An environmental (pre)history of European fishing: past and future archaeological contributions to sustainable fisheries

Large females connect Atlantic cod spawning sites

The Earth's ecosystems are increasingly deprived of large animals. Global simulations suggest that this downsizing of nature has serious consequences for biosphere functioning. However, the historical loss of large animals means that it is now often impossible to secure empirical data revealing their true ecological importance. We tracked 465 mature Atlantic cod (Gadus morhua) during their winter spawning season and show that large females (up to 114 centimeters in length), which are still found in mid-Norway, were characterized by more complex movement networks compared with smaller females. Large males were sparse but displayed similar movement patterns. Our finding implies that management programs promoting large fish will have positive impacts on population resilience by facilitating the continued use of a diversity of spawning habitats and the connectivity between them.

The potential of historical ecology to aid understanding of human-ocean interactions throughout the Anthropocene

Marine historical ecology emerged in the scholarly literature with the aim of understanding long-term dynamics in marine ecosystems and the outcomes of past human-ocean interactions. The use of historical sources, which differ in temporal scale and resolution to most scientific monitoring data, present both opportunities and challenges for informing our understanding of past marine ecosystems and the ways in which human communities made use of them. With an emphasis upon marine social-ecological changes over the past 200 years, I present an overview of the relevant historical ecology literature and summarise how this approach generates a richer understanding of human-ocean interactions and the legacies associated with human-induced ecosystem change. Marine historical ecology methodologies continue to be developed, whereas expanded inter- and multidisciplinary collaborations provide exciting avenues for future discoveries. Beyond scholarship, historical ecology presents opportunities to foster a more sustainable relationship with oceans going forward: by challenging ingrained perceptions of what is "normal" within marine ecosystems, reconnecting human communities to the oceans and providing cautionary lessons and exemplars of sustainable human-ocean interactions from the past. To leverage these opportunities, scholars must work alongside practitioners, managers and policy makers to foster mutual understanding, explore new opportunities to communicate historical findings and address the challenges of integrating historical data into modern-day frameworks.

Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation

Ecological disruption due to human impacts is evident worldwide, and a key to mitigation lies in characterizing the underlying mechanisms of species and ecosystem stability. Here we show that three extensive “supergenes” are maintained in Atlantic cod by stabilizing selection, tying these genes to the persistence of a keystone species distributed across the northern Atlantic Ocean. Removal of this species has caused severe ecosystem reshuffling in several areas of its range. Genomic inference of historic stock sizes further shows that cod has been under pressure in the North Sea system since the Viking period, in line with zooarchaeological records. Expansion of fisheries in Northern Europe through the past millennium is well documented and supports the inferred long-term declines.

Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological and climatic transitions through the history of our planet. Due to the increasing degree of ecological abruption caused by human influences many advocate that we now have entered the geological era of the Anthropocene, or “the age of man.” Considering the ongoing mass extinction and ecosystem reshuffling observed worldwide, a better understanding of the drivers of ecological stasis will be a requisite for identifying routes of intervention and mitigation. Ecosystem stability may rely on one or a few keystone species, and the loss of such species could potentially have detrimental effects. The Atlantic cod (Gadus morhua) has historically been highly abundant and is considered a keystone species in ecosystems of the northern Atlantic Ocean. Collapses of cod stocks have been observed on both sides of the Atlantic and reported to have detrimental effects that include vast ecosystem reshuffling. By whole-genome resequencing we demonstrate that stabilizing selection maintains three extensive “supergenes” in Atlantic cod, linking these genes to species persistence and ecological stasis. Genomic inference of historic effective population sizes shows continued declines for cod in the North Sea–Skagerrak–Kattegat system through the past millennia, consistent with an early onset of the marine Anthropocene through industrialization and commercialization of fisheries throughout the medieval period.

Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

Spiny head croaker (Collichthys lucidus), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23 Mb, with a contig N50 of 74.92 kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24 Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24 Mb, with an improved scaffold N50 of 26.58 Mb. Based on our phylogenetic analysis, we observed that C. lucidus is much closer to Larimichthys crocea than Miichthys miiuy. We also predicted that many gene families were significantly expanded (p-value <0.05) in spiny head croaker; among them, some are associated with "calcium signaling pathway" and potential "inner ear functions." In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae.

Early evidence for historical overfishing in the Gulf of Mexico

Fisheries encompass complex interplays between social, economic, and environmental factors, but limitations on historical fisheries data can hamper efforts to identify and contextualize the long-term spatiotemporal patterns that shape them. We integrate 2500 years of stable isotope (δ³⁴S, δ¹³C, and δ¹⁵N) and zooarchaeological evidence from Gulf of Mexico fisheries to assess cultural, demographic, and technological changes affecting sheepshead (Archosargus probatocephalus) populations and fishing practices in Louisiana, USA. Concurrent with human population growth, average sizes of sheepshead caught decreased from the 1720s to 1830s. The size of fish caught after the 1830s increased to pre-1720 levels at the same time that isotopic compositions of fish bone collagen show that fish were being caught from a more diverse range of ecosystems, including distant seagrass beds. Our findings provide the first evidence for large-scale depressions of historical sheepshead populations and the processes driving them, including rapid human population growth and sustained harvesting pressure.

Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

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.

An osteometric approach to reconstruct the length and weight of Lutjanus argentiventris (Perciformes: Lujtanidae) for archaeological and ecological purposes

ABSTRACT Lutjanus argentiventris presents a large intertropical distribution within the Eastern Pacific, which is as important to fisheries now as it was in the pre-Hispanic period. The purpose of this article is to present an allometric model that enables the size and weight of L. argentiventris to be predicted, using the isolated bones found in archaeological and paleontological contexts or the stomach contents of ichthyophagous species. A modern collection of L. argentiventris from Ecuador was used, composed of 37 individuals covering a wide range of sizes and weights. The total length (TL), standard length (SL), and total fresh weight (W) of each individual was gathered. The TL of the sample ranged between 210 and 760 mm, the SL between 164 and 627 mm and the W ranged between 123 and 6550 g. The most frequent bones (15) and otoliths were chosen and 39 measurements were taken. The total length-weight relationship was W = 6E-06 TL3.1513 with R 2 = 0.997. In general, it was observed that the relationships between the TL and the bone measurements had a strong correlation (R² > 0.95). The allometric model will be useful not only for archaeologists but also for biologists working on historical ecology.

Unlocking the potential of ancient fish DNA in the genomic era

Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.