Rebekah Oomen

• Maurstad, Marius Filomeno; Kusy, Dominik; Undheim, Eivind Andreas Baste; Jakobsen, Kjetill Sigurd; Böhne, Astrid & Monteiro, Rita [Show all 20 contributors for this article] (2026). ERGA-BGE chromosome-level genome assembly of the giant stream lacewing  Osmylus fulvicephalus (Scopoli, 1763). Open Research Europe. 6. doi: 10.12688/openreseurope.23457.3. Full text in Research Archive Show summary

  The giant stream lacewing, Osmylus fulvicephalus (Scopoli, 1763), is a widespread European species belonging to the insect order Neuroptera. Its cryptic larvae are predators found at the banks of streams and smaller rivers where they use their piercing, lance-shaped stylets to inject venom into their arthropod prey. Here, we present the reference genome of the giant stream lacewing as a crucial resource for uncovering the genetic basis of venom evolution in Neuroptera. The chromosome-level genome encompasses 674.7 Mb and is composed of 60 contigs and 24 scaffolds where 99.2% of the assembly is distributed among the 6 contiguous chromosomal pseudomolecules and two sex chromosomes (X and Y). Contig and scaffold N50 have a value of 51.5 Mb and 116.2 Mb, respectively. This reference genome is the first genomic resource from the family of lance lacewings, providing valuable data for clarifying the phylogenetic placement of the family Osmylidae within Neuroptera.

• Taboada, Sergi; Gracia-Sancha, Carlota; Galià-Camps, Carles; Böhne, Astrid; Monteiro, Rita & Marcussen, Thomas [Show all 18 contributors for this article] (2026). ERGA-BGE reference genome of Xylophaga dorsalis - a common deep-sea wood-boring bivalve with Atlantic-Mediterranean distribution. Open Research Europe. 6. doi: 10.12688/openreseurope.22692.2. Full text in Research Archive Show summary

  Xylophaga dorsalis is a common Atlantic-Mediterranean mollusc that plays a crucial role in deep-sea habitats, where it digests wood that reaches the seabed through a unique symbiosis with specialised bacteria. The reference genome of X. dorsalis thus offers a crucial resource for uncovering the genetic basis of the species adaptability to wood bore in deep-water ecosystems. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules (superscaffolds) and 1 mitochondrial genome. This chromosome-level assembly encompasses 0.451 Gb, composed of 1,259 contigs and 320 scaffolds, with contig and scaffold N50 values of 1.30 Mb and 25.4 Mb, respectively. The genome assembly encodes 19,441 protein-coding genes (34,405 transcripts) and 6,716 non-coding genes.

• Manzano-Marín, Alejandro; Böhne, Astrid; Monteiro, Rita; Marcussen, Thomas; Struck, Torsten H. & Oomen, Rebekah Alice [Show all 15 contributors for this article] (2026). ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech. Open Research Europe. 5. doi: 10.12688/openreseurope.21672.2. Full text in Research Archive Show summary

  Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana . Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.

• Lavergne, Sébastien; Rosa, Zoé; Peng, Chuan; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 20 contributors for this article] (2026). ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe. Open Research Europe. 5. doi: 10.12688/openreseurope.21922.1. Full text in Research Archive Show summary

  The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the highest altitudes where flowering plants can thrive and the speciation mechanisms of plants dwelling on high alpine sky islands. The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 413 Mb, composed of 253 contigs and 101 scaffolds, with contig and scaffold N50 values of 4.95 Mb and 21.2 Mb, respectively.

• Tomasello, Salvatore; Manzo, Eleonora; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 19 contributors for this article] (2026). ERGA-BGE genome of Xanthium orientale subsp. italicum (Moretti) Greuter. A plant of American origin, now widespread and, in some cases, invasive in Europe. Open Research Europe. 5, p. 367–367. doi: 10.12688/openreseurope.21891.1. Full text in Research Archive Show summary

  The Xanthium orientale subsp. italicum (Asterales: Asteraceae: Asteroideae) reference genome offers a valuable resource for understanding the genetic basis of invasiveness and fitness differences among congeneric species. The entirety of the genome sequence was assembled into 18 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.26 Gb, composed of 46 contigs and 32 scaffolds, with contig and scaffold N50 values of 98.8 Mb and 124 Mb, respectively.

