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Jaquier M, Albouy C, Bach W, Waldock C, Marques V, Maire E, Juhel JB, Andrello M, Valentini A, Manel S, Dejean T, Mouillot D, Pellissier L. Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands. Ecol Evol 2024; 14:e11337. [PMID: 38766310 PMCID: PMC11099785 DOI: 10.1002/ece3.11337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance-to-reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance-to-reef on β diversity variation using generalised linear mixed models and estimated species-specific distance-to-reef effects using a model-based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance-to-reef gradient. The analysis of β-diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance-to-reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale.
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Affiliation(s)
- Mélissa Jaquier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Camille Albouy
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Wilhelmine Bach
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
- CEFE, Univ. Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Eva Maire
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Marco Andrello
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | | | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
| | | | - David Mouillot
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
- Institut Universitaire de FranceParisFrance
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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2
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Andrello M, D'Aloia C, Dalongeville A, Escalante MA, Guerrero J, Perrier C, Torres-Florez JP, Xuereb A, Manel S. Evolving spatial conservation prioritization with intraspecific genetic data. Trends Ecol Evol 2022; 37:553-564. [PMID: 35450706 DOI: 10.1016/j.tree.2022.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.
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Affiliation(s)
- Marco Andrello
- Institute for the study of Anthropic impacts and Sustainability in the marine environment, National Research Council, CNR-IAS, Rome, Italy.
| | - Cassidy D'Aloia
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jimena Guerrero
- Sociedad Científica de Investigación Transdisciplinaria y Especialización (SCITE), Calimaya, México
| | - Charles Perrier
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade, Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Santos, Brazil
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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3
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Mathon L, Marques V, Mouillot D, Albouy C, Andrello M, Baletaud F, Borrero-Pérez GH, Dejean T, Edgar GJ, Grondin J, Guerin PE, Hocdé R, Juhel JB, Kadarusman, Maire E, Mariani G, McLean M, Polanco F. A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding. Proc Biol Sci 2022; 289:20220162. [PMID: 35440210 PMCID: PMC9019517 DOI: 10.1098/rspb.2022.0162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.
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Affiliation(s)
- Laetitia Mathon
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
| | - Virginie Marques
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Institut Universitaire de France, France
| | - Camille Albouy
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Nantes, France
| | - Marco Andrello
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Institute for the study of Anthropic Impacts and Sustainability in the marine environment, National Research Council (CNR-IAS), Rome, Italy
| | - Florian Baletaud
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- SOPRONER, groupe GINGER, 98000 Noumea, New Caledonia, France
| | - Giomar H. Borrero-Pérez
- Programa de Biodiversidad y Ecosistemas Marinos, Museo de Historia Natural Marina de Colombia (MHNMC), Instituto de Investigaciones Marinas y Costeras- INVEMAR, Santa Marta, Colombia
| | | | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Régis Hocdé
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | | | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, KKD BP Sumberdaya Genetik, Konservasi dan Domestikasi, Papua Barat, Indonesia
| | - Eva Maire
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Gael Mariani
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Matthew McLean
- Department of Biology, Dalhousie University, Halifax NSB3H4R2, Canada
| | - Andrea Polanco F.
