Climate-Driven Shifts in Marine Species Ranges: Scaling from Organisms to Communities

Annual Review of Marine Science, Journal Year: 2019, Volume and Issue: 12(1), P. 153 - 179

Published: Sept. 10, 2019

The geographic distributions of marine species are changing rapidly, with leading range edges following climate poleward, deeper, and in other directions trailing often contracting similar directions. These shifts have their roots fine-scale interactions between organisms environment-including mosaics gradients temperature oxygen-mediated by physiology, behavior, evolution, dispersal, interactions. reassemble food webs can dramatic consequences. Compared on land, more sensitive to but a greater capacity for colonization. differences suggest that cope change at different spatial scales the two realms across wide key mechanism sea. Additional research is needed understand how processes interact promote or constrain shifts, dominant responses vary among species, emergent communities future ocean will function.

Language: Английский

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Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(20), P. 5369 - 5406

Published: July 26, 2017

Abstract Whole‐genome resequencing ( WGR ) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. includes four approaches: the sequencing of individuals to high depth coverage with either unresolved or haplotypes, population genomes by mixing equimolar amounts unlabelled‐individual DNA (Pool‐seq) and multiple from low (lc ). These techniques require availability reference genome. This, along still cost shotgun large demand computing resources storage, has limited their implementation in nonmodel species scarce genomic fields such as conservation biology. Our goal here describe various methods, pros cons potential applications offers an unprecedented marker density surveys wide diversity genetic variations single nucleotide polymorphisms (e.g., structural variants mutations regulatory elements), increasing power detection signatures selection local adaptation well identification basis phenotypic traits diseases. Currently, though, no approach fulfils all requirements genetics, each its own limitations sources bias. We discuss proposed ways minimize biases. envision distant future where analysis whole becomes routine task many including

Language: Английский

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Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Evolutionary Applications, Journal Year: 2017, Volume and Issue: 11(7), P. 1035 - 1052

Published: Oct. 30, 2017

Abstract Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations restoration, rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, in some cases not a worthwhile use resources. Here, we offer an framework help conservation biologists managers decide genomics is likely effective detecting adaptation, how plan assessment address objectives. Studies using tools will inform many cases, including applications flow identifying units. In others, assessing diversity, inbreeding, demographics selectively neutral markers most useful. And assessed more efficiently alternative approaches common garden experiments. identify key considerations variation, provide road map successful collaborations with experts issues study design data analysis, guidelines interpreting results from assessments programs actions.

Language: Английский

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Harnessing the Power of Genomics to Secure the Future of Seafood

Trends in Ecology & Evolution, Journal Year: 2017, Volume and Issue: 32(9), P. 665 - 680

