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Article ; Online: Anemonefishes

Vincent Laudet / Marcela Herrera / Timothy Ravasi

F1000Research, Vol

A model system for evolutionary genomics [version 2; peer review: 2 approved]

2023 Volume 12

Abstract: Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the ... ...

Abstract	Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.
Keywords	adaptive radiation ; Amphiprion ; chromosome-scale assembly ; clownfish ; genome ; pigmentation ; eng ; Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sharks and their relatives

Aaron Hasenei / Jennifer M. Donelson / Timothy Ravasi / Jodie L. Rummer

Frontiers in Marine Science, Vol

can their past help predict their future?

2023 Volume 10

Abstract: Elasmobranchs (i.e., sharks, skates, and rays) have survived five mass extinction events and changed relatively little throughout their ~450-million-year evolutionary history. Therefore, elasmobranchs may provide critical evolutionary perspectives on how ...

Abstract	Elasmobranchs (i.e., sharks, skates, and rays) have survived five mass extinction events and changed relatively little throughout their ~450-million-year evolutionary history. Therefore, elasmobranchs may provide critical evolutionary perspectives on how species and populations can elicit phenotypic plasticity and adaptation responses to climate change. Unfortunately, despite their roles as critical apex- and meso-predators, most elasmobranch species are considered to be highly vulnerable to the impacts of fisheries exploitation and climate change, which is compounded by their K-selected life history strategies. Furthermore, the future of elasmobranchs is uncertain at best in the face of anthropogenic climate change because there have only been a handful of studies that have directly investigated the effects of climate change related stressors. Phenotypic plasticity in response to climate change, specifically ocean warming, may be a species’ best chance of resilience given the expedited rate of environmental change. However, despite extensive research on plasticity within and across generations in teleost fishes, there remains a knowledge gap for elasmobranch species, owing to their extended life spans and delayed sexual maturity. Here, we present four case studies on different elasmobranch species to lend perspectives on the capacity for phenotypic plasticity within the context of ocean warming. Furthermore, we discuss potential research avenues and modern technologies that may enable future investigations to empirically explore the capacity for phenotypic plasticity in elasmobranchs.
Keywords	plasticity ; adaptation ; elasmobranch ; climate change ; physiology ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	333
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular Response of the Brain to Cross-Generational Warming in a Coral Reef Fish

Moisés A. Bernal / Elliott Schmidt / Jennifer M. Donelson / Philip L. Munday / Timothy Ravasi

Frontiers in Marine Science, Vol

2022 Volume 9

Abstract: Ocean warming is a threat to marine biodiversity, as it can push marine species beyond their physiological limits. Detrimental effects can occur when marine poikilotherms are exposed to conditions beyond their thermal optima. However, acclamatory ... ...

Abstract	Ocean warming is a threat to marine biodiversity, as it can push marine species beyond their physiological limits. Detrimental effects can occur when marine poikilotherms are exposed to conditions beyond their thermal optima. However, acclamatory mechanisms, such as plasticity, may enable compensation of detrimental effects if warming is experienced during development or across generations. Studies evaluating the molecular responses of fishes to warming have mostly focused on liver, muscle, and gonads, and little is known about the effects on other vital organs, including the brain. This study evaluated the transcriptional program of the brain in the coral reef fish Acanthochromis polyacanthus, exposed to two different warming scenarios: +1.5°C and +3.0°C, across successive generations. Fish were exposed to these conditions in both developmental (F1 and F2) and transgenerational settings (F2 only), as well as a treatment with step-wise warming between generations. The largest differences in gene expression were between individuals of the first and second generation, a pattern that was corroborated by pairwise comparisons between Control F1 and Control F2 (7,500 DEGs) fish. This large difference could be associated with parental effects, as parents of the F1 generation were collected from the wild, whereas parents of the F2 generation were reared in captivity. A general response to warming was observed at both temperatures and in developmental and transgenerational treatments included protein folding, oxygen transport (i.e., myoglobin), apoptosis and cell death, modification of cellular structure, mitochondrial activity, immunity and changes in circadian regulation. Treatments at the highest temperature showed a reduction in synaptic activity and neurotransmission, which matches previous behavioral observations in coral reef fishes. The Transgenerational +3.0°C treatment showed significant activation of the gene pls3, which is known for the development of neuro-muscular junctions under heat-stress. F2 samples ...
Keywords	climate change ; gene expression ; ocean warming ; parental effects ; phenotypic plasticity ; poikilotherms ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	590
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Editorial

