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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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2
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Mo N, Shao S, Cui Z, Bao C. Roles of eyestalk in salinity acclimatization of mud crab (Scylla paramamosain) by transcriptomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101276. [PMID: 38935995 DOI: 10.1016/j.cbd.2024.101276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/29/2024] [Accepted: 06/12/2024] [Indexed: 06/29/2024]
Abstract
Salinity acclimatization refers to the physiological and behavioral adjustments made by crustaceans to adapt to varying salinity environments. The eyestalk, a neuroendocrine organ in crustaceans, plays a crucial role in salinity acclimatization. To elucidate the molecular mechanisms underlying eyestalk involvement in mud crab (Scylla paramamosain) acclimatization, we employed RNA-seq technology to analyze transcriptomic changes in the eyestalk under low (5 ppt) and standard (23 ppt) salinity conditions. This analysis revealed 5431 differentially expressed genes (DEGs), with 2372 upregulated and 3059 downregulated. Notably, these DEGs were enriched in crucial biological pathways like metabolism, osmoregulation, and signal transduction. To validate the RNA-seq data, we further analyzed 15 DEGs of interest using qRT-PCR. Our results suggest a multifaceted role for the eyestalk: maintaining energy homeostasis, regulating hormone synthesis and release, PKA activity, and downstream signaling, and ensuring proper ion and osmotic balance. Furthermore, our findings indicate that the crustacean hyperglycemic hormone (CHH) may function as a key regulator, modulating carbonic anhydrase expression through the activation of the PKA signaling pathway, thereby influencing cellular osmoregulation, and associated metabolic processes. Overall, our study provides valuable insights into unraveling the molecular mechanisms of mud crab acclimatization to low salinity environments.
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Affiliation(s)
- Nan Mo
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Shucheng Shao
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo 315020, China
| | - Chenchang Bao
- School of Marine Sciences, Ningbo University, Ningbo 315020, China.
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3
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Chen Y, Gao Y, Huang X, Li S, Zhang Z, Zhan A. Incorporating adaptive genomic variation into predictive models for invasion risk assessment. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 18:100299. [PMID: 37701243 PMCID: PMC10494315 DOI: 10.1016/j.ese.2023.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Global climate change is expected to accelerate biological invasions, necessitating accurate risk forecasting and management strategies. However, current invasion risk assessments often overlook adaptive genomic variation, which plays a significant role in the persistence and expansion of invasive populations. Here we used Molgula manhattensis, a highly invasive ascidian, as a model to assess its invasion risks along Chinese coasts under climate change. Through population genomics analyses, we identified two genetic clusters, the north and south clusters, based on geographic distributions. To predict invasion risks, we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability, respectively. These approaches yielded distinct predictions: the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster (i.e., lower invasion risks), while the species distribution model indicated higher future habitat suitability for the same cluster (i.e, higher invasion risks). By integrating these models, we found that the south cluster exhibited minor genome-niche disruptions in the future, indicating higher invasion risks. Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change. Moreover, incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yangchun Gao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
- Global Ocean and Climate Research Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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4
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Chen Y, Ni P, Fu R, Murphy KJ, Wyeth RC, Bishop CD, Huang X, Li S, Zhan A. (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2772. [PMID: 36316814 DOI: 10.1002/eap.2772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kieran J Murphy
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Cory D Bishop
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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5
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Green L, Faust E, Hinchcliffe J, Brijs J, Holmes A, Englund Örn F, Svensson O, Roques JAC, Leder EH, Sandblom E, Kvarnemo C. Invader at the edge - Genomic origins and physiological differences of round gobies across a steep urban salinity gradient. Evol Appl 2023; 16:321-337. [PMID: 36793700 PMCID: PMC9923490 DOI: 10.1111/eva.13437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Species invasions are a global problem of increasing concern, especially in highly connected aquatic environments. Despite this, salinity conditions can pose physiological barriers to their spread, and understanding them is important for management. In Scandinavia's largest cargo port, the invasive round goby (Neogobius melanostomus) is established across a steep salinity gradient. We used 12,937 SNPs to identify the genetic origin and diversity of three sites along the salinity gradient and round goby from western, central and northern Baltic Sea, as well as north European rivers. Fish from two sites from the extreme ends of the gradient were also acclimated to freshwater and seawater, and tested for respiratory and osmoregulatory physiology. Fish from the high-salinity environment in the outer port showed higher genetic diversity, and closer relatedness to the other regions, compared to fish from lower salinity upstream the river. Fish from the high-salinity site also had higher maximum metabolic rate, fewer blood cells and lower blood Ca2+. Despite these genotypic and phenotypic differences, salinity acclimation affected fish from both sites in the same way: seawater increased the blood osmolality and Na+ levels, and freshwater increased the levels of the stress hormone cortisol. Our results show genotypic and phenotypic differences over short spatial scales across this steep salinity gradient. These patterns of the physiologically robust round goby are likely driven by multiple introductions into the high-salinity site, and a process of sorting, likely based on behaviour or selection, along the gradient. This euryhaline fish risks spreading from this area, and seascape genomics and phenotypic characterization can inform management strategies even within an area as small as a coastal harbour inlet.