• Aguado-Ramsay, Pablo; Lara, Francisco; Draper, Isabel; Conejero, Maria; Böhne, Astrid & Monteiro, Rita [Show all 18 contributors for this article] (2026). ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia. Open Research Europe. 5. doi: 10.12688/openreseurope.21670.1. Full text in Research Archive Show summary

  The reference genome of Lewinskya acuminata (H. Philib.) F. Lara, Garilleti & Goffinet will enable phylogenomic, biogeographic, and evolutionary studies within the Orthotrichaceae and related bryophyte lineages at a depth previously inaccessible. This species of moss is among the most representative of the Mediterranean epiphytic communities and can be readily identified by its long-acuminate leaves, fusiform capsules with a vestigial exostome, a well-developed endostome of six broad segments, and a dark, puckered peristome mouth when dry. The entirety of the genome sequence was assembled into 6 contiguous chromosomal pseudomolecules, 1 mitochondrial genome, and 2 plastid genomes. This chromosome-level assembly encompasses 0.25 Gb, composed of 51 contigs and 13 scaffolds, with contig and scaffold N50 values of 11.5 Mb and 40.8 Mb, respectively.

• Faria, Rui; Vilela, Rocío Nieto; Lima, Fernando P; Monteiro, Rita; Böhne, Astrid & Marcussen, Thomas [Show all 18 contributors for this article] (2026). ERGA-BGE genome of Patella rustica Linnaeus, 1758: a resource to investigate responses to global warming in the intertidal. Open Research Europe. 5. doi: 10.12688/openreseurope.21608.2. Full text in Research Archive Show summary

  The reference genome of Patella rustica Linnaeus, 1758 will offer a unique opportunity to understand how intertidal organisms respond to the effects of global warming, contributing to improve our predictions about the impact of climate change on the maintenance and diversification of marine biodiversity. A total of 9 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 719 Mb, composed of 157 contigs and 24 scaffolds, with contig and scaffold N50 values of 8.52 Mb and 83.6 Mb, respectively.

• Oomen, Rebekah Alice; Cariani, Alessia; Chavarie, Louise; Leone, Agostino; Vella, Adriana & Vella, Noel [Show all 16 contributors for this article] (2026). The genome sequence of Atlantic Bluefin Tuna, Thunnus thynnus (Linnaeus, 1758). Wellcome Open Research. 10. doi: 10.12688/wellcomeopenres.23971.1. Full text in Research Archive Show summary

  We present a genome assembly from a specimen of Thunnus thynnus (Atlantic Bluefin Tuna; Chordata; Actinopteri; Scombriformes; Scombridae). The genome sequence has a total length of 799.05 megabases. Most of the assembly (99.17%) is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.53 kilobases. Gene annotation of this assembly on Ensembl identified 23,266 protein-coding genes.

• Hausdorf, Bernhard; Tapia, Elicio; Monteiro, Rita; Böhne, Astrid; Marcussen, Thomas & Struck, Torsten H [Show all 10 contributors for this article] (2026). ERGA-BGE genome of Anisus vorticulus (Troschel, 1834): the Lesser Ramshorn Snail, an endangered freshwater snail protected under the EU's Habitats and Species Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20499.1. Full text in Research Archive Show summary

  We have generated a high-quality reference genome for Anisus vorticulus to support monitoring of the genetic diversity of populations of this declining freshwater species. The chromosome-level genome assembly encompasses 1.04 Gb, composed of 835 contigs and 77 scaffolds, with contig and scaffold N50 values of 2.35 Mb and 59.2 Mb, respectively. The genome was assembled into 18 chromosomal pseudomolecules.

• Lopes, Ricardo Jorge; Böhne, Astrid; Marcussen, Thomas; Oomen, Rebekah Alice; Struck, Torsten H & Aguilera, Laura [Show all 12 contributors for this article] (2026). ERGA-BGE reference genome of the Azores Bullfinch - Pyrrhula murina Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal). Open Research Europe. 5, p. 1–16. doi: 10.12688/openreseurope.20666.3. Full text in Research Archive Show summary

  The reference genome of Pyrrhula murina’s reference genome will substantially enhance the current monitoring of genetic diversity and population viability and will allow us to understand the effective population size trends throughout time and recent bottlenecks and population expansions. A total of 42 contiguous chromosomal pseudomolecules were assembled from the genome sequence, using ONT, HI-C and Illumina data. This chromosome-level assembly encompasses 1.2 Gb, composed of 65 contigs and 60 scaffolds, with contig and scaffold N50 values of 65 Mb and 76 Mb, respectively.

