1
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Schmidt E, Donelson JM. Regional thermal variation in a coral reef fish. CONSERVATION PHYSIOLOGY 2024; 12:coae058. [PMID: 39139734 PMCID: PMC11320370 DOI: 10.1093/conphys/coae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/17/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024]
Abstract
How species respond to climate change will depend on the collective response of populations. Intraspecific variation in traits, evolved through genetic adaptation and phenotypic plasticity, can cause thermal performance curves to vary over species' distributions. Intraspecific variation within marine species has received relatively little attention due to the belief that marine systems lack dispersal barriers strong enough to promote locally adapted traits. Here we show that intraspecific variation is present between low- and high-latitude populations of a coral reef damselfish (Acanthochromis polyacanthus). Co-gradient variation was observed when examining aerobic physiology across a thermal gradient that reflected mean summer temperatures of high- and low-latitude regions, as well as projected future ocean temperatures (i.e. 27, 28.5, 30, 31.5°C). Whilst thermally sensitive, no significant differences were observed between high- and low-latitude regions when measuring immunocompetence, haematocrit and anaerobic enzyme activity. The presence of co-gradient variation suggests that dispersal limitations in marine systems can promote local adaptive responses; however, intraspecific variation may not be ubiquitous amongst traits. Identifying locally adapted traits amongst populations remains necessary to accurately project species responses to climate change and identify differences in adaptive potential.
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Affiliation(s)
- Elliott Schmidt
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Jennifer M Donelson
- College of Science and Engineering and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
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2
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Banousse G, Normandeau E, Semeniuk C, Bernatchez L, Audet C. Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study. G3 (BETHESDA, MD.) 2024; 14:jkae051. [PMID: 38478598 PMCID: PMC11075542 DOI: 10.1093/g3journal/jkae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 05/08/2024]
Abstract
Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerational plasticity) and offspring-rearing temperatures (within-generational plasticity) modify the brain transcriptome of Brook charr progeny (fry stage). Parents were exposed to either cold or warm temperatures during final gonad maturation and their progeny were reared at 5 or 8 °C during the first stages of development. Illumina Novaseq6000 was used to sequence the brain transcriptome at the yolk sac resorption stage. The number of differentially expressed genes was very low when comparing fry reared at different temperatures (79 differentially expressed genes). In contrast, 9,050 differentially expressed genes were significantly differentially expressed between fry issued from parents exposed to either cold or warm temperatures. There was a significant downregulation of processes related to neural and synaptic activity in fry originating from the warm parental group vs fry from the cold parental one. We also observed significant upregulation of DNA methylation genes and of the most salient processes associated with compensation to warming, such as metabolism, cellular response to stress, and adaptive immunity.
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Affiliation(s)
- Ghizlane Banousse
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5L 2Z9
| | - Eric Normandeau
- Plateforme de bio-informatique de l’IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada G1V 0A6
| | - Christina Semeniuk
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, Ont, Canada N9C 1A2
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5L 2Z9
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3
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Bonzi LC, Spinks RK, Donelson JM, Munday PL, Ravasi T, Schunter C. Timing-specific parental effects of ocean warming in a coral reef fish. Proc Biol Sci 2024; 291:20232207. [PMID: 38772423 DOI: 10.1098/rspb.2023.2207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/04/2024] [Indexed: 05/23/2024] Open
Abstract
Population and species persistence in a rapidly warming world will be determined by an organism's ability to acclimate to warmer conditions, especially across generations. There is potential for transgenerational acclimation but the importance of ontogenetic timing in the transmission of environmentally induced parental effects remains mostly unknown. We aimed to disentangle the effects of two critical ontogenetic stages (juvenile development and reproduction) to the new-generation acclimation potential, by exposing the spiny chromis damselfish Acanthochromis polyacanthus to simulated ocean warming across two generations. By using hepatic transcriptomics, we discovered that the post-hatching developmental environment of the offspring themselves had little effect on their acclimation potential at 2.5 months of life. Instead, the developmental experience of parents increased regulatory RNA production and protein synthesis, which could improve the offspring's response to warming. Conversely, parental reproduction and offspring embryogenesis in warmer water elicited stress response mechanisms in the offspring, with suppression of translation and mitochondrial respiration. Mismatches between parental developmental and reproductive temperatures deeply affected offspring gene expression profiles, and detrimental effects were evident when warming occurred both during parents' development and reproduction. This study reveals that the previous generation's developmental temperature contributes substantially to thermal acclimation potential during early life; however, exposure at reproduction as well as prolonged heat stress will likely have adverse effects on the species' persistence.