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Affiliation(s)
- Leon Green
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Ellika Faust
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - James Hinchcliffe
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Jeroen Brijs
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Institute of Marine Biology University of Hawai'i Kaneohe Hawai'i USA
| | - Andrew Holmes
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
| | - Felix Englund Örn
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
| | - Ola Svensson
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Educational Work University of Borås Borås Sweden
| | - Jonathan A C Roques
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Erica H Leder
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden.,Natural History Museum University of Oslo Oslo Norway
| | - Erik Sandblom
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
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6
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Farhadi A, Liu Y, Xu C, Han T, Wang X, Li E. Evidence from transcriptome analysis unravelled the roles of eyestalk in salinity adaptation in Pacific white shrimp (Litopenaeus vannamei). Gen Comp Endocrinol 2022; 329:114120. [PMID: 36055397 DOI: 10.1016/j.ygcen.2022.114120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/04/2022]
Abstract
Eyestalk is considered the main neuroendocrine organ in crustaceans. Eyestalk regulates reproduction, molting, and energy metabolism by secreting several neurohormones. However, the role of eyestalk in salinity adaptation in crustaceans remains unclear. To reveal the role of eyestalk in salinity adaptation in Litopenaeus vannamei, we performed RNA-seq to compare the transcriptomic response of the eyestalk under low salinity (salinity 3) with that of the control group (salinity 25) for 8 weeks. A total of 479 mRNAs, including 150 upregulated and 329 downregulated mRNAs, were differentially expressed between the two salinity groups. The majority of the differentially expressed genes (DEGs) were enriched in biological pathways related to osmoregulation, metabolism and energy production, and oxidative stress. The most important DEGs associated with osmoregulation were CA4, ATP1A, ATP2B, ABCB1, ABCC4, PhoA, PhoB, NOS1, ACE, ANPEP, and the V-type H+-ATPase E-subunit. The metabolism-related DEGs were divided into three main categories: carbohydrate and energy metabolism (i.e., G6PC, UGT), protein and amino acid metabolism (i.e., SLC15A1, AhcY, GFAT), and lipid and fatty acid metabolism (i.e., GPAT3_4, CYP2J). The key DEGs related to the oxidative stress response were UGT, NDUFB1, QCR7, QCR8, P5CDh, COX6B, and CES1. These results provide evidence for the existence of an eyestalk-salinity adaptation-stress endocrine axis in L. vannamei. These findings provide a better understanding of the molecular mechanism underlying salinity adaptation in L. vannamei.
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Affiliation(s)
- Ardavan Farhadi
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Yan Liu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Chang Xu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China
| | - Tao Han
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaodan Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Erchao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan 570228, China.
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7
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Hypo-Osmoregulatory Roles of Vasotocinergic and Isotocinergic Systems in the Intestines of Two European Sea Bass Lineages. Int J Mol Sci 2022; 23:ijms232113636. [PMID: 36362422 PMCID: PMC9655083 DOI: 10.3390/ijms232113636] [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: 10/04/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
European sea bass (Dicentrarchus labrax) are a major aquaculture species that live in habitats with fluctuating salinities that are sometimes higher than in seawater (SW). Atlantic and West-Mediterranean genetic lineages were compared regarding intestinal neuropeptide receptor expression in SW (36%) and following a two-week transfer to hypersalinity (HW, 55%). Phylogenetic analysis revealed seven neuropeptide receptors belonging to the arginine vasotocine (AVTR) family and two isotocin receptors (ITR). Among AVTR paralogs, the highest mRNA levels were recorded for v1a2, with a two- to fourfold upregulation in the European sea bass intestinal sections after transfer of fish to HW. Principal component analysis in posterior intestines showed that v1a2 expression grouped together with the expression and activity of main ion transporters and channels involved in solute-coupled water uptake, indicating a possible role of this receptor in triggering water absorption. v1a1 expression, however, was decreased or did not change after transfer to hypersaline water. Among ITR paralogs, itr1 was the most expressed paralog in the intestine and opposite expression patterns were observed following salinity transfer, comparing intestinal sections. Overall, different expression profiles were observed between genetic lineages for several analyzed genes which could contribute to different osmotic stress-related responses in D. labrax lineages.
