For example, let's say the Giant Anteater (Myrmecophaga tridactyla) benefits from the presence of fruit trees (even though their food chain numbers are not adjacent). We could assign the benefit based on a class (say, Magnoliopsida or similar) or genus (like Mangifera).
I propose this would be both more educational (since it actually encourages people to read/learn the Latin names) and make gameplay more meaningful. Given the potential for an explosion of species in the game, it doesn't make sense to pigeon-hole ourselves by referencing specific species names for in-game effects unless that's both relevant and factually accurate. For example, the Whalesucker (Remora australis) could have a Mutualism or Commensalism effect with any organism of Order Cetacea (though we are not currently displaying order or family).