15 Fully-funded PhD Studentships 2019 for PhD students or Early Stage Researchers, SeaChanges Network

Atlantic cod (Gadus morhua) is of profound economic and cultural value for communities around the North Atlantic Ocean. The history of exploitation for this species dates back millennia , which has made it difficult to quantify the extent of human impact since prehistory. For example, intensive harvest over the last century has been associated with phenotypic changes consistent with fisheries induced evolution (FIE), but it is unclear if analogous changes occurred in preceding periods. To address such questions, the long-term perspective that can be obtained through the comparative analysis of ancient and modern material is essential. ESR 1 will study demographic and evolutionary patterns through the analysis of DNA preserved in Atlantic cod bones from archaeological sites of up to 9000 years BP to now using state-of-the-art genomic tools and zooarchaeology.

ESR 1 will be trained to obtain and analyze genome-wide data from archaeological cod samples, selected from dozens of locations (in cooperation with ESR 2) across northern and western Europe with an aim to: (a) reconstruct long-term patterns of demography and selection in Atlantic cod populations; (b) resolve historic trade routes by identifying the target populations of fisheries industries during the Viking Age (AD 800-1050) and Middle Ages (AD 1050-1540); and (c) investigate associations between expanding fisheries, cod population declines or collapse, and anthropogenic selection. The candidate will also obtain experience in zooarchaeology by studying phenotypic characters via secondment at Cambridge University.

ESR 2: Noise into signal: identification challenges and the medieval fishing revolution (Cambridge)

Cod family fishes (Gadidae) were one of the most important trade goods of marine origin in medieval and early modern Europe. Yet the most abundant archaeological remains of these fishes, vertebrae, are often left unidentified to species and are almost always omitted from studies of changing fish-length distributions. These omissions occur because it is relatively difficult to identify gadid vertebrae beyond the level of family or genus, and to ascertain where within the vertebral column they belong—interrelated issues given variability in both morphology and size of vertebrae from anterior to posterior (‘head’ to ‘tail’). Much information regarding changes in fishing and fish-trade strategies is thus lost.

ESR 2 will develop protocols for replicable identification using quantitative image analysis of both 2D and 3D (CT-scanned) images of gadid vertebrae. The resulting method of classification will then be applied to archaeological material from rural fishing settlements around the North Atlantic and urban fish-consumption sites in Europe (e.g. London, York), to assess changes in the taxa and sizes exploited during the process of commercialisation and expanding trade. ZooMS collagen fingerprinting (secondment with York) and aDNA will be employed respectively to corroborate species identifications and—in cooperation with ESR 1—to detect specimens traded from distant populations .

ESR 3: Tracing the early origins of the Atlantic herring trade using ancient DNA (Oslo)

Herring (Clupea sp.) was among the first marine fish to see widespread exploitation in medieval Europe and, like Atlantic cod, has supported an important pan-European trade network for centuries. Its trade has been so significant to so many countries that it has been regarded as the most commercially important fishery, with strategic implications. During its long history, this trade was influenced by dramatic cycles in herring abundance —most likely due to climatic fluctuations— nonetheless, the origins of this trade are obscure, pre-dating documentary sources. In fact, very little is known about the historic population structure of the herring populations that supported this extensive trade. Increasingly sensitive ancient DNA (aDNA) and isotopic methods in combination with the detailed insights from modern whole genome sequencing data now provide the opportunity to explore long-term human and climatic impacts in this keystone species.

ESR 3 will train the candidate to generate and analyse genome-wide data from DNA preserved in ancient Atlantic (Clupea harengus) or Baltic (C. harengus membras) and isotope data from herring bones from archaeological sites from AD 700 onwards and compare these to contemporary specimens. This ESR aims to (a) identify the source populations and extent of historic trade routes, tracing the rise and fall of e.g. the high medieval Sound herring fishery and the Bohuslan herring periods in the late and post-medieval periods using both isotopic and aDNA methodology —via secondment with Cambridge University; (b) assess the long-term temporal variation of two major natural herring ecotypes (autumn vs. spring spawning herring) in association with climatic time series; (c) investigate the collapse of a herring population which was driven to extinction through the closure of a major inland sea in the early 20th century —through secondment with Groningen University.

