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• Atmore, Lane & Star, Bastiaan (2026). Beyond the scales: Marine archaeogenomics for the conservation and restoration of fisheries. Science. ISSN 0036-8075. 393(6810), p. 472–479. doi: 10.1126/science.aeg0333. Full text in Research Archive Show summary

  Protection and restoration of marine environments are essential for food security and climate change mitigation. Yet historical and archaeological research have shown that conservation and management often rely on arbitrary ecological baselines in ecosystems already shaped by long-term human impacts. Archaeogenomics, the combination of ancient DNA (aDNA) and whole-genome sequencing, provides invaluable insights into these impacts. Recent improvements in laboratory and computational techniques enable the assessment of past fish population dynamics, migration patterns, historical trade routes, long-term anthropogenic pressures, and responses to environmental change. This Review compiles aDNA research on archaeological fish remains, emphasizing studies from 2020 to 2025 that used whole-genome analysis to investigate historical fisheries and marine ecosystem change. We highlight the growing potential of archaeogenomics to inform restoration, conservation, sustainable fisheries management, and climate adaptation strategies worldwide.

• Buss, Danielle L.; O’Connell, Tamsin C.; Evans, Sally; Kneale, Catherine; Osborn, Joanna & Atmore, Lane [Show all 15 contributors for this article] (2025). Historical niche partitioning of baleen whales in the western South Atlantic. Marine Ecology Progress Series. ISSN 0171-8630. 765, p. 115–136. doi: 10.3354/meps14887. Full text in Research Archive
• Eriksen, Emma Falkeid; Andrews, Adam Jon; Nielsen, Svein Vatsvåg; Persson, Per; Malca, Estrella & Onar, Vedat [Show all 19 contributors for this article] (2025). Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA. Heredity. ISSN 0018-067X. 134, p. 175–185. doi: 10.1038/s41437-025-00745-1. Full text in Research Archive Show summary

  Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.

• Andrews, Adam Jon; Eriksen, Emma Falkeid; Star, Bastiaan; Præbel, Kim; Natale, Antonio Di & Malca, Estrella [Show all 19 contributors for this article] (2025). Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 122(21). doi: 10.1073/pnas.2409302122. Full text in Research Archive Show summary

  Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing 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 5,000 y ago, uncovering several 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 were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.

• Atmore, Lane; Jagt, Inge van der; Boilard, Aurélie; Häberle, Simone; Blevis, Rachel & Dierickx, Katrien Alfred C [Show all 11 contributors for this article] (2024). The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA. Global Change Biology. ISSN 1354-1013. 30(12). doi: 10.1111/gcb.70010. Full text in Research Archive Show summary

  Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools—including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)—that can accurately detect the population identity of individual fish. However, the biological relevance of such tools over longer periods of time remains unknown. Here, we demonstrate that diagnostic SNP panels designed for contemporary MSA in Atlantic herring have a millennium-long biological relevance and applicability. We assign the population identity of ancient Atlantic herring specimens—obtained through famously profitable historic fisheries—up to 1300 years old from eight archaeological sites across Europe. Analyzing contemporary and ancient whole-genome data, we obtain evidence for the long-term mixed-stock exploitation of Atlantic herring. Despite such mixed-stock exploitation, we exclusively identify autumn-spawning herring amongst these archaeological remains, indicative of a specific biological availability or cultural preference for certain herring ecotypes in the past. Moreover, our results show that herring demographic patterns were relatively stable until the dramatic disruptions and stock collapses during the 20th century. We find small but significant reductions in genetic diversity over time, indicating long-term evolutionary consequences from 20th-century stock declines. The long-term applicability of diagnostic SNP panels underscores their biological relevance and cost-effective application for the genetic monitoring of herring stocks and highlights the utility of ancient DNA to obtain insights in herring ecology and population dynamics.

