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Sarafidou G, Tsaparis D, Issaris Y, Chatzigeorgiou G, Grigoriou P, Chatzinikolaou E, Pavloudi C. Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea. PeerJ 2023; 11:e16491. [PMID: 38047017 PMCID: PMC10693241 DOI: 10.7717/peerj.16491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 10/29/2023] [Indexed: 12/05/2023] Open
Abstract
The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e., by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species' most suitable conservation management.
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Affiliation(s)
- Georgia Sarafidou
- Institute of Oceanography (IO), Hellenic Centre for Marine Research (HCMR), Anavyssos, Greece
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Dimitris Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Yiannis Issaris
- Institute of Oceanography (IO), Hellenic Centre for Marine Research (HCMR), Anavyssos, Greece
| | - Giorgos Chatzigeorgiou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Panos Grigoriou
- Cretaquarium, Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Eva Chatzinikolaou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Christina Pavloudi
- PSL Research University: EPHE-UPVD-CNRS, UAR CNRS 3278 Centre de Recherche Insulaire et Observatoire de l’Environnement (CRIOBE), Perpignan, France
- Laboratoire d’Excellence “CORAIL”, Centre de Recherche Insulaire et Observatoire de l’Environnement (CRIOBE), Moorea, French Polynesia
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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3
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Morris CJ, Nguyen KQ, Green JM. Comparison of lethal and non-lethal age-based growth estimation methodologies to assess an endemic bay population of Atlantic cod (Gadus morhua). J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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4
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Jeffery NW, Lehnert SJ, Kess T, Layton KKS, Wringe BF, Stanley RR. Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy. Front Genet 2022; 13:886494. [PMID: 35812740 PMCID: PMC9257101 DOI: 10.3389/fgene.2022.886494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/16/2022] [Indexed: 11/15/2022] Open
Abstract
A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New “big data” omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.
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Affiliation(s)
- Nicholas W. Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
- *Correspondence: Nicholas W. Jeffery,
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, NL, Canada
| | - Kara K. S. Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Brendan F. Wringe
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
| | - Ryan R.E. Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada
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Boulanger E, Benestan L, Guerin PE, Dalongeville A, Mouillot D, Manel S. Climate differently influences the genomic patterns of two sympatric marine fish species. J Anim Ecol 2021; 91:1180-1195. [PMID: 34716929 DOI: 10.1111/1365-2656.13623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.
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Affiliation(s)
- Emilie Boulanger
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France.,MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Laura Benestan
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre-Edouard Guerin
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | - David Mouillot
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Institut Universitaire de France, Paris, France
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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6
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Nikolopoulou S, Berov D, Klayn S, Dimitrov LI, Velkovsky K, Chatzinikolaou E, Chatzigeorgiou G, Karamfilov V, Pavloudi C. Benthic habitat mapping of Plazh Gradina - Zlatna ribka (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). Biodivers Data J 2021; 9:e71972. [PMID: 34531700 PMCID: PMC8405599 DOI: 10.3897/bdj.9.e71972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022] Open
Abstract
Background Habitat mapping is nеcessary for the efficient conservation and protection of marine ecosystems. In addition, it is a requirement for EU Member States as stated in the European Union (EU) Habitats Directive (92/43/EEC), as well as necessary for the achievement and maintenance of 'good environmental status (GES)' of benthic marine habitats in the framework of the EU Marine Strategy Framework Directive (2008/56/EC). New information This study provides baseline information on the marine benthic habitats of Sozopol Bay (Black Sea) and Karpathos and Saria Islands (Mediterranean Sea). These two Natura 2000 sites were selected as study sites of the RECONNECT project, which aimed at creating a transnational cooperative network to confront the environmental threats of ecosystems with a high natural and cultural interest, by the establishment of common practices and a joint regional strategy. The specific objective was to map the marine habitats using a defined a priori classification (EUNIS), with the ultimate purpose of supporting government marine spatial planning, management and decision-making processes through the development of a Decision Support System.
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Affiliation(s)
- Stamatina Nikolopoulou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500, Heraklion, Crete, Greece Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500 Heraklion, Crete Greece
| | - Dimitar Berov
- Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113, Sofia, Bulgaria Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113 Sofia Bulgaria
| | - Stefania Klayn
- Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113, Sofia, Bulgaria Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113 Sofia Bulgaria
| | - Lyubomir I Dimitrov
- Institute of Oceanology, Bulgarian Academy of Sciences, 40 First May St, 9000, Varna, Bulgaria Institute of Oceanology, Bulgarian Academy of Sciences, 40 First May St, 9000 Varna Bulgaria
| | - Kiril Velkovsky
- Centre for underwater archaeology, Khan Krum sq. 1, 8130, Sozopol, Bulgaria Centre for underwater archaeology, Khan Krum sq. 1, 8130 Sozopol Bulgaria
| | - Eva Chatzinikolaou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500, Heraklion, Crete, Greece Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500 Heraklion, Crete Greece
| | - Giorgos Chatzigeorgiou
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500, Heraklion, Crete, Greece Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500 Heraklion, Crete Greece
| | - Ventzislav Karamfilov
- Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113, Sofia, Bulgaria Laboratory of Marine Ecology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Major Yurii Gagarin Street, 1113 Sofia Bulgaria
| | - Christina Pavloudi
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500, Heraklion, Crete, Greece Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71500 Heraklion, Crete Greece
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7
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Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
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Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
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8
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Xuereb A, D'Aloia CC, Andrello M, Bernatchez L, Fortin MJ. Incorporating putatively neutral and adaptive genomic data into marine conservation planning. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:909-920. [PMID: 32785955 DOI: 10.1111/cobi.13609] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperature-associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.