Lisa N. S. Shama / Jennifer M. Donelson / Jose M. Eirin-Lopez / Timothy Ravasi

Frontiers in Marine Science, Vol

Adaptation and Phenotypic Plasticity to Climate Change

2022 Volume 9

Keywords	climate change ; adaptation ; plasticity ; epigenetics ; marine ; aquatic ectotherm ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Proteomic Responses to Ocean Acidification in the Brain of Juvenile Coral Reef Fish

Hin Hung Tsang / Megan J. Welch / Philip L. Munday / Timothy Ravasi / Celia Schunter

Frontiers in Marine Science, Vol

2020 Volume 7

Abstract: Elevated CO2 levels predicted to occur by the end of the century can affect the physiology and behavior of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation ... ...

Abstract	Elevated CO2 levels predicted to occur by the end of the century can affect the physiology and behavior of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation in the extent of behavioral impairment when exposed to elevated CO2 has been observed in previous studies. Whole brain transcriptomic data has further emphasized the importance of parental phenotypic variation in the response of juvenile fish to elevated CO2. In this study, we investigate the genome-wide proteomic responses of this variation in the brain of 5-week old spiny damselfish, Acanthochromis polyacanthus. We compared the accumulation of proteins in the brains of juvenile A. polyacanthus from two different parental behavioral phenotypes (sensitive and tolerant) that had been experimentally exposed to short-term, long-term and inter-generational elevated CO2. Our results show differential accumulation of key proteins related to stress response and epigenetic markers with elevated CO2 exposure. Proteins related to neurological development and glucose metabolism were also differentially accumulated particularly in the long-term developmental treatment, which might be critical for juvenile development. By contrast, exposure to elevated CO2 in the parental generation resulted in only three differentially accumulated proteins in the offspring, revealing potential for inter-generational acclimation. Lastly, we found a distinct proteomic pattern in juveniles due to the behavioral sensitivity of parents to elevated CO2, even though the behavior of the juvenile fish was impaired regardless of parental phenotype. Our data shows that developing juveniles are affected in their brain protein accumulation by elevated CO2, but the effect varies with the length of exposure as well as due to variation of parental phenotypes in the population.
Keywords	environmental proteomics ; climate change ; ocean acidification ; behavior ; tolerance ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	580
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The time course of molecular acclimation to seawater in a euryhaline fish

Lucrezia C. Bonzi / Alison A. Monroe / Robert Lehmann / Michael L. Berumen / Timothy Ravasi / Celia Schunter

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 16

Abstract: Abstract The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream ... ...

Abstract	Abstract The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds (“wadies”), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.
Keywords	Medicine ; R ; Science ; Q
Subject code	333
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Epigenetic Signature for Within-Generational Plasticity of a Reef Fish to Ocean Warming

Taewoo Ryu / Heather D. Veilleux / Philip L. Munday / Imgook Jung / Jennifer M. Donelson / Timothy Ravasi

Frontiers in Marine Science, Vol

2020 Volume 7

Abstract: Elevated temperature can have detrimental effects on the physiological performance of many marine organisms. However, phenotypic plasticity may enable some populations to maintain their performance under thermal stress. Two longitudinally separated ... ...

Abstract	Elevated temperature can have detrimental effects on the physiological performance of many marine organisms. However, phenotypic plasticity may enable some populations to maintain their performance under thermal stress. Two longitudinally separated populations of the coral reef fish, Acanthochromis polyacanthus from the Great Barrier Reef have shown differing capacities for thermal plasticity – the southernmost Heron Island population restored aerobic scope within one generation at a higher temperature, whereas the northernmost Palm Island population restored aerobic scope only when two generations were exposed to warmer conditions. We recently discovered an epigenetic signature associated with transgenerational plasticity in the Palm Island population. Here, we aimed to determine if epigenetic changes are also associated with the within-generational plasticity observed in the Heron Island population and, if so, how this epigenetic signature compares to the Palm Island transgenerational epigenome. By sequencing and analyzing the genome-wide DNA methylome of fish reared at control (+0°C) or elevated temperatures (+1.5 and +3°C) since early life, we identified 480 differentially methylated genomic regions and 372 adjacent protein-coding genes associated with within-generational plasticity in the Heron Island population. Functions related to insulin, cardiovascular capacity, development, and heat response were significantly enriched in differentially methylated genes, suggesting that these functions are the core mechanisms for within-generational restoration of aerobic scope. Comparison to the differentially methylated genes identified from F2 Palm Island population revealed little overlap of genes and enriched functions, indicating that distinct genetic toolkits may be used for within- and between-generational plasticity to ocean warming in the same species from different latitudes.
Keywords	climate change ; ocean warming ; coral reef fish ; epigenetics ; DNA methylation ; phenotypic plasticity ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	910 ; 590
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Viral ecogenomics across the Porifera

Cecília Pascelli / Patrick W. Laffy / Emmanuelle Botté / Marija Kupresanin / Thomas Rattei / Miguel Lurgi / Timothy Ravasi / Nicole S. Webster

Microbiome, Vol 8, Iss 1, Pp 1-

2020 Volume 22

Abstract: Abstract Background Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and ...