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Affiliation(s)
- L C Bonzi
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong , Hong Kong
| | - R K Spinks
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- Blue Carbon Section, Department of Climate Change, Energy, the Environment and Water, Australian Government , Brisbane 4000, Australia
| | - J M Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- College of Science and Engineering, James Cook University , Townsville 4810, Australia
| | - P L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- College of Science and Engineering, James Cook University , Townsville 4810, Australia
| | - T Ravasi
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4810, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University , Okinawa 904-0495, Japan
| | - C Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong , Hong Kong
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong , Hong Kong
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4
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Bonzi LC, Donelson JM, Spinks RK, Munday PL, Ravasi T, Schunter C. Matching maternal and paternal experiences underpin molecular thermal acclimation. Mol Ecol 2024:e17328. [PMID: 38520127 DOI: 10.1111/mec.17328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024]
Abstract
The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1.5°C) in a fully factorial design and analysing the F2 hepatic gene expression. Paternal and maternal effects showed not only common but also parent-specific components, with the father having the largest influence in shaping the offspring's transcriptomic profile. Fathers contributed to transcriptional transgenerational response to warming through transfer of epigenetically controlled stress-response mechanisms while mothers influenced increased gene expression associated with lipid metabolism regulation. However, the key to acclimation potential was matching thermal experiences of the parents. When both parents were exposed to the same condition, offspring showed increased expression of genes related to structural RNA production and transcriptional regulation, whereas environmental mismatch in parents resulted in maladaptive parental condition transfer, revealed by translation suppression and endoplasmic reticulum stress. Interestingly, the offspring's own environmental experience had the smallest influence on their hepatic transcription profiles. Taken together, our results show the complex nature of the interplay among paternal, maternal and offspring cue integration, and reveal that acclimation potential to ocean warming might depend not only on maternal and paternal contributions but importantly on congruent parental thermal experiences.
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Affiliation(s)
- L C Bonzi
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - J M Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - R K Spinks
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Blue Carbon Section, Australian Government Department of Climate Change, Energy, the Environment and Water, Canberra, Australian Capital Territory, Australia
| | - P L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - T Ravasi
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - C Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, Hong Kong SAR
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5
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Moore B, Jolly J, Izumiyama M, Kawai E, Ravasi T, Ryu T. Tissue-specific transcriptional response of post-larval clownfish to ocean warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168221. [PMID: 37923256 DOI: 10.1016/j.scitotenv.2023.168221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Anthropogenically driven climate change is predicted to increase average sea surface temperatures, as well as the frequency and intensity of marine heatwaves in the future. This increasing temperature is predicted to have a range of negative physiological impacts on multiple life-stages of coral reef fish. Nevertheless, studies of early-life stages remain limited, and tissue-specific transcriptomic studies of post-larval coral reef fish are yet to be conducted. Here, in an aquaria-based study we investigate the tissue-specific (brain, liver, muscle, and digestive tract) transcriptomic response of post-larval (20 dph) Amphiprion ocellaris to temperatures associated with future climate change (+3 °C). Additionally, we utilized metatranscriptomic sequencing to investigate how the microbiome of the digestive tract changes at +3 °C. Our results show that the transcriptional response to elevated temperatures is highly tissue-specific, as the number of differentially expressed genes (DEGs) and gene functions varied amongst the brain (102), liver (1785), digestive tract (380), and muscle (447). All tissues displayed DEGs associated with thermal stress, as 23 heat-shock protein genes were upregulated in all tissues. Our results indicate that post-larval clownfish may experience liver fibrosis-like symptoms at +3 °C as genes associated with extracellular matrix structure, oxidative stress, inflammation, glucose transport, and metabolism were all upregulated. We also observe a shift in the digestive tract microbiome community structure, as Vibrio sp. replace Escherichia coli as the dominant bacteria. This shift is coupled with the dysregulation of various genes involved in immune response in the digestive tract. Overall, this study highlights post-larval clownfish will display tissue-specific transcriptomic responses to future increases in temperature, with many potentially harmful pathways activated at +3 °C.