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Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Cassidy C D'Aloia
- Department of Biological Sciences, University of New Brunswick Saint John, 100 Tucker Park Road, Saint John, NB, E2L 4L5, Canada
| | - Marco Andrello
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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9
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Carr H, Abas M, Boutahar L, Caretti ON, Chan WY, Chapman ASA, de Mendonça SN, Engleman A, Ferrario F, Simmons KR, Verdura J, Zivian A. The Aichi Biodiversity Targets: achievements for marine conservation and priorities beyond 2020. PeerJ 2020; 8:e9743. [PMID: 33391861 PMCID: PMC7759131 DOI: 10.7717/peerj.9743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
In 2010 the Conference of the Parties (COP) for the Convention on Biological Diversity revised and updated a Strategic Plan for Biodiversity 2011–2020, which included the Aichi Biodiversity Targets. Here a group of early career researchers mentored by senior scientists, convened as part of the 4th World Conference on Marine Biodiversity, reflects on the accomplishments and shortfalls under four of the Aichi Targets considered highly relevant to marine conservation: target 6 (sustainable fisheries), 11 (protection measures), 15 (ecosystem restoration and resilience) and 19 (knowledge, science and technology). We conclude that although progress has been made towards the targets, these have not been fully achieved for the marine environment by the 2020 deadline. The progress made, however, lays the foundations for further work beyond 2020 to work towards the 2050 Vision for Biodiversity. We identify key priorities that must be addressed to better enable marine biodiversity conservation efforts moving forward.
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Affiliation(s)
- Hannah Carr
- The Joint Nature Conservation Committee, Peterborough, Cambridgeshire, UK
| | - Marina Abas
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Loubna Boutahar
- BioBio Research Center, BioEcoGen Laboratory, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.,Laboratorío de Biología Marina, Departamento de Zoología, Universidad de Sevilla, Sevilla, Spain
| | - Olivia N Caretti
- Department of Marine, Earth, & Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wing Yan Chan
- Australian Institute of Marine Science, Townsville, QLD, Australia.,School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Abbie S A Chapman
- School of Ocean and Earth Science, University of Southampton, Southampton, Hampshire, UK.,Centre for Biodiversity and Environment Research, University College London, London, UK
| | | | - Abigail Engleman
- Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Filippo Ferrario
- Québec-Ocean and Département de Biologie, Université Laval, Québec, QC, Canada
| | - Kayelyn R Simmons
- Department of Marine, Earth, & Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jana Verdura
- Institut d'Ecologia Aquàtica, Facultat de Ciències, Universitat de Girona, Girona, Spain
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10
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Yorisue T, Iguchi A, Yasuda N, Mizuyama M, Yoshioka Y, Miyagi A, Fujita Y. Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191731. [PMID: 33204436 PMCID: PMC7657918 DOI: 10.1098/rsos.191731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimp Parhippolyte misticia from three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns. Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.
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Affiliation(s)
- Takefumi Yorisue
- Integrative Aquatic Biology, Onagawa Field Center, Graduate School of Agricultural Science, Tohoku University, 3-1 Mukai, Konori-hama, Onagawa, Oshika, Miyagi 986-2242, Japan
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
- Institute of Natural and Environmental Sciences, University of Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
- Division of Nature and Environmental Management, Museum of Nature and Human Activities, Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Gakuenkibana-dai Nishi 1-1, Miyazaki 889-2192, Japan
| | - Masaru Mizuyama
- Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Yoshihisa Fujita
- General Educational Center, Okinawa Prefectural University of Arts, 1-4, Shuri Tounokura-cho, Naha-shi, Okinawa 903-8602, Japan
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11
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Fietz K, Trofimenko E, Guerin PE, Arnal V, Torres-Oliva M, Lobréaux S, Pérez-Ruzafa A, Manel S, Puebla O. New genomic resources for three exploited Mediterranean fishes. Genomics 2020; 112:4297-4303. [PMID: 32629099 DOI: 10.1016/j.ygeno.2020.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.
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Affiliation(s)
- Katharina Fietz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Elena Trofimenko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Pierre-Edouard Guerin
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Montserrat Torres-Oliva
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stéphane Lobréaux
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble-Alpes, Grenoble, France
| | - Angel Pérez-Ruzafa
- Departmento de Ecología e Hidrología, Facultad de Biología, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Oscar Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany; Leibniz Centre for Tropical Marine Research, Fahrenheitstrasse 6, 28359 Bremen, Germany
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