- Programa de Biodiversidad y Ecosistemas Marinos, Museo de Historia Natural Marina de Colombia (MHNMC), Instituto de Investigaciones Marinas y Costeras- INVEMAR, Santa Marta, Colombia
| | - Laurent Pouyaud
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Rick D. Stuart-Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Hagi Yulia Sugeha
- Research Center for Oceanography, National Research and Innovation Agency, Jl. Pasir Putih 1, Ancol Timur, Jakarta Utara 14430, Indonesia
| | | | - Laurent Vigliola
- ENTROPIE, Institut de Recherche pour le Développement (IRD), Univ. Réunion, UNC, CNRS, Q1 IFREMER, Nouméa, New Caledonia, France
| | - Indra B. Vimono
- Research Center for Oceanography, National Research and Innovation Agency, Jl. Pasir Putih 1, Ancol Timur, Jakarta Utara 14430, Indonesia
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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Andrello M, Darling ES, Wenger A, Suárez‐Castro AF, Gelfand S, Ahmadia GN. A global map of human pressures on tropical coral reefs. Conserv Lett 2021. [DOI: 10.1111/conl.12858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment National Research Council, CNR‐IAS Rome Italy
- MARBEC Université de Montpellier Montpellier France
| | - Emily S. Darling
- Wildlife Conservation Society, Marine Program Bronx New York USA
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
| | - Amelia Wenger
- Wildlife Conservation Society, Marine Program Bronx New York USA
- School of Earth and Environmental Sciences University of Queensland St. Lucia Queensland Australia
- Centre for Biodiversity and Conservation Science University of Queensland St. Lucia Queensland Australia
| | - Andrés F. Suárez‐Castro
- Centre for Biodiversity and Conservation Science University of Queensland St. Lucia Queensland Australia
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt Distrito Capital Bogotá Colombia
| | | | - Gabby N. Ahmadia
- Oceans Conservation World Wildlife Fund District of Colombia Washington USA
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5
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Stauffer S, Jucker M, Keggin T, Marques V, Andrello M, Bessudo S, Cheutin M, Borrero‐Pérez GH, Richards E, Dejean T, Hocdé R, Juhel J, Ladino F, Letessier TB, Loiseau N, Maire E, Mouillot D, Mutis Martinezguerra M, Manel S, Polanco Fernández A, Valentini A, Velez L, Albouy C, Pellissier L, Waldock C. How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? Ecol Evol 2021; 11:14630-14643. [PMID: 34765130 PMCID: PMC8571620 DOI: 10.1002/ece3.8150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
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Affiliation(s)
- Salomé Stauffer
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Meret Jucker
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Thomas Keggin
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine EnvironmentNational Research CouncilRomeItaly
| | - Sandra Bessudo
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | | | - Giomar Helena Borrero‐Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Eilísh Richards
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Régis Hocdé
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | | | - Felipe Ladino
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | - Tom B. Letessier
- Institute of ZoologyZoological Society of LondonLondonUK
- Marine Futures LabUniversity of Western AustraliaCrawleyWAAustralia
| | | | - Eva Maire
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Stéphanie Manel
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Andrea Polanco Fernández
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | | | - Laure Velez
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | - Camille Albouy
- IFREMERunité Écologie et Modèles pour l’HalieutiqueNantesFrance
| | - Loïc Pellissier
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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7
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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. Conserv Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Andrello M, Noirot C, Débarre F, Manel S. MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size. Mol Ecol Resour 2020; 21:596-608. [PMID: 33030758 DOI: 10.1111/1755-0998.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/05/2020] [Accepted: 09/23/2020] [Indexed: 11/27/2022]
Abstract
Multilocus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multilocus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements. These limitations increase with the number of simulated individuals. We developed a genetic simulator, MetaPopGen 2.0, to model multilocus population genetic processes in subdivided populations of arbitrarily large size. It allows for spatial and temporal variation in demographic parameters, age structure, adult and propagule dispersal, variable mutation rates and selection on survival and fecundity. We developed MetaPopGen 2.0 in the R environment to facilitate its use by non-modeler ecologists and evolutionary biologists. We illustrate the capabilities of MetaPopGen 2.0 for studying adaptation to water salinity in the striped red mullet Mullus surmuletus.
