A Darwinian Laboratory of Multiple Contact Zones

Trends in Ecology & Evolution, Journal Year: 2020, Volume and Issue: 35(11), P. 1021 - 1036

Published: Sept. 8, 2020

Barriers to gene flow are best studied where divergent populations in contact, and studies of single-taxon hybrid zones have generated important knowledge about the nature reproductive barriers.Marine environments, earlier considered host unstructured species due high connectivity, offer multispecies contact structured by simple physical gradients (e.g., salinity) ideal for comparative divergence speciation.Overlapping possibilities comparison barriers among various taxa, life histories, demographic backgrounds test role species-specific traits formation function barriers.Combining genome scans modelling, barrier regions can be located origin traced. With genetic maps, inversions that affect recombination rate (and hence flow) identified. between result (hybrid) zones. Locations multiple overlap used asking: what mechanisms maintain barriers; is variation involved; do differences history barriers? In a review 23 marine species' over postglacial salinity gradient, many showed steep clines supported selection and/or temporal or spatial segregation. Contacts were primary secondary shaped ancestral sometimes involving inversions. The dispersal potential seemed less shaping clines. Studies will increase our understanding speciation, but we need address taxonomic bias focus more on postzygotic isolation. Contact (see Glossary) laboratories taxa [1.Barton N.H. Hewitt G.M. Analysis zones.Annu. Rev. Ecol. Syst. 1985; 16: 113-148Crossref Scopus (2048) Google Scholar, 2.Hewitt Hybrid zones, natural evolutionary studies.Trends Evol. 1988; 3: 158-167Abstract Full Text PDF PubMed (612) 3.Abbot R.J. et al.Genomics hybridization its consequences.Mol. 2016; 25: 2325-2332Crossref (112) Scholar]. Genome-wide sequencing maps powered identification candidates loci investigations genomic landscape speciation [4.Wolf J.B.W. Ellegren H. Making sense islands differentiation light speciation.Nat. Genet. 2017; 18: 87-100Crossref (212) Divergence usually evolve either situ as different regimes acting side (primary contact) after already accumulated drift [5.Bierne N. al.The coupling hypothesis: why may fail map local adaptation genes.Mol. 2011; 20: 2044-2072Crossref (364) 6.Bierne geography introgression patchy environment thorn ecological speciation.Curr. Zool. 2013; 59: 72-86Crossref (97) 7.Ravinet M. al.Interpreting speciation: road finding flow.J. Biol. 30: 1450-1477Crossref (225) 8.Rougemont Q. Bernatchez L. Atlantic salmon (Salmo salar) across distribution range reconstructed from approximate Bayesian computations.Evolution. 2018; 72: 1261-1277Crossref (41) Scholar] (Box 1). both types central evolution maintenance Scholar,7.Ravinet Scholar,9.Faria R. al.Evolving inversions.Trends 2019; 34: 239-248Abstract (81) For example, roles selection, assortative mating (whether spatial, temporal, behavioural isolation), isolation caused intrinsic incompatibilities extrinsic against hybrids?Box 1Primary Secondary ContactA zone originates one two ways: (i) formed diverged during period prior contact; whereas (ii) when population expands an environmental transition under flow. Genomic patterns resulting hybridisation initially very [7.Ravinet Scholar], such difference haplotype structure. produce pattern characterised successively smaller 'pieces' original background haplotypes with increasing distance [87.Leitwein al.Using information conservation genomics.Trends 35: 245-258Abstract (35) This because repeated backcrossing breaks apart large introgressed pieces material (Figure I, 'young' contact). Primary contrast, emerge common occur sharing origin. (green brown loci/alleles Figure I) likely play key role: ancient adaptive remain while polymorphisms segregate selection. Over time, new (dark blue red I), mutations outside establish contribute barriers. form wherever isolated happen meet. However, neutral selected at first move until they become trapped density trough shift Scholar,5.Bierne shifts. Positions might sometime establishment modelling using nonadmixed can, however, help resolve their Also, components origin; instance, if standing evolved periods [85.Van Belleghem S.M. al.Evolution time frames: singular event fuel contemporary parallel evolution.PLoS 14e1007796Crossref (44) A single generate details involved give indication quantitative importance. Moreover, single-species cannot inform us invariable within life-history traits, traits). contacts same external conditions, allow assessments general importance origin, variation, architectures formation. They also enable investigate how dispersal, generation biology gene-flow barriers, prezygotic mechanisms. Multispecies (sometimes referred 'suture zones') present terrestrial [10.Hewitt Some consequences ice ages, speciation.Biol. J. Linn. Soc. 1996; 58: 247-276Crossref Scholar,11.Swenson N.G. Howard D.J. Clustering phylogeographic North America.Am. Nat. 2005; 166: 581-591Crossref (312) Scholar,12.Johannesson K. André C. Life margin - diversity loss peripheral ecosystem, Baltic Sea.Mol. 2006; 15: 2013-2029Crossref (289) 13.Patarnello T. al.Pillars Hercules: Atlantic–Mediterranean phylogeographical break?.Mol. 2007; 4426-4444Crossref (424) 14.DiBattista J.D. al.When biogeographical provinces collide: reef fishes crossroads Arabian Sea.J. Biogeogr. 2015; 42: 1601-1614Crossref (52) 15.Ding S. al.Characterization region inshore fish, Bostrychus sinensis, East China Sea.Heredity. 120: 51-62Crossref (10) 16.Stanley al.A climate-associated cryptic cline northwest Atlantic.Sci. Adv. 4eaaq0929Crossref (50) 17.El Ayari hidden major biogeographic boundary: wide mosaic divide reveals complex interaction mussels.Heredity. 122: 770-784Crossref (17) environments. Compiling recent data entrance Sea, here highlight questions approach address, support increased speciation. Sea (North-East Atlantic) brackish gradient steepest part Danish Straits 1, Key Figure). Importantly, low imposes strong physiological stress most organisms so this impacts heavily area. After 8000 years ago opening freshwater lake into Atlantic, was subsequently colonised subset living Sea. few these established along entire majority only outer [18.Ojaveer al.Status biodiversity Sea.PLoS One. 2010; 5e12467Crossref (207) Many show plasticity phenotypic [19.Kautsky al.Genotypic Mytilus edulis evaluated through reciprocal transplantations. 1. Growth morphology.Mar. Prog. Ser. 1990; 203-210Crossref 20.Wood H.L. al.Physiological presence isopod Idotea baltica (Pallas) Res. 2014; 85: 255-262Crossref (9) 21.Renborg E. al.Variable tolerance ascidian larvae primarily plastic response parental environment.Evol. 28: 561-572Crossref (21) 22.Johansson D. al.Reciprocal transplants plasticity-first scenario colonisation hyposaline basin macro alga.BMC 1714Crossref (11) Scholar]; addition, early had shown examples [23.Sick Haemoglobin polymorphism fishes.Nature. 