DOI: 10.5061/dryad.6h3q7
title: Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell

description: 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.
description: 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).