Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird

The systematics of Madagascar’s extinct elephant birds has remained unclear due to gaps in the fossil record and poor biomolecular preservation of skeletal specimens. Here, molecular analyses of ~1000-year-old fossil eggshells provide the first description of elephant bird phylogeography and illuminate the ecology and evolution of flightlessness. Mitochondrial genomes from across Madagascar reveal genetic divergence correlated with egg morphology, stable isotope composition, and geography. The elephant bird crown is dated to ~30 Ma, coincident with climatic shifts as Madagascar moved northward. High between-clade variation supports reclassifying Mullerornis into a separate family, while low within-clade variation suggests only two elephant bird genera existed in southern Madagascar during the Holocene. Notably, an eggshell collection from far northern Madagascar represents a unique lineage within Aepyornis. Divergence within Aepyornis coincides with early Pleistocene aridification (~1.5 Ma), consistent with highland fragmentation driving diversification and rapid evolution of extreme gigantism. The authors advocate for taxonomy that integrates palaeogenomic and palaeoecological data.