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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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Abdelnour SA, Naiel MAE, Said MB, Alnajeebi AM, Nasr FA, Al-Doaiss AA, Mahasneh ZMH, Noreldin AE. Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish. ENVIRONMENTAL RESEARCH 2024; 252:118799. [PMID: 38552831 DOI: 10.1016/j.envres.2024.118799] [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: 11/28/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Epigenetics plays a vital role in the interaction between living organisms and their environment by regulating biological functions and phenotypic plasticity. Considering that most aquaculture activities take place in open or natural habitats that are vulnerable to environmental changes. Promising findings from recent research conducted on various aquaculture species have provided preliminary evidence suggesting a link between epigenetic mechanisms and economically valuable characteristics. Environmental stressors, including climate changes (thermal stress, hypoxia, and water salinity), anthropogenic impacts such as (pesticides, crude oil pollution, nutritional impacts, and heavy metal) and abiotic factors (infectious diseases), can directly trigger epigenetic modifications in fish. While experiments have confirmed that many epigenetic alterations caused by environmental factors have plastic responses, some can be permanently integrated into the genome through genetic integration and promoting rapid transgenerational adaptation in fish. These environmental factors might cause irregular DNA methylation patterns in genes related to many biological events leading to organs dysfunction by inducing alterations in genes related to oxidative stress or apoptosis. Moreover, these environmental issues alter DNA/histone methylation leading to decreased reproductive competence. This review emphasizes the importance of understanding the effects of environmentally relevant issues on the epigenetic regulation of phenotypic variations in fish. The goal is to expand our knowledge of how epigenetics can either facilitate or hinder species' adaptation to these adverse conditions. Furthermore, this review outlines the areas that warrant further investigation in understanding epigenetic reactions to various environmental issues.
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Affiliation(s)
- Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt.
| | - Mohammed A E Naiel
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Mourad Ben Said
- Laboratory of Microbiology, National School of Veterinary Medicine of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia; Department of Basic Sciences, Higher Institute of Biotechnology of Sidi Thabet, University of Manouba, Manouba, 2010, Tunisia
| | - Afnan M Alnajeebi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fahd A Nasr
- Biology Department, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Amin A Al-Doaiss
- Biology Department, College of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Zeinab M H Mahasneh
- Department of Animal Production, School of Agriculture, The University of Jordan, Amman, 11942, Jordan
| | - Ahmed E Noreldin
- Department of Histology and Cytology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, Egypt
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3
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Han GD, Ma DD, Du LN, Zhao ZJ. Chromosomal-scale genome assembly of the Mediterranean mussel Mytilus galloprovincialis. Sci Data 2024; 11:644. [PMID: 38886364 PMCID: PMC11183127 DOI: 10.1038/s41597-024-03497-5] [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: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
The Mediterranean mussel, Mytilus galloprovincialis, is a significant marine bivalve species that has ecological and economic importance. This species is robustly resilient and highly invasive. Despite the scientific and commercial interest in studying its biology and aquaculture, there remains a need for a high-quality, chromosome-scale reference genome. In this study, we have assembled a high-quality chromosome-scale reference genome for M. galloprovincialis. The total length of our reference genome is 1.41 Gb, with a scaffold N50 sequence length of 96.9 Mb. BUSCO analysis revealed a 97.5% completeness based on complete BUSCOs. Compared to the four other available M. galloprovincialis assemblies, the assembly described here is dramatically improved in both contiguity and completeness. This new reference genome will greatly contribute to a deeper understanding of the resilience and invasiveness of M. galloprovincialis.
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Affiliation(s)
- Guo-Dong Han
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China.
| | - Dan-Dan Ma
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
| | - Li-Na Du
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
| | - Zhen-Jun Zhao
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
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4
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Camus L, Gautier M, Boitard S. Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability? Evol Appl 2024; 17:e13709. [PMID: 38884022 PMCID: PMC11178484 DOI: 10.1111/eva.13709] [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: 02/19/2024] [Revised: 04/30/2024] [Accepted: 05/04/2024] [Indexed: 06/18/2024] Open
Abstract
Predicting the risk of establishment and spread of populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation to a new environment with genomic data via so-called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species but have still rarely been used in this context. Here, we evaluated the relationship between GO and the establishment probability of a population in a new environment using both in silico and empirical data. First, we designed invasion simulations to evaluate the ability to predict establishment probability of two GO computation methods (Geometric GO and Gradient Forest) under several conditions. Additionally, we aimed to evaluate the interpretability of absolute Geometric GO values, which theoretically represent the adaptive genetic distance between populations from distinct environments. Second, utilizing public empirical data from the crop pest species Bactrocera tryoni, a fruit fly native from Northern Australia, we computed GO between "source" populations and a diverse range of locations within invaded areas. This practical application of GO within the context of a biological invasion underscores its potential in providing insights and guiding recommendations for future invasion risk assessment. Overall, our results suggest that GO statistics represent good predictors of the establishment probability and may thus inform invasion risk, although the influence of several factors on prediction performance (e.g., propagule pressure or admixture) will need further investigation.
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Affiliation(s)
- Louise Camus
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
| | - Simon Boitard
- CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier Montpellier France
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5
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Mestre A, Butlin RK, Hortal J, Rafajlović M. Adaptive colonization across a parasitism-mutualism gradient. Evol Lett 2024; 8:340-350. [PMID: 38818421 PMCID: PMC11134462 DOI: 10.1093/evlett/qrad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 06/01/2024] Open
Abstract
Adaptive colonization is a process wherein a colonizing population exhibits an adaptive change in response to a novel environment, which may be critical to its establishment. To date, theoretical models of adaptive colonization have been based on single-species introductions. However, given their pervasiveness, symbionts will frequently be co-introduced with their hosts to novel areas. We present an individual-based model to investigate adaptive colonization by hosts and their symbionts across a parasite-mutualist continuum. The host must adapt in order to establish itself in the novel habitat, and the symbiont must adapt to track evolutionary change in the host. First, we classify the qualitative shifts in the outcome that can potentially be driven by non-neutral effects of the symbiont-host interaction into three main types: parasite-driven co-extinction, parasite release, and mutualistic facilitation. Second, we provide a detailed description of a specific example for each type of shift. Third, we disentangle how the interplay between symbiont transmissibility, host migration, and selection strength determines: (a) which type of shift is more likely to occur and (b) the size of the interaction effects necessary to produce it. Overall, we demonstrate the crucial role of host and symbiont dispersal scales in shaping the impacts of parasitism and mutualism on adaptive colonization.
