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Miller AD, Coleman MA, Clark J, Cook R, Naga Z, Doblin MA, Hoffmann AA, Sherman CDH, Bellgrove A. Local thermal adaptation and limited gene flow constrain future climate responses of a marine ecosystem engineer. Evol Appl 2020; 13:918-934. [PMID: 32431743 PMCID: PMC7232764 DOI: 10.1111/eva.12909] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/13/2019] [Accepted: 12/09/2019] [Indexed: 01/02/2023] Open
Abstract
Rising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future trajectories under scenarios of climate change. We test the extent to which local differentiation in thermal tolerance is influenced by gene flow and local adaptation using a widely distributed intertidal seaweed (Hormosira banksii) from temperate Australia. Population surveys across ~2,000 km of the species range revealed strong genetic structuring at regional and local scales (global F ST = 0.243) reflecting extremely limited gene flow, while common garden experiments (14-day exposures to 15, 18, 21°C) revealed strong site differences in early development and mortality in response to elevated temperature. Embryos from many sites spanning a longitudinal thermal gradient showed suppressed development and increased mortality to elevated water temperatures, but populations originating from warmer and more variable thermal environments tended to be less susceptible to warming. Notably, there was significant local-scale variation in the thermal responses of embryos within regions which was corroborated by the finding of small-scale genetic differences. We expect the observed genetic and phenotypic differentiation to lead to uneven responses to warming sea surface temperatures in this important marine foundation species. The study highlights the challenges of predicting species responses to thermal stress and the importance of management strategies that incorporate evolutionary potential for "climate-proofing" marine ecosystems.
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Affiliation(s)
- Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Jennifer Clark
- Climate Change ClusterUniversity of Technology SydneySydneyNSWAustralia
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
| | - Rachael Cook
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVic.Australia
| | - Zuraya Naga
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVic.Australia
| | | | - Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
| | - Craig D. H. Sherman
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | - Alecia Bellgrove
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVic.Australia
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Li JJ, Hu ZM, Sun ZM, Yao JT, Liu FL, Fresia P, Duan DL. Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China. BMC Evol Biol 2017; 17:246. [PMID: 29216823 PMCID: PMC5721624 DOI: 10.1186/s12862-017-1089-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long-term survival in isolated marginal seas of the China coast during the late Pleistocene ice ages is widely believed to be an important historical factor contributing to population genetic structure in coastal marine species. Whether or not contemporary factors (e.g. long-distance dispersal via coastal currents) continue to shape diversity gradients in marine organisms with high dispersal capability remains poorly understood. Our aim was to explore how historical and contemporary factors influenced the genetic diversity and distribution of the brown alga Sargassum thunbergii, which can drift on surface water, leading to long-distance dispersal. RESULTS We used 11 microsatellites and the plastid RuBisCo spacer to evaluate the genetic diversity of 22 Sargassum thunbergii populations sampled along the China coast. Population structure and differentiation was inferred based on genotype clustering and pairwise F ST and allele-frequency analyses. Integrated genetic analyses revealed two genetic clusters in S. thunbergii that dominated in the Yellow-Bohai Sea (YBS) and East China Sea (ECS) respectively. Higher levels of genetic diversity and variation were detected among populations in the YBS than in the ECS. Bayesian coalescent theory was used to estimate contemporary and historical gene flow. High levels of contemporary gene flow were detected from the YBS (north) to the ECS (south), whereas low levels of historical gene flow occurred between the two regions. CONCLUSIONS Our results suggest that the deep genetic divergence in S. thunbergii along the China coast may result from long-term geographic isolation during glacial periods. The dispersal of S. thunbergii driven by coastal currents may facilitate the admixture between southern and northern regimes. Our findings exemplify how both historical and contemporary forces are needed to understand phylogeographical patterns in coastal marine species with long-distance dispersal.
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Affiliation(s)
- Jing-Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098 China
| | - Zi-Min Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| | - Zhong-Min Sun
- Laboratory of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
| | - Jian-Ting Yao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
| | - Fu-Li Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 China
| | - Pablo Fresia
- Unidad de Bioinform atica, Institut Pasteur de Montevideo, Mataojo, 2020 Montevideo, Uruguay
| | - De-Lin Duan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071 China
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Avia K, Coelho SM, Montecinos GJ, Cormier A, Lerck F, Mauger S, Faugeron S, Valero M, Cock JM, Boudry P. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus. Sci Rep 2017; 7:43241. [PMID: 28256542 PMCID: PMC5335252 DOI: 10.1038/srep43241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/20/2017] [Indexed: 02/06/2023] Open
Abstract
Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species.
