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Publications
Publications
Publications produced by the SeaChanges early-stage researchers in relation to their projects.
Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA
Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA
Lourdes Martínez-García, Angélica Pulido, Giada Ferrari, Anne Karin Hufthammer, Marianne Vedeler, Alex Hirons, Catherine Kneale, James H. Barrett and Bastiaan Star
Abstract
Abstract
Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ13C, δ15N, non-exchangeable δ2H and δ34S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ13C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries
Preprint online: 27 Nov 2024
Greenland Norse walrus exploitation deep into the Arctic
Greenland Norse walrus exploitation deep into the Arctic
Emily J. Ruiz-Puerta, Greer Jarrett, Morgan L. McCarthy, Shyong En Pan, Xénia Keighley, Magie Aiken, Giulia Zampirolo, Maarten J. J. E. Loonen, Anne Birgitte Gotfredsen, Lesley R. Howse, Paul Szpak, Snæbjörn Pálsson, Scott Rufolo, Hilmar J. Malmquist, Sean P. A. Desjardins, Morten Tange Olsen, and Peter D. Jordan.
Abstract
Abstract
Walrus ivory was a prized commodity in medieval Europe and was supplied by Norse intermediaries who expanded across the North Atlantic, establishing settlements in Iceland and Greenland. However, the precise sources of the traded ivory have long remained unclear, raising important questions about the sustainability of commercial walrus harvesting, the extent to which Greenland Norse were able to continue mounting their own long-range hunting expeditions, and the degree to which they relied on trading ivory with the various Arctic Indigenous peoples that they were starting to encounter. We use high-resolution genomic sourcing methods to track walrus artifacts back to specific hunting grounds, demonstrating that Greenland Norse obtained ivory from High Arctic waters, especially the North Water Polynya, and possibly from the interior Canadian Arctic. These results substantially expand the assumed range of Greenland Norse ivory harvesting activities and support intriguing archaeological evidence for substantive interactions with Thule Inuit, plus possible encounters with Tuniit (Late Dorset Pre-Inuit).
Preprint online: 27 Sept 2024
Ancient DNA reveals historical demographic decline and genetic erosion in the Atlantic bluefin tuna
Ancient DNA reveals historical demographic decline and genetic erosion in the Atlantic bluefin tuna
Adam Jon Andrews, Emma Falkeid Eriksen, Bastiaan Star, Kim Præbel, Antonio Di Natale, Estrella Malca, Glenn Zapfe, Vedat Onar, Veronica Aniceti, Gabriele Carenti, Gäel Piquès, Svein Vatsvåg Nielsen, Per Persson, Federica Piattoni, Francesco Fontani, Lane M. Atmore, Oliver Kersten, Fausto Tinti, Elisabetta Cilli, Alessia Cariani
Abstract
Abstract
Overexploitation has depleted fish stocks during the past century, nonetheless its genomic consequences remain poorly understood. Characterising the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n=49) and ancient (n=41) specimens dating up to 5000 years ago, uncovering several novel findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity was significantly lower in modern (2013-2020), than ancient (pre-1941) Mediterranean bluefin tuna, suggesting bluefin tuna underwent a genetic bottleneck. With this work we show how ancient DNA provides novel perspectives on ecological complexity with the potential to inform the management and conservation of fishes.
Preprint online: 19 Sept 2024
Finding the right plaice at the right time: Multi-molecular analysis of flatfish reveals historical catch habitats
Finding the right plaice at the right time: Multi-molecular analysis of flatfish reveals historical catch habitats
Katrien Dierickx, Peter Schauer, Jennifer Harland, Alan Pipe, Tarek Oueslati, Alexander Lehouck, Anton Ervynck, Wim Wouters, Matthew Von Tersch, David Orton, Michelle Alexander
Abstract
Abstract
Flatfish are ecologically diverse species that commonly occur in marine environments, but also in estuarine and riverine habitats. This complicates the examination of the potential role of flatfish in the ‘marine fish event horizon’, an economic shift in human exploitation from freshwater to marine fish species during the 10–11th centuries CE around the southern North Sea. This study represents the first multi-disciplinary investigation of flatfish remains to make species-specific interpretations of flatfish exploitation. Peptide mass fingerprinting and multi-isotope analysis of carbon (δ13C), nitrogen (δ15N) and sulphur (δ34S) was performed on collagen from 356 archaeological flatfish and 120 comparative archaeological marine or freshwater species to explore the catch habitat of individual flatfish species between 600 and 1600 CE from the North Sea area. European flounder show signals reflecting both freshwater and marine environments, while other flatfish show only those of marine habitats. A subtle shift towards more marine exploitation towards the end of the period is identified, corresponding to the observed transition in targeted species from flounder to plaice throughout the medieval period. Sites show slight differences in δ13C and δ34S within the same species, related to the local environments. Remarkable is the high abundance of marine plaice and flounder during the early medieval period, which shows clear marine or coastal exploitation of flatfish early on, well before the previously accepted onset of the marine fish event horizon. This indicates a gradual shift from coastal to open marine fish exploitation over the medieval period.