ESR 4: Flatfish and the origins of European Marine fishing (York)

Sea fishing was apparently rare in much of western Europe until a rapid expansion in exploitation of marine taxa, particularly herring and gadids, in the 10th and 11th centuries AD. Pleuronectid flatfish are amongst the earliest potentially marine taxa to be found in large numbers on medieval sites, often pre-dating this 'fish event horizon', but have largely been excluded from the debate due to (a) difficulty distinguishing the key species, particularly plaice (Pleuronectes platessa) and flounder (Platichthyes flesus), and (b) potential for flounder to be caught in estuarine as well as marine waters. Identification difficulties also hinder construction of taxon-specific time-series that might reveal changing exploitation patterns and/or the impact of fishing pressure on these species.

ESR 4 will undertake training in morphological identification of flatfish cranial bone―via secondment to Groningen―before developing ZooMS and geometric morphometric protocols for identifying flatfish vertebrae, and a stable isotope (carbon, nitrogen, sulphur) method for distinguishing marine and estuarine catches. These will be applied to samples from key medieval and early medieval sites in eastern England, northern France, and the Netherlands, to (a) refine understanding of the historically highly significant transition to marine fishing, and (b) produce taxon- and habitat-specific time series of metrical and capture age data (the latter from annuli in vertebral centra via secondment at CSIC Vigo), which can be used to track potential early impacts of fishing pressure on growth rates prior to industrialisation.

ESR 5: Tracking the decline of salmon in the North Sea basin (York)

As an anadromous fish that migrates annually inland to spawn, Atlantic salmon (Salmo salar) is potentially subject to human impact both from fishing and from modification of freshwater systems. Recent research based primarily upon historical data implicates damming and watermill construction in the collapse of salmon stocks around much of the North Sea basin, particularly the Rhine and Meuse systems. With relevant quantitative historical data extremely rare prior to c.AD 1500, however, archaeological remains are necessary to assess this hypothesis further. but their contribution has so far been limited by (a) difficulty distinguishing salmon from Atlantic trout (S. trutta) remains, and (b) the possibility that some remains represent northern imports from e.g. Scotland rather than locally caught fish.

ESR 5 will explore the impact of the medieval agricultural revolution and subsequent intensification on salmon through a systematic review of archaeological finds around the North Sea basin, employing ZooMS collagen fingerprinting and geometric morphometrics (GMM) to refine identifications. Working with an app developer partner, the ESR will develop the latter into a free mobile platform for automated on-site identification of Salmonidae scales—with potential to expand to other taxa in future, this should become a powerful tool for use in the field, fishmarket, or museum. Potential imports will be assessed via aDNA, working with Oslo and employing modern and ancient Scottish reference data. Additional guidance on salmon ecology and contemporary relevance will be provided by the Atlantic Salmon Trust, while the student will work closely with ESR 6 to understand wider ecosystems.

ESR 6: Sedimentary fish archives and diadromous taxa (Copenhagen)

Diadromous fish, i.e. those which migrate between rivers and seas during their spawning cycle, have been an important food resource in most regions of Europe for longer than their marine counterparts. Subject not only to fishing pressure but also to pollution and habitat modification in rivers and lakes, they are especially vulnerable to human activity. River-spawning anadromous fish, in particular, are often subject to intensive fishing during their spawning runs, which may also be disrupted by construction of dams and weirs. The presence of various migratory species in Europe’s rivers is known to have contracted significantly over the past century, but the true time-depth of this decline remains to be established, as does the relative contribution of fishing pressure vs. damming and other modifications to river systems.

ESR 6 will address this issue using sedimentary aDNA (sedaDNA). While historical records may reveal fluctuating prices, and archaeological remains provide evidence of consumed taxa, neither is direct evidence for the presence or relative abundance of migratory fish in particular freshwater systems. Continuously deposited lake sediments, by contrast, have recently been shown to contain genetic remains of past aquatic communities, each layer representing a temporal environmental archive in which we can identify and quantify the presence of migrating fish populations. Using sedaDNA analysis, combined with radiometric dating, the ESR will construct time-series of diadromous fish presence from cores taken in selected waters within the North Sea and Danube basins, and compare these with corresponding archaeological records to assess the complementarity of these sources. They will work closely with ESRs 5 (Atlantic salmon) and 15 (Black Sea fauna) to this end, and will work with NGO partners to explore potential of ancient sturgeon data for contemporary management and awareness-raising.