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Affiliation(s)
- Alexandre Mestre
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
| | - Roger K Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, United Kingdom
| | - Joaquín Hortal
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
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6
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Lin X, Yin J, Wang Y, Yao J, Li QQ, Latzel V, Bossdorf O, Zhang YY. Environment-induced heritable variations are common in Arabidopsis thaliana. Nat Commun 2024; 15:4615. [PMID: 38816460 PMCID: PMC11139905 DOI: 10.1038/s41467-024-49024-3] [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: 10/11/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yifan Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA
| | - Vit Latzel
- Institute of Botany of the CAS, Zamek 1, 252 43, Pruhonice, Czech Republic
| | - Oliver Bossdorf
- Institute of Evolution & Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
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7
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Acquafredda M, Guo X, Munroe D. Transcriptomic Response of the Atlantic Surfclam (Spisula solidissima) to Acute Heat Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:149-168. [PMID: 38240954 PMCID: PMC10869415 DOI: 10.1007/s10126-024-10285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
There is clear evidence that the oceans are warming due to anthropogenic climate change, and the northeastern coast of USA contains some of the fastest warming areas. This warming is projected to continue with serious biological and social ramifications for fisheries and aquaculture. One species particularly vulnerable to warming is the Atlantic surfclam (Spisula solidissima). The surfclam is a critically important species, linking marine food webs and supporting a productive, lucrative, and sustainable fishery. The surfclam is also emerging as an attractive candidate for aquaculture diversification, but the warming of shallow coastal farms threatens the expansion of surfclam aquaculture. Little is known about the adaptive potential of surfclams to cope with ocean warming. In this study, the surfclam transcriptome under heat stress was examined. Two groups of surfclams were subjected to heat stress to assess how artificial selection may alter gene expression. One group of clams had been selected for greater heat tolerance (HS) and the other was composed of random control clams (RC). After a 6-h exposure to 16 or 29 °C, gill transcriptome expression profiles of the four temperature/group combinations were determined by RNA sequencing and compared. When surfclams experienced heat stress, they exhibited upregulation of heat shock proteins (HSPs), inhibitors of apoptosis (IAPs), and other stress-response related genes. RC clams differentially expressed 1.7 times more genes than HS clams, yet HS clams had a stronger response of key stress response genes, including HSPs, IAPs, and genes involved with mitigating oxidative stress. The findings imply that the HS clams have a more effective response to heat stress after undergoing the initial selection event due to genetic differences created by the selection, epigenetic memory of the first heat shock, or both. This work provides insights into how surfclams adapt to heat stress and should inform future breeding programs that attempt to breed surfclam for greater heat tolerance, and ultimately bring greater resiliency to shellfish farms.
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Affiliation(s)
- Michael Acquafredda
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Daphne Munroe
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
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8
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Sol Dourdin T, Guyomard K, Rabiller M, Houssais N, Cormier A, Le Monier P, Sussarellu R, Rivière G. Ancestors' Gift: Parental Early Exposure to the Environmentally Realistic Pesticide Mixture Drives Offspring Phenotype in a Larger Extent Than Direct Exposure in the Pacific Oyster, Crassostrea gigas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1865-1876. [PMID: 38217500 DOI: 10.1021/acs.est.3c08201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Marine organisms are threatened by the presence of pesticides in coastal waters. Among them, the Pacific oyster is one of the most studied invertebrates in marine ecotoxicology where numerous studies highlighted the multiscale impacts of pesticides. In the past few years, a growing body of literature has reported the epigenetic outcomes of xenobiotics. Because DNA methylation is an epigenetic mark implicated in organism development and is meiotically heritable, it raises the question of the multigenerational implications of xenobiotic-induced epigenetic alterations. Therefore, we performed a multigenerational exposure to an environmentally relevant mixture of 18 pesticides (nominal sum concentration: 2.85 μg·L-1) during embryo-larval stages (0-48 hpf) of a second generation (F1) for which parents where already exposed or not in F0. Gene expression, DNA methylation, and physiological end points were assessed throughout the life cycle of individuals. Overall, the multigenerational effect has a greater influence on the phenotype than the exposure itself. Thus, multigenerational phenotypic effects were observed: individuals descending from exposed parents exhibited lower epinephrine-induced metamorphosis and field survival rates. At the molecular level, RNA-seq and Methyl-seq data analyses performed in gastrula embryos and metamorphosis-competent pediveliger (MCP) larvae revealed a clear F0 treatment-dependent discrimination. Some genes implicated into shell secretion and immunity exhibited F1:F0 treatment interaction patterns (e.g., Calm and Myd88). Those results suggest that low chronic environmental pesticide contamination can alter organisms beyond the individual scale level and have long-term adaptive implications.
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Affiliation(s)
- Thomas Sol Dourdin
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, 44311 Cedex 03 Nantes, France
| | - Killian Guyomard
- Ifremer, Plateforme Mollusques Marins Bouin, 85029 Bouin, France
| | | | - Nina Houssais
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, 44311 Cedex 03 Nantes, France
| | - Alexandre Cormier
- Ifremer, Service de Bioinformatique de l'Ifremer, 29280 Brest, France
| | - Pauline Le Monier
- Ifremer, Unité Contamination Chimique des Ecosystèmes Marins, 44311 Cedex 03 Nantes, France
| | - Rossana Sussarellu
- Ifremer, Physiologie et Toxines des Microalgues Toxiques, 44311 Cedex 03 Nantes, France
| | - Guillaume Rivière
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR7208, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche et Développement (IRD), Sorbonne Université (SU), Université de Caen Normandie (UCN), Université des Antilles (UA), 75231 Paris Cedex, France
- BOREA, UFR des Sciences, Université de Caen-Normandie, Esplanade de la Paix, 14032 Caen Cedex, France
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9
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Hu LS, Dong YW. Multiple genetic sources facilitate the northward range expansion of an intertidal oyster along China's coast. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2764. [PMID: 36259430 DOI: 10.1002/eap.2764] [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: 07/19/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Coastal artificial structures on the former mudflats provide available habitats for the rocky intertidal species which can establish new populations in these emerging habitats over their former distribution range limits. As a former southern species, the oyster Crassostrea sikamea has become a pioneer and rapidly invaded the artificial shorelines in northern China. We used a seascape genomics approach to investigate the population structure and genetic sources of C. sikamea on the coastal artificial structures, which is crucial for understanding the genetic mechanisms driving species distribution range expansion and invasion pathway of intertidal species. Five C. sikamea populations, including two artificial substrate populations (WGZ and ZAP), one oyster reef population (LS), and two natural rocky shore populations (ZS and XM), were measured using single nucleotide polymorphism (SNPs) obtained from double digest restriction-site associated DNA sequencing (ddRAD-Seq). Redundancy analyses (RDA) were implemented for investigating the relationship between local temperature variables and the temperature adaptability of C. sikamea. Genetic diversity, direction and strength of gene flow, and population structure all revealed that the LS and ZS populations were the genetic sources for the oyster populations on the emerging northern coastal artificial structures. Results of RDA showed that there were different adaptive potentials for northern and southern populations to local temperature variables and the oyster reef population which frequently suffers from heat stress owned high heat adaptability. The ZS population as a genetic source nearby the Yangtze River estuary provided mass larvae for the northern populations, and the other genetic source, the heat-tolerant LS population, in the oyster reef played an important role in the post-settlement success by providing preadapted genotypes. These results highlight the importance of multiple sources with divergent adaptative capabilities for biological invasion, and also emphasize the importance of the oyster reef in coastal biodiversity and conservation.
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Affiliation(s)
- Li-Sha Hu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
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10
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Hoste A, Capblancq T, Broquet T, Denoyelle L, Perrier C, Buzan E, Šprem N, Corlatti L, Crestanello B, Hauffe HC, Pellissier L, Yannic G. Projection of current and future distribution of adaptive genetic units in an alpine ungulate. Heredity (Edinb) 2024; 132:54-66. [PMID: 38082151 PMCID: PMC10798982 DOI: 10.1038/s41437-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/21/2024] Open
Abstract
Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.
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Affiliation(s)
- Amélie Hoste
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Thibaut Capblancq
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Thomas Broquet
- CNRS, Sorbonne Université, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Université Montpellier, Montpellier, France
| | - Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Luca Corlatti
- Stelvio National Park - ERSAF Lombardia, Via De Simoni 42, 23032, Bormio, Italy
- Chair of Wildlife Ecology and Management, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Barbara Crestanello
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Unit, Research and Innovation Centre, Fondazione E. Mach, Via E. Mach 1, 38098 S, Michele all'Adige, TN, Italy
| | - Loïc Pellissier
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zrich, Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Glenn Yannic
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
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11
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Tan Y, Sun YX, Zhu YJ, Liao ML, Dong YW. The impacts of thermal heterogeneity across microhabitats on post-settlement selection of intertidal mussels. iScience 2023; 26:108376. [PMID: 38034360 PMCID: PMC10682278 DOI: 10.1016/j.isci.2023.108376] [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: 06/07/2023] [Revised: 09/08/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Rapid genetic selection is critical for allowing natural populations to adapt to different thermal environments such as those that occur across intertidal microhabitats with high degrees of thermal heterogeneity. To address the question of how thermal regimes influence selection and adaptation in the intertidal black mussel Mytilisepta virgata, we continuously recorded environmental temperatures in both tidal pools and emergent rock microhabitats and then assessed genetic differentiation, gene expression patterns, RNA editing level, and cardiac performance. Our results showed that the subpopulations in the tidal pool and on emergent rocks had different genetic structures and exhibited different physiological and molecular responses to high-temperature stress. These results indicate that environmental heterogeneity across microhabitats is important for driving genetic differentiation and shed light on the importance of post-settlement selection for adaptively modifying the genetic composition and thermal responses of these intertidal mussels.