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Affiliation(s)
- Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Jeffrey Jolly
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
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Kottmann JS, Berge GM, Kousoulaki K, Østbye TKK, Ytteborg E, Gjerde B, Lein I. Welfare and performance of ballan wrasse (Labrus bergylta) reared at two different temperatures after a preparatory feeding trial with enhanced dietary eicosapentaenoic acid. JOURNAL OF FISH BIOLOGY 2023; 103:906-923. [PMID: 37321978 DOI: 10.1111/jfb.15482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023]
Abstract
Concerns have long been raised about the welfare of ballan wrasse (Labrus bergylta) used for the biological control of sea lice in Atlantic salmon (Salmo salar) aquaculture. This study assessed the effect of increased dietary eicosapentaenoic acid (EPA) levels and initial condition factor (CF) on the subsequent performance and welfare of ballan wrasse farmed in high and low water temperatures. Fish were fed a diet with either commercial or high EPA levels for 3 months at 15°C. Subsequently, fish were tagged with a passive integrated transponder, measured for their CF and divided into two groups consisting of fish from both treatments and reared for 4.5 months at either 15 or 6°C fed a commercial diet. Each fish was categorized as high (≥2.7) or low CF (<2.7) fish based on the calculated average CF of the population. Dietary composition influenced the fatty acid (FA) profile of the stored lipids without affecting the growth or welfare of ballan wrasse. Fish reared at 15°C showed higher growth, more fat and energy reserves and less ash content. Fish reared at 6°C lost weight, using up their body lipids at the end of the temperature trial. Gene expression analyses showed upregulation of the positive growth marker (GHrα) and two genes involved in the synthesis and oxidation of FAs (elovl5, cpt1) and downregulation of the negative growth marker (mstn) in fish reared at 15°C compared to those reared at 6°C. Fish reared at 6°C showed upregulated levels of il-6 compared to those reared at 15°C, suggesting an enhanced immune reaction in response to low temperature. Fish with high CF showed better survival, growth and performance compared to those with low CF. External welfare scoring showed higher prevalence and severity in emaciation, scale loss and the sum index score (of all measured welfare parameters) in fish reared at 6°C compared to those reared at 15°C and better welfare in fish with high CF compared to those with low CF. Histological examination of the skin showed that fish reared at 6°C had decreased epidermal thickness, a lower overall number of mucous cells in the inner and outer epidermis and a different organization of mucous cells compared to fish reared at 15°C, indicating stress in fish reared at 6°C. Overall, low water temperatures had profound effects on the performance and external and internal welfare parameters of ballan wrasse and can be considered a stressor likely affecting the delousing efficacy. These findings support the seasonal use of different cleaner fish species. High CF, but not increased dietary EPA levels, appeared to help fish cope better with low water temperatures and should thus be assessed and considered before deploying them in salmon cages.
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Affiliation(s)
- Johanna S Kottmann
- Department of Aquaculture Production Technology, Nofima, Sunndalsøra, Norway
| | - Gerd M Berge
- Department of Nutrition and Feed Technology, Nofima, Sunndalsøra, Norway
| | | | | | | | - Bjarne Gjerde
- Department of Breeding and Genetics, Nofima, Ås, Norway
| | - Ingrid Lein
- Department of Aquaculture Production Technology, Nofima, Sunndalsøra, Norway
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Herrera M, Ravasi T, Laudet V. Anemonefishes: A model system for evolutionary genomics. F1000Res 2023; 12:204. [PMID: 37928172 PMCID: PMC10624958 DOI: 10.12688/f1000research.130752.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
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.
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Affiliation(s)
- Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
- Marine Research Station, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi I-Lan 262, Taiwan
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Massey MD, Dalziel AC. Parental early life environments drive transgenerational plasticity of offspring metabolism in a freshwater fish ( Danio rerio). Biol Lett 2023; 19:20230266. [PMID: 37788714 PMCID: PMC10547547 DOI: 10.1098/rsbl.2023.0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
Parental experiences can lead to changes in offspring phenotypes through transgenerational plasticity (TGP). TGP is expected to play a role in improving the responses of offspring to changes in climate, but little is known about how the early lives of parents influence offspring TGP. Here, we use a model organism, zebrafish (Danio rerio), to contrast the effects of early and later life parental thermal environments on offspring routine metabolism. To accomplish this, we exposed both parents to either constant optimal (27°C) or environmentally realistic diel fluctuating (22-32°C) temperatures during early (embryonic and larval) and later (juvenile and adult) life in a factorial design. We found significant reduction of routine metabolic rates (greater than 20%) at stressful temperatures (22°C and 32°C) after biparental early life exposure to fluctuating temperatures, but little effect of later life parental temperatures on offspring metabolism. This reduction reflects metabolic compensation and is expected to enhance offspring body sizes under stressful temperatures. These changes occur over and above the effects of parental environments on egg size, suggesting alternate non-genetic mechanisms influenced offspring metabolic rates.