1961; 192: 894-896Crossref (93) Scholar,24.Christiansen F.B. Frydenberg O. Geographical four Zoarces viviparus evidence selection.Genetics. 1974; 77: 765-770PubMed We scanned published describing Sea–Baltic retrieved useful species. These represent (15 five invertebrates, macroalgae, microalga) histories (Table exception, recently invaded bay barnacle (Balanus improvisus) [25.Wrange A.L. story hitchhiker: invasive Balanus (Amphibalanus) improvisus Darwin 1854.PLoS 11e0147082Crossref (16) all zone. species, separation population, European flounder (Platichthys spp.) there additional subdivision inside populations. Original descriptions indicated 16 22 roughly overlapped 1), fitting enough (14 species) shows coincides although some slightly shifted towards lower salinities 2). 12 available allowed formal analysis supports stepped segmented ten clam [Limecola (Macoma) balthica] tends linear rather than 1).Table 1Species Available Genetic Data Transect Samples Covering TransitionSpeciesCommon nameDispersal potentiala'High' denotes several week-long pelagic highly mobile adults giving 'Low' short larval (or zygote/spore) stage sessile adults.Genetic databFigure number SNPs not specified.FST zoneOutlier distributionSelection agencyFitted modelcThe change analysed each taxon separately three models, which then compared Akaike criterion (AIC): model, model [84], regression relationships (R package 'segmented' [105]), compatible distance, respectively.Type zoneInferred fromBarrier strength; mechanismdSuggested experimentally confirmed followed '?'. Note other mechanisms, yet investigated, add barriers.RefsGadus morhuaAtlantic codHigh1.2 million0.040Three inversionsSalinity, temperatureToo dataSecondaryPhylogenyStrong; separate spawning times, adaptation[42.Berg P.R. al.Adaptation promotes cod (Gadus morhua L.).Genome 7: 1644-1663Crossref (111) 43.Fairweather al.Range-wide synthesis Transatlantic vicariance cod.Ecol. 8: 12140-12152Crossref (4) 44.Weist P. al.Assessing SNP-markers study mixing cod.PLoS 14e0218127Crossref 45.Nissling A. Westin Salinity requirements successful Belt stock interactions Sea.Mar. 1997; 152: 261-271Crossref (108) 46.Barth J.M.I. al.Genome architecture enables despite connectivity.Mol. 26: 4452-4466Crossref (75) 47.Barth al.Disentangling structural behavioral sea 1394-1411Crossref (37) 48.Kirubakaran T.G. al.Two adjacent migratory stationary ecotypes cod.Mol. 2130-2143Crossref (109) Scholar,69.Andersen al.Haemoglobin oxygen binding properties populations.Proc. Sci. 2009; 276: 833-841Crossref (71) Scholar]Clupea harengusAtlantic herringHigh6 million0.030Haplotype blocks, inversionSalinity, temperatureStepped clinePrimaryDemographyWeak; adaptation?[38.Martinez Barrio basis herring revealed sequencing.Elife. 5e12081Crossref (99) Scholar,56.Pettersson M.E. chromosome-level assembly – detection supergene signals selection.Genome 29: 1919-1928Crossref (38) Scholar,90.Berg F. al.Genetic factors effect growth, vertebrae otolith shape (Clupea harengus).PLoS 13e0190995Crossref (30) Scholar]Platichthys flesusEuropean flounderHigh54720.005Few scatteredSalinity, temperatureSegmented clineSecondaryDemographyWeak; adaptation?[39.Le Moan al.Beyond evolution: colonize gradient.bioRxiv. (Published online June 6, 2019. https://doi.org/10.1101/662569)Google Scholar,73.Hemmer-Hansen al.Adaptive environment: Hsc70 flesus L.).Heredity. 