For a long time the elephant birds were assumed to be closest to the African ostrich, which was geographically convenient. Ancient DNA recovered from eggshell and bone overturned that. Analyses place Aepyornithidae as sister group to the kiwi of New Zealand, an association nobody predicted from size or appearance.
The result reshaped thinking about ratite history. If a chicken-sized nocturnal bird and a half-tonne giant are each other's closest relatives on landmasses thousands of kilometres apart, flightlessness and gigantism must have arisen repeatedly and independently rather than once in a common flightless ancestor. Flying ancestors dispersing over water, then losing flight in place, fits the genetic tree better than slow drift on splitting continents.
The eggs remain the most striking evidence. Elephant bird eggs are the largest known of any animal, with volumes in the region of eight to nine litres, and intact examples periodically appear in museum collections that had catalogued them as replicas.