ESR 7: Impacts of industrial whaling: scale, ecological and evolutionary legacies (Groningen)

The large baleen whales were driven to near-extinction by industrial whaling during the 16th–20th centuries, largely by whaling fleets operating from European and North American ports. Several key questions remain about the effects of this large-scale removal, such as: (a) what were the abundances of pre-whaling populations; (b) did whaling and subsequent recovery lead to changes in population structure, connectivity and prey preferences; and (c) did the extreme population bottlenecks due to whaling result in long-term negative impacts, such as loss of adaptive genetic variation and/or an increase in mutational load, thereby endangering the long-term persistence of baleen whales? These questions can only be answered by the integration of modern and historic genomic data.

ESR 7 will conduct genome-wide scans and isotope analyses of historic bones collected at historic Antarctic and Arctic whaling stations to compare with similar data from modern baleen whale samples. Historic sample analyses will be conducted during secondment at University of British Columbia

ESR 8: Exploitation of Atlantic walruses by European whalers, c. AD 1600 to 1900 (Groningen)

ESR 8 will combine aDNA with historical records to explore the impact of recent-historic human exploitation of Atlantic walruses (Odobenus rosmarus rosmarus) in the waters around Greenland. From the early 17th to early 20th centuries, European whalers intensively exploited baleen whales in the waters between Greenland and Canada, as well as along the eastern Greenlandic coast and around Svalbard. Whenever possible, hunters also acquired walruses—abundant in area waters, and highly valued for their blubber and ivory. Though some scholarly attention has been paid to social, economic and ecological implications of whale stock depletion, less is known of the extent and impacts on walrus populations. Walruses in the Davis Strait stock are seasonally migratory, moving in and out of Canadian waters during the annual cycle, while the eastern Greenlandic stock is largely isolated and its animals tends not to migrate seasonally. Given what is known of the ecological conservatism of walruses and their sensitivity to human disturbance and habitat displacement, a working hypothesis is that even the ‘secondary’—or opportunistic—hunting of walruses by European whalers had a significant impact on many local stocks.

Drawing on (a) exceptionally well-preserved remains at Paleo- and Neo-Inuit (non-European Indigenous) archaeological sites, as well as (b) historical catchment records from whaling logbooks, ESR 8 will model walrus populations before the arrival of European hunters, and assess the impact of this hunting on genetic diversity of walruses across a range of different stocks (e.g. Davis Strait, Eastern Greenland, and potentially other areas including the Foxe basin, etc.). Based in Groningen with a secondment at Copenhagen, ESR 8 will compare historical catchment records with contemporary stock estimates, and will analyse archaeological walrus aDNA samples held in repositories in Canada and Denmark to elucidate genetic diversity across the region before industrial hunting.

ESR 9 : Scrimshaw: unlocking the cultural and biological archive of sea mammal art (Cambridge)

During the middle decades of the 19th century a folk-art tradition—scrimshaw—using the teeth of sperm whales (Physeter macrocephalus) flourished among the crews of industrial whaling ships. It is best known from New England whalers, but a London-based South Sea sperm whale industry resulted in many objects incorporating recognizably British motifs. An important selection is now held by the Scott Polar Research Institute (University of Cambridge), providing a unique pre-industrial biological archive of the cetacean population(s) exploited by the London whalers before the use of steamships and exploding harpoons.

ESR 9 will explore the use image analysis to infer associated groups of objects, and microCT-scanning to age the whales based on growth-layer groups. Moreover, samples drilled from the apex of the concave base of each tooth will facilitate aDNA analysis to assess genetic diversity vis-à-vis modern populations (secondment at Oslo) and stable isotope analysis to assess dietary/ecosystems heterogeneity. We will explore various genome-wide approaches for the comparative analyses of these specimens. This study has the potential to re-evaluate the time depth of the extremely low genetic heterogeneity of modern sperm whales and to produce an artefact-based ‘environmental history’ of the London whaling industry that is unparalleled in its interdisciplinary breadth and synergies.

ESR 10: Hindcasting to forecast: archaeobiology of the European hake fisheries (CSIC-Vigo)

Understanding of European hake (Merluccius merluccius) population structure and resilience is challenged by the shallow temporal window that existing fisheries data provide. While historical data are finally being recognised as essential for understanding long-term impacts of sustained exploitation on fisheries productivity, historic landing records can nevertheless be inaccurate or incomplete, and are usually only available for the last few centuries. By contrast, marine fishing intensification in the NE Atlantic dates back to at least AD 1,000, with hake amongst the best-represented marine fishes on archaeological sites in SW Europe. Historical information from a relatively recent past may thus yield ecological baselines already far removed from ‘pristine’ or pre-industrial (i.e. non-intensive) conditions.