Published online: 28 May 2024
The Once and Future Fish: 1300 years of Atlantic herring population structure and demography revealed through ancient DNA and mixed-stock analysis
The Once and Future Fish: 1300 years of Atlantic herring population structure and demography revealed through ancient DNA and mixed-stock analysis
Lane M. Atmore, Inge van der Jagt, Aurélie Boilard, Simone Häberle, Rachel Blevis, Katrien Dierickx, Liz M. Quinlan, David C. Orton, Anne Karin Hufthammer, James H. Barrett, Bastiaan Star
Abstract
Abstract
Atlantic herring populations have been the target of highly profitable coastal and pelagic fisheries in northern Europe for well over a thousand years. Their complex and intermingled population dynamics have sparked extensive debate over the impacts of historical overfishing and have complicated their sustainable management today. Recently developed tools – including diagnostic SNP panels for mixed-stock analysis – aim to improve population assignment for fisheries management, however, the biological relevance of such tools over long periods of time remains unknown. Here, we demonstrate the millennium-long applicability of diagnostic SNP panels and identify population perturbations associated with increasing exploitation pressure and climate change by analyzing whole genome data from modern and ancient herring specimens. We find that herring demographic cycles were likely within healthy ecosystem boundaries until the dramatic disruption of these cycles in the 20th century. We find only autumn-spawning herring in our archaeological remains spanning 900 years from 8 sites across Europe, supporting observations that the numerical dominance of specific spawning populations can demographically outcompete other herring types. We also obtain pre-archival aDNA evidence for the famous, cyclical “Bohuslän periods,” during which mass quantities of North Sea autumn-spawning herring congregated in the Skagerrak. Finally, the long-term applicability of diagnostic SNP panels underscores their highly cost-effective application for the genetic monitoring of herring stocks. Our results highlight the utility of ancient DNA and genomic analysis to obtain historical and natural insights in herring ecology and population dynamics with relevance for sustainable fisheries management.
Preprint online: 16 July 2024
Earliest records of Holocene cetaceans in the Black Sea
Earliest records of Holocene cetaceans in the Black Sea
Magie Aiken, Elena Gladilina, Canan Çakırlar, Serhii Telizhenko, Luminita Bejenaru, Maia Bukhsianidze, Morten Tange Olsen, Pavel Gol'din
Abstract
Abstract
The timing of the Holocene transition of the Black Sea from a brackish lake to a marine sea has long been debated. Here, we report on the earliest records of cetaceans in the Black Sea region as a proxy for the connection with the Mediterranean and the transition from a brackish to marine environment. We base our analysis on cetacean skeletal finds and archival data on cetacean skeletal remains from the Bosphorus, the western, northern and eastern Black Sea, and the Kerch Strait. We find that all three contemporary cetacean species in the Black Sea – the harbour porpoise, bottlenose dolphin and common dolphin – had migrated out of the Mediterranean to the Bosphorus and the Black Sea at least 8000–7000 years ago and reached the northern Black Sea by 5500 years ago at the latest. Our study suggests the establishment of a Mediterranean–Black Sea biogeographical connection for marine vertebrates at least 7000 years ago. The early presence of cetaceans in the Black Sea has implications for understanding its Holocene transition, as well as the evolutionary and ecological history of these species more generally.
