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’.

Radiocarbon dating legacy collections: A Bayesian analysis of high-precision AMS 14C dates from the Par-Tee site, Oregon

“…Advances in faunal identification methods through molecular fingerprinting provide researchers the opportunity to limit research impacts on museum archaeological collections (Buckley et al 2008;Collins et al 2010;Richter et al 2011) while maximizing data gathering potential. Collagen peptide mass fingerprinting (i.e., ZooMS) facilitates the use of highly fragmented faunal remains in research, allowing for the molecular barcoding of archaeological samples-even those in which ancient DNA (aDNA) is no longer readily retrieved-to family, genus, and in some cases, species level identification (Rybczynski et al 2013;Speller et al 2016). Collagen is the most abundant protein in bone and preserves for millions of years in some environments (Rybczynski et al 2013).…”

Animals and People in the Netherlands’ Past: >50 Years of Archaeozoology in the Netherlands

“…Hunting for cetaceans may therefore also have occurred in the Netherlands during the medieval period, as their remains are frequently encountered in ecclesiastical and high-status sites. The majority of the exploited cetaceans, however, probably derive from stranded individuals (Speller et al 2016).…”

“…Identified species are harbour porpoise (Phocoena phocoena), common bottlenose dolphin (Tursiops truncatus), killer whale (Orcinus orca), Atlantic right whale (Eubalaena glacialis), and sperm whale (Physeter macrocephalus). Most cetacean bones remain unidentified below the taxonomic level of family, a major problem in cetacean research in archaeozoology(Speller et al 2016).…”

Novel Universal Primers for Metabarcoding eDNA Surveys of Marine Mammals and Other Marine Vertebrates

“…The four loci described in this paper provide investigators with flexible options to target different barcode markers depending on priorities for their study objectives, tailored to requirements for taxonomic breadth, variation and resolution at different taxonomic levels, amplicon size where eDNA degradation is a concern (e.g. Speller et al 2016), and sensitivity to contamination from human DNA.…”