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Affiliation(s)
- Marco Andrello
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Christelle Noirot
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Florence Débarre
- Sorbonne Université, CNRS, INRAE, IRD, UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), UMR 7618, Paris, France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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Andrello M, de Villemereuil P, Carboni M, Busson D, Fortin MJ, Gaggiotti OE, Till-Bottraud I. Accounting for stochasticity in demographic compensation along the elevational range of an alpine plant. Ecol Lett 2020; 23:870-880. [PMID: 32216007 DOI: 10.1111/ele.13488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/02/2019] [Accepted: 02/17/2020] [Indexed: 12/17/2022]
Abstract
Demographic compensation arises when vital rates change in opposite directions across populations, buffering the variation in population growth rates, and is a mechanism often invoked to explain the stability of species geographic ranges. However, studies on demographic compensation have disregarded the effects of temporal variation in vital rates and their temporal correlations, despite theoretical evidence that stochastic dynamics can affect population persistence in temporally varying environments. We carried out a seven-year-long demographic study on the perennial plant Arabis alpina (L.) across six populations encompassing most of its elevational range. We discovered demographic compensation in the form of negative correlations between the means of plant vital rates, but also between their temporal coefficients of variation, correlations and elasticities. Even if their contribution to demographic compensation was small, this highlights a previously overlooked, but potentially important, role of stochastic processes in stabilising population dynamics at range margins.
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Affiliation(s)
- Marco Andrello
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études PSL, MNHN, CNRS, Sorbonne Université, Université des Antilles, Paris, France
| | - Marta Carboni
- Dipartimento di Scienze, Università Degli Studi di Roma Tre, viale Marconi 446, 00146, Roma, Italy
| | - Delphine Busson
- Univ Grenoble Alpes, CNRS, Univ Savoie Mont Blanc, LECA, Laboratoire d'Écologie Alpine, Grenoble, France
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Ontario, Canada
| | | | - Irène Till-Bottraud
- Université Clermont Auvergne, CNRS, GEOLAB, F-63000, Clermont-Ferrand, France
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Xuereb A, D’Aloia CC, Daigle RM, Andrello M, Dalongeville A, Manel S, Mouillot D, Guichard F, Côté IM, Curtis JMR, Bernatchez L, Fortin MJ. Marine Conservation and Marine Protected Areas. Population Genomics 2019. [DOI: 10.1007/13836_2018_63] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Dalongeville A, Andrello M, Mouillot D, Lobreaux S, Fortin M, Lasram F, Belmaker J, Rocklin D, Manel S. Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale. Evol Appl 2018; 11:1437-1447. [PMID: 30151051 PMCID: PMC6099820 DOI: 10.1111/eva.12638] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db-MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000 km), while larval dispersal was the major predictor at smaller spatial scale (<1,000 km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping-stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.
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Affiliation(s)
- Alicia Dalongeville
- EPHE, Biogéographie et Ecologie des VertébrésCEFE, UMR 5175, CNRSPSL Research UniversityUniversité de MontpellierUniversité Paul‐Valéry MontpellierMontpellierFrance
- MARBEC, UMR 9190, CNRS, IRDUniversité Montpellier – IfremerMontpellierFrance
| | - Marco Andrello
- EPHE, Biogéographie et Ecologie des VertébrésCEFE, UMR 5175, CNRSPSL Research UniversityUniversité de MontpellierUniversité Paul‐Valéry MontpellierMontpellierFrance
| | - David Mouillot
- MARBEC, UMR 9190, CNRS, IRDUniversité Montpellier – IfremerMontpellierFrance
| | - Stéphane Lobreaux
- Laboratoire d'Ecologie AlpineUMR‐CNRS 5553Université Joseph FourierGrenobleFrance
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Frida Lasram
- Laboratoire d'Océanologie et de GéosciencesUMR 8187 LOG CNRSUniversité du Littoral Côte d'OpaleWimereuxFrance
| | - Jonathan Belmaker
- Department of Zoology and the Steinhardt Museum of Natural HistoryTel Aviv UniversityTel AvivIsrael
| | - Delphine Rocklin
- Faculty of Humanities and Social SciencesDepartment of GeographyMemorial University of NewfoundlandSt John'sNLCanada
| | - Stéphanie Manel
- EPHE, Biogéographie et Ecologie des VertébrésCEFE, UMR 5175, CNRSPSL Research UniversityUniversité de MontpellierUniversité Paul‐Valéry MontpellierMontpellierFrance
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12
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Guerrero J, Andrello M, Burgarella C, Manel S. Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics. New Phytol 2018; 219:378-390. [PMID: 29696659 DOI: 10.1111/nph.15171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/14/2018] [Indexed: 05/22/2023]
Abstract
Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.