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Affiliation(s)
- Komlan Avia
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Susana M. Coelho
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Gabriel J. Montecinos
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Alexandre Cormier
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Fiona Lerck
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Stéphane Mauger
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Sylvain Faugeron
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Myriam Valero
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - J. Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l’Environnement Marin (UMR 6539 LEMAR, UBO, CNRS, IRD, Ifremer), Centre Bretagne – ZI de la Pointe du Diable, CS 10070, 29280 Plouzané, France
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4
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Hsu TH, Takata K, Onozato H, Gwo JC. Causes of the drastic loss of genetic variation in the Critically Endangered Formosa landlocked salmon of Taiwan. ENDANGER SPECIES RES 2015. [DOI: 10.3354/esr00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata. Gene 2014; 542:8-15. [DOI: 10.1016/j.gene.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 12/20/2013] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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Mosca E, González-Martínez SC, Neale DB. Environmental versus geographical determinants of genetic structure in two subalpine conifers. THE NEW PHYTOLOGIST 2014; 201:180-192. [PMID: 24102203 DOI: 10.1111/nph.12476] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/30/2013] [Indexed: 06/02/2023]
Abstract
Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation.
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Affiliation(s)
- Elena Mosca
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
| | | | - David B Neale
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, S. Michele all'Adige, 38010, Italy
- Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA
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Assis J, Castilho Coelho N, Alberto F, Valero M, Raimondi P, Reed D, Serrão EA. High and distinct range-edge genetic diversity despite local bottlenecks. PLoS One 2013; 8:e68646. [PMID: 23967038 PMCID: PMC3744244 DOI: 10.1371/journal.pone.0068646] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhiza polyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.
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Affiliation(s)
- Jorge Assis
- Centro de Ciências do Mar do Algarve, CIMAR-Laboratório Associado, University of Algarve, Campus de Gambelas, Faro, Portugal.
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8
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Thomas L, Bell JJ. Testing the consistency of connectivity patterns for a widely dispersing marine species. Heredity (Edinb) 2013; 111:345-54. [PMID: 23820580 DOI: 10.1038/hdy.2013.58] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/03/2013] [Accepted: 05/20/2013] [Indexed: 11/09/2022] Open
Abstract
Connectivity is widely recognized as an important component in developing effective management and conservation strategies. Although managers are generally most interested in demographic, rather than genetic connectivity, new analytic approaches are able to provide estimates of both demographic and genetic connectivity measures from genetic data. Combining such genetic data with mathematical models represents a powerful approach for accurately determining patterns of population connectivity. Here, we use microsatellite markers to investigate the genetic population structure of the New Zealand Rock Lobster, Jasus edwardsii, which has one of the longest known larval durations of all marine species (>2 years), a very large geographic range (>5500 km), and has been the subject of extensive dispersal modeling. Despite earlier mitochondrial DNA studies finding homogeneous genetic structure, the mathematical model suggests that there are source-sink dynamics for this species. We found evidence of genetic structure in J. edwardsii populations with three distinct genetic groups across New Zealand and a further Australian group; these groups and patterns of gene flow were generally congruent with the earlier mathematical model. Of particular interest was the consistent identification of a self-recruiting population/region from both modeling and genetic approaches. Although there is the potential for selection and harvesting to influence the patterns we observed, we believe oceanographic processes are most likely responsible for the genetic structure observed in J. edwardsii. Our results, using a species at the extreme end of the dispersal spectrum, demonstrate that source-sink population dynamics may still exist for such species.
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Affiliation(s)
- L Thomas
- 1] School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand [2] The Oceans Institute, School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
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9
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Jueterbock A, Tyberghein L, Verbruggen H, Coyer JA, Olsen JL, Hoarau G. Climate change impact on seaweed meadow distribution in the North Atlantic rocky intertidal. Ecol Evol 2013; 3:1356-73. [PMID: 23762521 PMCID: PMC3678489 DOI: 10.1002/ece3.541] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/22/2013] [Accepted: 03/04/2013] [Indexed: 01/14/2023] Open
Abstract
The North-Atlantic has warmed faster than all other ocean basins and climate change scenarios predict sea surface temperature isotherms to shift up to 600 km northwards by the end of the 21st century. The pole-ward shift has already begun for many temperate seaweed species that are important intertidal foundation species. We asked the question: Where will climate change have the greatest impact on three foundational, macroalgal species that occur along North-Atlantic shores: Fucus serratus, Fucus vesiculosus, and Ascophyllum nodosum? To predict distributional changes of these key species under three IPCC (Intergovernmental Panel on Climate Change) climate change scenarios (A2, A1B, and B1) over the coming two centuries, we generated Ecological Niche Models with the program MAXENT. Model predictions suggest that these three species will shift northwards as an assemblage or "unit" and that phytogeographic changes will be most pronounced in the southern Arctic and the southern temperate provinces. Our models predict that Arctic shores in Canada, Greenland, and Spitsbergen will become suitable for all three species by 2100. Shores south of 45° North will become unsuitable for at least two of the three focal species on both the Northwest- and Northeast-Atlantic coasts by 2200. If these foundational species are unable to adapt to the rising temperatures, they will lose their centers of genetic diversity and their loss will trigger an unpredictable shift in the North-Atlantic intertidal ecosystem.