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Affiliation(s)
- Yue Tan
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
| | - Yong-Xu Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ya-Jie Zhu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
| | - Yun-Wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
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12
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Schwaner C, Farhat S, Boutet I, Tanguy A, Barbosa M, Grouzdev D, Pales Espinosa E, Allam B. Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:997-1019. [PMID: 37864760 DOI: 10.1007/s10126-023-10255-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023]
Abstract
Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Isabelle Boutet
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier 29680, Roscoff, France
| | - Arnaud Tanguy
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier 29680, Roscoff, France
| | - Michelle Barbosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Denis Grouzdev
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
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13
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Richardson K, Steffen W, Lucht W, Bendtsen J, Cornell SE, Donges JF, Drüke M, Fetzer I, Bala G, von Bloh W, Feulner G, Fiedler S, Gerten D, Gleeson T, Hofmann M, Huiskamp W, Kummu M, Mohan C, Nogués-Bravo D, Petri S, Porkka M, Rahmstorf S, Schaphoff S, Thonicke K, Tobian A, Virkki V, Wang-Erlandsson L, Weber L, Rockström J. Earth beyond six of nine planetary boundaries. SCIENCE ADVANCES 2023; 9:eadh2458. [PMID: 37703365 PMCID: PMC10499318 DOI: 10.1126/sciadv.adh2458] [Citation(s) in RCA: 93] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/12/2023] [Indexed: 09/15/2023]
Abstract
This planetary boundaries framework update finds that six of the nine boundaries are transgressed, suggesting that Earth is now well outside of the safe operating space for humanity. Ocean acidification is close to being breached, while aerosol loading regionally exceeds the boundary. Stratospheric ozone levels have slightly recovered. The transgression level has increased for all boundaries earlier identified as overstepped. As primary production drives Earth system biosphere functions, human appropriation of net primary production is proposed as a control variable for functional biosphere integrity. This boundary is also transgressed. Earth system modeling of different levels of the transgression of the climate and land system change boundaries illustrates that these anthropogenic impacts on Earth system must be considered in a systemic context.
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Affiliation(s)
- Katherine Richardson
- Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Will Steffen
- Australian National University, Canberra, Australia
| | - Wolfgang Lucht
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Department of Geography, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jørgen Bendtsen
- Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Sarah E. Cornell
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Jonathan F. Donges
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Markus Drüke
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Ingo Fetzer
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Govindasamy Bala
- Centre for Atmospheric and Oceanic Sciences, Indian Institute of Science, Bangalore, Karnataka – 560012, India
| | - Werner von Bloh
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Georg Feulner
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Stephanie Fiedler
- GEOMAR Helmholtz Centre for Ocean Research Kiel and Faculty for Mathematics and Natural Sciences, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dieter Gerten
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Department of Geography, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tom Gleeson
- Department of Civil Engineering, University of Victoria, Victoria, British Columbia, Canada
- School of Earth and Ocean Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Matthias Hofmann
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Willem Huiskamp
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Matti Kummu
- Water and Development Research Group, Aalto University, Espoo, Finland
| | - Chinchu Mohan
- GEOMAR Helmholtz Centre for Ocean Research Kiel and Faculty for Mathematics and Natural Sciences, Christian-Albrechts-University Kiel, Kiel, Germany
- Global Institute for Water Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Waterplan (YC S21), San Francisco, CA, USA
| | - David Nogués-Bravo
- Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Petri
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Miina Porkka
- Water and Development Research Group, Aalto University, Espoo, Finland
| | - Stefan Rahmstorf
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Sibyll Schaphoff
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Kirsten Thonicke
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
| | - Arne Tobian
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Vili Virkki
- Water and Development Research Group, Aalto University, Espoo, Finland
| | - Lan Wang-Erlandsson
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Lisa Weber
- GEOMAR Helmholtz Centre for Ocean Research Kiel and Faculty for Mathematics and Natural Sciences, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Johan Rockström
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, Potsdam, Germany
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
- Institute for Environmental Science and Geography, University of Potsdam, Potsdam, Germany
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14
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Guo F, Ye Y, Zhu K, Lin S, Wang Y, Dong Z, Yao R, Li H, Wang W, Liao Z, Guo B, Yan X. Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing. Int J Mol Sci 2023; 24:13641. [PMID: 37686445 PMCID: PMC10488143 DOI: 10.3390/ijms241713641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.
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Affiliation(s)
- Feng Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
| | - Shuangrui Lin
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yuxia Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhenyu Dong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Ronghui Yao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Hongfei Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Weifeng Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
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15
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Leiva C, Pérez-Portela R, Lemer S. Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO 2 seeps. Commun Biol 2023; 6:769. [PMID: 37481685 PMCID: PMC10363134 DOI: 10.1038/s42003-023-05103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/06/2023] [Indexed: 07/24/2023] Open
Abstract
Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.
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Affiliation(s)
- Carlos Leiva
- University of Guam Marine Laboratory, 303 University Drive, 96923, Mangilao, Guam, USA.
| | - Rocío Pérez-Portela
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sarah Lemer
- University of Guam Marine Laboratory, 303 University Drive, 96923, Mangilao, Guam, USA
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16
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Diaz Caballero J, Wheatley RM, Kapel N, López-Causapé C, Van der Schalk T, Quinn A, Shaw LP, Ogunlana L, Recanatini C, Xavier BB, Timbermont L, Kluytmans J, Ruzin A, Esser M, Malhotra-Kumar S, Oliver A, MacLean RC. Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients. Nat Commun 2023; 14:4083. [PMID: 37438338 DOI: 10.1038/s41467-023-39416-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.
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Affiliation(s)
| | - Rachel M Wheatley
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Natalia Kapel
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Angus Quinn
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Liam P Shaw
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Lois Ogunlana
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark Esser
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - R Craig MacLean
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK.
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17
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Haye PA, Segovia NI. Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel. Heredity (Edinb) 2023; 130:402-413. [PMID: 37024547 PMCID: PMC10238476 DOI: 10.1038/s41437-023-00615-8] [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: 11/13/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.
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Affiliation(s)
- Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile
| | - Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile.
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18
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Nedoluzhko A. Sea of opportunities: marine genomics in an era of global environmental change. BMC Genomics 2023; 24:286. [PMID: 37237270 DOI: 10.1186/s12864-023-09392-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Overexploitation of natural resources and pollution of seas, acidification of the ocean, and rising temperatures all contribute to the destruction of marine habitats and, in 2015, the protection of the ocean became one of the UN Sustainable Development Goals (SDG 14: Life Below Water). This collection aims to highlight the molecular genetic changes currently happening in marine organisms.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at St. Petersburg, 6/1A Gagarinskaya Street, St. Petersburg, 191187, Russia.