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Affiliation(s)
- Jimena Guerrero
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Marco Andrello
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Concetta Burgarella
- UMR DIADE Institut de Recherche pour le Developpement (IRD), Centre de Montpellier, BP 64501, Montpellier Cedex 5, France
- UMR AGAP Centre de Coopération International en Recherche Agronomique pour le Développement (CIRAD), Avenue Agropolis, 34398, Montpellier, France
| | - Stephanie Manel
- CEFE-CNRS, Centre D'Ecologie Fonctionelle et Evolutive, Route de Mende, 34090, Montpellier, France
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Manel S, Andrello M, Henry K, Verdelet D, Darracq A, Guerin PE, Desprez B, Devaux P. Predicting genotype environmental range from genome-environment associations. Mol Ecol 2018; 27:2823-2833. [DOI: 10.1111/mec.14723] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/12/2018] [Accepted: 05/02/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Stéphanie Manel
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
| | - Marco Andrello
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
| | | | | | | | - Pierre-Edouard Guerin
- EPHE; PSL Research University; CNRS, UM, SupAgro, IND, INRA; UMR 5175 CEFE; Montpellier France
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Andrello M, Devaux C, Quétier F, Till-Bottraud I. Paying for conservation: A bioeconomic analysis of the effects of land management options on the viability of an endangered species,Eryngium alpinum. J Appl Ecol 2018. [DOI: 10.1111/1365-2664.13112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Andrello
- CEFE; CNRS; Université de Montpellier; Université Paul Valéry Montpellier 3; EPHE; PSL Research University; IRD; Montpellier France
| | - Caroline Devaux
- Laboratoire d’Écologie Alpine; Université Grenoble Alpes; CNRS; LECA; Grenoble France
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15
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Magris RA, Andrello M, Pressey RL, Mouillot D, Dalongeville A, Jacobi MN, Manel S. Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning. Conserv Lett 2018. [DOI: 10.1111/conl.12439] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Rafael A. Magris
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
- Chico Mendes Institute for Biodiversity Conservation; Ministry of Environment; Brasilia DF 70.670-350 Brazil
- School of Environmental Studies; University of Victoria; Victoria BC V8W 2Y2 Canada
| | - Marco Andrello
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier; Université Paul-Valéry Montpellier, EPHE, Biogeographie et Ecologie des Vertébrés; Montpellier France
| | - Robert L. Pressey
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
| | - David Mouillot
- Australian Research Council Centre of Excellence for Coral Reef Studies; James Cook University; Townsville QLD 4811 Australia
- MARBEC UMR 9190, CNRS - IRD; Universite Montpellier - Ifremer; 34095 Montpellier France
| | - Alicia Dalongeville
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier; Université Paul-Valéry Montpellier, EPHE, Biogeographie et Ecologie des Vertébrés; Montpellier France
- MARBEC UMR 9190, CNRS - IRD; Universite Montpellier - Ifremer; 34095 Montpellier France
| | - Martin N. Jacobi
- Complex Systems Group, Department of Energy and Environment; Chalmers University of Technology; SE-412 96 Gothenburg Sweden
| | - Stéphanie Manel
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier; Université Paul-Valéry Montpellier, EPHE, Biogeographie et Ecologie des Vertébrés; Montpellier France
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Andrello M, Henry K, Devaux P, Verdelet D, Desprez B, Manel S. Insights into the genetic relationships among plants of Beta section Beta using SNP markers. Theor Appl Genet 2017; 130:1857-1866. [PMID: 28589246 DOI: 10.1007/s00122-017-2929-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/30/2017] [Indexed: 05/23/2023]
Abstract
Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.