Published online: 6 March 2024
Grouping groupers in the Mediterranean: ecological baselines revealed by ancient proteins
Grouping groupers in the Mediterranean: ecological baselines revealed by ancient proteins
Rachel M. Winter, Willemien de Kock, Meaghan Mackie, Max Ramsøe, Elena Desiderà, Matthew Collins, Paolo Guidetti, Samantha Presslee, Marta Munoz Alegre, Tarek Oueslati, Arturo Morales Muniz, Dimitris Michailidis, Youri van den Hurk, Alberto J. Taurozzi, Canan Çakirlar
Abstract
Abstract
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 if 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 a northeastern 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. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.
Published online: 23 October 2023
Holocene deglaciation drove rapid genetic diversification of Atlantic walrus
Holocene deglaciation drove rapid genetic diversification of Atlantic walrus
Emily J. Ruiz-Puerta, Xénia Keighley, Sean P. A. Desjardins, Anne Birgitte Gotfredsen, Shyong En Pan, Bastiaan Star, Sanne Boessenkool, James H. Barrett, Morgan L. McCarthy, Liselotte W. Andersen, Erik W. Born, Lesley R. Howse, Paul Szpak, Snæbjörn Pálsson, Hilmar J. Malmquist, Scott Rufolo, Peter D. Jordan and Morten Tange Olsen
Abstract
Abstract
Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.
Published online: 27 September 2023
Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries
Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries
Adam J. Andrews, Christophe Pampoulie, Antonio Di Natale, Piero Addis, Darío Bernal-Casasola, Veronica Aniceti, Gabriele Carenti, Verónica Gómez-Fernández, Valerie Chosson, Alice Ughi, Matt Von Tersch, Maria Fontanols-Col, Elisabetta Cilli, Vedat Onar, Fausto Tinti, Michelle Alexander.
Abstract
Abstract
During recent decades, the health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution and anthropogenic-driven climate change. Due to a lack of long-term ecological data, we have a poor grasp of the true impact on the diet and habitat use of fishes. This information is vital if we are to recover depleted fish populations and predict their future dynamics. Here, we trace the long-term diet and habitat use of Atlantic bluefin tuna (BFT), Thunnus thynnus, a species that has had one of the longest and most intense exploitation histories, owing to its tremendous cultural and economic importance. Using carbon, nitrogen and sulphur stable isotope analyses of modern and ancient BFT including 98 archaeological and archival bones from 11 Mediterranean locations ca. 1st century to 1941 CE, we infer a shift to increased pelagic foraging around the 16th century in Mediterranean BFT. This likely reflects the early anthropogenic exploitation of inshore coastal ecosystems, as attested by historical literature sources. Further, we reveal that BFT which migrated to the Black Sea–and that disappeared during a period of intense exploitation and ecosystem changes in the 1980s–represented a unique component, isotopically distinct from BFT of NE Atlantic and Mediterranean locations. These data suggest that anthropogenic activities had the ability to alter the diet and habitat use of fishes in conditions prior to those of recent decades. Consequently, long-term data provide novel perspectives on when marine ecosystem modification began and the responses of marine populations, with which to guide conservation policy.
Published Online: 10 August 2023
Geometric morphometric analysis of Pleuronectiformes vertebrae: A new tool to identify archaeological fish remains?
Geometric morphometric analysis of Pleuronectiformes vertebrae: A new tool to identify archaeological fish remains?
Katrien Dierickx, Tarek Oueslati, Antonio Profico.
Abstract
Abstract
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.
Published Online: 26 July 2023
Threatened North African seagrass meadows have supported green turtle populations for millennia
Threatened North African seagrass meadows have supported green turtle populations for millennia
Willemien de Kock, Meaghan Mackie, Max Ramsøe, Morten E. Allentoft, Annette C. Broderick, Julia C. Haywood, Brendan J. Godley, Robin T. E. Snape, Phil J. Bradshaw, Hermann Genz, Matthew von Tersch, Michael W. Dee, Per J. Palsbøll, Michelle Alexander, Alberto J. Taurozzi, and Canan Çakırlar
Abstract
Abstract
“Protect and restore ecosystems and biodiversity” is the second official aim of the current UN Ocean Decade (2021 to 2030) calling for the identification and protection of critical marine habitats. However, data to inform policy are often lacking altogether or confined to recent times, preventing the establishment of long-term baselines. The unique insights gained from combining bioarchaeology (palaeoproteomics, stable isotope analysis) with contemporary data (from satellite tracking) identified habitats which sea turtles have been using in the Eastern Mediterranean over five millennia. Specifically, our analysis of archaeological green turtle (Chelonia mydas) bones revealed that they likely foraged on the same North African seagrass meadows as their modern-day counterparts. Here, millennia-long foraging habitat fidelity has been directly demonstrated, highlighting the significance (and long-term dividends) of protecting these critical coastal habitats that are especially vulnerable to global warming. We highlight the potential for historical ecology to inform policy in safeguarding critical marine habitats.