• Wellenreuther, Maren; Oomen, Rebekah Alice; Han, Kwi Young; Krohman, Rebecca & Reusch, Thorsten B.H. (2025). Beyond supergenes: the diverse roles of inversions in trait evolution. Trends in Ecology & Evolution. ISSN 0169-5347. 40(11), p. 1054–1065. doi: 10.1016/j.tree.2025.08.004. Full text in Research Archive Show summary

  Chromosomal inversions are ubiquitous across the Tree of Life, with genome-wide studies revealing a bias toward smaller inversions, yet research has disproportionately focused on large, supergene-like inversions linked to discrete phenotypes. This limits our understanding of inversions' roles in trait evolution, as their size affects their potential functional impact. Investigation of smaller inversions and multi-inversion genotypes is crucial to elucidate their role in shaping continuous traits and evolutionary adaptation. Addressing this requires a shift towards a systematic study of smaller inversions and the use of experimental assays and functional annotation to identify the evolutionary forces driving different genomic trait architectures.

• Aurelle, Didier; Guillemain, Dorian; Zuberer, Frédéric; Malengros, Denys; Böhne, Astrid & Monteiro, Rita [Show all 19 contributors for this article] (2025). ERGA-BGE reference genome of Eunicella cavolini, an IUCN Near Threatened Gorgonian of the Mediterranean Sea. Open Research Europe. 5. doi: 10.12688/openreseurope.21514.1. Full text in Research Archive Show summary

  The Eunicella cavolini reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.

• Vila, Marta; Marí-Mena, Neus; Vila, Roger; Riesgo, Ana; García-Souto, Daniel & Lopez-Vaamonde, Carlos [Show all 20 contributors for this article] (2025). ERGA-BGE genome of the Spanish moon moth Actias isabellae Graells, 1849: a nocturnal lepidopteran protected by the Habitats Directive. Open Research Europe. 5. doi: 10.12688/openreseurope.20658.2. Full text in Research Archive Show summary

  High-quality reference genomes are critical resources for understanding biodiversity and supporting conservation efforts. We present the chromosome-level assembly of the Spanish moon moth, Actias isabellae (Graells, 1849), a nocturnal lepidopteran protected under the EU Habitats Directive. The assembly spans 0.56 Gb across 31 pseudomolecules, including the Z chromosome, with a contig N50 of 18.9 Mb and a scaffold N50 of 20.4 Mb. The mitochondrial genome was also assembled into a 15,247 bp circular sequence. Annotation identified 11,805 protein-coding genes and 2,238 non-coding genes, with a BUSCO completeness of over 94%. Notably, no W chromosome was detected, suggesting a ZZ/Z0 sex determination system. This reference genome provides an essential foundation for studying sex chromosome evolution in Lepidoptera and enables advanced population genomics monitoring of this protected species. More broadly, it contributes to ongoing efforts within the European Reference Genome Atlas and the Earth BioGenome Project to harness genomics for biodiversity conservation.

• 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. 81(5), p. 815–822. doi: 10.1093/icesjms/fsae039. Full text in Research Archive Show summary

  The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species and is a key instrument in global biodiversity conservation efforts. Our understanding of the structure and value of genetic biodiversity below the species level is rapidly increasing. Nonetheless, the IUCN assessment criteria overlook genetic variation within species. Here, we address this blind spot and discuss the principles of species conservation status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive in heterogeneous environments known to drive genetic differentiation. The focal example species, Atlantic cod and sugar kelp, have contrasting life histories, are ecologically and economically important constituents of the coastal ecosystem, and are currently not classified as threatened in Norway and Canada. We expose important variation in population structure, the presence of ecotypes and genetic-environment covariation, as well as loss of ecotypes that threatens the conservation of these species. Because the genetic makeup of species directly influences their resilience, omitting this information from conservation status assessments can result in loss of adaptive capacity to future stressors, such as climate change. Consequently, recognizing and preserving intraspecific variation emerges as vital for species’ abilities to adapt to and survive in future ocean conditions.

• Cartney, Ann M. Mc; Formenti, Giulio; Mouton, Alice; Panis, Diego De; Marins, Luísa S. & Leitão, Henrique G. [Show all 203 contributors for this article] (2024). The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj biodiversity. 3(1), p. 1–17. doi: 10.1038/s44185-024-00054-6. Full text in Research Archive Show summary

  A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

• Böhne, Astrid; Fernández, Rosa; Leonard, Jennifer A.; McCartney, Ann M.; McTaggart, Seanna & Melo-Ferreira, José [Show all 10 contributors for this article] (2024). Contextualising samples: supporting reference genomes of European biodiversity through sample and associated metadata collection. npj biodiversity. 3(1), p. 1–11. doi: 10.1038/s44185-024-00053-7. Full text in Research Archive Show summary

