1
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Dilworth J, Million WC, Ruggeri M, Hall ER, Dungan AM, Muller EM, Kenkel CD. Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression. Proc Biol Sci 2024; 291:20232447. [PMID: 38531406 DOI: 10.1098/rspb.2023.2447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.
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Affiliation(s)
| | | | - Maria Ruggeri
- University of Southern California, Los Angeles, CA, USA
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2
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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3
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Lafuente E, Duneau D, Beldade P. Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation. Mol Ecol 2024; 33:e17294. [PMID: 38366327 DOI: 10.1111/mec.17294] [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: 09/13/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.
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Affiliation(s)
- E Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - D Duneau
- UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - P Beldade
- cE3c (Center for Ecology, Evolution and Environmental Changes) & CHANGE (Global Change and Sustainability Institute), FCUL, Lisboa, Portugal
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Russo D, Jones G, Martinoli A, Preatoni DG, Spada M, Pereswiet‐Soltan A, Cistrone L. Climate is changing, are European bats too? A multispecies analysis of trends in body size. Ecol Evol 2024; 14:e10872. [PMID: 38333101 PMCID: PMC10850807 DOI: 10.1002/ece3.10872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024] Open
Abstract
Animal size, a trait sensitive to spatial and temporal variables, is a key element in ecological and evolutionary dynamics. In the context of climate change, there is evidence that some bat species are increasing their body size via phenotypic responses to higher temperatures at maternity roosts. To test the generality of this response, we conducted a >20-year study examining body size changes in 15 bat species in Italy, analysing data from 4393 individual bats captured since 1995. In addition to examining the temporal effect, we considered the potential influence of sexual dimorphism and, where relevant, included latitude and altitude as potential drivers of body size change. Contrary to initial predictions of a widespread increase in size, our findings challenge this assumption, revealing a nuanced interplay of factors contributing to the complexity of bat body size dynamics. Specifically, only three species (Myotis daubentonii, Nyctalus leisleri, and Pipistrellus pygmaeus) out of the 15 exhibited a discernible increase in body size over the studied period, prompting a reassessment of bats as reliable indicators of climate change based on alterations in body size. Our investigation into influencing factors highlighted the significance of temperature-related variables, with latitude and altitude emerging as crucial drivers. In some cases, this mirrored patterns consistent with Bergmann's rule, revealing larger bats recorded at progressively higher latitudes (Plecotus auritus, Myotis mystacinus, and Miniopterus schreibersii) or altitudes (Pipistrellus kuhlii). We also observed a clear sexual dimorphism effect in most species, with females consistently larger than males. The observed increase in size over time in three species suggests the occurrence of phenotypic plasticity, raising questions about potential long-term selective pressures on larger individuals. The unresolved question of whether temperature-related changes in body size reflect microevolutionary processes or phenotypic plastic responses adds further complexity to our understanding of body size patterns in bats over time and space.
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Affiliation(s)
- Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di AgrariaUniversità degli Studi di Napoli Federico IIPorticiItaly
- School of Biological SciencesUniversity of BristolBristolUK
| | - Gareth Jones
- School of Biological SciencesUniversity of BristolBristolUK
| | - Adriano Martinoli
- Unità di Analisi e Gestione delle Risorse Ambientali, Guido Tosi Research Group, Dipartimento di Scienze Teoriche ed ApplicateUniversità degli Studi dell'InsubriaVareseItaly
| | - Damiano G. Preatoni
- Unità di Analisi e Gestione delle Risorse Ambientali, Guido Tosi Research Group, Dipartimento di Scienze Teoriche ed ApplicateUniversità degli Studi dell'InsubriaVareseItaly
| | | | | | - Luca Cistrone
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di AgrariaUniversità degli Studi di Napoli Federico IIPorticiItaly
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Kang J, Chung A, Suresh S, Bonzi LC, Sourisse JM, Ramirez‐Calero S, Romeo D, Petit‐Marty N, Pegueroles C, Schunter C. Long non-coding RNAs mediate fish gene expression in response to ocean acidification. Evol Appl 2024; 17:e13655. [PMID: 38357358 PMCID: PMC10866067 DOI: 10.1111/eva.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The majority of the transcribed genome does not have coding potential but these non-coding transcripts play crucial roles in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in shaping an organism's response to environmental changes, ultimately impacting their survival and persistence as population or species face global change. However, the roles of long non-coding RNAs (lncRNAs), when confronted with environmental changes, remain largely unclear. To explore the potential role of lncRNAs in fish exposed to ocean acidification (OA), we analyzed publicly available brain RNA-seq data from a coral reef fish Acanthochromis polyacanthus. We annotated the lncRNAs in its genome and examined the expression changes of intergenic lncRNAs (lincRNAs) between A. polyacanthus samples from a natural CO2 seep and a nearby control site. We identified 4728 lncRNAs, including 3272 lincRNAs in this species. Remarkably, 93.03% of these lincRNAs were species-specific. Among the 125 highly expressed lincRNAs and 403 differentially expressed lincRNAs in response to elevated CO2, we observed that lincRNAs were either neighboring or potentially trans-regulating differentially expressed coding genes associated with pH regulation, neural signal transduction, and ion transport, which are known to be important in the response to OA in fish. In summary, lncRNAs may facilitate fish acclimation and mediate the responses of fish to OA by modulating the expression of crucial coding genes, which offers insight into the regulatory mechanisms underlying fish responses to environmental changes.