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19
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Pierron F, Daffe G, Daramy F, Heroin D, Barré A, Bouchez O, Clérendeau C, Romero-Ramirez A, Nikolski M. Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131579. [PMID: 37163897 DOI: 10.1016/j.jhazmat.2023.131579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023]
Abstract
Evidence has emerged that environmentally-induced epigenetic changes can have long-lasting effects on gene transcription across generations. These recent findings highlight the need to investigate the transgenerational impacts of pollutants to assess their long term effects on populations. In this study, we investigated the transgenerational effect of cadmium on zebrafish across 4 generations. A first whole methylome approach carried out on fish of the first two generations led us to focus our investigations on the estradiol receptor alpha gene (esr1). We observed a sex-dependent transgenerational inheritance of Cd-induced DNA methylation changes up to the last generation. These changes were associated with single nucleotide polymorphisms (SNPs) that were themselves at the origin of the creation or deletion of methylation sites. Thus, Cd-induced genetic selection gave rise to DNA methylation changes. We also analyzed the transcription level of various sections of esr1 as well as estrogen responsive genes. While Cd triggered transgenerational disorders, Cd-induced epigenetic changes in esr1 contributed to the rapid transgenerational adaptation of fish to Cd. Our results provide insight into the processes underpinning rapid adaptation and highlight the need to maintain genetic diversity within natural populations to bolster the resilience of species faced with the global environmental changes.
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Affiliation(s)
- Fabien Pierron
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France.
| | - Guillemine Daffe
- Univ. Bordeaux, CNRS, INRAE, La Rochelle Univ., UMS 2567 POREA, F-33615 Pessac, France
| | - Flore Daramy
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Débora Heroin
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33600 Pessac, France
| | - Aurélien Barré
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, 31326, France
| | | | | | - Macha Nikolski
- Univ. Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, France; Univ. Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux 33077, France
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20
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Alves F, Banks SC, Edworthy M, Stojanovic D, Langmore NE, Heinsohn R. Using conservation genetics to prioritise management options for an endangered songbird. Heredity (Edinb) 2023; 130:289-301. [PMID: 37016134 PMCID: PMC10162965 DOI: 10.1038/s41437-023-00609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.
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Affiliation(s)
- Fernanda Alves
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia.
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT, Australia
| | - Max Edworthy
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Naomi E Langmore
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
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21
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RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification. Int J Mol Sci 2023; 24:ijms24043661. [PMID: 36835072 PMCID: PMC9961701 DOI: 10.3390/ijms24043661] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.
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22
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Gold DA, Vermeij GJ. Deep resilience: An evolutionary perspective on calcification in an age of ocean acidification. Front Physiol 2023; 14:1092321. [PMID: 36818444 PMCID: PMC9935589 DOI: 10.3389/fphys.2023.1092321] [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: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
The success of today's calcifying organisms in tomorrow's oceans depends, in part, on the resilience of their skeletons to ocean acidification. To the extent this statement is true there is reason to have hope. Many marine calcifiers demonstrate resilience when exposed to environments that mimic near-term ocean acidification. The fossil record similarly suggests that resilience in skeletons has increased dramatically over geologic time. This "deep resilience" is seen in the long-term stability of skeletal chemistry, as well as a decreasing correlation between skeletal mineralogy and extinction risk over time. Such resilience over geologic timescales is often attributed to genetic canalization-the hardening of genetic pathways due to the evolution of increasingly complex regulatory systems. But paradoxically, our current knowledge on biomineralization genetics suggests an opposing trend, where genes are co-opted and shuffled at an evolutionarily rapid pace. In this paper we consider two possible mechanisms driving deep resilience in skeletons that fall outside of genetic canalization: microbial co-regulation and macroevolutionary trends in skeleton structure. The mechanisms driving deep resilience should be considered when creating risk assessments for marine organisms facing ocean acidification and provide a wealth of research avenues to explore.
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23
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Schwaner C, Farhat S, Barbosa M, Boutet I, Tanguy A, Pales Espinosa E, Allam B. Molecular Features Associated with Resilience to Ocean Acidification in the Northern Quahog, Mercenaria mercenaria. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:83-99. [PMID: 36417051 DOI: 10.1007/s10126-022-10183-3] [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: 09/29/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
The increasing concentration of CO2 in the atmosphere and resulting flux into the oceans will further exacerbate acidification already threatening coastal marine ecosystems. The subsequent alterations in carbonate chemistry can have deleterious impacts on many economically and ecologically important species including the northern quahog (Mercenaria mercenaria). The accelerated pace of these changes requires an understanding of how or if species and populations will be able to acclimate or adapt to such swift environmental alterations. Thus far, studies have primarily focused on the physiological effects of ocean acidification (OA) on M. mercenaria, including reductions in growth and survival. However, the molecular mechanisms of resilience to OA in this species remains unclear. Clam gametes were fertilized under normal pCO2 and reared under acidified (pH ~ 7.5, pCO2 ~ 1200 ppm) or control (pH ~ 7.9, pCO2 ~ 600 ppm) conditions before sampled at 2 days (larvae), 32 days (postsets), 5 and 10 months (juveniles) and submitted to RNA and DNA sequencing to evaluate alterations in gene expression and genetic variations. Results showed significant shift in gene expression profiles among clams reared in acidified conditions as compared to their respective controls. At 10 months of exposure, significant shifts in allele frequency of single nucleotide polymorphisms (SNPs) were identified. Both approaches highlighted genes coding for proteins related to shell formation, bicarbonate transport, cytoskeleton, immunity/stress, and metabolism, illustrating the role these pathways play in resilience to OA.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Michelle Barbosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Isabelle Boutet
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier, 29680, Roscoff, France
| | - Arnaud Tanguy
- Station Biologique de Roscoff, CNRS/Sorbonne Université, Place Georges Teissier, 29680, Roscoff, France
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
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24
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Pfenninger M, Foucault Q, Waldvogel AM, Feldmeyer B. Selective effects of a short transient environmental fluctuation on a natural population. Mol Ecol 2023; 32:335-349. [PMID: 36282585 DOI: 10.1111/mec.16748] [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: 02/15/2022] [Revised: 09/21/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023]
Abstract
Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygenic traits, but the underlying genomic dynamics and architecture are poorly understood. In this study, we took advantage of a natural experiment in an insect population of the non-biting midge Chironomus riparius by monitoring genome-wide allele frequencies before and after a cold snap event. Whole genome pooled sequencing of time series samples revealed 10 selected haplotypes carrying ancient polymorphisms, partially with signatures of balancing selection. By constantly cold exposing genetically variable individuals in the laboratory, we could demonstrate with whole genome resequencing (i) that among the survivors, the same alleles rose in frequency as in the wild, and (ii) that the identified variants additively predicted fitness (survival time) of its bearers. Finally, by simultaneously sequencing the genome and the transcriptome of cold exposed individuals we could tentatively link some of the selected SNPs to the cis- and trans-regulation of genes and pathways known to be involved in cold response of insects, such as cytochrome P450 and fatty acid metabolism. Altogether, our results shed light on the strength and speed of selection in natural populations and the genomic architecture of its underlying polygenic trait. Population genomic time series data thus appear as promising tool for measuring the selective tracking of fluctuating selection in natural populations.