Published online: 17 July 2023
Prehistoric and historic exploitation of marine mammals in the Black Sea
Prehistoric and historic exploitation of marine mammals in the Black Sea
Magie Aiken, Elena Gladilina, Canan Çakırlar, Serhii Telizhenko, Youri van den Hurk, Luminita Bejenaru, Morten Tange Olsen, Pavel Gol'din
Abstract
Abstract
The recent exploitation of marine species is relatively well documented and understood in terms of impacts on species abundance, distribution, and resource use. In contrast, ancient exploitation of marine mammals remains poorly documented; in part, because a detailed meta-analysis of their presence in the zooarchaeological record is lacking. This is true in the Black Sea, where cetaceans are reported in the zooarchaeological record but have not yet been studied comprehensively. Here, we synthesize all available published and unpublished zooarchaeological data from 27 sites around the Black Sea, dating from the Mesolithic and Neolithic periods (6500-6000 BCE) to the Medieval period (641–1475 CE), to document the extent and nature of the exploitation of the Black Sea cetacean species. The results suggest that cetacean exploitation was practised continuously in the Black Sea over a period of 8500 years from the Neolithic through to the Medieval period. This suggests a much longer history of marine mammal exploitation in the Black Sea than previously understood, pushing back the timeline of human impacts on the Black Sea marine fauna.
Published online: 13 July 2023
Isotopic life-history signatures are retained in modern and ancient Atlantic bluefin tuna vertebrae
Isotopic life-history signatures are retained in modern and ancient Atlantic bluefin tuna vertebrae
Adam J. Andrews, David Orton, Vedat Onar, Piero Addis, Fausto Tinti, Michelle Alexander
Abstract
Abstract
Isotopic, tagging and diet studies of modern-day teleosts lacked the ability to contextualise life-history and trophic dynamics with a historical perspective, when exploitation rates were lower and climatic conditions differed. Isotopic analysis of vertebrae, the most plentiful hard-part in archaeological and museum collections, can potentially fill this data-gap. Chemical signatures of habitat and diet use during growth are retained by vertebrae during bone formation. Nonetheless, to fulfil their potential to reveal life-history and trophic dynamics, we need a better understanding of the time frame recorded by vertebrae, currently lacking due to a poor understanding of fish bone remodelling. To address this issue, the authors serially-sectioned four vertebral centra of the highly migratory Atlantic bluefin tuna (Thunnus thynnus; BFT) captured off Sardinia (Italy) and analysed their isotopic composition. They show how carbon (δ13C), nitrogen (δ15N) and sulphur (δ34S) isotope values can vary significantly across BFT vertebrae growth-axes, revealing patterning in dietary life histories. Further, they find that similar patterns are revealed through incremental isotopic analysis of inner and outer vertebrae centra samples from 13 archaeological BFT vertebrae dating between the 9th and 13th centuries CE. The results indicate that multi-year foraging signatures are retained in vertebrae and allow for the study of life histories in both modern and paleo-environments. These novel methods can be extended across teleost taxa owing to their potential to inform management and conservation on how teleost trophic dynamics change over time and what their long-term environmental, ecological and anthropological drivers are.
