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

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).