DOI: 10.5061/dryad.jm5251f
title: Data from: Avian mitochondrial genomes retrieved from museum eggshell

description: Avian eggshell is a bio-ceramic material with exceptional properties for
 preserving DNA within its crystalline structure, presenting an opportunity
 to retrieve genomic information from extinct or historic populations of
 birds. However, intracrystalline DNA has only been recovered from the
 large, thick eggshell of palaeognaths; members of their more-diverse
 sister group (neognaths) lay smaller, thinner eggs that may not exhibit
 the same propensity for DNA preservation. Here, we use three 40-60
 year-old museum eggshell specimens of Australian neognath birds to
 determine the minimum mass of eggshell from which intracrystalline DNA can
 be retrieved, and to characterise the yield and quality of such DNA. In
 doing so, we describe the first protocol for successful extraction of
 intractrystalline DNA from neognath eggshells, with the view to unlocking
 the potential of vast museum egg collections for genetic research. We were
 able to retrieve DNA fragments over 200 bp in length from 10 mg of
 eggshell powder from all three specimens, and demonstrate that expanding
 the existing blow-hole can allow sufficient material to be collected for
 DNA extraction while minimising damage to the appearance and structural
 integrity of the egg. Furthermore, we were able to reconstruct
 near-complete mitochondrial genomes at a coverage of 40-83X through
 shotgun sequencing of these extracts on three NextSeq lanes. Given the
 current extinction and extirpation rates of many avian species world-wide,
 genetic data from eggshell could provide a rapid and cost-effective
 approach to examining temporal changes in avian diversity, which is not
 only becoming crucial for conservation management, but also serve to
 deepen our understanding of genome-wide evolutionary processes.
description: Mitochondrial_partitioned_alignmentsAlignments used for phylogenetic inference, separated by mitochondrial partition in both .fasta and .phy format. Unstable blocks in these alignments were removed through the Gblocks program.MitogenomesFinal mitogenomes reconstructed in .fasta format.RAXML_inputInput files used for phylogenetic genetic inference using RAXML.Mitochondrial_partitions_gblocksAlignments of mitochondrial partitions in NEXUS format. Unstable blocks were removed using the Gblocks program.BarcodesRaw: Barcode sequence data, sorted by index and trimmed but not filtered; Filtering_pipeline: Pipeline used to quality filter, chimera filter, and abidance filter barcode data before BLAST; Filtered: Barcode data, post-filtering, that was then BLAST as described in the main manuscript.Filtered_mapped_readsReads used to reconstruct the final mitogenomes of each organism. The pipeline used to quality filter mapped reads after de novo assembly (as described in the main manuscript) is included as a .sh file.Subset_for_BLASTUnfiltered: a random selection of 1,000,000 merged sequences for blast, not quality filtered; Shotgun_filtering_pipeline.sh: the pipeline used to quality filter shotgun reads prior to BLAST; Filtered: the final selection of filtered sequences that were BLAST as outlined in the main manuscript.Aquila_audaxShotgun data: all merged NextSeq reads for Aquila audax, unfiltered. Unmerged reads are available upon request from the corresponding author.Cracticus_tibicenShotgun data: all merged NextSeq reads for Cracticus tibicen, unfiltered. Unmerged reads are available upon request from the corresponding author.Turnix_veloxShotgun data: all merged NextSeq reads for Turnix velox, unfiltered. Unmerged reads are available upon request from the corresponding author.Extraction_controlShotgun data: all merged NextSeq reads for the extraction control, unfiltered. Unmerged reads are available upon request from the corresponding author.No_template_controlShotgun data: all merged NextSeq reads for the no-template control, unfiltered. Unmerged reads are available upon request from the corresponding author.