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Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Arthur Chung
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sneha Suresh
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Lucrezia C. Bonzi
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Jade M. Sourisse
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Sandra Ramirez‐Calero
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Daniele Romeo
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Natalia Petit‐Marty
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
| | - Cinta Pegueroles
- Department of Genetics, Microbiology and Statistics, Institute for Research on Biodiversity (IRBio)University of BarcelonaBarcelonaSpain
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological SciencesThe University of Hong KongPokfulamHong Kong SAR
- State Key Laboratory of Marine Pollution and Department of ChemistryCity University of Hong KongHong Kong SARChina
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6
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Deng Z, Zhang X, Wolinska J, Blair D, Hu W, Yin M. Climate has contributed to population diversification of Daphnia galeata across Eurasia. Mol Ecol 2023; 32:5110-5124. [PMID: 37548328 DOI: 10.1111/mec.17094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Climate is a fundamental abiotic factor that plays a key role in driving the evolution, distribution and population diversification of species. However, there have been few investigations of genomic signatures of adaptation to local climatic conditions in cladocerans. Here, we have provided the first high-quality chromosome-level genome assembly (~143 Mb, scaffold N50 12.6 Mb) of the waterflea, Daphnia galeata, and investigated genomic variation in 22 populations from Central Europe and Eastern China. Our ecological-niche models suggested that the historic distribution of D. galeata in Eurasia was significantly affected by Quaternary climate fluctuations. We detected pronounced genomic and morphometric divergences between European and Chinese D. galeata populations. Such divergences could be partly explained by genomic signatures of thermal adaptation to distinct climate regimes: a set of candidate single-nucleotide polymorphisms (SNPs) potentially associated with climate were detected. These SNPs were in genes significantly enriched in the Gene ontology terms "determination of adult lifespan" and "translation repressor activity", and especially, mthl5 and SOD1 involved in the IIS pathway, and EIF4EBP2 involved in the target of the rapamycin signalling pathway. Our study indicates that certain alleles might be associated with particular temperature regimes, playing a functional role in shaping the population structure of D. galeata at a large geographical scale. These results highlight the potential role of molecular variation in the response to climate variation, in the context of global climate change.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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Huang X, Li H, Shenkar N, Zhan A. Multidimensional plasticity jointly contributes to rapid acclimation to environmental challenges during biological invasions. RNA (NEW YORK, N.Y.) 2023; 29:675-690. [PMID: 36810233 PMCID: PMC10159005 DOI: 10.1261/rna.079319.122] [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: 06/16/2022] [Accepted: 02/01/2023] [Indexed: 05/06/2023]
Abstract
Rapid plastic response to environmental changes, which involves extremely complex underlying mechanisms, is crucial for organismal survival during many ecological and evolutionary processes such as those in global change and biological invasions. Gene expression is among the most studied molecular plasticity, while co- or posttranscriptional mechanisms are still largely unexplored. Using a model invasive ascidian Ciona savignyi, we studied multidimensional short-term plasticity in response to hyper- and hyposalinity stresses, covering the physiological adjustment, gene expression, alternative splicing (AS), and alternative polyadenylation (APA) regulations. Our results demonstrated that rapid plastic response varied with environmental context, timescales, and molecular regulatory levels. Gene expression, AS, and APA regulations independently acted on different gene sets and corresponding biological functions, highlighting their nonredundant roles in rapid environmental adaptation. Stress-induced gene expression changes illustrated the use of a strategy of accumulating free amino acids under high salinity and losing/reducing them during low salinity to maintain the osmotic homoeostasis. Genes with more exons were inclined to use AS regulations, and isoform switches in functional genes such as SLC2a5 and Cyb5r3 resulted in enhanced transporting activities by up-regulating the isoforms with more transmembrane regions. The extensive 3'-untranslated region (3'UTR) shortening through APA was induced by both salinity stresses, and APA regulation predominated transcriptomic changes at some stages of stress response. The findings here provide evidence for complex plastic mechanisms to environmental changes, and thereby highlight the importance of systemically integrating different levels of regulatory mechanisms in studying initial plasticity in evolutionary trajectories.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