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Affiliation(s)
- Marco Andrello
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Karine Henry
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Pierre Devaux
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | | | - Bruno Desprez
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Stéphanie Manel
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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Andrello M, Guilhaumon F, Albouy C, Parravicini V, Scholtens J, Verley P, Barange M, Sumaila UR, Manel S, Mouillot D. Global mismatch between fishing dependency and larval supply from marine reserves. Nat Commun 2017; 8:16039. [PMID: 28691710 PMCID: PMC5508853 DOI: 10.1038/ncomms16039] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems.
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Affiliation(s)
- Marco Andrello
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293 Montpellier, France
| | - François Guilhaumon
- UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Université de Montpellier, 34095 Montpellier, France
| | - Camille Albouy
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland.,IFREMER, Unité Ecologie et Modèles pour l'Halieutique, 44300 Nantes Cedex 3, France
| | - Valeriano Parravicini
- CRIOBE, USR 3278 CNRS-EPHE-UPVD, Labex 'Corail', University of Perpignan, 66860 Perpignan, France
| | - Joeri Scholtens
- MARE Centre for Maritime Research, Amsterdam Institute for Social Science Research, University of Amsterdam, Plantage Muidergracht 14, 1018 Amsterdam, The Netherlands
| | - Philippe Verley
- IRD, UMR AMAP, TA A51/PS2, Montpellier, 05 34398 Cedex, France
| | - Manuel Barange
- Plymouth Marine Laboratory, Prospect Place, PL1 3DH Plymouth, UK.,Food and Agriculture Organization of the UN, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - U Rashid Sumaila
- Fisheries Economics Research Unit, Institute for Oceans and Fisheries &Liu Institute for Global Studies, the University of British Columbia, Vancouver, Canada V6T 1Z
| | - Stéphanie Manel
- EPHE, PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, Biogéographie et Ecologie des Vertébrés, 1919 route de Mende, 34293 Montpellier, France
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-IFREMER-UM, Université de Montpellier, 34095 Montpellier, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811 Queens Land, Australia
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Andrello M, Henry K, Devaux P, Desprez B, Manel S. Taxonomic, spatial and adaptive genetic variation of Beta section Beta. Theor Appl Genet 2016; 129:257-271. [PMID: 26526552 DOI: 10.1007/s00122-015-2625-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/17/2015] [Indexed: 06/05/2023]
Abstract
KEY MESSAGE The genetic variation of Beta section Beta is structured into four taxonomic and spatial clusters. There are significant associations between molecular markers and environmental variables. ABSTRACT We investigated the genetic diversity of Beta section Beta, which includes the wild and cultivated relatives of the sugar beet. The taxa included in the study were: Beta vulgaris subsp. maritima, B. vulgaris subsp. adanensis, B. macrocarpa, B. patula and B. vulgaris subsp. vulgaris (garden beet, leaf beet and swiss chards). We collected 1264 accessions originating from the entire distribution area of these taxa and genotyped them for 4436 DArT markers (DArTs). We showed that the genetic variation of these accessions is structured into four taxonomic and spatial clusters: (1) samples of Beta macrocarpa, (2) samples of Beta vulgaris subsp. adanensis, (3) Mediterranean and Asian samples and (4) Atlantic and Northern European samples. These last two clusters were mainly composed of samples of Beta vulgaris subsp. maritima. We investigated in deeper detail the genetic structure of B. vulgaris subsp. maritima, which constituted the majority (80%) of the wild samples. This subspecies exhibited a clinal genetic variation from South-East to North-West. We detected some markers significantly associated to environmental variables in B. vulgaris subsp. maritima. These associations are interpreted as results of natural selection. The variable most often involved in the associations was annual mean temperature. Therefore, these markers can be useful for the development of frost-tolerant winter beets and drought-tolerant rain-fed beets.
