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

Abstract

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'.

Keywords: ancient DNA; archaeozoology; cetaceans; collagen peptide mass fingerprinting; species identification; zooarchaeology by mass spectrometry.

Figure 1.

Location of southern North Sea archaeological sites with cetacean remains (including the east coast of England (n = 27), the French region of Nord-Pas-de-Calais (n = 2), Belgium (n = 4), The Netherlands (n = 56) and the North Sea coast of Germany (n = 13).

Figure 2.

Two established methods for the molecular identification of ancient cetacean remains: (a) DNA barcoding: DNA is extracted from the sample in a clean room, and PCR-amplified targeting short fragments of mtDNA. Resulting sequences are compared with a databank of known sequences for taxonomic identification. (b) ZooMS: samples are (1) demineralized in a weak acid solution; (2) collagen is gelatinized by heating at 65°C in an ammonium bicarbonate buffer; the collagen is then (3) enzymatically cleaved into peptides, which are spotted with a matrix onto a target plate. The masses of the peptides are measured following desorption/ionization of the sample using laser energy (MALDI) and (4) the peptide masses estimated by time of flight (TOF). The presence of specific peptides (5) is used for taxonomic identification.

Figure 3.

Map displaying locations of confirmed [68] palaeontological gray whale finds in the northeast Atlantic (filled squares, and shaded area representing southern bight of the North Sea) and the locations of the Mediterranean archaeological sites tested here (circled numbers: (1) Saint Sauveur; (2) Cougourlude and Saint Martin; (3) Villa Sant'Imbenia; (4) Porto Torres; (5) Nuraghe Lu Brandali and (6) San Rocchino.

Figure 4.

DNA hybridization capture coupled to NGS: (1) DNA is extracted in a clean room and (2) NGS libraries are built from the extract; (3) the libraries are enriched for specific DNA sequences by hybridization to custom designed baits, and non-target templates are washed away; (4) enriched libraries are sequenced on a NGS platform, and the resulting data are analysed bioinformatically.