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Affiliation(s)
- Melanie D. Massey
- Department of Biology Life Science Centre, Dalhousie University, 1355 Oxford Street, PO Box 15000, Halifax, Nova Scotia, Canada B3H 4R2
| | - Anne C. Dalziel
- Biology Department, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia, Canada B3H 3C3
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Liu MJ, Gao J, Guo HY, Zhu KC, Liu BS, Zhang N, Sun JH, Zhang DC. Transcriptomics Reveal the Effects of Breeding Temperature on Growth and Metabolism in the Early Developmental Stage of Platax teira. BIOLOGY 2023; 12:1161. [PMID: 37759561 PMCID: PMC10525949 DOI: 10.3390/biology12091161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/16/2023] [Accepted: 08/10/2023] [Indexed: 09/29/2023]
Abstract
The growth, development, and survival of fish, especially in the early stages of development, is influenced by a complex of environmental factors, among which temperature is one of the most important. Although the physiological effects of environmental stress in fish have been extensively studied, the molecular mechanisms are poorly understood. However, recent advances in transcriptomic techniques have facilitated the study of the molecular mechanisms of environmental stress responses in aquatic species. Here, we aimed to elucidate the effects of breeding temperatures (21, 24, 27, and 30 °C) on the growth and nutrient metabolism in the early developmental stage of Platax teira, using transcriptomic techniques. Transcriptomic analysis identified 5492, 6937, and 4246 differentially expressed genes (DEGs) in the 21 vs. 24 °C, 27 vs. 24 °C, and 30 vs. 24 °C comparisons, respectively, most of which were involved in cell processes, single organism, metabolism, catalytic activity, and cell part, based on gene ontology (GO) functional annotations. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly enriched in pathways related to metabolism of matter and energy, protein digestion and absorption, and glucose and lipid metabolism. Additionally, the expression of genes related to energy, lipid, and glucose metabolism in the fish liver was upregulated under a low-temperature condition (21 °C), although increasing the temperature within the acceptable threshold improved nutrient metabolism and growth in the fish. Meanwhile, nutrient metabolism and growth were suppressed by an extremely high temperature (30 °C) owing to oxidative stress. Overall, it was shown that nutrient metabolism pathways were involved in thermal stress responses in P. teira, and the optimal breeding temperature range was 24-27 °C. Through transcriptomics, the regulatory mechanism of larval development in P. teira under different growth temperatures was elucidated, with the goal of establishing a theoretical basis for industrial breeding.
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Affiliation(s)
- Ming-Jian Liu
- College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Jie Gao
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Hua-Yang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Ke-Cheng Zhu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Bao-Suo Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Nan Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Jin-Hui Sun
- College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Dian-Chang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
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10
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Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Hum Genomics 2022; 16:56. [PMID: 36369063 PMCID: PMC9652883 DOI: 10.1186/s40246-022-00429-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA.
| | - Rittika Mallik
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Moisés A Bernal
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Daniel W Nebert
- Department of Environmental Health, Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati, OH, 45267, USA
- Department of Pediatrics and Molecular Developmental Biology, Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, 45229, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Laurel R Yohe
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey P Townsend
- Department of Bioinformatics and Genomics, UNC-Charlotte, Charlotte, NC, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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11
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Ragsdale A, Ortega-Recalde O, Dutoit L, Besson AA, Chia JHZ, King T, Nakagawa S, Hickey A, Gemmell NJ, Hore T, Johnson SL. Paternal hypoxia exposure primes offspring for increased hypoxia resistance. BMC Biol 2022; 20:185. [PMID: 36038899 PMCID: PMC9426223 DOI: 10.1186/s12915-022-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia. RESULTS We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 6-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that other epigenetic mechanisms are responsible for alterations in gene expression. CONCLUSIONS Overall, our findings suggest that an epigenetic memory of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.
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Affiliation(s)
| | | | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Anne A Besson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Jolyn H Z Chia
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Tania King
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Anthony Hickey
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sheri L Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand.
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12
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Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis. Nat Commun 2022; 13:3804. [PMID: 35778405 PMCID: PMC9249911 DOI: 10.1038/s41467-022-31350-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
At the current rate of climate change, it is unlikely that multicellular organisms will be able to adapt to changing environmental conditions through genetic recombination and natural selection alone. Thus, it is critical to understand alternative mechanisms that allow organisms to cope with rapid environmental changes. Here, we use the sea anemone Nematostella vectensis, which has evolved the capability of surviving in a wide range of temperatures and salinities, as a model to investigate the microbiota as a source of rapid adaptation. We long-term acclimate polyps of Nematostella to low, medium, and high temperatures, to test the impact of microbiota-mediated plasticity on animal acclimation. Using the same animal clonal line, propagated from a single polyp, allows us to eliminate the effects of the host genotype. The higher thermal tolerance of animals acclimated to high temperature can be transferred to non-acclimated animals through microbiota transplantation. The offspring fitness is highest from F0 females acclimated to high temperature and specific members of the acclimated microbiota are transmitted to the next generation. These results indicate that microbiota plasticity can contribute to animal thermal acclimation and its transmission to the next generation may represent a rapid mechanism for thermal adaptation. This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.
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13
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Chan SKN, Suresh S, Munday P, Ravasi T, Bernal MA, Schunter C. The alternative splicing landscape of a coral reef fish during a marine heatwave. Ecol Evol 2022; 12:e8738. [PMID: 35342554 PMCID: PMC8933327 DOI: 10.1002/ece3.8738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n = 40) genes during the onset of the heatwave (i.e., 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding, and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n = 26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.
