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

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.

Mining museums for historical DNA: advances and challenges in museomics

“…the first historical specimens to reliably produce hDNA and have since become a frequent sampling target. But recent efforts have obtained DNA from a broader array of museum specimen types and taxonomic groups, including sampling microbial communities from herbarium specimens [18], isolating retroviruses in koala (Phascolarctos cinereus) specimens [19], genetic barcoding of eggshells [20], genotyping century-old insect specimens [21], obtaining mitogenomes from 130 year-old dry Bryozoans [22], and collecting genomic loci from formalinpreserved specimens [23]. Of major significance, the use of museum specimens as a source for DNA greatly increases the scale of genetic resources available for research, and consequently, will accelerate comparative studies by substantially increasing taxonomic inclusion, reducing or eliminating field costs, and saving research time.…”

Unlocking inaccessible historical genomes preserved in formalin

“…The comprehensive metadata associated with each specimen (collection date, location, sex, weight, age, etc), phenotypic data (e.g., colour, size, gut contents) and genomic data can be used to monitor ecosystem health and study the mechanisms driving adaptation, evolution, speciation and extinction (Holmes et al, 2016; Meineke et al, 2018). The value of collections as sources of historical genetic material has been recognized for the past 30 years, with numerous pathways emerging to retrieve high‐quality DNA from challenging archival vertebrate tissues such as skins (Martínková & Searle, 2006), feathers (Rawlence et al, 2009; Sefc et al, 2003), eggshells (Grealy et al, 2019, 2021) and toe pads (Tsai et al, 2020).…”

Oological collections and egg collectors of Brazilian birds: an overview

“…Egg sets without specific locality and specific collecting date are of limited scientific value for most studies but can be very useful for destructive analyses (Russell et al, 2010). However, recent development of genetic barcoding of eggshell collections can allow the identification of these eggs and improve the reliability and use of egg collections (Grealy et al, 2021). Egg sets that lack locality, many collected before 1900, could have their habitat reconstructed and their region traced with isotopic analyses (Barrick, 1998;Johnson et al, 1998;Niespolo et al, 2020).…”