Published Online: 26 April 2023
Rapid collagen peptide mass fingerprinting as a tool to authenticate Pleuronectiformes in the food industry
Rapid collagen peptide mass fingerprinting as a tool to authenticate Pleuronectiformes in the food industry
Katrien Dierickx, Sam Presslee, Virginia L. Harvey
Abstract
Abstract
Reliable species identification of specimens in the food chain is crucial for detecting mislabelling fraud. While visual identification, DNA-analyses, and proteomic approaches have been used in the past, this research provides an alternative proteomic technique that has been trialled here to identify tissue samples from species within the order Pleuronectiformes (flatfish). Previously, archaeological research has used peptide mass fingerprinting to identify fish remains to species by extracting collagen Type I preserved in bones. As this type of collagen can also be found in the fins, skin and muscle of fishes (types of tissue that can be found throughout the food chain), collagen peptide mass fingerprinting has been applied here to identify modern fish specimens to species. In this study, MALDI-ToF MS peptide fingerprints are obtained from enzymatic digestion of collagen Type I from fin (or skin if fin was not available) and muscle tissues from six specimens of Pleuronectiformes. Using the already available diagnostic collagen peptide biomarkers for flatfish, all six specimens could be identified to the correct species for each of the tissue types. We recommend using this rapid approach for future screenings of modern flatfish in the food chain to detect mislabelling fraud, and also in more general applications of modern ecological studies of this order. It is likely that the methods can be applied to other Actinopterygian fishes.
Published Online: 14 February 2023
Catch of the day: abundance and size data of groupers (Epinephelidae) and combers (Serranidae) from Middle to Late Holocene Levantine archaeological contexts
Catch of the day: abundance and size data of groupers (Epinephelidae) and combers (Serranidae) from Middle to Late Holocene Levantine archaeological contexts
Rachel Winter, Elena Desidera, Paolo Guidetti, Shyama Vermeersch, Nazli Demirel, Canan Çakırlar
Abstract
Abstract
Groupers (Epinephelidae) are ecologically, commercially, and culturally important carnivorous fishes found throughout the world’s tropical, subtropical, and temperate coastal marine waters. Due to various life history traits (e.g., late maturity, sequential hermaphroditism) and behavior (e.g., sedentary, small home ranges) groupers are susceptible to overfishing, including small-scale and recreational fishing (especially spearfishing), and their populations are declining worldwide. The eastern Mediterranean coast, home to some of the world’s longest continuously occupied urban settlements, hosts important but declining grouper populations. This paper investigates how grouper and comber (fishes in the Serranidae family with similar ecology and osteomorphology, but smaller in size) abundance and catch size changed in the eastern Mediterranean from the Middle to Late Holocene, coinciding with early coastal urbanization, by estimating their relative frequency and reconstructing their size. Size reconstructions have been done from a large sample of bones (Number of Identified Specimens = 1851) recovered from Kinet Höyük in Turkey, and Tell Fadous-Kfarabida and Tell el-Burak in Lebanon, habitation sites along the Levantine coast. Our results imply that groupers in the past reached >100 cm more often than is observed today in areas open to commercial fishing. Furthermore, the apparent lack of large groupers by the Hellenistic Period at Kinet Höyük suggests fishing efforts were intense enough to have either had an appreciable effect on the size structure of local grouper populations or brought about a behavioral change to the fishes of moving to deeper waters.
Published Online: 23 December 2022
Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics
Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics
Lane M. Atmore, Lourdes Martínez-García, Daniel Makowiecki, Carl André, Lembi Lõugas, James H. Barrett, Bastiaan Star
Abstract
Abstract
The world’s oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first “industrial” fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.
Published Online: 25 October 2022
Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe
Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe
Lourdes Martínez-García, Giada Ferrari, Angélica Cuevas, Lane M. Atmore, Begoña López-Arias, Mark Culling, Laura Llorente-Rodríguez, Arturo Morales-Muñiz, Eufrasia Roselló-Izquierdo, Juan Antonio Quirós, Ricard Marlasca-Martín, Bernd Hänfling, William F. Hutchinson, Kjetill S. Jakobsen, Sissel Jentoft, David Orton, Bastiaan Star and James H. Barrett
Abstract
Abstract
Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050–1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.
Published Online: 19 October 2022
Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters
Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters
Katrien Dierickx, Samantha Presslee, Richard Hagan, Tarek Oueslati, Jennifer Harland, Jessica Hendy, David Orton, Michelle Alexander and Virginia L. Harvey
Abstract
Abstract
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.
Published Online: 27 July 2022
Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene
Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene
Lourdes Martínez-García, Giada Ferrari, Anne Karin Hufthammer, Kjetill S. Jakobsen, Sissel Jentoft, James H. Barrett and Bastiaan Star
Abstract
Abstract
Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, 14C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.