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Affiliation(s)
- Stanley Kin Nok Chan
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Sneha Suresh
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
| | - Phillip Munday
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
| | - Moisés A. Bernal
- Department of Biological SciencesCollege of Science and MathematicsAuburn UniversityAuburnAlabamaUSA
| | - Celia Schunter
- Swire Institute of Marine ScienceSchool of Biological SciencesThe University of Hong KongHong Kong SARChina
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14
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Bernal MA, Ravasi T, Rodgers GG, Munday PL, Donelson JM. Plasticity to ocean warming is influenced by transgenerational, reproductive, and developmental exposure in a coral reef fish. Evol Appl 2022; 15:249-261. [PMID: 35233246 PMCID: PMC8867710 DOI: 10.1111/eva.13337] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/10/2021] [Indexed: 11/28/2022] Open
Abstract
Global warming is expected to drive some ectothermic species beyond their thermal tolerance in upcoming decades. Phenotypic plasticity, via developmental or transgenerational acclimation, is a critical mechanism for compensation in the face of environmental change. Yet, it remains to be determined if the activation of beneficial phenotypes requires direct exposure throughout development, or if compensation can be obtained just through the experience of previous generations. In this study, we exposed three generations of a tropical damselfish to combinations of current-day (Control) and projected future (+1.5°C) water temperatures. Acclimation was evaluated with phenotypic (oxygen consumption, hepatosomatic index, physical condition) and molecular (liver gene expression) measurements of third-generation juveniles. Exposure of grandparents/parents to warm conditions improved the aerobic capacity of fish regardless of thermal conditions experienced afterwards, representing a true transgenerational effect. This coincided with patterns of gene expression related to inflammation and immunity seen in the third generation. Parental effects due to reproductive temperature significantly affected the physical condition and routine metabolic rate (oxygen consumption) of offspring, but had little impact on gene expression of the F3. Developmental temperature of juveniles, and whether they matched conditions during parental reproduction, had the largest influence on the liver transcriptional program. Using a combination of both phenotypic and molecular approaches, this study highlights how the conditions experienced by both previous and current generations can influence plasticity to global warming in upcoming decades.
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Affiliation(s)
- Moisés A. Bernal
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Timothy Ravasi
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐son, OkinawaJapan
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
| | - Giverny G. Rodgers
- College of Science and EngineeringJames Cook UniversityTownsvilleQLDAustralia
| | - Philip L. Munday
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
| | - Jennifer M. Donelson
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
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15
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Alfonso S, Gesto M, Sadoul B. Temperature increase and its effects on fish stress physiology in the context of global warming. JOURNAL OF FISH BIOLOGY 2021; 98:1496-1508. [PMID: 33111333 DOI: 10.1111/jfb.14599] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/14/2020] [Accepted: 10/27/2020] [Indexed: 05/07/2023]
Abstract
The capacity of fishes to cope with environmental variation is considered to be a main determinant of their fitness and is partly determined by their stress physiology. By 2100, global ocean temperature is expected to rise by 1-4°C, with potential consequences for stress physiology. Global warming is affecting animal populations worldwide through chronic temperature increases and an increase in the frequency of extreme heatwave events. As ectotherms, fishes are expected to be particularly vulnerable to global warming. Although little information is available about the effects of global warming on stress physiology in nature, multiple studies describe the consequences of temperature increases on stress physiology in controlled laboratory conditions, providing insight into what can be expected in the wild. Chronic temperature increase constitutes a physiological load that can alter the ability of fishes to cope with additional stressors, which might compromise their fitness. In addition, rapid temperature increases are known to induce acute stress responses in fishes and might be of ecological relevance in particular situations. This review summarizes knowledge about effects of temperature increases on the stress physiology of fishes and discusses these in the context of global warming.
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Affiliation(s)
- Sébastien Alfonso
- COISPA Tecnologia & Ricerca, Stazione Sperimentale per lo Studio delle Risorse del Mare, Bari, Italy
| | - Manuel Gesto
- Section for Aquaculture, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Bastien Sadoul
- MARBEC, Ifremer, IRD, UM2, CNRS, Sète, France
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes Cedex, France
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16
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Lefevre S, Wang T, McKenzie DJ. The role of mechanistic physiology in investigating impacts of global warming on fishes. J Exp Biol 2021; 224:224/Suppl_1/jeb238840. [PMID: 33627469 DOI: 10.1242/jeb.238840] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Warming of aquatic environments as a result of climate change is already having measurable impacts on fishes, manifested as changes in phenology, range shifts and reductions in body size. Understanding the physiological mechanisms underlying these seemingly universal patterns is crucial if we are to reliably predict the fate of fish populations with future warming. This includes an understanding of mechanisms for acute thermal tolerance, as extreme heatwaves may be a major driver of observed effects. The hypothesis of gill oxygen limitation (GOL) is claimed to explain asymptotic fish growth, and why some fish species are decreasing in size with warming; but its underlying assumptions conflict with established knowledge and direct mechanistic evidence is lacking. The hypothesis of oxygen- and capacity-limited thermal tolerance (OCLTT) has stimulated a wave of research into the role of oxygen supply capacity and thermal performance curves for aerobic scope, but results vary greatly between species, indicating that it is unlikely to be a universal mechanism. As thermal performance curves remain important for incorporating physiological tolerance into models, we discuss potentially fruitful alternatives to aerobic scope, notably specific dynamic action and growth rate. We consider the limitations of estimating acute thermal tolerance by a single rapid measure whose mechanism of action is not known. We emphasise the continued importance of experimental physiology, particularly in advancing our understanding of underlying mechanisms, but also the challenge of making this knowledge relevant to the more complex reality.