99: 592-600Crossref (130) Scholar]P. flesus/Platichthys solemdaliBaltic flounderLow20510.025SalinityToo dataSecondaryDemographyStrong; habitats, adaptation[51.Momigliano al.Extraordinarily rapid fish.Proc. Natl. Acad. U. 114: 6074-6079Crossref (64) Scholar,52.Momigliano al.Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): Sea.Front. Mar. 5: 225Crossref (22) Scholar]Scophthalmus maximusTurbotHigh33480.012Many scatteredSalinityStepped clinePrimaryDemographyModerate; unknown[31.Momigliano al.Biases process speciation.bioRxiv. 2020; 5, 2020. https://doi.org/10.1101/2020.06.03.128298)Google Scholar]Pleuronectus platessaEuropean plaiceHigh66850.013Two inversionsSalinityToo dataPrimaryDemographyWeak; unknown[39.Le Scholar]Limanda limandaCommon dabHigh34680.008ClusteredSalinityStepped Scholar]Solea soleaCommon soleHigh37140.003Very fewToo dataPrimaryDemographyVery weak; unknown[40.Diopere al.Seascape genetics flatfish levels flow.ICES 75: 675-689Crossref (32) Scholar,41.Le al.Fine scale structure linked sole (Solea solea), fish capacity.bioRxiv. https://doi.org/10.1101/662619)Google Scholar]Ammodytes tobianusSmall sandeelHigh40390.041Salinity, clineStrong; times?[91.Christensen al.Sandeel (Ammodytes marinus) transport individual-based hydrodynamic egg model.Can. Fish. Aquat. 2008; 65: 1498-1511Crossref Scholar,92.Fietz al.Mind gut: insights gut microbial composition keystone species.Microbiome. 682Crossref Scholar]Hyperoplus lanceolatusGreater sandeelHigh43280.039Salinity, times?[92.Fietz Scholar,93.Lynam C.P. al.Spatial trends abundance sandeels Sea: 1950–2005.ICES 70: 540-553Crossref (18) Scholar]Symphodus melopsCorkwing wrasseLow50 1300.120Only spurious outliersStepped clineSecondaryDemographyStrong; trough[49.Mattingsdal al.Demographic history, adaptation, has strongly differentiated corkwing wrasse Northern Europe.Mol. 160-171Crossref Scholar]Labrus bergyltaBallan wrasseLow820.027Stepped clineModerate; trough[50.Seljestad G.W. cleaner break: geographic groups sympatric phenotypes ballan (Labrus bergylta).Ecol. 10: 6120-6135Crossref (6) Scholar]Pomatoschistus minutusSandgobyLow22 1900.020DistributedSalinity, turbidityToo dataSecondaryDemographyModerate; adaptation[94.Larmuseau M.H.D. al.To see seas: rhodopsin sand goby (Pomatoschistus minutus).Mol. 4227-4239Crossref (47) Scholar,95.Leder E.H. al.Postglacial locally adapted gradient.J. 23, https://doi.org/10.1111/jeb.13668)Crossref Scholar]Gasterosterus aculeatusThree-spined sticklebackLow30 0000.015Enriched regionsSalinity, dataPrimaryDemographyModerate; adaptation[67.DeFaveri Merilä Local three-spined stickleback?.J. 27: 290-302Crossref Scholar,96.Guo B. al.Population sticklebacks.BMC 1319Crossref (83) Scholar]Salmo salarAtlantic salmonHigh50340.132Too areas[8.Rougemont Scholar,97.Nilsson al.Matrilinear phylogeography salar L.) Europe colonization area.Mol. 2001; 89-102Crossref (128) Scholar]Ciona intestinalisVase tunicateLow16530.180SalinityVertical (no test)SecondaryDemographyStrong; partly adaptation[53.Dybern B.I. Ciona intestinalis (L.) f. typica special reference waters around southern Scandinavia.Ophelia. 1967; 4: 207-226Crossref (40) Scholar,55.Hudson al.Secondary admixture genotypes amphiatlantic epibenthic invertebrate.Evol. Appl. 13: 600-612Crossref (12) Scholar]Idotea baltica'Isopod'Low33 7740.024SalinityLinear clineWeak; unknown[98.De Wit crustacean herbivore highlights considerations management.Evol. 974-990Crossref (8) Scholar]Balanus improvisusBay barnacleHighmtDNA, microsatellites0.011No outliersNo clineNo barriers[25.Wrange Scholar,99.Wrange al.