Published Online: 04 May 2022
Length estimation of Atlantic bluefin tuna (Thunnus thynnus) using vertebrae
Length estimation of Atlantic bluefin tuna (Thunnus thynnus) using vertebrae
Adam J. Andrews, Dimitra Mylona, Lucia Rivera-Charún, Rachel Winter, Vedat Onar, Abu B. Siddiq, Fausto Tinti, Arturo Morales-Muniz
Abstract
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) is a large (up to 3.3 m in length) pelagic predator which has been exploited throughout the eastern Atlantic and Mediterranean since prehistoric times, as attested by its archeological remains. One key insight derivable from these remains is body size, which can indicate past fishing abilities, the impact of fishing, and past migration behavior. Despite this, there exists no reliable method to estimate the size of BFT found in archeological sites. Here, 13 modern Thunnus spp. skeletons were studied to provide power regression equations that estimate body length from vertebra dimensions. In modern specimens, the majority of BFT vertebrae can be differentiated by their morphological features, and thus, individual regression equations can be applied for each rank (position in vertebral column). In an archeological context, poor preservation may limit one's ability to identify rank; hence, “types” of vertebrae were defined, which enable length estimates when rank cannot be determined. At least one vertebra dimension, height, width, or length correlated highly with body length when vertebrae were ranked (R2 > 0.97) or identified to types (R2 > 0.98). Whether using rank or type, length estimates appear accurate to approximately ±10%. Finally, the method was applied to a sample of Roman-era BFT vertebrae to demonstrate its potential. It is acknowledged that further studies with larger sample sizes would provide more precision in BFT length estimates.
Published Online: 23 January 2022
Exploitation history of Atlantic bluefin tuna in the eastern Atlantic and Mediterranean—insights from ancient bones
Exploitation history of Atlantic bluefin tuna in the eastern Atlantic and Mediterranean—insights from ancient bones
Adam J Andrews, Antonio Di Natale, Darío Bernal-Casasola, Veronica Aniceti, Vedat Onar, Tarek Oueslati, Tatiana Theodropoulou, Arturo Morales-Muñiz, Elisabetta Cilli, Fausto Tinti
Abstract
Abstract
Overexploitation has directly, negatively affected marine fish populations in the past half-century, modifying not only their abundance but their behaviour and life-history traits. The recovery and resilience of such populations is dependent upon their exploitation history, which often extends back millennia. Hence, data on when exploitation intensified and how populations were composed in historical periods, have the potential to reveal long-term population dynamics and provide context on the baselines currently used in fisheries management and conservation. Here, we setup a framework for investigations on the exploitation history of Atlantic bluefin tuna (Thunnus thynnus; BFT) in the eastern Atlantic and Mediterranean by collating records of their zooarchaeological remains and critically reviewing these alongside the literature. Then, we outline how novel multidisciplinary applications on BFT remains may be used to document long-term population dynamics. Our review of literature provides clear evidence of BFT overexploitation during the mid-20th century CE. Furthermore, a strong case could be made that the intensification of BFT exploitation extends back further to at least the 19th century CE, if not the 13th–16th century CE, in the eastern Atlantic and Mediterranean. However, a host of archaeological evidence would suggest that BFT exploitation may have been intensive since antiquity. Altogether, this indicates that by the currently used management baselines of the 1970s, population abundance and complexity was already likely to have declined from historical levels, and we identify how biomolecular and morphometric analyses of BFT remains have the potential to further investigate this.
Published Online: 18 January 2022
Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment
Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment
Lane M. Atmore, Magie Aiken and Fabricio Furni
Abstract
Abstract
Current research on anthropogenic impacts on marine ecosystems often relies on the concept of a “baseline,” which aims to describe ecosystems prior to human contact. Recent research is increasingly showing that humans have been involved in marine ecosystems for much longer than previously understood. We propose a theoretical framework oriented around a system of “thresholds” referring to system-wide changes in human culture, ecosystem dynamics, and molecular evolution. The concept of the threshold allows conceptual space to account for the fluid nature of ecosystems throughout time while providing a critical framework for understanding drivers of ecosystem change. We highlight practical research approaches for exploring thresholds in the past and provide key insights for future adaptation to a changing world. To ensure ecological and societal goals for the future are met, it is critical that research efforts are contextualized into a framework that incorporates human society as integral to ecology and evolution.