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Affiliation(s)
- Sjannie Lefevre
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Tobias Wang
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | - David J McKenzie
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, Ifremer, IRD, 34000 Montpellier, France
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17
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Cerqueira NNCD, Rotundo MM, Marceniuk AP, Cruz VPD, Foresti F, Oliveira C. Molecular identification of Brachygenys and Haemulon species (Perciformes: Haemulidae) from the Brazilian coast. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2020-0109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract The fishes of the Haemulidae family are currently allocated to 19 genera with a worldwide distribution in the tropical and subtropical waters of the world’s oceans. Brachygenys and Haemulon are important genera of reef fish in Brazil, as they occur in large shoals, which are both ecologically and commercially valuable. This study identified the Brazilian species of the genera Brachygenys and Haemulon using DNA barcodes. While we found only a single lineage in Brachygenys chrysargyrea, Haemulon melanurum, H. parra, and H. squamipinna, more than one molecular operational taxonomic unit (MOTU) was identified in H. atlanticus, H. aurolineatum, and H. plumieri, indicating the possible existence of discrete populations or cryptic species.
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Affiliation(s)
| | | | | | | | - Fausto Foresti
- Universidade Estadual Paulista Júlio de Mesquita Filho IBB/UNESP, Brazil
| | - Claudio Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho IBB/UNESP, Brazil
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18
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Lopes AF, Faria AM, Dupont S. Elevated temperature, but not decreased pH, impairs reproduction in a temperate fish. Sci Rep 2020; 10:20805. [PMID: 33257710 PMCID: PMC7705697 DOI: 10.1038/s41598-020-77906-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/17/2020] [Indexed: 12/27/2022] Open
Abstract
Fish reproductive success is linked to the ability of couples to mate and produce clutches that successfully hatch. Environmental stressors like high temperature and low pH can jeopardize this energetically costly process. In this study, exposure to high temperature and low pH was tested on a marine temperate species, Gobiusculus flavescens, to evaluate effects on reproductive performance. Breeding pairs were assigned to different temperatures (+ 0 °C, + 3 °C relative to in situ temperature) and pH levels (8.0, 7.6), in a cross-factorial design for a 3-month period. Reproduction activity, success, and paternal investment were measured throughout the exposure period. Results show reproduction is impaired by elevated temperature, while low pH had little impact. Breeding pairs under high temperature had 3% to 10% hatching success, up to 30% less eggs and eggs up to 20% smaller. Although paternal investment was not affected by tested parameters, males of breeding pairs exposed to elevated temperature had smaller gonadosomatic indexes, which might indicate a lack of investment in the reproductive process. Overall, results show that elevated temperature, expected more frequently in the near future, as a consequence of global warming, may impair key processes like reproduction in temperate fish, with potential consequences for fitness and population replenishment.
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Affiliation(s)
- Ana F Lopes
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, 1149-041, Lisbon, Portugal.
| | - Ana M Faria
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, 1149-041, Lisbon, Portugal
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Gothenburg, 566 Kristineberg, 45178, Fiskebäckskil, Sweden
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19
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Monroe AA, Zhang H, Schunter C, Ravasi T. Probing SWATH-MS as a tool for proteome level quantification in a nonmodel fish. Mol Ecol Resour 2020; 20:1647-1657. [PMID: 32687632 PMCID: PMC7689905 DOI: 10.1111/1755-0998.13229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/09/2020] [Accepted: 07/08/2020] [Indexed: 12/27/2022]
Abstract
Quantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data‐independent acquisition (SWATH/DIA‐MS), an accurate, sensitive and reproducible method for analysing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species‐specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for nonmodel organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins under fish exposure to elevated pCO2 and temperature, we validated the application and usefulness of these different spectral libraries. Successful identification of significant differentially expressed proteins from different environmental exposures occurred using the library with a combination of data‐independent and data‐dependent acquisition methods as well as both tissue types. Further analysis revealed expected patterns of significantly up‐regulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a nonmodel organism. It represents a useful guide for future building of accurate spectral library references in nonmodel organisms allowing the discovery of ecologically relevant changes in the proteome.