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Affiliation(s)
- Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Quentin Foucault
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Ann-Marie Waldvogel
- Department of Ecological Genomics, Institute of Zoology, University of Cologne, Köln, Germany
| | - Barbara Feldmeyer
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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25
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Chakraborty A, Walter GM, Monro K, Alves AN, Mirth CK, Sgrò CM. Within-population variation in body size plasticity in response to combined nutritional and thermal stress is partially independent from variation in development time. J Evol Biol 2023; 36:264-279. [PMID: 36208146 PMCID: PMC10092444 DOI: 10.1111/jeb.14099] [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: 11/25/2021] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Ongoing climate change has forced animals to face changing thermal and nutritional environments. Animals can adjust to such combinations of stressors via plasticity. Body size is a key trait influencing organismal fitness, and plasticity in this trait in response to nutritional and thermal conditions varies among genetically diverse, locally adapted populations. The standing genetic variation within a population can also influence the extent of body size plasticity. We generated near-isogenic lines from a newly collected population of Drosophila melanogaster at the mid-point of east coast Australia and assayed body size for all lines in combinations of thermal and nutritional stress. We found that isogenic lines showed distinct underlying patterns of body size plasticity in response to temperature and nutrition that were often different from the overall population response. We then tested whether plasticity in development time could explain, and therefore regulate, variation in body size to these combinations of environmental conditions. We selected five genotypes that showed the greatest variation in response to combined thermal and nutritional stress and assessed the correlation between response of developmental time and body size. While we found significant genetic variation in development time plasticity, it was a poor predictor of body size among genotypes. Our results therefore suggest that multiple developmental pathways could generate genetic variation in body size plasticity. Our study emphasizes the need to better understand genetic variation in plasticity within a population, which will help determine the potential for populations to adapt to ongoing environmental change.
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Affiliation(s)
| | - Greg M Walter
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - André N Alves
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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26
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Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
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27
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Wenne R, Zbawicka M, Prądzińska A, Kotta J, Herkül K, Gardner JPA, Apostolidis AP, Poćwierz-Kotus A, Rouane-Hacene O, Korrida A, Dondero F, Baptista M, Reizopoulou S, Hamer B, Sundsaasen KK, Árnyasi M, Kent MP. Molecular genetic differentiation of native populations of Mediterranean blue mussels, Mytilus galloprovincialis Lamarck, 1819, and the relationship with environmental variables. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2086306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- R. Wenne
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - M. Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - A. Prądzińska
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - J. Kotta
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - K. Herkül
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - J. P. A. Gardner
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - A. P. Apostolidis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A. Poćwierz-Kotus
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - O. Rouane-Hacene
- Department of Biology, Faculty of Nature and Life Sciences, University of Oran 1 - Ahmed Ben Bella, Algeria
| | - A. Korrida
- High Institute of Nursing Professions and Health Techniques, ISPITS-Agadir, Moroccan Ministry of Health and Social Protection, Kingdom of Morocco
| | - F. Dondero
- Department of Science and Technological Innovation (DISIT), Ecotoxicology and Ecology, Università del Piemonte Orientale “Amedeo Avogadro”, Novara, 15121, Italy
| | - M. Baptista
- Marine and Environmental Sciences Centre, University of Lisbon, Portugal
| | - S. Reizopoulou
- Department of Biological Oceanography, Institute of Oceanography, Hellenic Centre for Marine Research, Athens Sounio, 19013 Anavyssos, Greece
| | - B. Hamer
- Ruđer Bošković Institute, Center for Marine Research Rovinj, Rovinj, Croatia
| | - K. K. Sundsaasen
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. Árnyasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. P. Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
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28
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Pfenninger M, Foucault Q. Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes. Integr Comp Biol 2022; 62:1812-1826. [PMID: 35762661 DOI: 10.1093/icb/icac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/05/2023] Open
Abstract
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.
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Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Quentin Foucault
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany
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29
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Andersson A, Karlsson S, Ryman N, Laikre L. Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator. Mol Ecol 2022; 31:6422-6439. [PMID: 36170147 PMCID: PMC10091952 DOI: 10.1111/mec.16710] [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: 11/29/2021] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST , respectively) and assess the effective population size (Ne -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.
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Affiliation(s)
- Anastasia Andersson
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
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30
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Jin P, Wan J, Zhou Y, Gao K, Beardall J, Lin J, Huang J, Lu Y, Liang S, Wang K, Ma Z, Xia J. Increased genetic diversity loss and genetic differentiation in a model marine diatom adapted to ocean warming compared to high CO 2. THE ISME JOURNAL 2022; 16:2587-2598. [PMID: 35948613 PMCID: PMC9561535 DOI: 10.1038/s41396-022-01302-y] [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: 03/30/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 05/30/2023]
Abstract
Although high CO2 and warming could act interactively on marine phytoplankton, little is known about the molecular basis for this interaction on an evolutionary scale. Here we explored the adaptation to high CO2 in combination with warming in a model marine diatom Phaeodactylum tricornutum. Whole-genome re-sequencing identifies, in comparison to populations grown under control conditions, a larger genetic diversity loss and a higher genetic differentiation in the populations adapted for 2 years to warming than in those adapted to high CO2. However, this diversity loss was less under high CO2 combined with warming, suggesting that the evolution driven by warming was constrained by high CO2. By integrating genomics, transcriptomics, and physiological data, we found that the underlying molecular basis for this constraint is associated with the expression of genes involved in some key metabolic pathways or biological processes, such as the glyoxylate pathway, amino acid and fatty acid metabolism, and diel variability. Our results shed new light on the evolutionary responses of marine phytoplankton to multiple environmental changes in the context of global change and provide new insights into the molecular basis underpinning interactions among those multiple drivers.
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Affiliation(s)
- Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science & College of Ocean and Earth Sciences, Xiamen University, 361005, Xiamen, China
| | - John Beardall
- State Key Laboratory of Marine Environmental Science & College of Ocean and Earth Sciences, Xiamen University, 361005, Xiamen, China
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Kaiqiang Wang
- Gene Denovo Biotechnology Co, Guangzhou, 510006, China
| | - Zengling Ma
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
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31
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Pierron F, Heroin D, Daffe G, Daramy F, Barré A, Bouchez O, Romero-Ramirez A, Gonzalez P, Nikolski M. Genetic and epigenetic interplay allows rapid transgenerational adaptation to metal pollution in zebrafish. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac022. [PMID: 36474803 PMCID: PMC9716877 DOI: 10.1093/eep/dvac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/21/2022] [Accepted: 10/21/2022] [Indexed: 05/26/2023]
Abstract
Despite still being a matter of debate, there is growing evidence that pollutant-induced epigenetic changes can be propagated across generations. Whereas such modifications could have long-lasting effects on organisms and even on population, environmentally relevant data from long-term exposure combined with follow-up through multiple generations remain scarce for non-mammalian species. We performed a transgenerational experiment comprising four successive generations of zebrafish. Only fish from the first generation were exposed to an environmentally realistic concentration of cadmium (Cd). Using a whole methylome analysis, we first identified the DNA regions that were differentially methylated in response to Cd exposure and common to fish of the first two generations. Among them, we then focused our investigations on the exon 3 (ex3) of the cep19 gene. We indeed recorded transgenerational growth disorders in Cd-exposed fish, and a mutation in this exon is known to cause morbid obesity in mammals. Its methylation level was thus determined in zebrafish from all the four generations by means of a targeted and base resolution method. We observed a transgenerational inheritance of Cd-induced DNA methylation changes up to the fourth generation. However, these changes were closely associated with genetic variations, mainly a single nucleotide polymorphism. This single nucleotide polymorphism was itself at the origin of the creation or deletion of a methylation site and deeply impacted the methylation level of neighboring methylation sites. Cd-induced epigenetic changes were associated with different mRNA transcripts and an improved condition of Cd fish. Our results emphasize a tight relationship between genetic and epigenetic mechanisms and suggest that their interplay and pre-existing diversity can allow rapid adaptation to anthropogenic environmental changes.
