pay off!
OK, this is gonna get a little confusing. There's Classical Latin, and there's Ecclesiastical Latin; pronunciations are a bit different in the two, and most modern users of Latin learned one or the other, so there'll be some disagreement there. Then there's a sort of informal scientific Latin pronunciation, which differs from both and is highly variable from country to country, field to field, and individual to individual. It's a real pain to try to keep up with. The best bet is to just hang out with workers in your field and pick up their pronunciations.
Classical Latin pronounces "-ii" as "-ee-ee". I'm not sure on Ecclesiastical, but I believe it does the same or else elides the two syllables into one "-ee". But most scientists (at least in the US) say "-ee-eye" as noted above, probably just to emphasize the second "i".
Some other general notes on Classical pronunciation: "c" and "ch" are always hard (sound like "k"). This rule is usually followed by scientists when it comes to "ch", but is often ignored when it comes to "c"; for example, most English speakers would pronounce "pomacea" as "po-mase-ee-uh", not the Classically correct "po-mah-kay-ah".
"G" is also always hard, as in "good", never soft, as in "gelatin". "V" or "u" before a vowel is usually pronounced like English "w". "J" or "i" before a vowel is usually pronounced like English consonantal "y".
There are no silent "e"s; think of "anemone" and you'll do well. Classical vowels have very different values from English vowels, but that's something so haphazardly followed as to be unhelpful for you to learn.
When words of non-Latin or Greek origin appear, just pronounce them as you normally would. There are lots of proper names from other languages in scientific names.
"Bichir" is confusing. This word is African in origin, but the spelling is French; the French scientists who described the species wrote down the local name as it sounded to them. This means that "bichir" is pronounced as a Frenchman would say it, not a Roman: "buh-sheer".