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Affiliation(s)
- Alison A Monroe
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Huoming Zhang
- King Abdullah University of Science and Technology, Core Labs, Thuwal, Saudi Arabia
| | - Celia Schunter
- Swire Institute of Marine Science, The School of Biological Sciences, The University of Hong Kong, Hong Kong SAR
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna-son, Japan
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20
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Brandl SJ, Johansen JL, Casey JM, Tornabene L, Morais RA, Burt JA. Extreme environmental conditions reduce coral reef fish biodiversity and productivity. Nat Commun 2020; 11:3832. [PMID: 32737315 PMCID: PMC7395083 DOI: 10.1038/s41467-020-17731-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022] Open
Abstract
Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world’s hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth’s hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss. Brandl, Johansen et al. compare organismal traits, community structure, and productivity dynamics of cryptobenthic reef fishes across two locations, the Arabian Gulf and the Gulf of Oman, the former of which harbors the world’s hottest coral reefs. They show that environmental extremes in the Arabian Gulf result in dramatically less diverse, abundant, and productive cryptobenthic fish assemblages, which could foreshadow the future of coral reef biodiversity and functioning.
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Affiliation(s)
- Simon J Brandl
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada. .,CESAB-FRB, 5 Rue de l'École de Médecine, 34000, Montpellier, France. .,PSL Université Paris: CNRS-EPHE-UPVD USR3278 CRIOBE, Université de Perpignan, Perpignan, France. .,Laboratoire d'Excellence "CORAIL,", Perpignan, France.
| | - Jacob L Johansen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Kane'ohe, HI, USA. .,Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Jordan M Casey
- PSL Université Paris: CNRS-EPHE-UPVD USR3278 CRIOBE, Université de Perpignan, Perpignan, France.,Laboratoire d'Excellence "CORAIL,", Perpignan, France
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Renato A Morais
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A Burt
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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21
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Bernal MA, Schunter C, Lehmann R, Lightfoot DJ, Allan BJM, Veilleux HD, Rummer JL, Munday PL, Ravasi T. Species-specific molecular responses of wild coral reef fishes during a marine heatwave. SCIENCE ADVANCES 2020; 6:eaay3423. [PMID: 32206711 PMCID: PMC7080449 DOI: 10.1126/sciadv.aay3423] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
The marine heatwave of 2016 was one of the longest and hottest thermal anomalies recorded on the Great Barrier Reef, influencing multiple species of marine ectotherms, including coral reef fishes. There is a gap in our understanding of what the physiological consequences of heatwaves in wild fish populations are. Thus, in this study, we used liver transcriptomes to understand the molecular response of five species to the 2016 heatwave conditions. Gene expression was species specific, yet we detected overlap in functional responses associated with thermal stress previously reported in experimental setups. The molecular response was also influenced by the duration of exposure to elevated temperatures. This study highlights the importance of considering the effects of extreme warming events when evaluating the consequences of climate change on fish communities.
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Affiliation(s)
- Moisés A. Bernal
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biological Sciences, College of Science and Mathematics, Auburn University, Auburn, AL 36849, USA
| | - Celia Schunter
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Robert Lehmann
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Damien J. Lightfoot
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Bridie J. M. Allan
- Department of Marine Science, University of Otago, Dunedin 9054, New Zealand
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - Heather D. Veilleux
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Jodie L. Rummer
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - Philip L. Munday
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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22
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The effects of water temperature on the juvenile performance of two tropical damselfishes expatriating to temperate reefs. Sci Rep 2019; 9:13937. [PMID: 31558794 PMCID: PMC6763422 DOI: 10.1038/s41598-019-50303-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Ocean warming associated with global climate change is already inducing geographic range shifts of marine species. Juvenile coral reef fishes transported into temperate latitudes (termed ‘vagrant’ fishes) can experience winter water temperatures below their normal thermal minimum. Such environmental extremes may increase energetic costs for such fishes, resulting in reduced performance, which may be the governing factor that limits the potential for poleward range expansion of such fishes. This study compared the juvenile physiological performance and behaviour of two congeneric tropical damselfishes which settle during austral summer months within temperate eastern Australia: Abudefduf vaigiensis have an extended southern range, and lower threshold survival temperature than the congeneric A. whitleyi. Physiological and behavioural performance parameters that may be affected by cooler temperature regimes at higher latitudes were measured in aquaria. Lower water temperature resulted in reduced growth rates, feeding rates, burst escape speed and metabolic rates of both species, with significantly reduced performance (up to six-fold reductions) for fishes reared at 18 °C relative to 22 °C and 26 °C. However, A. whitleyi exhibited lower growth rates than A. vaigiensis across all temperatures, and lower aerobic capacity at the lowest temperature (18 °C). This difference between species in growth and metabolic capacity suggests that the extended southern distribution and greater overwintering success of A. vaigiensis, in comparison to A. whitleyi is related to thermal performance parameters which are critical in maintaining individual health and survival. Our results support previous findings in the region that water temperature below 22 °C represents a critical physiological threshold for tropical Abudefduf species expatriating into temperate south-eastern Australia.
