Rebekah Oomen

• Norderhaug, Kjell Magnus; Knutsen, Halvor; Filbee-Dexter, Karen; Sodeland, Marte; Jorde, Per Erik & Wernberg, Thomas [Show all 8 contributors for this article] (2024). The International Union for Conservation of Nature Red List does not account for intraspecific diversity. ICES Journal of Marine Science. ISSN 1054-3139. doi: 10.1093/icesjms/fsae039.
• Kao, Albert B.; Hund, Amanda K.; Santos, Fernando P.; Young, Jean-Gabriel; Bhat, Deepak & Garland, Joshua [Show all 8 contributors for this article] (2023). Opposing Responses to Scarcity Emerge from Functionally Unique Sociality Drivers. The American Naturalist. ISSN 0003-0147. 202(3), p. 302–321. doi: 10.1086/725426. Full text in Research Archive Show summary

  From biofilms to whale pods, organisms across taxalive in groups, thereby accruing numerous diverse benefits of soci-ality. All social organisms, however, pay the inherent cost of in-creased resource competition. One expects that when resources be-come scarce, this cost will increase, causing group sizes to decrease.Indeed, this occurs in some species, but there are also species forwhich group sizes remain stable or even increase under scarcity.What accounts for these opposing responses? We present a concep-tual framework, literature review, and theoretical model demon-strating that differing responses to sudden resource shifts can beexplained by which sociality benefit exerts the strongest selectionpressure on a particular species. We categorize resource-relatedbenefits of sociality into six functionally distinct classes and modeltheir effect on the survival of individuals foraging in groups underdifferent resource conditions. Wefind that whether, and to what de-gree, the optimal group size (or correlates thereof) increases, de-creases, or remains constant when resource abundance declinesdepends strongly on the dominant sociality mechanism. Existingdata, although limited, support our model predictions. Overall,we show that across a wide diversity of taxa, differences in howgroup size shifts in response to resource declines can be driven bydifferences in the primary benefits of sociality.

• Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar & Bleidorn, Christoph [Show all 55 contributors for this article] (2023). How genomics can help biodiversity conservation. Trends in Genetics. ISSN 0168-9525. 39(7), p. 545–559. doi: 10.1016/j.tig.2023.01.005. Full text in Research Archive Show summary

  The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

• Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano & Bleidorn, Christoph [Show all 59 contributors for this article] (2022). The era of reference genomes in conservation genomics. Trends in Ecology & Evolution. ISSN 0169-5347. 37(3), p. 197–202. doi: 10.1016/j.tree.2021.11.008. Full text in Research Archive
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2022). Warming Accelerates the Onset of the Molecular Stress Response and Increases Mortality of Larval Atlantic Cod. Integrative and Comparative Biology. ISSN 1540-7063. 62(6), p. 1784–1801. doi: 10.1093/icb/icac145. Full text in Research Archive
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2022). Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. Journal of Animal Ecology. ISSN 0021-8790. 91(6), p. 1073–1087. doi: 10.1111/1365-2656.13707. Full text in Research Archive Show summary

  Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common-garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common-garden-gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco-evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high-dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco-evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common-garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.

• Rasmussen, Jeppe Have; Moyano, Marta; Fuiman, Lee A. & Oomen, Rebekah Alice (2022). FishSizer: Software solution for efficiently measuring larval fish size. Ecology and Evolution. ISSN 2045-7758. 12(3), p. 1–10. doi: 10.1002/ece3.8672. Full text in Research Archive Show summary

  Length and depth of fish larvae are part of the fundamental measurements in many marine ecology studies involving early fish life history. Until now, obtaining these measurements has required intensive manual labor and the risk of inter- and intra-observer variability. We developed an open-source software solution to semi-automate the measurement process and thereby reduce both time consumption and technical variability. Using contrast-based edge detection, the software segments images of a fish larva into “larva” and “background.” Length and depth are extracted from the “larva” segmentation while taking curvature of the larva into consideration. The graphical user interface optimizes workflow and ease of usage, thereby reducing time consumption for both training and analysis. The software allows for visual verification of all measurements. A comparison of measurement methods on a set of larva images showed that this software reduces measurement time by 66%–78% relative to commonly used software. Using this software instead of the commonly used manual approach has the potential to save researchers from many hours of monotonous work. No adjustment was necessary for 89% of the images regarding length (70% for depth). Hence, the only workload on most images was the visual inspection. As the visual inspection and manual dimension extraction works in the same way as currently used software, we expect no loss in accuracy.