  The European Reference Genome Atlas (ERGA) consortium aims to generate a reference genome catalogue for all of Europe's eukaryotic biodiversity. The biological material underlying this mission, the specimens and their derived samples, are provided through ERGA’s pan-European network. To demonstrate the community’s capability and capacity to realise ERGA’s ambitious mission, the ERGA Pilot project was initiated. In support of the ERGA Pilot effort to generate reference genomes for European biodiversity, the ERGA Sampling and Sample Processing committee (SSP) was formed by volunteer experts from ERGA’s member base. SSP aims to aid participating researchers through (i) establishing standards for and collecting of sample/specimen metadata; (ii) prioritisation of species for genome sequencing; and (iii) development of taxon-specific collection guidelines including logistics support. SSP serves as the entry point for sample providers to the ERGA genomic resource production infrastructure and guarantees that ERGA’s high-quality standards are upheld throughout sample collection and processing. With the volume of researchers, projects, consortia, and organisations with interests in genomics resources expanding, this manuscript shares important experiences and lessons learned during the development of standardised operational procedures and sample provider support. The manuscript details our experiences in incorporating the FAIR and CARE principles, species prioritisation, and workflow development, which could be useful to individuals as well as other initiatives.

• 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.

• 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.

• 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.

• 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 Show summary

  Temperature profoundly affects ectotherm physiology. Although differential thermal responses influence fitness, thus driving population dynamics and species distributions, our understanding of the molecular architecture underlying these responses is limited, especially during the critical larval stage. Here, using RNA-sequencing of laboratory-reared Atlantic cod (Gadus morhua) larvae of wild origin, we find changes in gene expression in thousands of transcripts consistent with a severe cellular stress response at both ambient and projected (+2°C and +4°C) temperatures. In addition, specific responses to stress, heat, and hypoxia were commonly identified in gene ontology enrichment analyses and 33 of the 44 genes comprising the minimum stress proteome of all organisms were upregulated. Earlier onset of the stress response was evident at higher temperatures; concomitant increased growth and mortality suggests a reduction in fitness. Temporal differences in gene expression levels do not correspond to differences in growing degree days, suggesting negative physiological consequences of warming beyond accelerated development. Because gene expression is costly, we infer that the upregulation of thousands of transcripts in response to warming in larval cod might act as an energetic drain. We hypothesize that the energetically costly stress response, coupled with increased growth rate at warmer temperatures, leads to faster depletion of energy reserves and increased risk of mortality in larval cod. As sea surface temperatures continue to rise over the next century, reduced fitness of Atlantic cod larvae might lead to population declines in this ecologically and socioeconomically important species. Further, our findings expand our understanding of transcriptomic responses to temperature by ectothermic vertebrate larvae beyond the critical first-feeding stage, a time when organisms begin balancing the energetic demands of growth, foraging, development, and maintenance. Linking the molecular basis of a thermal response to key fitness-related traits is fundamentally important to predicting how global warming will affect ectotherms.

• 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 Show summary

  Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.

• Rasmussen, Jeppe Have; Moyano, Marta; Fuiman, Lee A. & Oomen, Rebekah Alice (2022). FishSizer: Software solution for efficiently measuring larval fish size. Ecology and Evolution. 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.

• Deininger, Anne; Martin, Angela Helen; Pardo, Juan; Berg, Paul Ragnar; Bhardwaj, Jyotirmoy & Catarino, Diana Sofia de Oliveira [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. 8. doi: 10.3389/fmars.2021.634999. Full text in Research Archive Show summary

  The value of interdisciplinarity for solving complex coastal problems is widely recognized. Many early career researchers (ECRs) therefore actively seek this type of collaboration through choice or necessity, for professional development or project funding. However, establishing and conducting interdisciplinary research collaborations as an ECR has many challenges. Here, we identify these challenges through the lens of ECRs working in different disciplines on a common ecosystem, the Norwegian Skagerrak coast. The most densely populated coastline in Norway, the Skagerrak coast, is experiencing a multitude of anthropogenic stressors including fishing, aquaculture, eutrophication, climate change, land runoff, development, and invasive species. The Skagerrak coastline has also been the focus of environmental science research for decades, much of which aims to inform management of these stressors. The region provides a fantastic opportunity for interdisciplinary collaboration, both within and beyond the environmental sciences. This perspective article identifies the barriers ECRs in Norway face in establishing interdisciplinary and collaborative research to inform management of coastal ecosystems, along with their root causes. We believe our discussion will be of broad interest to all research institutions who employ or educate ECRs (in Norway and worldwide), and to those who develop funding mechanisms for ECRs and interdisciplinary research.