• Buss, Danielle L.; Atmore, Lane; Zicos, Maria H.; Goodall-Copestake, William P.; Brace, Selina & Archer, Frederick I. [Show all 15 contributors for this article] (2023). Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales. Genes. 14(5), p. 1–23. doi: 10.3390/genes14051038. Full text in Research Archive Show summary

  Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

• Kersten, Oliver Sven; Star, Bastiaan; Krabberød, Anders Kristian; Atmore, Lane; Tørresen, Ole K. & Anker-Nilssen, Tycho [Show all 12 contributors for this article] (2023). Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. Science Advances. 9(40). doi: 10.1126/sciadv.adh1407. Full text in Research Archive Show summary

  The Arctic is experiencing the fastest rates of global warming,leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidenc eof recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins(Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F.a. naumanni and the temperate, smaller-sized subspecies F.a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F.a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations.Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.

• Atmore, Lane & Buss, Danielle Lia (2023). Historical land use patterns provide insight into contemporary insect diversity loss. Molecular Ecology. ISSN 0962-1083. 32(13), p. 3353–3355. doi: 10.1111/mec.17044. Full text in Research Archive Show summary

  Healthy insect populations are vital for maintaining natural ecosystems and essential to global food security. The ongoing dramatic loss of insect species and biomass is thus a global cause for concern, with much focus on this topic in the media. Yet, determining the mechanism behind these declines remains difficult, particularly when attempting to differentiate between anthropogenic drivers of biodiversity loss and long-term natural fluctuations. In a From the Cover manuscript in this issue of Molecular Ecology, Crossley et al. (2022) examined the long-term impact of land use change on freshwater insects by estimating levels of genetic diversity with publicly available data for the cytochrome c oxidase subunit 1 (CO1) mitochondrial locus from >700 aquatic insect species across the United States. Contemporary genetic diversity measures reflect both current and past demography and therefore are related to both past and present habitat change. Crossley et al. found that environments with greater cropland extent over the last 200 years were associated with lower genetic diversity in contemporary aquatic insect populations. This indicates that historical land use is an important factor in contemporary population dynamics. Most critically, in regions of historical cropland cover that have been converted towards other uses (such as urban environments) more recently, aquatic insect populations exhibited higher levels of genetic diversity, indicating a possible rebound in insect populations after cessation of agricultural activity. This study highlights the power of using publicly available data to answer crucial questions regarding the current biospheric emergency.

• Garcia, Lourdes Martinez; Ferrari, Giada; Cuevas, Angelica; Atmore, Lane Margaret; López-Arias, Begoña & Culling, Mark [Show all 18 contributors for this article] (2022). Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 289(1985). doi: 10.1098/rspb.2022.1107. Full text in Research Archive Show summary

  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.

• Atmore, Lane Margaret; Ferrari, Giada; Garcia, Lourdes Martinez; Jagt, Inge van der; Blevis, Rachel & Granado, José [Show all 14 contributors for this article] (2022). Ancient DNA sequence quality is independent of fish bone weight. Journal of Archaeological Science. ISSN 0305-4403. 149. doi: 10.1016/j.jas.2022.105703. Full text in Research Archive Show summary

  The field of ancient DNA (aDNA) typically uses between 50 and 200 mg of minimum input weight of bone material for the extraction of DNA from archaeological remains. While laboratory and analysis techniques have focused on improved efficiency of extracting useable sequence data from older and poorer quality remains, bone material input requirements have rarely been critically evaluated. Here, we present the aDNA analysis of 121 size-constrained Atlantic herring remains – weighing between <10 and 70 mg – that were individually sequenced to explore the capacity of successful aDNA retrieval from small archaeological remains. We statistically evaluate the relationship between bone weight and several response variables, including library success, endogenous DNA content, and library complexity, i.e., the number of unique molecules that are obtained. Remarkably, we find no relationship between bone weight and library success, levels of endogenous DNA, or library complexity. Our results imply that – at least in the case of fish bone – even minute bones can yield positive results and that the presumed minimum sample size required should be re-evaluated. Archaeological site, instead of bone size, is the primary driver of DNA sequence quality. Our work expands the number of specimens considered suitable for aDNA analyses, and therefore facilitates efforts to minimize the destructive impact of aDNA research and mediate some of the ethical concerns surrounding destructive analysis.

