Hi Egyption Arrow
Fossils [that were] clearly intermediate, or transitional, between land mammals and cetaceans were missing until recently.The author has topicalized the phrase 'missing until recently' giving:
Missing until recently were fossils ... .
Fossils ... were missing until recently.
The rule is this, when you topicalize, or bring a phrase to the front of a clause, the subject and verb invert:
Fossils were missing => missing were fossilsAbove, the subject-verb set 'fossils were' becomes 'were fossils'.