Take species A. For whatever reason, species A splits into two groups, A1 and A2. A1 and A2 are (initially) the same species, but the split causes them to be separated for a long time (hundreds, thousands, tens-of-thousands, hundreds-of-thousands, millions of years).

You have already accepted that A1 and A2 will adapt to their surroundings. What prevents those adaptations from eventually making A1 and A2 no longer able to mate?