Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

Sarkissian, Clio Der; Möller, Per; Hofman, Courtney A.; Ilsøe, Peter; Rick, Torben C.; Schiøtte, Tom; Sørensen, Martin V.; Dalén, Love; Orlando, Ludovic

doi:10.3389/fevo.2020.00037

Cited by 34 publications

(32 citation statements)

References 146 publications

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“…Using a set of 25 worked coral samples, we evaluated which one of five candidate DNA extraction protocols is most suited to retrieve DNA from worked precious coral samples. Each of the five tested methods (abbreviated as "W", "F", "B", "E", "Y") have earlier proven to be useful in extracting DNA from biomineralized material 29,[39][40][41][42][43][44][45][46][47][48] . DNA was extracted from each of the 25 worked coral skeletal samples with all five techniques, and DNA purity and quantity were assessed using real-time quantitative PCR (qPCR) technology.…”

Section: Resultsmentioning

confidence: 99%

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DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

Lendvay

Cartier

Gysi

et al. 2020

Sci Rep

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Precious coral species have been used to produce jewelry and ornaments since antiquity. Due to the high value and demand for corals, some coral beds have been heavily fished over past centuries. Fishing and international trade regulations were put in place to regulate fishing practices in recent decades. To this date, the control of precious coral exploitation and enforcement of trade rules have been somewhat impaired by the fact that different species of worked coral samples can be extremely difficult to distinguish, even for trained experts. Here, we developed methods to use DNA recovered from precious coral samples worked for jewelry to identify their species. We evaluated purity and quantity of DNA extracted using five different techniques. Then, a minimally invasive sampling protocol was tested, which allowed genetic analysis without compromising the value of the worked coral objects.The best performing DNA extraction technique applies decalcification of the skeletal material with EDTA in the presence of laurylsarcosyl and proteinase, and purification of the DNA with a commercial silica membrane. This method yielded pure DNA in all cases using 100 mg coral material and in over half of the cases when using "quasi non-destructive" sampling with sampled material amounts as low as 2.3 mg. Sequence data of the recovered DNA gave an indication that the range of precious coral species present in the trade is broader than previously anticipated. Precious corals are among the most appreciated and oldest known gems. They are valued for their color, texture and workability (polishing, carving), and have thus been collected and used for adornment for millennia 1-3. Growing demand, particularly in Asia in recent years, has led to an increase in prices of precious corals used in jewelry 4-6. The most valuable precious coral species belong to the Coralliidae family within the Octocorallia subclass of the Anthozoa. The precious coral material used for jewelry is the worked (i.e. cut, carved and polished) hard coral skeletal axis, which is a biogenic material created by a biomineralization process 7. In this process, closely packed magnesium-rich calcite crystals are secreted by coral polyps (1-2 mm in size) to build up a skeleton over decades. The polyps can thrive on the surface of the skeleton as colonies connected and surrounded by a 0.5-1 mm thick surface tissue (coenenchyme) 8. The Coral Commission of The World Jewellery Confederation (CIBJO) lists eight Coralliidae species as significant in the precious coral jewelry industry 9,10. Precious coral products are sold worldwide, with production centers located in Italy, Japan and Taiwan and large-scale trade of raw material between these areas 5,6,11. Until recent decades, the populations of these highly coveted marine animals experienced exploitation in boom and bust cycles where the discovery of precious coral beds led to rushes by coral fishers and these beds were exploited as long as it remained economically feasible 12,13. Local and international regulations were put...

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Section: Resultsmentioning

confidence: 99%

“…Oskam and Bunce 45 "Y" method subfossil bones 46 , subfossil and modern clam shells 47,48 EDTA solution with N-laurylsarcosyl and Proteinase-K…”

Section: Methodsmentioning

confidence: 99%

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

Lendvay

Cartier

Gysi

et al. 2020

Sci Rep

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“…The 'ancient' DNA that remains in molluscan shells and other material, including subfossil and museum species, also has the potential to transform our study of the past ecological and evolutionary dynamics. In this latter respect, several new studies have provided successful proof-of-principle [155][156][157]. While the methods for the extraction of ancient DNA have been available for some time, improved and cheaper sequencing technologies have enabled substantial recent progress in the insights that can be generated from this DNA.…”

Section: Improved Extraction Of High-molecular Weight Dnamentioning

confidence: 99%

Mobilising molluscan models and genomes in biology

Davison¹,

Neiman²

2020

Preprint

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Molluscs are amongst the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to ‘model’ status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution.

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“…Passive eDNA sampling using natural substrates is a promising solution to overcome filtration challenges. Organisms such as marine sponges (Mariani et al, 2019), molluscs (Der Sarkissian et al, 2020) and biofilms (Rivera et al, 2021) can trap and accumulate eDNA particles in water. Minerals can also accumulate and protect DNA from enzymatic degradation (Alvarez et al, 1998;Levy-Booth et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

Verdier

Konecny‐Dupré

Marquette

et al. 2021

Preprint

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1. The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. 2. We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. 3. We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. 4. By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.

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Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells

Cited by 34 publications

References 146 publications

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry

Mobilising molluscan models and genomes in biology

Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

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