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Affiliation(s)
- Marco Andrello
- Laboratoire Biogeographie et écologie des vertébrés, CEFE UMR 5175, CNRS - Universite de Montpellier - Universite Paul-Valery Montpellier - EPHE, 34293, Montpellier Cedex 5, France.
| | - Karine Henry
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Pierre Devaux
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Bruno Desprez
- Florimond Desprez, 59242, Cappelle En Pévèle, France
| | - Stéphanie Manel
- Laboratoire Biogeographie et écologie des vertébrés, CEFE UMR 5175, CNRS - Universite de Montpellier - Universite Paul-Valery Montpellier - EPHE, 34293, Montpellier Cedex 5, France
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Andrello M, Manel S. MetaPopGen: anrpackage to simulate population genetics in large size metapopulations. Mol Ecol Resour 2015; 15:1153-62. [DOI: 10.1111/1755-0998.12371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/27/2014] [Accepted: 01/01/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Andrello
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Stéphanie Manel
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
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Andrello M, Mouillot D, Somot S, Thuiller W, Manel S. Additive effects of climate change on connectivity between marine protected areas and larval supply to fished areas. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12250] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Marco Andrello
- IRD; Aix Marseille Université; LPED UMR 151 Marseille France
- LECA; Univ. Grenoble Alpes; F-38000 Grenoble France
- CNRS; LECA; F-38000 Grenoble France
| | - David Mouillot
- UMR 5119 - Écologie des Systèmes marins côtiers; Université Montpellier 2; cc 093 Place E. Bataillon 34095 Montpellier Cedex 5 France
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
| | - Samuel Somot
- Météo-France; Centre National de Recherches Météorologiques CNRM-GAME; 42 Avenue Gaspard Coriolis 31057 Toulouse Cedex France
| | - Wilfried Thuiller
- LECA; Univ. Grenoble Alpes; F-38000 Grenoble France
- CNRS; LECA; F-38000 Grenoble France
| | - Stéphanie Manel
- IRD; Aix Marseille Université; LPED UMR 151 Marseille France
- Centre de coopération internationale en recherche agronomique pour le développement; UMR AMAP; Montpellier France
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Andrello M, Mouillot D, Beuvier J, Albouy C, Thuiller W, Manel S. Low connectivity between Mediterranean marine protected areas: a biophysical modeling approach for the dusky grouper Epinephelus marginatus. PLoS One 2013; 8:e68564. [PMID: 23861917 PMCID: PMC3704643 DOI: 10.1371/journal.pone.0068564] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 05/30/2013] [Indexed: 11/24/2022] Open
Abstract
Marine protected areas (MPAs) are major tools to protect biodiversity and sustain fisheries. For species with a sedentary adult phase and a dispersive larval phase, the effectiveness of MPA networks for population persistence depends on connectivity through larval dispersal. However, connectivity patterns between MPAs remain largely unknown at large spatial scales. Here, we used a biophysical model to evaluate connectivity between MPAs in the Mediterranean Sea, a region of extremely rich biodiversity that is currently protected by a system of approximately a hundred MPAs. The model was parameterized according to the dispersal capacity of the dusky grouper Epinephelus marginatus, an archetypal conservation-dependent species, with high economic importance and emblematic in the Mediterranean. Using various connectivity metrics and graph theory, we showed that Mediterranean MPAs are far from constituting a true, well-connected network. On average, each MPA was directly connected to four others and MPAs were clustered into several groups. Two MPAs (one in the Balearic Islands and one in Sardinia) emerged as crucial nodes for ensuring multi-generational connectivity. The high heterogeneity of MPA distribution, with low density in the South-Eastern Mediterranean, coupled with a mean dispersal distance of 120 km, leaves about 20% of the continental shelf without any larval supply. This low connectivity, here demonstrated for a major Mediterranean species, poses new challenges for the creation of a future Mediterranean network of well-connected MPAs providing recruitment to the whole continental shelf. This issue is even more critical given that the expected reduction of pelagic larval duration following sea temperature rise will likely decrease connectivity even more.
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Affiliation(s)
- Marco Andrello
- UMR 151 - Laboratoire Population Environnement et Développement, Institut de Recherche pour le Développement - Université Aix-Marseille, Marseille, France.
