Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Abstract

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so‐called bio‐swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high‐yield sources of DNA for genomic‐scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

The importance of considering genetic diversity in shark and ray conservation policies

“…Genetic monitoring, as defined by Schwartz et al (2007), is the quantification of temporal changes in population genetic parameters or other population data generated using molecular markers. This technique can be performed using ancient DNA (aDNA) from the dried jaws and vertebrae of sharks and rays archived in museums and private collections and even kept as exotic souvenirs (Nielsen et al 2016). These data allow for retrospective monitoring to assess historical conditions, such as the temporal stability of the population structure, the loss of genetic diversity, and changes in the Ne, which are difficult to determine using traditional methods (Schwartz et al 2007;Nielsen and Hansen 2008).…”

Historical DNA Metabarcoding of the Prey and Microbiome of Trematomid Fishes Using Museum Samples

“…Amongst the first reports of successful DNA extraction from archived samples was the study of Higuchi et al (1984) targeting the extinct quagga, a member of the horse family. Molecular analysis of museum samples, sometimes also referred to as "ancient DNA" studies, have gained popularity since (e.g., Lambert et al, 2002;Nielsen et al, 2017). Advances of high-throughput sequencing techniques applied to museum samples have changed the possible scale and effort needed for archived DNA investigations and shown how powerful and valuable these can be (Bi et al, 2012(Bi et al, , 2013Nielsen et al, 2017).…”

“…Molecular analysis of museum samples, sometimes also referred to as "ancient DNA" studies, have gained popularity since (e.g., Lambert et al, 2002;Nielsen et al, 2017). Advances of high-throughput sequencing techniques applied to museum samples have changed the possible scale and effort needed for archived DNA investigations and shown how powerful and valuable these can be (Bi et al, 2012(Bi et al, , 2013Nielsen et al, 2017). To date, studies using museum samples have mainly focused on the host (e.g., extracting DNA from bones, otoliths, teeth), whereas organisms that lived on or within the host, as well as ingested prey organisms are mostly ignored.…”

An environmental DNA sampling method for aye‐ayes from their feeding traces

“…Yet, improved efficacy of the method to increase amount of aye‐aye DNA obtained and therefore reduce the cost per sample could make it a more attractive application for conservation monitoring (Ekblom & Galindo, ). Low proportions of on‐target, unique sequence reads recovered are common when working with environmental samples (Ávila‐Arcos et al., ; Nielsen et al., ) and adequate sampling effort is required to account for this issue. A mode of three different samples was taken per feeding trace, and it would be feasible to double this number.…”

“…Low proportions of on-target, unique sequence reads recovered are common when working with environmental samples (Ávila-Arcos et al, 2015;Nielsen et al, 2017) and adequate sampling effort is required to account for this issue. A mode of three different samples was taken per feeding trace, and it would be feasible to double this number.…”