To explore long-term human impact on Iberian hake fisheries, ESR 10 will pair zooarchaeological and biomolecular analyses of bones from archaeological sites across Europe, dating back to the 5th century BC, with modern hake samples, to construct a baseline of changes in life-history, biology, and ecology. Analyses will include (a) bone morphometrics, allowing estimation of size and growth patterns; (b) ancient DNA analysis (via secondment in Bologna), identifying SNPs to reveal population structure and adaptation (resilience) in different historical times; and (c) historical records of landings, current knowledge on hake biology, and reconstruction of paleoclimatic changes. These tools will be combined to understand long-term impacts of sustained exploitation on fisheries productivity, adopting the ‘hindcasting first to forecast after’ approach to enhance our perception of hake biology and ecology, and improve population management. It is expected to identify past regime shifts in productivity associated with environmental and exploitation factors, improving capacity to predict future changes in a key commercial species.

ESR 11: Current and historical threats to dolphins in the Atlantic and the Mediterranean (CSIC-Vigo)

Historical abundance trends in small cetaceans are poorly understood, with baselines for current conservation efforts in Europe being based on relatively recent abundance estimates from sighting surveys. Common dolphins, Delphinus delphis, are currently the most abundant cetacean in European Atlantic waters but this species has declined substantially in the Mediterranean. Differences in the history of fishery exploitation may help account for this discrepancy, with overfishing believed to have caused depletion of common dolphin prey in the Mediterranean. However, the evidence underlying this view is largely anecdotal and limited to the modern era, and the ecologically similar striped dolphin Stenella coeruleoalba may have expanded its range. This ESR project aims to improve understanding of small cetacean population trajectories and their drivers in the Atlantic (Iberian coast) and Mediterranean.

ESR 11 will: (a) apply novel tools—photogrammetry, sampling and analysis of breath microbiota (supported by a secondment at Copenhagen)—to provide indices of individual health status and condition that can be used to infer population status; (b) reconstruct dolphin trophic interactions and investigate impacts of fishing by analysing stomach contents and stable isotopes (SI) in stranded and bycaught animals; (c) extend results on diet through lifetimes by SI analysis of growth rings in dolphin teeth and into deeper time using museum and archaeological specimens; (d) use data from necropsies and interviews with fishermen to assess fishery bycatch mortality; (e) analyse historical and archaeological records to construct timelines of fishery activity and dolphin population status in the study areas (secondment at Groningen); and (f) explore historical scenarios of dolphin-fishery interactions by adapting contemporary ecosystem models.

ESR 12: Exploring the correlations between environmental/ecological drivers and past/contemporary genetic diversity of Atlantic and Mediterranean bluefin tuna populations (Bologna)

Among the many fish species commercially exploited since prehistoric times, bluefin tuna (BFT, Thunnus thynnus) is both one of the most economically significant and one of the most threatened. ESR 12 will explore and highlight correlations between environmental and ecological drivers (including anthropogenic ones) and past and present genetic diversity of the Atlantic and Mediterranean BFT populations, by measuring (a) temporal variation in environmental and ecological proxies and (b) paleo- and neo-genomic adaptive variation in BFT. The ESR will take a multidisciplinary approach, combining omics' methods (ancient DNA, genomics, palaeoproteomics) with stable carbon and nitrogen isotope analyses, applying these to both archaeological/historical (c. 2,000 – 100 BP) and contemporary BFT specimens, either already in-hand or available via project partners

Using genome scan techniques, ESR 12 will evaluate the effects that environmental disturbances (habitat changes, pollution, stock overexploitation) have on biological adaptation, through analysis of the evolution of structural/functional genomic components such as adaptive traits. The ESR will use ZooMS for initial identification/screening of ancient tuna remains, expanding this technique to Scombridae for the first time via a secondment at Copenhagen. Stable isotope analyses, via secondment at York, will provide signatures of environmental and ecological conditions. The student will cooperate with ESR 15 regarding potential additional ancient samples from the Black Sea.

