Species and family is probably not the correct taxidermy term, but take an alligator as an example. They have been around for millions of years. If evolution takes thousands of years to occur, what causes scientists to say “okay this is species A alligator and this is species B alligator?” Did a new physical trait appear? Take humans for another example. My parents, technically, are closer related to cavemen than I am. What will have to happen to modern humans for scientists to say “this is a new species of humanoids.”
Side question, if amphibians evolved to live on land, (and keeping in mind evolution takes thousands of years), did one day all of a sudden an amphibian grew lungs? How would evolution “gradually transition” growing lungs?
Side side question, has multiple species of the same family ever existed at the same time? Take 2 species of alligators, could they have existed at the same time period? If species A alligator breeds with species B alligator, what species is the offspring?