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Affiliation(s)
- Fabien Pierron
- *Correspondence address. UMR 5805 EPOC – OASU, Station Marine d’Arcachon, Université de Bordeaux, Place du Docteur Bertrand Peyneau, Arcachon 33120, France. Tel: +335 56 22 39 33; Fax: +335 40 70 85 04; E-mail:
| | - Débora Heroin
- University of Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac 33600, France
| | - Guillemine Daffe
- University of Bordeaux, CNRS, INRAE, La Rochelle University, UMS 2567 POREA, Pessac 33615, France
| | - Flore Daramy
- University of Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac 33600, France
| | - Aurélien Barré
- University of Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, 33076, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan 31326, France
| | | | - Patrice Gonzalez
- University of Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac 33600, France
| | - Macha Nikolski
- University of Bordeaux, Bordeaux Bioinformatics Center, Bordeaux, 33076, France
- University of Bordeaux, CNRS, IBGC, UMR 5095, Bordeaux 33077, France
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Aguilera VM, Bednaršek N. Variations in phenotypic plasticity in a cosmopolitan copepod species across latitudinal hydrographic gradients. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.925648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Studies assessing latitudinal variations in habitat conditions and phenotypic plasticity among populations yield evidence of the mechanisms governing differentiation in the potential to adapt to current/future habitat changes. The cosmopolitan copepod species Acartia tonsa thrives across ocean clines delimiting Seasonal (30–40° S) and Permanent (10–30° S) Upwelling coastal provinces established during the middle–late Pliocene (3.6–1.8 Ma) alongshore the South East Pacific (SEP), nowadays exhibiting contrasting variability features related to several ocean drivers (temperature, salinity, pH, and food availability). Latitudinal variation across the range of environmental conditions of the coastal provinces can contribute toward shaping divergent A. tonsa’s phenotypes, for example, through specific patterns of phenotypic plasticity in morphological and physiological traits and tolerance to environmental drivers. With the aim of contributing to the understanding of these adaptive processes in a relatively little studied oceanic region, here we compared the expression of parental (i.e., adult size, egg production, and ingestion rate) and offspring (i.e., egg size) traits in relation to variation in environmental habitat conditions across different cohorts of two distant (> 15° latitude) A. tonsa populations inhabiting estuarine and upwelling habitats located in the Seasonal and Permanent Upwelling province, respectively. Mean conditions and ranges of variability in the habitat conditions and phenotypic plasticity of parental and offspring traits within and among cohorts of A. tonsa populations varied significantly across the different examined regions (i.e., Seasonal vs. Permanent). We also found significant differences in the coupling of habitat variability and trait expression, suggesting that the differences in trait expressions might be related to habitat variability. The phenotypic divergence was translated to cohort-related patterns of trait trade-offs regulating reproduction and tolerance of egg production efficiency that can jointly determine the level of plasticity, genetic structure, or local adaptation. The current findings provide novel evidence of how divergent phenotypes might sustain A. tonsa populations across variable coastal provinces of the SEP.
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Barbosa M, Schwaner C, Pales Espinosa E, Allam B. A Transcriptomic Analysis of Phenotypic Plasticity in Crassostrea virginica Larvae under Experimental Acidification. Genes (Basel) 2022; 13:1529. [PMID: 36140697 PMCID: PMC9498863 DOI: 10.3390/genes13091529] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
Ocean acidification (OA) is a major threat to marine calcifiers, and little is known regarding acclimation to OA in bivalves. This study combined physiological assays with next-generation sequencing to assess the potential for recovery from and acclimation to OA in the eastern oyster (Crassostrea virginica) and identify molecular mechanisms associated with resilience. In a reciprocal transplant experiment, larvae transplanted from elevated pCO2 (~1400 ppm) to ambient pCO2 (~350 ppm) demonstrated significantly lower mortality and larger size post-transplant than oysters remaining under elevated pCO2 and had similar mortality compared to those remaining in ambient conditions. The recovery after transplantation to ambient conditions demonstrates the ability for larvae to rebound and suggests phenotypic plasticity and acclimation. Transcriptomic analysis supported this hypothesis as genes were differentially regulated under OA stress. Transcriptomic profiles of transplanted and non-transplanted larvae terminating in the same final pCO2 converged, further supporting the idea that acclimation underlies resilience. The functions of differentially expressed genes included cell differentiation, development, biomineralization, ion exchange, and immunity. Results suggest acclimation as a mode of resilience to OA. In addition, the identification of genes associated with resilience can serve as a valuable resource for the aquaculture industry, as these could enable marker-assisted selection of OA-resilient stocks.
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Affiliation(s)
| | | | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Sony Brook University, Stony Brook, NY 11790, USA
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Kapsenberg L, Bitter MC, Miglioli A, Aparicio-Estalella C, Pelejero C, Gattuso JP, Dumollard R. Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis. iScience 2022; 25:104677. [PMID: 35847553 PMCID: PMC9283884 DOI: 10.1016/j.isci.2022.104677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022] Open
Abstract
Predicting the potential for species adaption to climate change is challenged by the need to identify the physiological mechanisms that underpin species vulnerability. Here, we investigated the sensitivity to ocean acidification in marine mussels during early development, and specifically the trochophore stage. Using RNA and DNA sequencing and in situ RNA hybridization, we identified developmental processes associated with abnormal development and rapid adaptation to low pH. Trochophores exposed to low pH seawater exhibited 43 differentially expressed genes. Gene annotation and in situ hybridization of differentially expressed genes point to pH sensitivity of (1) shell field development and (2) cellular stress response. Five genes within these two processes exhibited shifts in allele frequencies indicative of a potential for rapid adaptation. This case study contributes direct evidence that protecting species’ existing genetic diversity is a critical management action to facilitate species resilience to climate change. Marine mussel larval development and genetic adaptation in low pH seawater RNA and DNA responses reveal impacts on shell field development and cell stress Five genes exhibited both physiological sensitivity and long-term adaptive potential Conserving standing genetic variation could bolster resilience to global change
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Affiliation(s)
- Lydia Kapsenberg
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer à Villefranche (IMEV), 181 chemin du Lazaret, 06230 Villefranche-sur-mer, France
| | - Mark C Bitter
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Angelica Miglioli
- Sorbonne Université/CNRS, Institut de la Mer, UMR7009 Laboratoire de Biologie du Développement, Chemin du Lazaret, 06230 Villefranche-sur-Mer, France.,Università degli studi di Genova, Dipartimento di Scienze della Terra, dell'Ambiente e della Vita (DISTAV), Corso Europa 26, 16132 Genova, Italy
| | - Clàudia Aparicio-Estalella
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Lighthouse Field Station, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Carles Pelejero
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (CSIC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Jean-Pierre Gattuso
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), Institut de la Mer à Villefranche (IMEV), 181 chemin du Lazaret, 06230 Villefranche-sur-mer, France.,Institute for Sustainable Development and International Relations, Sciences Po, 27 rue Saint Guillaume, 75007 Paris, France
| | - Rémi Dumollard
- Sorbonne Université/CNRS, Institut de la Mer, UMR7009 Laboratoire de Biologie du Développement, Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
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35
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Gurr SJ, Trigg SA, Vadopalas B, Roberts SB, Putnam HM. Acclimatory gene expression of primed clams enhances robustness to elevated pCO 2. Mol Ecol 2022; 31:5005-5023. [PMID: 35947503 DOI: 10.1111/mec.16644] [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: 04/24/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022]
Abstract
Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO2 improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO2 (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO2 treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO2 , and a third 7-day exposure to two pCO2 treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO2 and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO2 priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.
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Affiliation(s)
- Samuel J Gurr
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Shelly A Trigg
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | | | - Steven B Roberts
- University of Washington, School of Aquatic and Fishery Sciences, Seattle, WA, USA
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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36
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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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37
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Stern DB, Anderson NW, Diaz JA, Lee CE. Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. Nat Commun 2022; 13:4024. [PMID: 35821220 PMCID: PMC9276764 DOI: 10.1038/s41467-022-31622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
The role of epistasis in driving adaptation has remained an unresolved problem dating back to the Evolutionary Synthesis. In particular, whether epistatic interactions among genes could promote parallel evolution remains unexplored. To address this problem, we employ an Evolve and Resequence (E&R) experiment, using the copepod Eurytemora affinis, to elucidate the evolutionary genomic response to rapid salinity decline. Rapid declines in coastal salinity at high latitudes are a predicted consequence of global climate change. Based on time-resolved pooled whole-genome sequencing, we uncover a remarkably parallel, polygenic response across ten replicate selection lines, with 79.4% of selected alleles shared between lines by the tenth generation of natural selection. Using extensive computer simulations of our experiment conditions, we find that this polygenic parallelism is consistent with positive synergistic epistasis among alleles, far more so than other mechanisms tested. Our study provides experimental and theoretical support for a novel mechanism promoting repeatable polygenic adaptation, a phenomenon that may be common for selection on complex physiological traits.