| | - Hanxi Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801 Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
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Londoño GA, Gomez JP, Sánchez-Martínez MA, Levey DJ, Robinson SK. Changing patterns of nest predation and predator communities along a tropical elevation gradient. Ecol Lett 2023; 26:609-620. [PMID: 36855287 DOI: 10.1111/ele.14189] [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: 06/27/2022] [Revised: 02/02/2023] [Accepted: 02/12/2023] [Indexed: 03/02/2023]
Abstract
Tropical montane communities host the world's highest beta diversity of birds, a phenomenon usually attributed to community turnover caused by changes in biotic and abiotic factors along elevation gradients. Yet, empirical data on most biotic factors are lacking. Nest predation is thought to be especially important because it appears to be common and can change selective pressures underlying life history traits, which can alter competitive interactions. We monitored 2538 nests, 338 of which had known nest predators, to evaluate if nest predation changes along a tropical elevational gradient. We found that nest predation decreased with elevation, reflecting the loss of lowland predators that do not tolerate colder climates. We found different "super" nest predators at each elevation that accounted for a high percentage of events, suggesting that selection pressures exerted by nest predator communities may be less diffuse than has been hypothesized, at least for birds nesting in the understory.
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Affiliation(s)
- Gustavo A Londoño
- Facultad de Ciencias Naturales, Departamento de Ciencias Biológicas, Universidad Icesi, Cali, Colombia
| | - Juan Pablo Gomez
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Manuel A Sánchez-Martínez
- Facultad de Ciencias Naturales, Departamento de Ciencias Biológicas, Universidad Icesi, Cali, Colombia
| | - Douglas J Levey
- Division of Environmental Biology, National Science Foundation, Alexandria, Virginia, USA
| | - Scott K Robinson
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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Gates K, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Laporte M, Bernatchez L, Beheregaray LB. Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish. Heredity (Edinb) 2023:10.1038/s41437-023-00612-x. [PMID: 36997655 DOI: 10.1038/s41437-023-00612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractTo conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.
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Kuo HC, Yao CT, Liao BY, Weng MP, Dong F, Hsu YC, Hung CM. Weak gene-gene interaction facilitates the evolution of gene expression plasticity. BMC Biol 2023; 21:57. [PMID: 36941675 PMCID: PMC10029303 DOI: 10.1186/s12915-023-01558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited. RESULTS Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship. CONCLUSIONS Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.
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Affiliation(s)
- Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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Liu M, Liu X, Zhou P, Jiang S, Huang JG, Dong Z. Environmental factors have a major effect in shaping the gene expression of Siberian larch in the Altai Mountains of China. THE PLANT GENOME 2022; 15:e20240. [PMID: 35818680 DOI: 10.1002/tpg2.20240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The differentiation of gene expression is an important link between genotype and phenotype and has important contributions to species adaptation and ecosystem evolution. As a major component of the world's forests, boreal forests play an important role in regulating the global climate, and the phenology of tree species has been and is undergoing changes during global warming. Here, to understand the impact of global warming on gene expression in boreal forest species, we used PacBio and Illumina sequencing methods to study the transcriptome of natural populations of Siberian larch (Larix sibirica Ledeb.) from the Altai Mountains in Xinjiang, China. We found that populations in this area had low genetic differentiation, but individuals were genetically clustered together when they had close geographic distance. Environmental factors, especially temperature, dominated differential gene expression of Siberian larch, while the contribution of genetic variation is relatively small. We speculate that Siberian larch adapts to changes in temperature and precipitation by altering its own gene expression. These results not only predict the tolerance of boreal forests to higher temperatures in the future, but also inform forest management strategies under global climate change.