ESR 13: Foraging ecology and catch size in Mediterranean groupers before and after the rise of coastal urbanism, c. 2500 BC – AD 500 (Groningen)

Groupers (Epinephelus) are a keystone taxon for the rocky shorelines of the Mediterranean Sea. As such, they are crucial to conservation efforts, especially in Marine Protected Areas (MPAs). Mediterranean Groupers are under increasing anthropogenic pressure, especially caused by overfishing and habitat loss. Assessment and management strategies, however, typically lack the long-term ecological perspective required critically to assess ecological baselines. Groupers were fished in the Mediterranean throughout the Holocene. Their relative abundance in the archaeological record increases at times of increased urbanisation and elite trade, for example during the Late Bronze Age (1600-1200 BC), and systematic exploitation takes place from the Greek colony period (750 BC) onwards. Their archaeological record has unfulfilled potential to define variation in groupers’ status under distinct environmental conditions and exploitation intensity through time. Archaeological grouper bones can provide catch intensity, catch size, and trophic level data from zooarchaeological and nitrogen and carbon isotopic analyses.

ESR 13 will employ ZooMS, metrics, and stable isotope analyses of recent and archaeological groupers to reveal the long-term ecological history of groupers in the eastern Mediterranean, from prehistoric times to the Late Roman Period in comparison with modern data from MPAs. Training in rocky reef ecology will be provided via partners in Nice; ZooMS and stable isotopes via secondment at York.

ESR 14: Green sea turtle population dynamics and foraging ecology in the ancient Mediterranean (Groningen)

ESR 14 will combine genetic and stable isotope analyses of ancient green sea turtle (Chelonia mydas) mater to assess effects of changes in human exploitation and foraging ecology upon connectivity and effective population size in the eastern Mediterranean c. 2500 BC – AD 500. Sea turtles are endangered marine flagship species for which effective conservation relies upon knowledge of their ecology and past population dynamics. While humans have exploited sea turtles in the Mediterranean since the Late Quaternary, periodic increases in relative abundance of sea turtle bones at archaeological sites coincide with periods of urbanisation, technological advancement, and intensified maritime interconnectivity, e.g. during the Iron Age, when coastal towns grew under the influence of Phoenician trade networks.

ESR 14 will analyse stable isotopes and DNA from archaeological sea turtle material from periods of both intensive and small-scale exploitation during the Late Iron Age and Roman periods. Ancient DNA data will serve as the basis to infer temporal changes in population sizes and connectivity, while nitrogen and carbon isotopes (secondment at York) will provide data on diet and habitat use, which will be used to explore any linkage between population dynamics and dietary habits. Custom-made aDNA capture methods will be employed in conjunction with massive parallel sequencing methods (secondment at Geogenetics, Copenhagen).

ESR 15: Exploitation and collapse of the Black Sea marine fauna (Copenhagen)

The archaeological record of the Black Sea region exhibits a great variety of economic and cultural practices dating back millennia. Marine resources appears to have played an important role in economy and diet, as documented by the recovery of small cetaceans and key fish species at archaeological sites from the Chalcolithic to Byzantine ages (c. 4000 BC–AD 1300). The cetaceans inhabiting the Black Sea (harbour porpoise, common dolphin, and bottlenose dolphin) are recognised as separate subspecies of special management and conservation concern, with IUCN listings as endangered or threatened. These have all been subject to periods of extensive hunting, and are now affected by fisheries bycatch and consequences of ctenophore invasion, undermining their trophic base. Similarly, overexploitation has decimated some fish stocks and led to the extermination of others. How did past marine resource use and environmental changes affect Black Sea cetaceans and key fish species? Did it reduce gene flow or adaptive genetic variation? Did cumulative pressures lead to trophic alterations, and how have these shaped the current marine ecosystem?

To address these questions, ESR 15 will review the Black Sea zooarchaeological record and modern ecological data (working with project partners in Ukraine) before applying genomic, proteomic, and isotopic analyses to track changes in the genomes, demography, and trophic interactions of Black Sea cetaceans, turbot, and anchovies in response to major shifts in environment and in human cultural and economic practices. This will serve to identify past and present pressures on marine species, understand their past and present cultural and economic role, and provide recommendations for their conservation and management. Genomic and proteomic expertise is available in Copenhagen; dietary insights and predator-prey interactions will be addressed via secondment at CSIC-Vigo, where the student will benefit from comparison with ESR 11’s work on small cetaceans in the Mediterranean and Atlantic.

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