• Goodwin, Morten; Halvorsen, Kim Aleksander Tallaksen; Jiao, Lei; Knausgård, Kristian Muri; Martin, Angela Helen & Moyano, Marta [Show all 10 contributors for this article] (2022). Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook. ICES Journal of Marine Science. ISSN 1054-3139. 79(2), p. 319–336. doi: 10.1093/icesjms/fsab255. Full text in Research Archive Show summary

  The deep learning (DL) revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. New methods provide analysis of data from sensors, cameras, and acoustic recorders, even in real time, in ways that are reproducible and rapid. Off-the-shelf algorithms find, count, and classify species from digital images or video and detect cryptic patterns in noisy data. These endeavours require collaboration across ecological and data science disciplines, which can be challenging to initiate. To promote the use of DL towards ecosystem-based management of the sea, this paper aims to bridge the gap between marine ecologists and computer scientists. We provide insight into popular DL approaches for ecological data analysis, focusing on supervised learning techniques with deep neural networks, and illustrate challenges and opportunities through established and emerging applications of DL to marine ecology. We present case studies on plankton, fish, marine mammals, pollution, and nutrient cycling that involve object detection, classification, tracking, and segmentation of visualized data. We conclude with a broad outlook of the field’s opportunities and challenges, including potential technological advances and issues with managing complex data sets.

• Raatikainen, Kaisa; Purhonen, Jenna; Pohjanmies, Tähti; Peura, Maiju; Nieminen, Eini & Mustajärvi, Linda [Show all 30 contributors for this article] (2021). Pathways towards a sustainable future envisioned by early-career conservation researchers. Conservation Science and Practice (CSP). ISSN 2578-4854. 3(9). doi: 10.1111/csp2.493. Full text in Research Archive Show summary

  Scientists have warned decision-makers about the severe consequences of the global environmental crisis since the 1970s. Yet ecological degradation continues and little has been done to address climate change. We investigated early-career conservation researchers' (ECR) perspectives on, and prioritization of, actions furthering sustainability. We conducted a survey (n = 67) and an interactive workshop (n = 35) for ECR attendees of the 5th European Congress of Conservation Biology (2018). Building on these data and discussions, we identified ongoing and forthcoming advances in conservation science. These include increased transdisciplinarity, science communication, advocacy in conservation, and adoption of a transformation-oriented social–ecological systems approach to research. The respondents and participants had diverse perspectives on how to achieve sustainability. Reformist actions were emphasized as paving the way for more radical changes in the economic system and societal values linked to the environment and inequality. Our findings suggest that achieving sustainability requires a strategy that (1) incorporates the multiplicity of people's views, (2) places a greater value on nature, and (3) encourages systemic transformation across political, social, educational, and economic realms on multiple levels. We introduce a framework for ECRs to inspire their research and practice within conservation science to achieve real change in protecting biological diversity.