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23
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Fox RJ, Donelson JM, Schunter C, Ravasi T, Gaitán-Espitia JD. Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180174. [PMID: 30966962 PMCID: PMC6365870 DOI: 10.1098/rstb.2018.0174] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2018] [Indexed: 12/18/2022] Open
Abstract
How populations and species respond to modified environmental conditions is critical to their persistence both now and into the future, particularly given the increasing pace of environmental change. The process of adaptation to novel environmental conditions can occur via two mechanisms: (1) the expression of phenotypic plasticity (the ability of one genotype to express varying phenotypes when exposed to different environmental conditions), and (2) evolution via selection for particular phenotypes, resulting in the modification of genetic variation in the population. Plasticity, because it acts at the level of the individual, is often hailed as a rapid-response mechanism that will enable organisms to adapt and survive in our rapidly changing world. But plasticity can also retard adaptation by shifting the distribution of phenotypes in the population, shielding it from natural selection. In addition to which, not all plastic responses are adaptive-now well-documented in cases of ecological traps. In this theme issue, we aim to present a considered view of plasticity and the role it could play in facilitating or hindering adaption to environmental change. This introduction provides a re-examination of our current understanding of the role of phenotypic plasticity in adaptation and sets the theme issue's contributions in their broader context. Four key themes emerge: the need to measure plasticity across both space and time; the importance of the past in predicting the future; the importance of the link between plasticity and sexual selection; and the need to understand more about the nature of selection on plasticity itself. We conclude by advocating the need for cross-disciplinary collaborations to settle the question of whether plasticity will promote or retard species' rates of adaptation to ever-more stressful environmental conditions. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.
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Affiliation(s)
- Rebecca J. Fox
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jennifer M. Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4810, Australia
| | - Celia Schunter
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan D. Gaitán-Espitia
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
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Bernal MA, Dixon GB, Matz MV, Rocha LA. Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ 2019; 7:e6541. [PMID: 30842908 PMCID: PMC6398375 DOI: 10.7717/peerj.6541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/29/2019] [Indexed: 01/21/2023] Open
Abstract
Background Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic. Methods Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise d N/d S) and patterns of gene expression between the three species. Results Pairwise d N/d S analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior-posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium. Discussion Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.
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Affiliation(s)
- Moisés A Bernal
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Groves B Dixon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Luiz A Rocha
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
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Domenici P, Allan BJM, Lefrançois C, McCormick MI. The effect of climate change on the escape kinematics and performance of fishes: implications for future predator-prey interactions. CONSERVATION PHYSIOLOGY 2019; 7:coz078. [PMID: 31723432 PMCID: PMC6839432 DOI: 10.1093/conphys/coz078] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/27/2019] [Accepted: 10/18/2019] [Indexed: 05/21/2023]
Abstract
Climate change can have a pronounced impact on the physiology and behaviour of fishes. Notably, many climate change stressors, such as global warming, hypoxia and ocean acidification (OA), have been shown to alter the kinematics of predator-prey interactions in fishes, with potential effects at ecological levels. Here, we review the main effects of each of these stressors on fish escape responses using an integrative approach that encompasses behavioural and kinematic variables. Elevated temperature was shown to affect many components of the escape response, including escape latencies, kinematics and maximum swimming performance, while the main effect of hypoxia was on escape responsiveness and directionality. OA had a negative effect on the escape response of juvenile fish by decreasing their directionality, responsiveness and locomotor performance, although some studies show no effect of acidification. The few studies that have explored the effects of multiple stressors show that temperature tends to have a stronger effect on escape performance than OA. Overall, the effects of climate change on escape responses may occur through decreased muscle performance and/or an interference with brain and sensory functions. In all of these cases, since the escape response is a behaviour directly related to survival, these effects are likely to be fundamental drivers of changes in marine communities. The overall future impact of these stressors is discussed by including their potential effects on predator attack behaviour, thereby allowing the development of potential future scenarios for predator-prey interactions.
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Affiliation(s)
- Paolo Domenici
- CNR-IAS, Oristano, 09170 Italy
- Corresponding author: CNR-IAS, Oristano 09170, Italy.
| | - Bridie J M Allan
- Department of Marine Science, University of Otago, Dunedin 9054, New Zealand
| | | | - Mark I McCormick
- Department of Marine Biology and Aquaculture, ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
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