In Star Trek IV: The Voyage Home, we learn that humpback whales are extinct by the time of the Federation. My question is simple: are there any other species native to Earth that are extinct by that time?
According to TNG: New Ground, several prominent Earth species went extinct in the 21st and 22nd Century
KYLE: The eating habits of Gilvos are very similar to those of Earth's Draco lizards, which died out over three hundred years ago...
KYLE: ... as the value of their horns increased, the number of white Rhinos in the wild kept falling until they finally became extinct about two centuries ago.
By the 23rd Century (TOS: Man Trap), the Buffalo was only a memory
SPOCK: The Earth buffalo. What about it?
CRATER: Once there were millions of them prairies black with them. One herd covered three whole states, and when they moved they were like thunder.
SPOCK: And now they're gone. Is that what you mean?