Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

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.publishedVersio

Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

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.publishedVersionpublishedVersionPaid Open Acces

A roadmap for understanding the evolutionary significance of structural genomic variation

Author's accepted manuscriptStructural 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.acceptedVersio

FishSizer: Software solution for efficiently measuring larval fish size

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.publishedVersio

Warming Accelerates the Onset of the Molecular Stress Response and Increases Mortality of Larval Atlantic Cod

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Warming Accelerates the Onset of the Molecular Stress Response and Increases Mortality of Larval Atlantic Cod

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.publishedVersio

Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook

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.publishedVersionPaid Open Acces

Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook

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Coastal Research Seen Through an Early Career Lens—A Perspective on Barriers to Interdisciplinarity in Norway

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.publishedVersio

The era of reference genomes in conservation genomics

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