Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins.

Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past biogeography of Mediterranean groupers, we investigated whether Zooarchaeology by Mass Spectrometry (ZooMS) can be used for identifying intra-genus grouper bones to species level. We discovered 22 novel, species-specific ZooMS biomarkers for groupers. Applying these biomarkers to Kinet Höyük, a Mediterranean archaeological site, demonstrated 4000 years of regional Epinephelus aeneus dominance and resiliency through millennia of fishing pressures, habitat degradation and climatic changes. Combining ZooMS identifications with catch size reconstructions revealed the Epinephelus aeneus capacity for growing 30 cm larger than hitherto documented, revising the maximum Total Length from 120 to 150 cm. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.

Geometric morphometric analysis of Pleuronectiformes vertebrae: A new tool to identify archaeological fish remains?

Flatfish (Pleuronectiformes) vertebrae are difficult to identify to species due to the lack of diagnostic features. This has resulted in a lack of understanding of the species abundances across archaeological sites, hindering interpretations of historical fisheries in the North Sea area. We use a new approach, utilising a combined 2D landmark-based geometric morphometric analysis as an objective and non-destructive method for species identification of flatfish vertebrae from the North Sea area. Modern specimens were used as a reference to describe the morphological variation between taxa using principal component analysis (PCA) and to trial an automated classification using linear discriminant analysis. Although there is limited distinction between taxa using PCAs, the classification shows high accuracies, indicating that flatfish species identifications using geometric morphometrics are possible. Bone samples (n = 105) from two archaeological sites in the United Kingdom and France were analysed using this approach and their identifications were verified using collagen peptide mass fingerprinting. The success rate of species identification was usually less than 50%, indicating that this technique has limited applicability due to preservation/fragmentation of archaeological fish bone. Nonetheless, this could prove a valuable tool for modern and non-fragmented samples. Furthermore, the technique applied in this study can be easily adapted to work on other landmark datasets.

Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters.

Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples (n = 202) from three archaeological sites in the UK and France dating to the medieval period (ca seventh-sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history.

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.