Published Online: 19 November 2021
An accurate assignment test for extremely low-coverage whole-genome sequence data
An accurate assignment test for extremely low-coverage whole-genome sequence data
Giada Ferrari, Lane M. Atmore, Sissel Jentoft, Kjetill S. Jakobsen, Daniel Makowiecki, James H. Barrett, Bastiaan Star
Abstract
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
Published Online: 14 November 2021
Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean
Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean
Adam J. Andrews, Gregory N. Puncher, Darío Bernal-Casasola, Antonio Di Natale, Francesco Massari, Vedat Onar, Nezir Yaşar Toker, Alex Hanke, Scott A. Pavey, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Elisabetta Cilli, Arturo Morales-Muñiz, Barbara Mantovani, Fausto Tinti & Alessia Cariani
Abstract
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
Published Online: 20 October 2021
Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes
Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes
Lourdes Martínez-García, Giada Ferrari, Tom Oosting, Rachel Ballantyne, Inge van der Jagt, Ingrid Ystgaard, Jennifer Harland, Rebecca Nicholson, Sheila Hamilton-Dyer, Helle Tessand Baalsrud, Marine Servane Ono Brieuc, Lane M. Atmore, Finlay Burns, Ulrich Schmölcke, Kjetill S. Jakobsen, Sissel Jentoft, David Orton, Anne Karin Hufthammer, James H. Barrett and Bastiaan Star
Abstract
Abstract
Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.
Published Online: 4 June 2021
Potential applications of biomolecular archaeology to the ecohistory of sea turtles and groupers in Levant coastal antiquity
Potential applications of biomolecular archaeology to the ecohistory of sea turtles and groupers in Levant coastal antiquity
Rachel M.Winter, Willemien de Kock, Per J.Palsbøll, Canan Çakirlar
Abstract
Abstract
Humans have been exploiting marine resources along the Levantine coast for millennia. Advances in biomolecular archaeology present novel opportunities to understand the exploitation of these taxa in antiquity. We discuss the potential insights generated by applying collagen peptide fingerprinting, ancient DNA analysis, and stable isotope analysis to groupers (Serranidae) and sea turtles (Chelonia mydas and Caretta caretta) in the Levant. When combined with traditional zooarchaeological techniques, biomolecular archaeology offers utility to further investigate human impacts on marine ecosystem
Published Online: 6 March 2021
Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries
Exploitation shifted trophic ecology and habitat preferences of Mediterranean and Black Sea bluefin tuna over centuries
Adam J. Andrews, Christophe Pampoulie, Antonio Di Natale, Piero Addis, Darío Bernal-Casasola, Veronica Aniceti, Gabriele Carenti, Verónica Gómez-Fernández, Valerie Chosson, Alice Ughi, Matt Von Tersch, Maria Fontanals-Coll, Elisabetta Cilli, Vedat Onar, Fausto Tinti, Michelle Alexander
Abstract
Abstract
During recent decades, the health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution and anthropogenic-driven climate change. Due to a lack of long-term ecological data, we have a poor grasp of the true impact on the diet and habitat use of fishes. This information is vital if we are to recover depleted fish populations and predict their future dynamics. Here, we trace the long-term diet and habitat use of Atlantic bluefin tuna (BFT), Thunnus thynnus, a species that has had one of the longest and most intense exploitation histories, owing to its tremendous cultural and economic importance. Using carbon, nitrogen and sulphur stable isotope analyses of modern and ancient BFT including 98 archaeological and archival bones from 11 Mediterranean locations ca. 1st century to 1941 CE, we infer a shift to increased pelagic foraging around the 16th century in Mediterranean BFT. This likely reflects the early anthropogenic exploitation of inshore coastal ecosystems, as attested by historical literature sources. Further, we reveal that BFT which migrated to the Black Sea–and that disappeared during a period of intense exploitation and ecosystem changes in the 1980s–represented a unique component, isotopically distinct from BFT of NE Atlantic and Mediterranean locations. These data suggest that anthropogenic activities had the ability to alter the diet and habitat use of fishes in conditions prior to those of recent decades. Consequently, long-term data provide novel perspectives on when marine ecosystem modification began and the responses of marine populations, with which to guide conservation policy.
Published online: 10 August 2023
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