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Affiliation(s)
- Min Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
| | - Xiaobin Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
| | - Peng Zhou
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Shaowei Jiang
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Jian-Guo Huang
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou, 510650, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Univ., Guangzhou, 510006, China
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12
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Fortuna MA. The phenotypic plasticity of an evolving digital organism. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220852. [PMID: 36117864 PMCID: PMC9470259 DOI: 10.1098/rsos.220852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Climate change will fundamentally reshape life on Earth in the coming decades. Therefore, understanding the extent to which species will cope with rising temperatures is of paramount importance. Phenotypic plasticity is the ability of an organism to change the morphological and functional traits encoded by its genome in response to the environment. I show here that plasticity pervades not only natural but also artificial systems that mimic the developmental process of biological organisms, such as self-replicating and evolving computer programs-digital organisms. Specifically, the environment can modify the sequence of instructions executed from a digital organism's genome (i.e. its transcriptome), which results in changes in its phenotype (i.e. the ability of the digital organism to perform Boolean logic operations). This genetic-based pathway for plasticity comes at a fitness cost to an organism's viability and generation time: the longer the transcriptome (higher fitness cost), the more chances for the environment to modify the genetic execution flow control, and the higher the likelihood for the genome to encode novel phenotypes. By studying to what extent a digital organism's phenotype is influenced by both its genome and the environment, I make a parallelism between natural and artificial evolving systems on how natural selection might slide trait regulation anywhere along a continuum from total environmental control to total genomic control, which harbours lessons not only for designing evolvable artificial systems, but also for synthetic biology.
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Affiliation(s)
- Miguel A. Fortuna
- Computational Biology Lab, Estación Biológica de Doñana (EBD), Spanish National Research Council (CSIC), Seville, Spain
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13
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Marshall IR, Brauer CJ, Wedderburn SD, Whiterod NS, Hammer MP, Barnes TC, Attard CRM, Möller LM, Beheregaray LB. Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13889. [PMID: 35023224 DOI: 10.1111/cobi.13889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.
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Affiliation(s)
- Imogen R Marshall
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Scotte D Wedderburn
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nick S Whiterod
- Aquasave-Nature Glenelg Trust, Victor Harbor, South Australia, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Thomas C Barnes
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, New South Wales, Australia
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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14
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Wang J, Cheng ZY, Dong YW. Demographic, physiological, and genetic factors linked to the poleward range expansion of the snail Nerita yoldii along the shoreline of China. Mol Ecol 2022; 31:4510-4526. [PMID: 35822322 DOI: 10.1111/mec.16610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 05/23/2022] [Accepted: 07/04/2022] [Indexed: 12/01/2022]
Abstract
Species range shift is one of the most significant consequences of climate change in the Anthropocene. A comprehensive study, including demographic, physiological, and genetic factors linked to poleward range expansion, is crucial for understanding how the expanding population occupies the new habitat. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km over the former biogeographic break of the Yangtze River Estuary during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modelling analysis revealed that the new marginal populations experienced a strong genetic bottleneck followed by recent demographic expansion. Successful expansion that overcame the founder effect might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Lower transcriptional plasticity was observed in the new marginal populations. These results suggest a new biogeographic pattern of N. yoldii has formed with the occurrence of demographic, physiologic, and genetic changes, and emphasize the roles of adaptation of marginal populations during range expansion.
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Affiliation(s)
- Jie Wang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, PR China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Zhi-Yuan Cheng
- State Key Laboratory of Marine Environmental Science, College of Marine and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, PR China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
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15
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Swaegers J, Koch EL. Gene expression studies of plastic and evolutionary responses to global warming. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100918. [PMID: 35390507 DOI: 10.1016/j.cois.2022.100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Phenotypic plasticity can be a rapid response for coping with global warming, yet may be insufficient to protect species from extinction. Evolutionary adaptation may reinforce adaptive or oppose maladaptive plastic responses. With advances in technology whole transcriptomes can provide us with an unprecedented overview of genes and functional processes underlying the interplay between plasticity and evolution. We advocate that insects provide ideal opportunities to study plasticity in non-adapted and thermally adapted populations to infer reaction norms across the whole transcriptome ('reactionomes'). This can advance our understanding of how the interplay between plasticity and evolution shapes responses to warming. So far, a limited number of studies suggest predominantly maladaptive plastic responses to novel environments that are reduced with time, but much more research is needed to infer general patterns.