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Affiliation(s)
- David B Stern
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA.
- National Biodefense Analysis and Countermeasures Center (NBACC), Operated by Battelle National Biodefense Institute (BNBI) for the U.S. Department of Homeland Security Science and Technology Directorate, Fort Detrick, MD, 21702, USA.
| | - Nathan W Anderson
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA
| | - Juanita A Diaz
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA
| | - Carol Eunmi Lee
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Birge Hall, Madison, WI, 53706, USA.
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38
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Johnston NM, Murphy EJ, Atkinson A, Constable AJ, Cotté C, Cox M, Daly KL, Driscoll R, Flores H, Halfter S, Henschke N, Hill SL, Höfer J, Hunt BPV, Kawaguchi S, Lindsay D, Liszka C, Loeb V, Manno C, Meyer B, Pakhomov EA, Pinkerton MH, Reiss CS, Richerson K, Jr. WOS, Steinberg DK, Swadling KM, Tarling GA, Thorpe SE, Veytia D, Ward P, Weldrick CK, Yang G. Status, Change, and Futures of Zooplankton in the Southern Ocean. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.624692] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In the Southern Ocean, several zooplankton taxonomic groups, euphausiids, copepods, salps and pteropods, are notable because of their biomass and abundance and their roles in maintaining food webs and ecosystem structure and function, including the provision of globally important ecosystem services. These groups are consumers of microbes, primary and secondary producers, and are prey for fishes, cephalopods, seabirds, and marine mammals. In providing the link between microbes, primary production, and higher trophic levels these taxa influence energy flows, biological production and biomass, biogeochemical cycles, carbon flux and food web interactions thereby modulating the structure and functioning of ecosystems. Additionally, Antarctic krill (Euphausia superba) and various fish species are harvested by international fisheries. Global and local drivers of change are expected to affect the dynamics of key zooplankton species, which may have potentially profound and wide-ranging implications for Southern Ocean ecosystems and the services they provide. Here we assess the current understanding of the dominant metazoan zooplankton within the Southern Ocean, including Antarctic krill and other key euphausiid, copepod, salp and pteropod species. We provide a systematic overview of observed and potential future responses of these taxa to a changing Southern Ocean and the functional relationships by which drivers may impact them. To support future ecosystem assessments and conservation and management strategies, we also identify priorities for Southern Ocean zooplankton research.
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Hedgecock D. No evidence for temporally balanced selection on larval Pacific oysters Crassostrea gigas: a comment on Durland et al. (2021). Proc Biol Sci 2022; 289:20212579. [PMID: 35642361 PMCID: PMC9156931 DOI: 10.1098/rspb.2021.2579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
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40
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Durland E, Wit PD, Langdon C. Genetic changes in larval oysters are more abundant and dynamic than can be explained by rare events or error: a response to Hedgecock (2022). Proc Biol Sci 2022; 289:20220197. [PMID: 35642372 PMCID: PMC9156927 DOI: 10.1098/rspb.2022.0197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Pierre De Wit
- Marine Sciences, Goteborgs Universitet, Strömstad, Sweden
| | - Chris Langdon
- Department of Fisheries, Oregon State University College of Agricultural Sciences, Newport, OR, USA
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42
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Cornman RS, Cryan PM. Positively selected genes in the hoary bat ( Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PeerJ 2022; 10:e13130. [PMID: 35317076 PMCID: PMC8934532 DOI: 10.7717/peerj.13130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov-Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.
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Saleh D, Chen J, Leplé J, Leroy T, Truffaut L, Dencausse B, Lalanne C, Labadie K, Lesur I, Bert D, Lagane F, Morneau F, Aury J, Plomion C, Lascoux M, Kremer A. Genome-wide evolutionary response of European oaks during the Anthropocene. Evol Lett 2022; 6:4-20. [PMID: 35127134 PMCID: PMC8802238 DOI: 10.1002/evl3.269] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.
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Affiliation(s)
- Dounia Saleh
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Jun Chen
- College of Life SciencesZhejiang UniversityHangzhou310058China
| | | | - Thibault Leroy
- Department of Botany and Biodiversity ResearchUniversity of ViennaVienna1010Austria
| | - Laura Truffaut
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - Céline Lalanne
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | - Karine Labadie
- Genoscope, Institut de Biologie François Jacob, Commissariat à l’énergie atomique (CEA)Université de Paris‐SaclayEvry91057France
| | | | - Didier Bert
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
| | | | - François Morneau
- Département Recherche Développement InnovationOffice National des ForêtsBoigny‐Sur‐Bionne45760France,Current Address: Service de l'Information Statistique Forestière et EnvironnementaleInstitut National de l'Information géographique et ForestièreNogent‐sur‐Vernisson45290France
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRSUniv Evry, Université Paris‐SaclayEvry91057France
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSE‐75236Sweden
| | - Antoine Kremer
- UMR BIOGECO, INRAEUniversité de BordeauxCestas33612France
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Albecker MA, Wilkins LGE, Krueger-Hadfield SA, Bashevkin SM, Hahn MW, Hare MP, Kindsvater HK, Sewell MA, Lotterhos KE, Reitzel AM. Does a complex life cycle affect adaptation to environmental change? Genome-informed insights for characterizing selection across complex life cycle. Proc Biol Sci 2021; 288:20212122. [PMID: 34847763 PMCID: PMC8634620 DOI: 10.1098/rspb.2021.2122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Complex life cycles, in which discrete life stages of the same organism differ in form or function and often occupy different ecological niches, are common in nature. Because stages share the same genome, selective effects on one stage may have cascading consequences through the entire life cycle. Theoretical and empirical studies have not yet generated clear predictions about how life cycle complexity will influence patterns of adaptation in response to rapidly changing environments or tested theoretical predictions for fitness trade-offs (or lack thereof) across life stages. We discuss complex life cycle evolution and outline three hypotheses—ontogenetic decoupling, antagonistic ontogenetic pleiotropy and synergistic ontogenetic pleiotropy—for how selection may operate on organisms with complex life cycles. We suggest a within-generation experimental design that promises significant insight into composite selection across life cycle stages. As part of this design, we conducted simulations to determine the power needed to detect selection across a life cycle using a population genetic framework. This analysis demonstrated that recently published studies reporting within-generation selection were underpowered to detect small allele frequency changes (approx. 0.1). The power analysis indicates challenging but attainable sampling requirements for many systems, though plants and marine invertebrates with high fecundity are excellent systems for exploring how organisms with complex life cycles may adapt to climate change.
