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

Madagascar’s extinct elephant birds are the least studied of the ratites,
yet in recent years have proven to be critical for understanding the
evolution of all birds. With large spatio-temporal gaps in the fossil
record and poor biomolecular preservation of skeletal specimens, the
systematics of these flightless giants remains controversial. Here, we
overcome these limitations using a comprehensive molecular analysis of
1000-year-old fossil eggshells to provide the first description of
elephant bird phylogeography and reveal new insights into the ecology of
the world’s largest birds. High-throughput sequencing of 21 mitochondrial
genomes from across Madagascar reveals genetic variation that is
correlated with eggshell morphology, stable isotope composition, and
geographic distribution. The elephant bird crown is dated to ca. 30 Mya
during the Eocene-Oligocene, a period of marked global cooling when
Madagascar’s local palaeoclimate is estimated to have become less arid as
the island moved northward. High levels of between-clade genetic variation
argue for the reclassification of Mullerornis into a new family.
Low levels of within-clade genetic variation are unexpected and suggest
that there were only two elephant bird genera, with one species per genus
existing in southern Madagascar during the Holocene. However, we reveal a
newly discovered eggshell collection from Madagascar’s far north that is
phylogenetically, morphologically, and ecologically distinct, representing
a unique lineage of Aepyornis. Furthermore, molecular dating
estimates that divergence within Aepyornis coincides
with the aridification of Madagascar during the early Pleistocene ca. 1.5
Ma, and is consistent with the fragmentation of populations in the
highlands driving diversification, as well as the evolution of extreme
gigantism over short timescales. Molecular analysis thus provides the
first insight into elephant bird speciation, and we advocate for a
revision of their taxonomy that integrates palaeogenomic and
palaeoecological perspectives.