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Affiliation(s)
- Janne Swaegers
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Charles Deberiotstraat 32, Leuven B-3000, Belgium.
| | - Eva L Koch
- School of Biociences, University of Sheffield, Sheffield, United Kingdom
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16
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Sentis A, Veselý L, Let M, Musil M, Malinovska V, Kouba A. Short‐term thermal acclimation modulates predator functional response. Ecol Evol 2022; 12:e8631. [PMID: 35222981 PMCID: PMC8855023 DOI: 10.1002/ece3.8631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 11/10/2022] Open
Abstract
Phenotypic plastic responses to temperature can modulate the kinetic effects of temperature on biological rates and traits and thus play an important role for species adaptation to climate change. However, there is little information on how these plastic responses to temperature can influence trophic interactions. Here, we conducted an experiment using marbled crayfish and their water louse prey to investigate how short‐term thermal acclimation at two temperatures (16 and 24°C) modulates the predator functional response. We found that both functional response parameters (search rate and handling time) differed between the two experimental temperatures. However, the sign and magnitudes of these differences strongly depended on acclimation time. Acclimation to 16°C increased handling time and search rate whereas acclimation to 24°C leads to the opposite effects with shorter handling time and lower search rate for acclimated predators. Moreover, the strength of these effects increased with acclimation time so that the differences in search rate and handing time between the two temperatures were reversed between the treatment without acclimation and after 24 h of acclimation. Overall, we found that the magnitude of the acclimation effects can be as strong as the direct kinetic effects of temperature. Our study highlights the importance of taking into account short‐term thermal plasticity to improve our understanding of the potential consequences of global warming on species interactions.
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Affiliation(s)
- Arnaud Sentis
- INRAE Aix Marseille University UMR RECOVER Aix‐en‐Provence France
| | - Lukas Veselý
- Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic
| | - Marek Let
- Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic
| | - Martin Musil
- Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic
| | - Viktoriia Malinovska
- Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic
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17
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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: 8] [Impact Index Per Article: 4.0] [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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18
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Attard CRM, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Schmarr D, Bernatchez L, Beheregaray LB. Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert. Evolution 2021; 76:171-183. [PMID: 34778944 DOI: 10.1111/evo.14399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/31/2021] [Indexed: 11/26/2022]
Abstract
How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Schmarr
- Inland Waters and Catchment Ecology Program, SARDI Aquatic Sciences, Henley Beach, SA, 5022, Australia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Québec, QC, G1V 0A6, Canada
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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19
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Li A, Dai H, Guo X, Zhang Z, Zhang K, Wang C, Wang X, Wang W, Chen H, Li X, Zheng H, Li L, Zhang G. Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity. Commun Biol 2021; 4:1287. [PMID: 34773106 PMCID: PMC8590024 DOI: 10.1038/s42003-021-02823-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.
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Affiliation(s)
- Ao Li
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - He Dai
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Ximing Guo
- grid.430387.b0000 0004 1936 8796Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ USA
| | - Ziyan Zhang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Kexin Zhang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Chaogang Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinxing Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.9227.e0000000119573309National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hongju Chen
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Xumin Li
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Hongkun Zheng
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,University of Chinese Academy of Sciences, Beijing, China. .,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
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20
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Wang C, Liu H, Li Y, Dong B, Qiu C, Yang J, Zong Y, Chen H, Zhao Y, Zhang Y. Study on habitat suitability and environmental variable thresholds of rare waterbirds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147316. [PMID: 33932675 DOI: 10.1016/j.scitotenv.2021.147316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
The conservation level of rare waterbirds reflects the quality of the regional ecological environment and wetlands, and suitable habitat patches and good environmental conditions are bases to support the activities of rare species in habitats. Establishing these conditions is also an important goal of habitat landscape and functional restoration. However, lack of these conditions limits population protection and habitat restoration of rare species. Based on the random forest (RF) algorithm and threshold indicator taxa analysis (TITAN), this paper performed habitat suitability assessment and environmental variable threshold analysis of rare waterbird species in Yancheng coastal wetlands. The results showed that the suitable area proportion of three waterbird species at different habitat sites was less than 20%. The unsuitable area proportions of red-crowned cranes and oriental storks at the CA habitat site were the highest, reaching 86.73% and 85.17%, respectively. In addition, analysis of the importance of environmental variables showed that the main influencing variables affecting the suitable habitat distribution of the three rare waterbirds were habitat type (T_hab), habitat area (A_hab), vegetation coverage (P_fvc), distance to farmland (D_far), distance to reeds (D_ree), ponds density (Ponds), distance to water surface (D_wat) and distance to main roads or seawalls (D_swa). These variables covered the type, area, coverage and distance indicators. With the exception of D_far, Ponds and D_swa, rare waterbirds had response thresholds to each environmental indicator, and these results supported the restoration of landscape structure and function of each habitat site. This study emphasized the importance of foods, water resources and hidden conditions for habitat selection in rare waterbirds. Finally, we proposed the maintenance and restoration patterns of the landscape structure and function of rare waterbird habitats, which are available for other coastal tidal wetlands.