Abstract	Abstract Background Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. Results Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. Conclusions Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses ...
Keywords	Viromics ; Viral ecology ; Functional diversity ; AMGs ; Coral reef sponges ; Microbial ecology ; QR100-130
Subject code	572
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Inductively actuated micro needles for on-demand intracellular delivery

Mincho N. Kavaldzhiev / Jose E. Perez / Rachid Sougrat / Ptissam Bergam / Timothy Ravasi / Jürgen Kosel

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 9

Abstract: Abstract Methods that provide controlled influx of molecules into cells are of critical importance for uncovering cellular mechanisms, drug development and synthetic biology. However, reliable intracellular delivery without adversely affecting the cells ... ...

Abstract	Abstract Methods that provide controlled influx of molecules into cells are of critical importance for uncovering cellular mechanisms, drug development and synthetic biology. However, reliable intracellular delivery without adversely affecting the cells is a major challenge. We developed a platform for on-demand intracellular delivery applications, with which cell membrane penetration is achieved by inductive heating of micro needles. The micro needles of around 1 μm in diameter and 5 μm in length are made of gold using a silicon-based micro fabrication process that provides flexibility with respect to the needles’ dimensions, pitch, shell thickness and the covered area. Experiments with HCT 116 colon cancer cells showed a high biocompatibility of the gold needle platform. Transmission electron microscopy of the cell-needle interface revealed folding of the cell membrane around the needle without penetration, preventing any delivery, which was confirmed using the EthD-1 fluorescent dye. The application of an alternating magnetic field, however, resulted in the delivery of EthD-1 by localized heating of the micro needles. Fluorescence quantification showed that intracellular delivery, with as high as 75% efficiency, is achieved for specific treatment times between 1 and 5 minutes. Overexposure of the cells to the heated micro needles, i.e. longer magnetic field application, leads to an increase in cell death, which can be exploited for cleaning the platform. This method allows to perform intracellular deliver by remotely activating the micro needles via a magnetic field, and it is controlled by the application time, making it a versatile and easy to use method. The wireless actuation could also be an attractive feature for in-vivo delivery and implantable devices.
Keywords	Medicine ; R ; Science ; Q
Subject code	621
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular Response to Extreme Summer Temperatures Differs Between Two Genetically Differentiated Populations of a Coral Reef Fish

Heather D. Veilleux / Taewoo Ryu / Jennifer M. Donelson / Timothy Ravasi / Philip L. Munday

Frontiers in Marine Science, Vol

2018 Volume 5

Abstract: Extreme thermal events are increasing in frequency and duration as the climate continues to warm, with potential detrimental effects on marine organisms. However, the effects of heatwaves may differ among geographically separated populations depending on ...

Abstract	Extreme thermal events are increasing in frequency and duration as the climate continues to warm, with potential detrimental effects on marine organisms. However, the effects of heatwaves may differ among geographically separated populations depending on their capacity for thermal plasticity. Here, we compared the response to simulated summer heatwave temperatures (+1.5 and +3.0°C above average) in two populations of a coral reef damselfish with different capacities for thermal plasticity. We found that the more thermally tolerant population had greater plasticity of gene expression and had significantly more downregulated genes, which may provide more energy to repair damage associated with thermal stress and to maintain basic functions at these extreme temperatures. In contrast, the thermally sensitive population exhibited higher basal levels of heat shock proteins and had three times fewer changes in gene expression overall. The limited changes in gene regulation suggest that individuals have reduced genome plasticity to tolerate thermal fluctuations and consequently may not have enough energy to repair damage and resume cellular homeostasis at extreme temperatures. Thus, we have identified the molecular signatures of how two genetically distinct fish populations cope with an extreme thermal event, and why they differ in their capacity for thermal plasticity.
Keywords	climate change ; heatwaves ; ocean warming ; transcriptomics ; genomics ; local adaptation ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	612
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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