• 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). 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. 11(20), p. 13624–13632. doi: 10.1002/ece3.8106. Full text in Research Archive Show summary

  The usage of preprint servers in ecology and evolution is increasing, allowing research to be rapidly disseminated and available through open access at no cost. Early Career Researchers (ECRs) often have limited experience with the peer review process, which can be challenging when trying to build publication records and demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions. ECRs face different challenges relative to researchers with permanent positions and established research programs. These challenges might also vary according to institution size and country, which are factors associated with the availability of funding for open access journals. We predicted that the career stage and institution size impact the relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we showed that ECRs generated more preprints relative to non-ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal association between first author, institution size, and preprint usage, whereby the number of preprints tends to increase with institution size for ECRs. The United States and United Kingdom contributed the greatest number of preprints by ECRs, whereas non-Western countries contributed relatively fewer preprints. This empirical evidence that preprint usage varies with the career stage, institution size, and country helps to identify barriers surrounding large-scale adoption of preprinting in ecology and evolution.

• 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 Show summary

  Structural genomic variants (SVs) take diverse forms and are ubiquitous drivers of ecological and evolutionary processes. Most studies of SVs focus on the adaptive significance of gene duplications and large inversions. Future studies should catalog SVs of all types and sizes and systematically test their evolutionary implications. We propose a roadmap and definitions for the study of SVs in ecological and evolutionary genomics. Best practices for SV detection are needed to facilitate comparisons across studies. Integrating population genomic, theoretical, and experimental approaches to SVs will more comprehensively characterize genomic variation, uncover the adaptive and neutral processes shaping the evolutionary trajectory of SVs, and identify the mechanisms by which SVs impact adaptation and speciation.

• 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 Show summary

  Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.

• 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. 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. p. 1–11. doi: 10.1002/ece3.4615. Full text in Research Archive Show summary

  Successful resource‐management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4,000 offspring, we document fine‐scaled temporal differences in individual reproductive success for two spatially adjacent (<10 km) populations of a broadcast‐spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from inner‐ and outer‐fjord populations were allowed to compete for mating and reproductive opportunities. After accounting for phenotypic variability in several traits, reproductive success of outer‐fjord cod was significantly lower than that of inner‐fjord cod. This finding, given that genomically different cod ecotypes inhabit inner‐ and outer‐fjord waters, raises the intriguing hypothesis that the populations might be diverging because of ecological speciation. Individual reproductive success, skewed within both sexes (more so among males), was positively affected by body size, which also influenced the timing of reproduction, larger individuals spawning later among females but earlier among males. Our work suggests that spatial mismatches between management and biological units exist in marine fishes and that studies of reproductive interactions between putative populations or ecotypes can provide an informative basis on which determination of the scale of local adaptation can be ascertained.

• Oomen, Rebekah Alice & Hutchings, Jeffrey (2017). Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing. FACETS. 2, p. 610–641. doi: 10.1139/facets-2017-0015. Full text in Research Archive Show summary

  The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

• 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. 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. Full text in Research Archive
• 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. Full text in Research Archive
• 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. 3:cov027(1). doi: 10.1093/conphys/cov027. Full text in Research Archive

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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. p. 19–19. Full text in Research Archive
• 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. 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. Full text in Research Archive
• Oomen, Rebekah Alice; Thorbjørnsen, Susanna Huneide; Goodwin, Morten & Stenseth, Nils Christian (2020). Torsken vår bruker antakelig sørlandsdialekt. Agderposten. ISSN 0805-3723. Full text in Research Archive 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. Full text in Research Archive
• Oomen, Rebekah Alice (2017). Genetic and environmental drivers of gene expression in Atlantic cod. Full text in Research Archive
• 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. Full text in Research Archive
• Oomen, Rebekah Alice (2016). Transcriptomic responses to environmental change in fishes: insights from RNA-seq. Full text in Research Archive
• Oomen, Rebekah Alice (2015). The transcriptomic response of cod to temperature. Full text in Research Archive
• 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. Full text in Research Archive
• Oomen, Rebekah Alice; Knutsen, Halvor; Olsen, Esben Moland; Jentoft, Sissel; Stenseth, Nils Christian & Hutchings, Jeffrey (2015). The transcriptomic response of cod to temperature. Full text in Research Archive
• 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. Full text in Research Archive
• 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. Full text in Research Archive
• Oomen, Rebekah Alice (2013). Genetic variability in population responses of Atlantic cod to environmental change. Full text in Research Archive

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