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Affiliation(s)
- Cheng Wang
- School of Geography, Nanjing Normal University, Nanjing 210023, China; Key Laboratory of Virtual Geographic Environment, Nanjing Normal University, Ministry of Education, Nanjing 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China.
| | - Hongyu Liu
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Yufeng Li
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Bin Dong
- School of Science, Anhui Agricultural University, Hefei 230036, China
| | - Chunqi Qiu
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jialing Yang
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ying Zong
- School of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Hao Chen
- Jiangsu Yancheng Wetland National Nature Reserve, Rare Birds, Yancheng, Jiangsu 224057, China
| | - Yongqiang Zhao
- Jiangsu Yancheng Wetland National Nature Reserve, Rare Birds, Yancheng, Jiangsu 224057, China
| | - Yanan Zhang
- Jiangsu Yancheng Wetland National Nature Reserve, Rare Birds, Yancheng, Jiangsu 224057, China
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21
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Huang Z, Xiao Q, Yu F, Gan Y, Lu C, Peng W, Zhang Y, Luo X, Chen N, You W, Ke C. Comparative Transcriptome and DNA Methylation Analysis of Phenotypic Plasticity in the Pacific Abalone ( Haliotis discus hannai). Front Physiol 2021; 12:683499. [PMID: 34267674 PMCID: PMC8277243 DOI: 10.3389/fphys.2021.683499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/07/2021] [Indexed: 01/20/2023] Open
Abstract
Phenotypic plasticity is an adaptive mechanism used by organisms to cope with environmental fluctuations. Pacific abalone (Haliotis discus hannai) are large-scale farmed in the temperate area of northern China and in the warmer waters of southern China. RNA-seq and comparative transcriptomic analysis here were performed to determine if the northern and southern populations have evolved divergent plasticity and if functional differences are associated with protein synthesis and growth-related biological progress. The DNA methylation (5mC) landscape of H. discus hannai from the two populations using whole genomic bisulfite sequencing (WGBS), exhibited different epigenetic patterns. The southern population had significant genomic hypo-methylation that may have resulted from long-term acclimation to heat stress. Combining 790 differentially expressed genes (DEGs) and 7635 differentially methylated genes (DMGs), we found that methylation within the gene body might be important in predicting abalone gene expression. Genes related to growth, development, transduction, and apoptosis may be regulated by methylation and could explain the phenotypic divergence of H. discus hannai. Our findings not only emphasize the significant roles of adaptive plasticity in the acclimation of H. discus hannai to high temperatures but also provide a new understanding of the epigenetic mechanism underlying the phenotypic plasticity in adaptation to climate change for marine organisms.