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Andrello M, Nicolè F, Till-Bottraud I, Gaggiotti OE. Effect of stage-specific vital rates on population growth rates and effective population sizes in an endangered iteroparous plant. Conserv Biol 2012; 26:208-217. [PMID: 22268810 DOI: 10.1111/j.1523-1739.2011.01815.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Effective population size (N(e)) determines the strength of genetic drift and can influence the level of genetic diversity a population can maintain. Assessing how changes in demographic rates associated with environmental variables and management actions affect N(e) thus can be crucial to the conservation of endangered species. Calculation of N(e) through demographic models makes it possible to use elasticity analyses to study this issue. The elasticity of N(e) to a given vital rate is the proportional change in N(e) associated with a proportional increase in that vital rate. In addition, demographic models can be used to study N(e) and population growth rate (λ) simultaneously. Simultaneous examination is important because some vital rates differ diametrically in their associations with λ and N(e). For example, in some cases increasing these vital rates increases λ and decreases N(e). We used elasticity analysis to study the effect of stage-specific survival and flowering rates on N(e), annual effective population size (N(a)), and λ in seven populations of the endangered plant Austrian dragonhead (Dracocephalum austriacum). In populations with λ ≥ 1, the elasticities of N(e) and N(a) were similar to those of λ. Survival rates of adults were associated with greater elasticities than survival rates of juveniles, flowering rates, or fecundity. In populations with λ < 1, N(e) and N(a) exhibited greater elasticities to juvenile than to adult vital rates. These patterns are similar to those observed in other species with similar life histories. We did not observe contrasting effects of any vital rate on λ and N(e); thus, management actions that increase the λ of populations of Austrian dragonhead will not increase genetic drift. Our results show that elasticity analyses of N(e) and N(a) can complement elasticity analysis of λ. Moreover, such analyses do not require more data than standard matrix models of population dynamics.
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Affiliation(s)
- Marco Andrello
- Université de Grenoble 1, CNRS UMR 5553, LECA, BP53, F-38041 Grenoble Cedex 09, France.
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Andrello M, Bevacqua D, Maes GE, De Leo GA. An integrated genetic-demographic model to unravel the origin of genetic structure in European eel (Anguilla anguilla L.). Evol Appl 2010; 4:517-33. [PMID: 25568002 PMCID: PMC3352426 DOI: 10.1111/j.1752-4571.2010.00167.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 09/27/2010] [Indexed: 11/30/2022] Open
Abstract
The evolutionary enlightened management of species with complex life cycles often requires the development of mathematical models integrating demographic and genetic data. The genetic structure of the endangered European eel (Anguilla anguilla L.) has been thoroughly analyzed in several studies in the past years. However, the interpretation of the key demographic and biologic processes that determine the observed spatio-temporal genetic structure has been very challenging owing to the complex life cycle of this catadromous species. Here, we present the first integrated demographic-genetic model applied to the European eel that explicitly accounts for different levels of larval and adult mixing during oceanic migrations and allows us to explore alternative hypotheses on genetic differentiation. Our analyses show that (i) very low levels of mixing occurring during larval dispersal or adult migration are sufficient to erase entirely any genetic differences among sub-populations; (ii) small-scale temporal differentiation in recruitment can arise if the spawning stock is subdivided in distinct reproductive groups; and (iii) the geographic differentiation component might be overestimated if a limited number of temporal recruits are analyzed. Our study can inspire the scientific debate on the interpretation of genetic structure in other species characterized by complex life cycle and long-range migrations.
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Affiliation(s)
- Marco Andrello
- Dipartimento di Scienze Ambientali, Università degli Studi di Parma Parma, Italy
| | - Daniele Bevacqua
- Dipartimento di Scienze Ambientali, Università degli Studi di Parma Parma, Italy
| | - Gregory E Maes
- Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven Leuven, Belgium
| | - Giulio A De Leo
- Dipartimento di Scienze Ambientali, Università degli Studi di Parma Parma, Italy
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