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8
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Bereza D, Shenkar N. Shipping voyage simulation reveals abiotic barriers to marine bioinvasions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155741. [PMID: 35525364 DOI: 10.1016/j.scitotenv.2022.155741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The shipping industry is considered the main vector of introduction of marine non-indigenous species (NIS). NIS distributions are often a consequence of frequent trade activities that are affected by economic trends. A dominant trend in the shipping industry is the operation of Ultra Large Container Vessels (ULCV), which are over 395 m long and sail mostly on the East-Asia - northern-Europe route. Understanding the risk of NIS introduction by this emerging shipping category is needed for devising strategies for sustainable shipping. Here, we conducted a controlled simulation of key abiotic factors that determine marine bioinvasion success: temperature, salinity, and food availability along selected routes, under two treatments: ULCV and intermediate-size vessels. We tested the effect of each treatment and the varying environmental conditions on the survival of two invasive ascidians (Chordata, Ascidiacea). We used survival analysis methods to locate predictors of ascidian mortality; Environmental conditions at ports with high mortality were used to identify similar major ports on a global scale as potential abiotic barriers. The key factors in ascidian mortality varied between the two species, but for both species, the treatment and salinity were dominant predictors for survival. We identified Port Klang, Rotterdam, and Dammam as ports with high mortality and located several globally distributed major ports that present similar environmental conditions. Our results highlight the potential role of selected major ports as abiotic barriers to fouling organisms during ocean voyages. The tolerance of the tropical-origin Microcosmus exasperatus to the northern-Europe conditions, and of the temperate/sub-tropical origin Styela plicata, to high temperature conditions, point out the urgent need to modify international fouling regulations in view of global change. Further studies on the survival of fouling organisms during a cascade of changing environmental conditions will contribute to the advancement of science-based regulations to reduce the adverse effects of NIS.
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Affiliation(s)
- Doron Bereza
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel; The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel Aviv, Israel.
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9
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Gao Y, Chen Y, Li S, Huang X, Hu J, Bock DG, MacIsaac HJ, Zhan A. Complementary genomic and epigenomic adaptation to environmental heterogeneity. Mol Ecol 2022; 31:3598-3612. [PMID: 35560847 DOI: 10.1111/mec.16500] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri, using reduced-representation methods. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dan G Bock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Yunnan, 650091, China.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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10
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Zhang Z, Li A, She Z, Wang X, Jia Z, Wang W, Zhang G, Li L. Adaptive divergence and underlying mechanisms in response to salinity gradients between two Crassostrea oysters revealed by phenotypic and transcriptomic analyses. Evol Appl 2022; 16:234-249. [PMID: 36793677 PMCID: PMC9923467 DOI: 10.1111/eva.13370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Comparing the responses of closely related species to environmental changes is an efficient method to explore adaptive divergence, for a better understanding of the adaptive evolution of marine species under rapidly changing climates. Oysters are keystone species thrive in intertidal and estuarine areas where frequent environmental disturbance occurs including fluctuant salinity. The evolutionary divergence of two sister species of sympatric estuarine oysters, Crassostrea hongkongensis and Crassostrea ariakensis, in response to euryhaline habitats on phenotypes and gene expression, and the relative contribution of species effect, environment effect, and their interaction to the divergence were explored. After a 2-month outplanting at high- and low-salinity locations in the same estuary, the high growth rate, percent survival, and high tolerance indicated by physiological parameters suggested that the fitness of C. ariakensis was higher under high-salinity conditions and that of C. hongkongensis was higher under low-salinity conditions. Moreover, a transcriptomic analysis showed the two species exhibited differentiated transcriptional expression in high- and low-salinity habitats, largely caused by the species effect. Several of the important pathways enriched in divergent genes between species were also salinity-responsive pathways. Specifically, the pyruvate and taurine metabolism pathway and several solute carriers may contribute to the hyperosmotic adaptation of C. ariakensis, and some solute carriers may contribute to the hypoosmotic adaptation of C. hongkongensis. Our findings provide insights into the phenotypic and molecular mechanisms underlying salinity adaptation in marine mollusks, which will facilitate the assessment of the adaptive capacity of marine species in the context of climate change and will also provide practical information for marine resource conservation and aquaculture.
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Affiliation(s)
- Ziyan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,University of Chinese Academy of SciencesBeijingChina,Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Zhicai She
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine SciencesBeibu Gulf UniversityQinzhouChina
| | - Xuegang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Zhen Jia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine SciencesBeibu Gulf UniversityQinzhouChina
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,University of Chinese Academy of SciencesBeijingChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
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