Language: Английский

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Speciation in marine environments: Diving under the surface

Journal of Evolutionary Biology, Journal Year: 2021, Volume and Issue: 34(1), P. 4 - 15

Published: Jan. 1, 2021

Abstract Marine environments are inhabited by a broad representation of the tree life, yet our understanding speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing more comprehensive picture requires that we 'dive under surface' studying wider range taxa necessary for speciation. Although evolutionary processes often challenging, recent technological advances different fields, from maritime engineering to genomics, making it increasingly possible study life forms across diverse taxa. Motivated research field, including 14 contributions this issue, highlight discuss six axes think will deepen realm: (a) broader organisms; (b) identify reproductive barriers driving between taxa; (c) understand role genomic architectures underlying isolation; (d) infer history divergence using model‐based approaches; (e) patterns hybridization introgression (f) implement highly interdisciplinary, collaborative programmes. In outlining these goals, hope inspire researchers continue filling critical knowledge gap surrounding origins biodiversity.

Language: Английский

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How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map

Annual Review of Animal Biosciences, Journal Year: 2023, Volume and Issue: 12(1), P. 1 - 20

Published: Oct. 31, 2023

Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most these species are abundant and therefore important ecosystems food security. Here, we present road map how population genomics can promote sustainable fisheries. In species, development reference genomes whole genome sequencing key, because differentiation at neutral loci usually low due to large sizes gene flow. First, baseline allele frequencies representing genetically differentiated populations within must be established. These then used accurately determine composition mixed samples, forming basis demographic analysis inform sustainably set fish quotas. SNP-chip cost-effective method determining identification samples. Finally, describe marker transform stock management.

Language: Английский

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Fine Scale Patterns of Population Structure and Connectivity in Scandinavian Flat Oysters in Scandinavia (Ostrea edulis L.)

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(4)

Published: March 31, 2025

ABSTRACT Stocks of the European flat oyster, Ostrea edulis , have collapsed due to overfishing, habitat destruction, and pathogen outbreaks across most their distribution range. Nonetheless, as a result lower exploitation pressure absence pathogens in northern part range, large remaining wild population can be found relatively high densities Scandinavia, region Northern Europe. However, despite recent studies focusing on oyster structure along coast, little is known about oysters Skagerrak marginal sea how it related neighbouring regions. This study, therefore, aimed investigate with special emphasis Skagerrak. We gathered low‐coverage whole‐genome sequencing data from Sweden, Norway, Denmark, three countries that border Genetic diversity appeared homogeneously distributed over sampled area Skagerrak, while samples collected east coast Denmark location historical farming activity Norwegian West Coast were genetically distinct samples. A genetic barrier analysis indicated barriers gene flow Baltic Sea transition zone west Norway. Overall, our results suggest Swedish coasts form single panmictic seas, potentially allowing for regional management stocks restoration translocations area. composition donor recipient should assessed case‐by‐case basis, effects hatchery practices monitored, biosecurity measures need considered prior any movement stock.

Language: Английский

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Population Genetic Structure of Three‐Spined Sticklebacks in the St. Lawrence: A Gradient of Change

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT Understanding how environmental gradients shape population genetic structure is critical for elucidating evolutionary dynamics in heterogeneous landscapes. The St. Lawrence Estuary, spanning fluvial, middle, and marine zones, presents a steep salinity gradient that serves as an ideal setting to study such question. Three‐spined sticklebacks ( Gasterosteus aculeatus ) thrive across these offering model system investigate the interplay of gene flow natural selection shaping structure. Using whole‐genome resequencing from 12 sites, this aimed resolve fine‐scale diversity differentiation are influenced by flow. By integrating single nucleotide polymorphisms (SNPs) structural variants (SVs), we assessed patterns, examined clinal variation, evaluated relative roles dynamics. Our findings reveal clear between fluvial saltwater populations, with Baie‐Saint‐Paul forming potential third group. Salinity emerged key driver structure, variation allele frequencies suggesting ongoing adaptation along gradient. Demographic modeling indicated history secondary contact recent weak Structural variants, particularly indels, complemented SNP‐based analyses, underscoring their importance detecting These results highlight complex forces biodiversity transitional environments, providing basis exploring local connected populations contributing broader efforts conservation genomics.

Language: Английский

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Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae)

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Jan. 4, 2021

Abstract As a promising novel marine fish model for future research on ecotoxicology as well an animal of human disease, the genome information yellowstripe goby ( Mugilogobius chulae ) remains unknown. Here we report first annotated chromosome-level reference assembly goby. A 20.67-cM sex determination region was discovered chromosome 5 and seven potential sex-determining genes were identified. Based combined transcriptome data, identified three key lipid metabolic pathways high-fat accumulation in liver The changes expression patterns MGLL CPT1 at different development stage liver, expansion ABCA1 gene, innate immune gene TLR23 , TRIM family may help balancing storage hepatocytes steatohepatitis. These results provide insights into understanding molecular mechanisms fishes.