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Affiliation(s)
- Molly A Albecker
- Department of Biology, Utah State University, Logan, UT 84321, USA
| | - Laetitia G E Wilkins
- Max Planck Institute for Marine Microbiology (MPIMM), Celsiusstrasse 1, 28209 Bremen, Germany
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA
| | - Samuel M Bashevkin
- Delta Science Program, Delta Stewardship Council, 715 P Street 15-300, Sacramento, CA 95814, USA
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd St., Bloomington, IN 47405, USA
| | - Matthew P Hare
- Department of Natural Resources and the Environment, Cornell University, 205 Fernow Hall, Ithaca, NY 14853, USA
| | - Holly K Kindsvater
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mary A Sewell
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Katie E Lotterhos
- Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA 01918, USA
| | - Adam M Reitzel
- University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA
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45
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Griffiths JS, Johnson KM, Kelly MW. Evolutionary Change in the Eastern Oyster, Crassostrea Virginica, Following Low Salinity Exposure. Integr Comp Biol 2021; 61:1730-1740. [PMID: 34448845 DOI: 10.1093/icb/icab185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The presence of standing genetic variation will play a role in determining a population's capacity to adapt to environmentally relevant stressors. In the Gulf of Mexico, extreme climatic events and anthropogenic changes to local hydrology will expose productive oyster breeding grounds to stressful low salinity conditions. We identified genetic variation for performance under low salinity (due to the combined effects of low salinity and genetic load) using a single-generation selection experiment on larvae from two populations of the eastern oyster, Crassostrea virginica. We used pool-sequencing to test for allele frequency differences at 152 salinity-associated genes for larval families pre- and post-low salinity exposure. Our results have implications for how evolutionary change occurs during early life history stages at environmentally relevant salinities. Consistent with observations of high genetic load observed in oysters, we demonstrate evidence for purging of deleterious alleles at the larval stage in C. virginica. In addition, we observe increases in allele frequencies at multiple loci, suggesting that natural selection for low salinity performance at the larval stage can act as a filter for genotypes found in adult populations.
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Affiliation(s)
- Joanna S Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Kevin M Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.,California Sea Grant, University of California San Diego, La Jolla, CA 92093, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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46
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Matoo OB, Neiman M. Bringing Disciplines and People Together to Characterize the Plastic and Genetic Responses of Molluscs to Environmental Change. Integr Comp Biol 2021; 61:1689-1698. [PMID: 34435639 PMCID: PMC8699093 DOI: 10.1093/icb/icab186] [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] [Indexed: 11/12/2022] Open
Abstract
Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs as a "common currency" to demonstrate how organismal and evolutionary biologists can use natural systems to make phenotype-genotype connections in the context of changing environments. In parallel, we emphasize the critical need to collaborate and integrate findings across taxa and disciplines in order to use new data and information to advance our understanding of mollusc biology in the context of global environmental change. We end with a brief synthetic summary of the papers inspired by the 2021 SICB Symposium "Genomic Perspectives in Comparative Physiology of Molluscs: Integration across Disciplines".
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Affiliation(s)
- Omera B Matoo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City 52242, IA, USA.,Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City 52242, IA, USA
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47
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Xuereb A, Rougemont Q, Tiffin P, Xue H, Phifer-Rixey M. Individual-based eco-evolutionary models for understanding adaptation in changing seas. Proc Biol Sci 2021; 288:20212006. [PMID: 34753353 PMCID: PMC8580472 DOI: 10.1098/rspb.2021.2006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/15/2021] [Indexed: 01/09/2023] Open
Abstract
As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fuelled in part by developments in modelling frameworks that allow simulation of increasingly complex ecological, genetic and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: (i) effects of genetic architecture and non-genetic responses on adaptive potential; (ii) capacity for gene flow to facilitate rapid adaptation; and (iii) impacts of multiple stressors on persistence. Finally, we demonstrate the approach using simple simulations and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.
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Affiliation(s)
- Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, Université Laval, 3050 Avenue de la Médecine, Québec, Quebec, Canada G1 V 0A6
| | - Quentin Rougemont
- CEFE, Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Huijie Xue
- School of Marine Sciences, University of Maine, 5706 Aubert Hall, Orono, ME 04469-5706, USA
| | - Megan Phifer-Rixey
- Department of Biology, Monmouth University, 400 Cedar Avenue, West Long Branch, NJ, USA
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48
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Yang Z, Sun F, Liao H, Zhang Z, Dou Z, Xing Q, Hu J, Huang X, Bao Z. Genome-wide association study reveals genetic variations associated with ocean acidification resilience in Yesso scallop Patinopecten yessoensis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 240:105963. [PMID: 34547702 DOI: 10.1016/j.aquatox.2021.105963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/22/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Ocean acidification (OA), which refers to a gradual decrease in seawater pH due to the absorption of atmospheric carbon dioxide, profoundly affects the growth, development and survival of bivalves. Relatively limited studies have assessed the resilience of bivalve to OA. In the present study, Patinopecten yessoensis, an economically and ecologically significant species, were exposed to low pH (pH = 7.5) for 4 weeks. Forty-seven scallops that died in the first week were considered pH-sensitive population, and 20 that were alive at the end of the experiment were considered pH-tolerant population. A genome-wide association study was conducted to identify the genomic loci associated the resilience of P. yessoensis to OA. Twenty-one single nucleotide polymorphisms were significantly associated with resilience, which were distributed in 11 linkage groups. Within the linkage disequilibrium block region (± 300 kb) surrounding the 21 SNPs, 193 candidate genes were successfully identified. Particularly, five associated SNPs were directly located on five genes, including SP24, CFDH, 5HTR3, HSDL1 and ZFP346. The GO enrichment and KEGG pathway analyses showed that the molecular response of P. yessoensis to OA mainly involved neural signal transmission, energy metabolism and redox reaction. Candidate genes were expressed during larval development and in adult tissues. Furthermore, the expression of 30 candidate genes changed significantly under low pH stress in the mantle. Our results reveal certain SNPs and candidate genes that could elucidate the different responses of P. yessoensis to OA. The genetic variations indicated molecular resilience in P. yessoensis populations, which may enable adaptation to future acidification stress.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanhua Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Zhengrui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zheng Dou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
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49
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Durland E, De Wit P, Langdon C. Temporally balanced selection during development of larval Pacific oysters ( Crassostrea gigas) inherently preserves genetic diversity within offspring. Proc Biol Sci 2021; 288:20203223. [PMID: 34465244 PMCID: PMC8437028 DOI: 10.1098/rspb.2020.3223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.
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Affiliation(s)
- Evan Durland
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Chris Langdon
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
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Hellwig T, Abbo S, Sherman A, Ophir R. Prospects for the natural distribution of crop wild-relatives with limited adaptability: The case of the wild pea Pisum fulvum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110957. [PMID: 34315583 DOI: 10.1016/j.plantsci.2021.110957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/12/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Plant breeders and conservationist depend on knowledge about the genetic variation of their species of interest. Pisum fulvum, a wild relative of domesticated pea, has attracted attention as a genetic resource for crop improvement, yet little information about its diversity in the wild has been published hitherto. We sampled 15 populations of P. fulvum from Israeli natural habitats and conducted genotyping by sequencing to analyse their genetic diversity and adaptive state. We also attempted to evaluate the species past demography and the prospects of its future reaction to environmental changes. The results suggest that genetic diversity of P. fulvum is low to medium and is distributed between well diverged populations. Surprisingly, with 56 % in the total population the selfing rate was found to be significantly lower than expected from a species that is commonly assumed to be a predominant selfer. We found a strong genetic bottleneck during the last glacial period and only limited patterns of isolation by distance and environment, which explained 13 %-18 % of the genetic variation. Despite the weak signatures of genome-wide IBE, 1,354 markers were significantly correlated with environmental factors, 1,233 of which were located within known genes with a nonsynonymous to synonymous ratio of 0.382. Species distribution modelling depicted an ongoing fragmentation and decreased habitable area over the next 80 years under two different socio-economic pathways. Our results suggest that complex interactions of substantial drift and selection shaped the genome of P. fulvum. Climate changeis likely to cause further erosion of genetic diversity in P. fulvum. Systematic ex-situ conservation may be advisable to safeguard genetic variability for future utilization of this species.
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Affiliation(s)
- Timo Hellwig
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel; Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Shahal Abbo
- R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot, 761001, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, P.O.B 15159, Rishon LeZion, 7505101, Israel.
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