• Wolf, Jesse F.; MacKay, Layla; Haworth, Sarah E.; Cossette, Marie-Laurence; Dedato, Morgan N. & Young, Kiana B. [Show all 8 contributors for this article] (2021). Preprinting is positively associated with early career researcher status in ecology and evolution. Ecology and Evolution. ISSN 2045-7758. 11(20), p. 13624–13632. doi: 10.1002/ece3.8106. Full text in Research Archive
• Oomen, Rebekah Alice; Kuparinen, Anna & Hutchings, Jeffrey (2020). Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change. Journal of Heredity. ISSN 0022-1503. 111(4), p. 319–332. doi: 10.1093/jhered/esaa020. Full text in Research Archive
• Mérot, Claire; Oomen, Rebekah Alice; Tigano, Anna & Wellenreuther, Maren (2020). A roadmap for understanding the evolutionary significance of structural genomic variation. Trends in Ecology & Evolution. ISSN 0169-5347. 35(7), p. 561–572. doi: 10.1016/j.tree.2020.03.002. Full text in Research Archive
• Roney, Nancy; Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland & Hutchings, Jeffrey (2018). Fine-Scale Population Differences in Atlantic Cod Reproductive Success: A Potential Mechanism for Ecological Speciation in a Marine Fish. Ecology and Evolution. ISSN 2045-7758. p. 1–11. doi: 10.1002/ece3.4615. Full text in Research Archive
• Roney, Nancy; Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland & Hutchings, Jeffrey (2018). Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish. ICES Journal of Marine Science. ISSN 1054-3139. 75(4), p. 1353–1361. doi: 10.1093/icesjms/fsx232.
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2017). Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. FACETS. ISSN 2371-1671. 2, p. 610–641. doi: 10.1139/facets-2017-0015. Full text in Research Archive
• Kuparinen, Anna; Roney, Nancy E.; Oomen, Rebekah Alice; Hutchings, Jeffrey & Olsen, Esben Moland (2016). Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units. ICES Journal of Marine Science. ISSN 1054-3139. 73(2), p. 286–292. doi: 10.1093/icesjms/fsv181.
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2016). Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes. Canadian Journal of Zoology. ISSN 0008-4301. 94(4), p. 257–264. doi: 10.1139/cjz-2015-0186.
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2015). Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish. Conservation Physiology. ISSN 2051-1434. 3:cov027(1). doi: 10.1093/conphys/cov027.
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2015). Genetic variability in reaction norms in fishes. Environmental Reviews. ISSN 1181-8700. 23(3), p. 353–366. doi: 10.1139/er-2014-0077.

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• Lien, Anne; Nygård, Malene Østreng; Laugen, Ane Timenes; Lie, Asbjørn; Slettan, Audun & Johansen, Beate Strøm [Show all 33 contributors for this article] (2023). Utbygging vil ødelegge for biologisk mangfold på campus Gimlemoen. NB! 34 forfattere totalt. Fædrelandsvennen. ISSN 0805-3790. p. 19–19.
• Oomen, Rebekah Alice; Knutsen, Halvor; Moland, Even; Olsen, Esben Moland; Knutsen, Jan Atle & Bernatchez, Louis [Show all 8 contributors for this article] (2022). Nothing so boundless, nothing so patient: Obituary for Professor Jeffrey Alexander Hutchings (1958–2022). Fish and Fisheries. ISSN 1467-2960. 23(3), p. 519–521. doi: 10.1111/faf.12661.
• Deininger, Anne; Martin, Angela Helen; Pardo, Juan; Berg, Paul Ragnar; Bhardwaj, Jyotirmoy & de Oliveira Catarino, Diana Sofia [Show all 15 contributors for this article] (2021). Coastal Research Seen Through an Early Career Lens—A Perspective on Barriers to Interdisciplinarity in Norway. Frontiers in Marine Science. ISSN 2296-7745. 8. doi: 10.3389/fmars.2021.634999. Full text in Research Archive
• Oomen, Rebekah Alice & Hutchings, Jeffrey (2020). Evolution of Reaction Norms. In Futuyma, Douglas J. (Eds.), Oxford Bibliographies in Evolutionary Biology. Oxford University Press. ISSN 9780199941728.
• Oomen, Rebekah Alice; Thorbjørnsen, Susanna Huneide; Goodwin, Morten & Stenseth, Nils Christian (2020). Torsken vår bruker antakelig sørlandsdialekt. Agderposten. ISSN 0805-3723. Show summary

  FORSKNINGSDAGENE: Unike dialekter blant fiskene kan hjelpe torsk til å velge partnere som ligner den selv.

• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Chr. & Hutchings, Jeffrey (2018). Transcriptomic variability in population responses of Atlantic cod to temperature.
• Oomen, Rebekah Alice (2017). Genetic and environmental drivers of gene expression in Atlantic cod.
• Oomen, Rebekah Alice (2016). Transcriptomic responses to environmental change in fishes: insights from RNA-seq.
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2016). Genetic variability in population responses of Atlantic cod to temperature.
• Oomen, Rebekah Alice (2015). The transcriptomic response of cod to temperature.
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2015). The transcriptomic response of cod to temperature.
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2015). Genetic variability in population responses of Atlantic cod to temperature.
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2015). Genetic variability in population responses of Atlantic cod to environmental change and the transcriptomic response to temperature.
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey A. (2014). Genetic variability in population responses of Atlantic cod to environmental change.
• Oomen, Rebekah Alice (2013). Genetic variability in population responses of Atlantic cod to environmental change.

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