Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell

Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable. Here, we use ancient DNA (aDNA) extracted from fossil eggshell, together with target enrichment and next-generation sequencing techniques, to reconstruct an additional new mitogenome from Aepyornis sp. with 33.5X coverage. We also recover the first elephant bird nuclear aDNA, represented by 12,500 bp of exonic information. While we confirm that elephant birds are sister taxa to the kiwi, our data suggests that, like neognaths, palaeognaths underwent an explosive radiation between 69 and 52 Ma—well after the break-up of Gondwana, and more rapidly than previously estimated from mitochondrial data alone. These results further support the idea that ratites primarily diversified immediately following the Cretaceous-Palaeogene mass extinction and convergently evolved flightlessness. Our study reinforces the importance of including information from the nuclear genome of extinct taxa for recovering deep evolutionary relationships. Furthermore, with approximately 3% endogenous aDNA retrieved, avian eggshell can be a valuable substrate for recovering high quality aDNA. We suggest that elephant bird whole genome recovery is ultimately achievable, and will provide future insights into the evolution these birds. RaxML_inputsInput phylip files (.phy) and partition files (_part.txt) used for maximum likelihood tree generation in RaxML for various data sets (mt=mitochondrial, nuc=nuclear, ry=ry-coded, m3=mitochondrial third codon positions, loops=mitochondrial rRNA loops). Note that RY coded bases are given by a 0 (R) or 1 (Y).MrBayes_inputsInput nexus files (.nex) used for Bayesian phylogenetic inference for various datasets (mt=mitochondrial, nuc=nuclear, nt=standard coded (nucleotide), ry=ry-coded, m3=mitochondrial third codon positions, loops=mitochondrial rRNA loops)Nuclear_sequence_alignmentsNon-partitioned multiple sequence alignments for various nuclear loci in FASTA format (.fasta).MCMCTree_inputsInputs in phylip format (.phy) for molecular dating analysis conducted in MCMCTree for several datasets (mt=mitochondrial, nuc=nuclear, nt=standard coded (nucleotide), ry=ry-coded, m3=mitochondrial third codon positions). Note that RY-coded data are represented by R and Y. Tree topologies (.trees) used as input are shown: for mitochondrial and combined mitochondrial/nuclear datasets, two topologies were tested, one in which moa/tinamous are sister to the remaining notopalaeognathae, and one where rheas are sister to the remaining notopalaeognathae. For the nuclear dataset, the topology derived from phylogenetic inference on the nuclear data alone was used. MCMCTree control files (.ctl) are not shown as parameters used are described in text.FASTQTotal shotgun NGS (combined Ion Torrent Proton, Ion Torrent PGM, and MiSeq data as well as enriched and non-enriched libraries) reads (trimmed, quality filtered and unfiltered) in FASTQ format (.fastq).