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Genetic barcoding of museum eggshell improves data integrity of avian biological collections

Citation

Grealy, Alicia; Langmore, Naomi; Joseph, Leo; Holleley, Clare (2020), Genetic barcoding of museum eggshell improves data integrity of avian biological collections, Dryad, Dataset, https://doi.org/10.5061/dryad.k3j9kd55x

Abstract

Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird’s egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen’s appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species’ accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.

Methods

DNA was extracted from museum eggshell specimens. Two mitochondrial mini barcodes (12S rDNA) were amplified via PCR and sequenced via NGS. 

Usage Notes

The dataset provided includes demultiplexed, quality filtered and dereplicated .fasta sequence files, and BLAST tables in .txt format. 

The naming convention is as follows: Sample ID - DNA extraction ID - Substrate - Barcode - Forward index ID - Reverse index ID - "Quality Filtered" - 
"Dereplicated" - "Chimera filtered" - "Denoised" - "Abundance Filtered".fasta

 

Funding

CSIRO Strategic Investment Funds (NRCA)

Centre for Biodiversity Analysis Ignition Grant

Australian Research Council, Award: DP180100021

CSIRO Strategic Investment Funds (NRCA)

Centre for Biodiversity Analysis Ignition Grant