Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes

Vincent Biard; Pavel Gol'din; Elena Gladilina; Karina Vishnyakova; Krista McGrath; Filipe Jorge Garrett Vieira; Nathan Wales; Michael C. Fontaine; Camilla Speller; Morten Tange Olsen

doi:10.1016/j.jasrep.2017.07.008

Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes

Vincent Biard^*, Pavel Gol'din, Elena Gladilina, Karina Vishnyakova, Krista McGrath, Filipe Jorge Garrett Vieira, Nathan Wales, Michael C. Fontaine, Camilla Speller, Morten Tange Olsen

^*Corresponding author for this work

3 Citations (Scopus)

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Abstract

A critical challenge of the 21st century is to understand and minimise the effects of human activities on biodiversity. Cetaceans are a prime concern in biodiversity research, as many species still suffer from human impacts despite decades of management and conservation efforts. Zooarchaeology constitutes a valuable approach for informing conservation and management decisions by providing baseline information on the past distribution and human uses of species. However, traditional morphological species identification of mixed assemblage bones can be challenging, particularly in the case of cetaceans. To address this issue, we applied and evaluated the performance of three biomolecular approaches – Sanger sequencing, shotgun sequencing and collagen peptide fingerprinting (ZooMS) – for species identification in a mixed assemblage of 800 to 1600 years old odontocete (toothed whale) samples from the site of Chersonesus in Crimea, Ukraine. We found that ZooMS allowed for identification to the taxonomic level for 28 of our 30 samples (> 90%), identifying them as either “porpoise” or “dolphin”, and approximately half of those samples could be further identified to species level with the shotgun sequencing approach. In addition, shotgun sequencing produced several complete ancient odontocete mitogenomes and auxiliary nuclear genomic data for further exploration in a population genetic context. In contrast, both morphological identification and Sanger sequencing lacked taxonomic resolution and/or resulted in misclassification of samples. We found that the combination of ZooMS and shotgun sequencing provides a powerful tool in zooarchaeology, and here allowed for a deeper understanding of past marine resource use and its implication for current management and conservation of Black Sea odontocetes.

Original language	English
Journal	Journal of Archaeological Science: Reports
Volume	15
Pages (from-to)	262-271
Number of pages	10
ISSN	2352-409X
DOIs	https://doi.org/10.1016/j.jasrep.2017.07.008
Publication status	Published - Oct 2017

Keywords

Mitogenome
Mixed assemblage
Odontocete
Sanger sequencing
Shotgun sequencing
Species identification
ZooMS

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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title = "Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes",

abstract = "A critical challenge of the 21st century is to understand and minimise the effects of human activities on biodiversity. Cetaceans are a prime concern in biodiversity research, as many species still suffer from human impacts despite decades of management and conservation efforts. Zooarchaeology constitutes a valuable approach for informing conservation and management decisions by providing baseline information on the past distribution and human uses of species. However, traditional morphological species identification of mixed assemblage bones can be challenging, particularly in the case of cetaceans. To address this issue, we applied and evaluated the performance of three biomolecular approaches – Sanger sequencing, shotgun sequencing and collagen peptide fingerprinting (ZooMS) – for species identification in a mixed assemblage of 800 to 1600 years old odontocete (toothed whale) samples from the site of Chersonesus in Crimea, Ukraine. We found that ZooMS allowed for identification to the taxonomic level for 28 of our 30 samples (> 90%), identifying them as either “porpoise” or “dolphin”, and approximately half of those samples could be further identified to species level with the shotgun sequencing approach. In addition, shotgun sequencing produced several complete ancient odontocete mitogenomes and auxiliary nuclear genomic data for further exploration in a population genetic context. In contrast, both morphological identification and Sanger sequencing lacked taxonomic resolution and/or resulted in misclassification of samples. We found that the combination of ZooMS and shotgun sequencing provides a powerful tool in zooarchaeology, and here allowed for a deeper understanding of past marine resource use and its implication for current management and conservation of Black Sea odontocetes.",

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author = "Vincent Biard and Pavel Gol'din and Elena Gladilina and Karina Vishnyakova and Krista McGrath and {Garrett Vieira}, {Filipe Jorge} and Nathan Wales and Fontaine, {Michael C.} and Camilla Speller and Olsen, {Morten Tange}",

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AU - Gol'din, Pavel

AU - Gladilina, Elena

AU - Vishnyakova, Karina

AU - McGrath, Krista

AU - Garrett Vieira, Filipe Jorge

AU - Wales, Nathan

AU - Fontaine, Michael C.

AU - Speller, Camilla

AU - Olsen, Morten Tange

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JO - Journal of Archaeological Science: Reports

JF - Journal of Archaeological Science: Reports

ER -

Genomic and proteomic identification of Late Holocene remains: setting baselines for Black Sea odontocetes

Abstract

Keywords

UN SDGs

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