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Affiliation(s)
- Zekun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Qizhen Xiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Feng Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Yang Gan
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Chengkuan Lu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Yifang Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Xuan Luo
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Nan Chen
- College of Fisheries, Jimei University, Xiamen, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen University, Xiamen China
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22
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O'Brien KM, Joyce W, Crockett EL, Axelsson M, Egginton S, Farrell AP. Resilience of cardiac performance in Antarctic notothenioid fishes in a warming climate. J Exp Biol 2021; 224:268390. [PMID: 34042975 DOI: 10.1242/jeb.220129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Warming in the region of the Western Antarctic Peninsula is occurring at an unprecedented rate, which may threaten the survival of Antarctic notothenioid fishes. Herein, we review studies characterizing thermal tolerance and cardiac performance in notothenioids - a group that includes both red-blooded species and the white-blooded, haemoglobinless icefishes - as well as the relevant biochemistry associated with cardiac failure during an acute temperature ramp. Because icefishes do not feed in captivity, making long-term acclimation studies unfeasible, we focus only on the responses of red-blooded notothenioids to warm acclimation. With acute warming, hearts of the white-blooded icefish Chaenocephalus aceratus display persistent arrhythmia at a lower temperature (8°C) compared with those of the red-blooded Notothenia coriiceps (14°C). When compared with the icefish, the enhanced cardiac performance of N. coriiceps during warming is associated with greater aerobic capacity, higher ATP levels, less oxidative damage and enhanced membrane integrity. Cardiac performance can be improved in N. coriiceps with warm acclimation to 5°C for 6-9 weeks, accompanied by an increase in the temperature at which cardiac failure occurs. Also, both cardiac mitochondrial and microsomal membranes are remodelled in response to warm acclimation in N. coriiceps, displaying homeoviscous adaptation. Overall, cardiac performance in N. coriiceps is malleable and resilient to warming, yet thermal tolerance and plasticity vary among different species of notothenioid fishes; disruptions to the Antarctic ecosystem driven by climate warming and other anthropogenic activities endanger the survival of notothenioids, warranting greater protection afforded by an expansion of marine protected areas.
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Affiliation(s)
- Kristin M O'Brien
- Institute of Arctic Biology , University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
| | - William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Michael Axelsson
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Stuart Egginton
- School of Biomedical Sciences , University of Leeds, Leeds LS2 9JT, UK
| | - Anthony P Farrell
- Department of Zoology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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23
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Spinks RK, Bonzi LC, Ravasi T, Munday PL, Donelson JM. Sex- and time-specific parental effects of warming on reproduction and offspring quality in a coral reef fish. Evol Appl 2021; 14:1145-1158. [PMID: 33897826 PMCID: PMC8061261 DOI: 10.1111/eva.13187] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 01/24/2023] Open
Abstract
Global warming can disrupt reproduction or lead to fewer and poorer quality offspring, owing to the thermally sensitive nature of reproductive physiology. However, phenotypic plasticity may enable some animals to adjust the thermal sensitivity of reproduction to maintain performance in warmer conditions. Whether elevated temperature affects reproduction may depend on the timing of exposure to warming and the sex of the parent exposed. We exposed male and female coral reef damselfish (Acanthochromis polyacanthus) during development, reproduction or both life stages to an elevated temperature (+1.5°C) consistent with projected ocean warming and measured reproductive output and newly hatched offspring performance relative to pairs reared in a present-day control temperature. We found female development in elevated temperature increased the probability of breeding, but reproduction ceased if warming continued to the reproductive stage, irrespective of the male's developmental experience. Females that developed in warmer conditions, but reproduced in control conditions, also produced larger eggs and hatchlings with greater yolk reserves. By contrast, male development or pairs reproducing in higher temperature produced fewer and poorer quality offspring. Such changes may be due to alterations in sex hormones or an endocrine stress response. In nature, this could mean female fish developing during a marine heatwave may have enhanced reproduction and produce higher quality offspring compared with females developing in a year of usual thermal conditions. However, male development during a heatwave would likely result in reduced reproductive output. Furthermore, the lack of reproduction from an average increase in temperature could lead to population decline. Our results demonstrate how the timing of exposure differentially influences females and males and how this translates to effects on reproduction and population sustainability in a warming world.
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Affiliation(s)
- Rachel K. Spinks
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Lucrezia C. Bonzi
- Red Sea Research CenterDivision of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Timothy Ravasi
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Marine Climate Change UnitOkinawa Institute of Science and Technology Graduate UniversityKunigami‐gunJapan
| | - Philip L. Munday
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Jennifer M. Donelson
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
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24
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Emami-Khoyi A, Knapp IS, Monsanto DM, van Vuuren BJ, Toonen RJ, Teske PR. Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient. Mar Genomics 2021; 58:100847. [PMID: 33637426 DOI: 10.1016/j.margen.2021.100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/15/2020] [Accepted: 01/29/2021] [Indexed: 11/30/2022]
Abstract
Environmental gradients between marine biogeographical provinces separate distinct faunal communities. However, the absence of absolute dispersal barriers allows numerous species to occur on both sides of such boundaries. While the regional populations of such widespread species are often morphologically indistinguishable from each other, genetic evidence suggests that they represent unique ecotypes, and likely even cryptic species, that may be uniquely adapted to their local environment. Here, we explored genomic divergence in four sympatric southern African decapod crustaceans whose ranges span the boundary between the cool-temperate west coast (south-eastern Atlantic) and the warm-temperate south coast (south-western Indian Ocean) near the southern tip of the African continent. Using genome-wide data, we found that all four species comprise distinct west coast and south coast ecotypes, with molecular dating suggesting divergence during the Pleistocene. Transcriptomic data from the hepatopancreas of twelve specimens of one of these species, the mudprawn Upogebia africana, which were exposed to either 10 °C or 20 °C, showed a clear difference in gene expression profiles between the west- and south coast ecotypes. This difference was particularly clear at 10 °C, where individuals from the south coast experienced a 'transcriptomic shock'. This low temperature is more typical of the west coast during upwelling events, and the physiological stress experienced by the south coast ecotype under such conditions may explain its absence from that coastline. Our results shed new light on the processes involved in driving genomic divergence and incipient speciation along coastlines with porous dispersal barriers.