Language: Английский

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The Next Generation Is Here: A Review of Transcriptomic Approaches in Marine Ecology

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: May 10, 2022

As we enter the United Nations Decade of Ocean Science for Sustainable Development, extensive efforts to reverse decline ocean health are taking place. Moreover, need utilize innovative and integrative approaches aid in these address marine ecological questions urgent. Transcriptomic technologies provide tools further our understanding an organism’s biology by allowing researchers rapidly gain information on genetic variation populations regulation cellular processes pathways through gene presence, absence, expression. Here, review application transcriptomics field ecology over last decade, following a systematic literature approach. We found 478 articles that fit search criteria using transcriptomic hypotheses, with 70% studies occurring within 5 years. Among analysed articles, 51.7% involved type stressor, 16.6% used study adaptation, another 15.9% researched interactions. Most investigated species from kingdom Animalia, high representation both molluscs (19.5%) chordates (13.3%), only 22% had fieldwork component. Our demonstrates how use techniques is increasing they being applied. Although there still challenges experience such techniques, particularly when annotating genes non-model those no prior genomic resources, extremely valuable investigating differential expression, molecular pathways, generating resources.

Language: Английский

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Predicting the future of our oceans—Evaluating genomic forecasting approaches in marine species

Global Change Biology, Journal Year: 2024, Volume and Issue: 30(3)

Published: March 1, 2024

Abstract Climate change is restructuring biodiversity on multiple scales and there a pressing need to understand the downstream ecological genomic consequences of this change. Recent advancements in field eco‐evolutionary genomics have sought include evolutionary processes forecasting species' responses climate (e.g., offset), but date, much work has focused terrestrial species. Coastal offshore species, fisheries they support, may be even more vulnerable than their counterparts, warranting critical appraisal these approaches marine systems. First, we synthesize knowledge about basis adaptation then discuss few examples where been applied Next, identify key challenges validating offset estimates advocate for inclusion historical sampling data hindcasting validation phase. Lastly, describe workflow guide managers incorporating predictions into decision‐making process.

Language: Английский

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Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crabCarcinus maenas

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(7), P. 1980 - 1994

Published: Jan. 26, 2022

Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge larvae of coastal species is to return nursery habitats. Shore crab (Carcinus maenas L.) are known show tidal rhythmicity in vertical migration areas and circadian microtidal areas, which seems increase successful settlement. We studied genome-wide differentiation based on 24,000 single nucleotide polymorphisms 12 native populations shore sampled from large amplitude gradient macrotidal (~8 m) (~0.2 m). Dispersal recruitment success was assessed Lagrangian biophysical model, showed strong effect behaviour long-term connectivity, dispersal barriers partly coincided different environments. The genetic population structure subdivision the samples into three clusters, represent micro-, meso- areas. mostly driven by 0.5% outlier loci, allelic clines located at limits between Demographic modelling suggested two have origins. Differential gene expression clock genes (cyc pdp1) further highlighted phenotypic differences among clusters potentially linked behaviour. Taken together, our seascape genomic study suggests regime acts as selection force structure, consistent affecting success.

Language: Английский

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The Risk for Novel and Disappearing Environmental Conditions in the Baltic Sea

Frontiers in Marine Science, Journal Year: 2021, Volume and Issue: 8

Published: Oct. 1, 2021

Future climate biogeochemical projections indicate large changes in the ocean with environmental conditions not experienced at present referred to as novel, or may even disappear. These climate-induced will most likely affect species distribution via growth, behavior, evolution, dispersal, and interactions. However, future risk of novel disappearing is poorly understood, particular for compound effects nutrient management changes. We map occurrence conditions, analyze outcome scenarios world’s largest estuary, Baltic Sea, potential consequences three charismatic species. Overall, show, expected, an increase novelty over time. The reduction that improves eutrophication status Sea contributes conditions. show fundamental niches under different scenarios. This first step toward comprehensively analyzing a marine system illustrates urgent need include projection outputs Earth System Models. Our results further illustrate adaptive needed account emergence related interplay multiple drivers. our analysis provides strong support expectation ecological communities systems, which ecosystem services, needs be accounted sustainable plans oceans.

Language: Английский

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