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Affiliation(s)
- Alexander Jueterbock
- Faculty of Biosciences and Aquaculture, University of Nordland 8049, Bodø, Norway
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10
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Riquet F, Daguin‐Thiébaut C, Ballenghien M, Bierne N, Viard F. Contrasting patterns of genome‐wide polymorphism in the native and invasive range of the marine molluscCrepidula fornicata. Mol Ecol 2013; 22:1003-18. [PMID: 23286428 DOI: 10.1111/mec.12161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/15/2012] [Accepted: 10/29/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Florentine Riquet
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Claire Daguin‐Thiébaut
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Marion Ballenghien
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution Laboratory Phylogénie et Evolution moléculaire UMR 5554 Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Nicolas Bierne
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution UMR 5554 Station Méditerranéenne de l'Environnement Littoral, 2 rue des Chantiers 34200 Sète France
| | - Frédérique Viard
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
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11
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Coelho SM, Simon N, Ahmed S, Cock JM, Partensky F. Ecological and evolutionary genomics of marine photosynthetic organisms. Mol Ecol 2012; 22:867-907. [PMID: 22989289 DOI: 10.1111/mec.12000] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/10/2012] [Accepted: 07/15/2012] [Indexed: 01/05/2023]
Abstract
Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing (NGS) technologies. Building on information generated by NGS-based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms (MPOs) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPOs. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPOs and illustrate how their genomes are yielding information on the specific features of these organisms.
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Affiliation(s)
- Susana M Coelho
- UPMC-Université Paris 06, Station Biologique de Roscoff, Roscoff, France.
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12
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Diekmann OE, Serrão EA. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina. Mol Ecol 2012; 21:1647-57. [PMID: 22369278 DOI: 10.1111/j.1365-294x.2012.05500.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value.
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Affiliation(s)
- Onno E Diekmann
- CCMAR, CIMAR-Laboratório Associado, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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In silico mining and characterization of 12 EST-SSRs for the invasive slipper limpet Crepidula fornicata. Mar Genomics 2011; 4:291-5. [PMID: 22118642 DOI: 10.1016/j.margen.2011.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/29/2011] [Accepted: 08/03/2011] [Indexed: 11/23/2022]
Abstract
In silico mining of an expressed sequence tags (ESTs) library was found to be efficient at isolating simple sequence repeats (SSRs) loci in the non-indigenous marine mollusc Crepidula fornicata. Twelve SSR loci were developed for routine genotyping. Cross-species amplification to 8 other Crepidula species showed that the 12 loci are highly specific for C. fornicata. Mendelian inheritance was shown for 11 of them (1 being monomorphic in the analyzed offspring array). The genetic diversity for 88 adults was found to be variable across the 12 loci (2-40 alleles, expected heterozygosity between 0.023 and 0.898) with a high overall exclusion probability of 0.99. The degree of genetic polymorphism found here is similar to that shown for 7 anonymous SSRs previously developed and here used on the same samples. This set of 12 specific loci is relevant to perform reliable population and relatedness analyses in Crepidula fornicata.
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Wahl M, Jormalainen V, Eriksson BK, Coyer JA, Molis M, Schubert H, Dethier M, Karez R, Kruse I, Lenz M, Pearson G, Rohde S, Wikström SA, Olsen JL. Stress ecology in fucus: abiotic, biotic and genetic interactions. ADVANCES IN MARINE BIOLOGY 2011; 59:37-105. [PMID: 21724018 DOI: 10.1016/b978-0-12-385536-7.00002-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stress regimes defined as the synchronous or sequential action of abiotic and biotic stresses determine the performance and distribution of species. The natural patterns of stress to which species are more or less well adapted have recently started to shift and alter under the influence of global change. This was the motivation to review our knowledge on the stress ecology of a benthic key player, the macroalgal genus Fucus. We first provide a comprehensive review of the genus as an ecological model including what is currently known about the major lineages of Fucus species with respect to hybridization, ecotypic differentiation and speciation; as well as life history, population structure and geographic distribution. We then review our current understanding of both extrinsic (abiotic/biotic) and intrinsic (genetic) stress(es) on Fucus species and how they interact with each other. It is concluded that (i) interactive stress effects appear to be equally distributed over additive, antagonistic and synergistic categories at the level of single experiments, but are predominantly additive when averaged over all studies in a meta-analysis of 41 experiments; (ii) juvenile and adult responses to stress frequently differ and (iii) several species or particular populations of Fucus may be relatively unaffected by climate change as a consequence of pre-adapted ecotypes that collectively express wide physiological tolerences. Future research on Fucus should (i) include additional species, (ii) include marginal populations as models for responses to environmental stress; (iii) assess a wider range of stress combinations, including their temporal fluctuations; (iv) better differentiate between stress sensitivity of juvenile versus adult stages; (v) include a functional genomic component in order to better integrate Fucus' ecological and evolutionary responses to stress regimes and (vi) utilize a multivariate modelling approach in order to develop and understand interaction networks.
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