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Affiliation(s)
- Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa.
| | - Ingrid S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, Honolulu, HI, USA
| | - Daniela M Monsanto
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, Honolulu, HI, USA
| | - Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa.
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25
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Komoroske LM, Jeffries KM, Whitehead A, Roach JL, Britton M, Connon RE, Verhille C, Brander SM, Fangue NA. Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish. Evol Appl 2020. [DOI: 10.1111/eva.13172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Lisa M. Komoroske
- Department of Environmental Conservation University of Massachusetts Amherst Amherst MA USA
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
| | - Ken M. Jeffries
- Department of Biological Sciences University of Manitoba Winnipeg MB Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Jennifer L. Roach
- Department of Environmental Toxicology University of California, Davis Davis CA USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center University of California, Davis Davis CA USA
| | - Richard E. Connon
- Department of Anatomy, Physiology & Cell Biology, School of Veterinary Medicine University of California, Davis Davis CA USA
| | | | - Susanne M. Brander
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station Oregon State University Corvallis OR USA
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology University of California, Davis Davis CA USA
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26
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Akman M, Carlson JE, Latimer AM. Climate explains population divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea. Mol Ecol 2020; 30:255-273. [PMID: 33098695 DOI: 10.1111/mec.15705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Long-term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up-regulation of stress-related and down-regulation of growth-related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment-dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses of P. repens populations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.
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Affiliation(s)
- Melis Akman
- Department of Plant Sciences, UC Davis, Davis, CA, USA.,Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
| | - Jane E Carlson
- Department of Biology, Nicholls State University, Thibodaux, LA, USA.,Gulf Coast Network Inventory and Monitoring Program, National Park Services, Washington, DC, USA
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27
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Smith S, Brauer CJ, Sasaki M, Unmack PJ, Guillot G, Laporte M, Bernatchez L, Beheregaray LB. Latitudinal variation in climate-associated genes imperils range edge populations. Mol Ecol 2020; 29:4337-4349. [PMID: 32930432 DOI: 10.1111/mec.15637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates. We generated and integrated information from environmental mapping, phenotypic variation and genome-wide data from across the geographical range of the rainbowfish Melanotaenia duboulayi, an emerging aquatic system for studies of climate change. We detected, after controlling for spatial population structure, strong interactions between genotypes and environment associated with variation in stream flow and temperature. Some of these hydroclimate-associated genes were found to interact within functional protein networks that contain genes of adaptive significance for projected future climates in rainbowfish. Hydroclimatic selection was also associated with variation in phenotypic traits, including traits known to affect fitness of rainbowfish exposed to different flow environments. Consistent with predictions from the "climatic variability hypothesis," populations exposed to extremes of important environmental variables showed stronger adaptive divergence and less variation in climate-associated genes compared to populations at the centre of the environmental gradient. Our findings suggest that populations that evolved at environmental range margins and at geographical range edges may be more vulnerable to changing climates, a finding with implications for predicting adaptive resilience and managing biodiversity under climate change.
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Affiliation(s)
- Steve Smith
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia.,Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chris J Brauer
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia
| | - Minami Sasaki
- Molecular Ecology Lab, Flinders University, Bedford Park, SA, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, University of Canberra, Bruce, ACT, Australia
| | - Gilles Guillot
- International Prevention Research Institute, Dardilly, France
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Quebec City, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Quebec City, QC, Canada
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