Many of the worlds you'll build will have multiple continents, and if you're doing things correctly, each of those continents will have their own biodiversity. Each one will have its own specific native plants and animals that may or may not be domesticatible, and the nature of those species help determine the civilizations that thrive there.
But sooner or later in the history of your world, those two cultures are going to meet, and when they do... interesting things will happen.
Some call when that happened in our world-- when Eurasian/African biodiversity met American-- the Columbian Exchange. Now, just ignoring the political and social elements of what happened when Columbus and those that followed him came to Americas, on a pure level of biological exchange, it was incredibly uneven for the Americas.
By which I mean, the Columbian Exchange meant that the cultures of Europe, Asia and Africa got. to name a few: potatoes, beans, corn, blueberries, peppers, tomatoes, chocolate and vanilla. Foodstuffs and flavors that were nutritiously dense and became integral parts of the diets of those cultures, and helped result in population booms throughout those continents. And the Americas got a Disease Apocalypse. Yes, the Americas also got horses, pigs, cattle and wheat, but those mostly came with settlers who moved into the Americas, which was relatively easy to do, what with the Disease Apocalypse, killing an estimate 80% of the population.
So, that's the big question: does your worldbuilding take into account what may (or did) happen when Culture A crosses the ocean and meets up with Culture B? Will that exchange be relatively equal, or will it strongly weigh in favor of one or the other? How will those cultures see each other? Will there be unintended consequences from that meeting? How will your world be changed?
In my Daermad Cycle, in times past, European Celts (circa 4th century which research shows there were tribes left) arrived in Rune, which is not part of this world. They carried with them the diseases we'd expect of old Europe and a disease that I based on chicken pox infected the Runic peoples. It didn't kill all of them, but it set up the collapse of the entire web of societies, allowing the Celts to become the dominant group.
The Runic peoples had never seen horses before, which also gave the "celts" an advantage. I record the reaction of one culture eating the foods of the other cultures and finding them odd, but in the main body of the story, my "celts" have been in Rune so long that they don't find the landscape odd anymore -- though they're still in denial about how true natives can channel the energies of that world.
Since my main peoples are pre-Columbian European in origin, I do take care never to have them eat potatoes, etc. Even if what they are eating isn't really turnips, I call them turnips because I figure the early celtic invaders would have called them turnips.
But, you've given me food for thought. I do have other continents that occasionally interact with my main continent and biodiversity should be reflected in their interactions. I had given some thought about their cultural difference, but not so much about native plants and animals.
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