Minimally destructive DNA extraction from archaeological artefacts made from whale baleen

Sinding, Mikkel‐Holger S.; Gilbert, M. Thomas P.; Grønnow, Bjarne; Gulløv, Hans Christian; Toft, Peter Andreas; Foote, Andrew D.

doi:10.1016/j.jas.2012.06.020

Cited by 11 publications

(11 citation statements)

References 20 publications

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“…As with modern whale product identification, studies of ancient specimens primarily concentrated on recovering short diagnostic fragments of mtDNA control region [ 40 , 41 ], cyt b gene [ 42 ] or both [ 43 , 44 ] for accurate taxonomic identification. In addition to archaeological bone, DNA analysis has been applied to other whale products, such as museum samples of baleen [ 45 , 46 ], whale ivory or scrimshaw [ 40 ], with relative success. Although there has been the occasional large-scale study identifying hundreds of samples [ 47 ], DNA-based studies have been primarily applied to demonstrate the feasibility of these molecular techniques, or at the site level, to identify the range of species exploited within a geographically restricted region.…”

Section: Opportunities From Molecular Identification Techniquesmentioning

confidence: 99%

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Speller

Hurk

Charpentier

et al. 2016

Phil. Trans. R. Soc. B

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Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue ‘From DNA barcodes to biomes’.

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Section: Opportunities From Molecular Identification Techniquesmentioning

confidence: 99%

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Speller

Hurk

Charpentier

et al. 2016

Phil. Trans. R. Soc. B

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“…Genetic material has been retrieved from a variety of tissues from museum specimens: bones and teeth, plant tissues, insects, feathers and skins [ 1 ]. DNA has also been successfully recovered from baleen plates, some over a hundred years old [ 9 , 10 ], and from historical [ 11 ] and archaeological [ 12 , 13 ] artefacts fashioned from baleen. This work has shown that analyses of baleen can contribute to studies of population genetics, conservation and exploitation and use of Mysticeti whales in past and recent times.…”

Section: Introductionmentioning

confidence: 99%

Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections

et al. 2017

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Baleen has been harvested by indigenous people for thousands of years, as well as collected by whalers as an additional product of commercial whaling in modern times. Baleen refers to the food-filtering system of Mysticeti whales; a full baleen rack consists of dozens of plates of a tough and flexible keratinous material that terminate in bristles. Due to its properties, baleen was a valuable raw material used in a wide range of artefacts, from implements to clothing. Baleen is not widely used today, however, analyses of this biomolecular tissue have the potential to contribute to conservation efforts, studies of genetic diversity and a better understanding of the exploitation and use of Mysticeti whales in past and recent times. Fortunately, baleen is present in abundance in museum natural history collections. However, it is often difficult or impossible to make a species identification of manufactured or old baleen. Here, we propose a new tool for biomolecular identification of baleen based on its main structural component alpha-keratin (the same protein that makes up hair and fingernails). With the exception of minke whales, alpha-keratin sequences are not yet known for baleen whales. We therefore used peptide mass fingerprinting to determine peptidic profiles in well documented baleen and evaluated the possibility of using this technique to differentiate species in baleen samples that are not adequately identified or are unidentified. We examined baleen from ten different species of whales and determined molecular markers for each species, including species-specific markers. In the case of the Bryde’s whales, differences between specimens suggest distinct species or sub-species, consistent with the complex phylogeny of the species. Finally, the methodology was applied to 29 fragments of baleen excavated from archaeological sites in Labrador, Canada (representing 1500 years of whale use by prehistoric people), demonstrating a dominance of bowhead whale (Balaena mysticetus) in the archaeological assemblage and the successful application of the peptide mass fingerprinting technique to identify the species of whale in unidentified and partially degraded samples.

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“…The keratin structure of hair, claws and baleen is thought to protect endogenous DNA from contamination [ 61 , 62 ], and several studies have successfully retrieved endogenous DNA from human and animal hair [ 62 , 63 , 64 ] and whale baleen [ 65 , 66 ] preserved in Danish and Greenlandic archaeological contexts. Preservation of claws in archaeological contexts is rare; however, research on natural history collections (NHC) indicates that DNA can be sufficiently well preserved for analysis of this substrate [ 67 , 68 ], with potentially the same success rate as ancient bone [ 69 ].…”

Section: Novel Substratesmentioning

confidence: 99%

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

Green

Speller

2017

Genes

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Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively “novel”. Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.

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Minimally destructive DNA extraction from archaeological artefacts made from whale baleen

Cited by 11 publications

References 20 publications

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Molecular markers in keratins from Mysticeti whales for species identification of baleen in museum and archaeological collections

Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

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