• Atmore, Lane Margaret; Garcia, Lourdes Martinez; Makowiecki, Daniel; André, Carl; Lõugas, Lembi & Barrett, James [Show all 7 contributors for this article] (2022). Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 119(45). doi: 10.1073/pnas.2208703119. Full text in Research Archive Show summary

  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.

• Racimo, Fernando; Valentini, Elia; León, Gaston Rijo De; Santos, Teresa L.; Norberg, Anna & Atmore, Lane Margaret [Show all 11 contributors for this article] (2022). The biospheric emergency calls for scientists to change tactics. eLIFE. 11. doi: 10.7554/eLife.83292. Full text in Research Archive Show summary

  Our current economic and political structures have an increasingly devastating impact on the Earth’s climate and ecosystems: we are facing a biospheric emergency, with catastrophic consequences for both humans and the natural world on which we depend. Life scientists – including biologists, medical scientists, psychologists and public health experts – have had a crucial role in documenting the impacts of this emergency, but they have failed to drive governments to take action in order to prevent the situation from getting worse. Here we, as members of the movement Scientist Rebellion, call on life scientists to re-embrace advocacy and activism – which were once hallmarks of academia – in order to highlight the urgency and necessity of systemic change across our societies. We particularly emphasise the need for scientists to engage in nonviolent civil resistance, a form of public engagement which has proven to be highly effective in social struggles throughout history.

• Padilla-Iglesias, Cecilia; Atmore, Lane Margaret; Olivero, Jesús; Lupo, Karen; Manica, Andrea & Isaza, Epifanía Arango [Show all 8 contributors for this article] (2022). Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 119(21). doi: 10.1073/pnas.2113936119. Full text in Research Archive Show summary

  The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here, we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density are explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also estimate the range of hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by our newly compiled dataset of dated archaeological sites. Finally, we show that genomic estimates of divergence times between CAHG groups match our ecological estimates of periods favoring population splits, and that recoveries of connectivity would have facilitated subsequent gene flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.

• Garcia, Lourdes Martinez; Ferrari, Giada; Oosting, Tom; Ballantyne, Rachel; Jagt, Inge van der & Ystgaard, Ingrid [Show all 20 contributors for this article] (2021). Historical demographic processes dominate genetic variation in ancient Atlantic cod mitogenomes. Frontiers in Ecology and Evolution. 9, p. 1–14. doi: 10.3389/fevo.2021.671281. Full text in Research Archive Show summary

  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.

• Atmore, Lane Margaret; Aiken, Magie & Furni, Fabricio (2021). Shifting Baselines to Thresholds: Reframing Exploitation in the Marine Environment. Frontiers in Marine Science. 8, p. 1–15. doi: 10.3389/fmars.2021.742188. Full text in Research Archive Show summary

  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.

• Ferrari, Giada; Atmore, Lane Margaret; Jentoft, Sissel; Jakobsen, Kjetill Sigurd; Makowiecki, Daniel & Barrett, James [Show all 7 contributors for this article] (2021). An accurate assignment test for extremely low-coverage whole-genome sequence data. Molecular Ecology Resources. ISSN 1755-098X. p. 1–15. doi: 10.1111/1755-0998.13551. Full text in Research Archive Show summary

  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.

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• Atmore, Lane Margaret (2021). Using extremely low-coverage sequence data to accurately assign structural variation haplotypes in ancient specimens. Full text in Research Archive
• Atmore, Lane Margaret; Aiken, Magie & Furni, Fabricio (2021). Shifting Thresholds to Baselines: Reframing Exploitation in the Marine Environment. Full text in Research Archive
• Atmore, Lane (2020). What is Nature? A Personal and Theoretical Journey. Full text in Research Archive

View all works in NVA