Published: Aug. 14, 2017

Advancements of genetic technologies now allow the collection genome-wide data in nonmodel species a cost -effective manner. These genomic-informed addressing comprehensive spectrum needs and applications relevant to fisheries, aquaculture , biosecurity. Genomics tools also improve our understanding how aquatic organisms adapt respond environment, ability monitor environmental variation exploited species. Genomic approaches are rapidly replacing traditional markers, but their application fisheries management has stagnated when compared agriculture where they have long been used for improved production. There is no reason further delay genomic Best use scientific knowledge required maintain fundamental role seafood human nutrition. While it acknowledged that genomic-based methods powerful data, value inform management, biosecurity remains underestimated. We review relevance sustainable resources, illustrate benefits of, identify barriers integration. conclude information towards securing future does not need be demonstrated. Instead, we immediate efforts remove structural roadblocks focus on ways support integration into production practices. propose solutions pave way forward. Seafood plays meeting current food [1Béné C. et al.Contribution security poverty reduction: assessing evidence.World Dev. 2016; 79: 177-196Crossref Scopus (409) Google Scholar]. Capture only remaining wild animal protein source, fastest growing sector world. Together provide 4.5 billion people with at least 15% [2Béné Small-scale fisheries: contribution rural livelihoods developing countries.FAO Fisheries Circular. FAO, 2006Google Scholar, 3McIntyre P.B. al.Linking freshwater fishery global biodiversity conservation.Proc. Nat. Acad. Sci. U. S. A. 113: 12880-12885Crossref (139) The population may exceed 9 by 2050, so pressing question whether can help alleviate issues [3McIntyre answer this unknown. some developed countries longer sustained from local fish stocks increasingly supplemented elsewhere [4Pauly D. Zeller Catch reconstructions reveal marine catches higher than reported declining.Nat. Commun. 7: 10244Crossref PubMed (707) This trend will probably remain or increase over time, as several near above limits [5Hilborn R. Stokes K. Defining overfished stocks: lost plot?.Fisheries. 2010; 35: 113-120Crossref (61) 6Rose G.A. Rowe Northern cod comeback.Can. J. Fish. Aquat. 2015; 72: 1789-1798Crossref (69) Scholar], many overexploited collapse 7Worm B. al.Rebuilding fisheries.Science. 2009; 325: 578-585Crossref (1578) 8Osio G.C. al.Assessing vulnerability Mediterranean demersal predicting exploitation status un-assessed stocks.Fish. Res. 171: 110-121Crossref (35) For example, 95% Black Seas overharvested [8Osio being severely affected worldwide cumulative effects habitat degradation, climate change,and diseases [39Bhattacharya M. al.DNA barcoding fishes: directions.Mitochondrial DNA Part 27: 2744-2752PubMed finfish reached volume [10Béné al.Feeding 2050–Putting back menu.Food Secur. 261-274Crossref (424) growth expected decelerate response shortage, lack suitable locations, increasing feed costs [11Food Agriculture Organization State World Aquaculture 2016. Contributing nutrition all.STECF: Scientific, Technical Economic Committee Fisheries. Publications Office European Union, 2016Google Moreover, other industries (e.g., shellfish) suffering setbacks due disease outbreaks ocean acidification [12S al.An Updated Synthesis Impacts Ocean Acidification Marine Biodiversity. Secretariat Convention Biological Diversity, 2014Google Careful strategies industry, making critical best informs decision-making 4Pauly 13Melnychuk M.C. al.Fisheries impacts target status.Proc. 2017; 114: 178-183Crossref (100) Traditional relies stock assessment models predict variability stock–recruitment relationships determine catch [7Worm 14Myers R.A. Stock recruitment: generalizations about maximum reproductive rate, density dependence, using meta-analytic approaches.ICES Mar. 2001; 58: 937-951Crossref (208) 15Beddington J.R. al.Current problems 2007; 316: 1713-1716Crossref (457) Genetic [16Waples R.S. al.Integrating resources: do better?.Fish 2008; 9: 423-449Crossref (235) however, (Box 1). Consequently, despite demonstrated delineate populations accurately (see section below), units predominantly based administrative units, which often closely connected biology 17Borja al.Overview integrative systems: ecosystem approach practice.Front. 3: 20Crossref (180) contradicts basis science whereby Maximum Sustainable Yield (MSY) achieved efficient distinct 16Waples 18Utter F.M. Biochemical genetics management: an historical perspective.J. Fish Biol. 1991; 39: 1-20Crossref (147) Scholar].Box 1Why Data Has Seldom Been Incorporated Management, What Do itThe explosion began 1980 s propelled allelic interpretation electrophoretic mobility proteins accelerated genomics revolution 9Snapper9 [49Ryman N. Utter F. Genetics past, present future.in: Ryman Population management. University Washington, 1987: 1-20Google Sadly, exclamations practical conservation largely fallen deaf ears. Despite trouble-shooting experts 50Hauser L. Carvalho G.R. Paradigm shifts genetics: ugly hypotheses slain beautiful facts.Fish 333-362Crossref (449) impediments downstream still remain.To systematically address this, three user groups were consulted one-to-one structured interviews [51Dichmont, C.M. al. (2012) Scoping tools, limitations Final Report. Australian Research & Development Corporation Project 2011/035.Google scientists (n = 26), managers 24), fishing industry representatives 12) Australia, Europe, North South America, Western Pacific, Africa New Zealand. purpose was qualitatively assess attitudes perceptions context if there uptake might improved. Over 90% interviewees familiar structure (Theme II [52Ovenden al.Ocean's eleven: evaluation population, evolutionary molecular fisheries.Fish 16: 125-159Crossref (113) Scholar]). awareness ten themes poor moderate. Industry viewed more positively scientists. positive recognition general usefulness genetics, particular defining spatial populations. Where negative perception interviewees, reasons provided:•A potential information,•A studies expensive,•A results 'oversold',•A consistency interpretations geneticists,•The importance far outweighed inputs decisions.All agreed effectiveness could suggestions grouped two categories: communication technical. Improvements (around 70% suggestions) considered essential. Specific included: across plain language; greater among scientists, geneticists, industry; utility groups; accessibility research geneticists. improvement included reducing projects; robust reliable techniques; sampling designs.Unhappily, challenges roadblock wake-up call those involved security. glimmers hope changing. survey showed most understand its power sympathetic, knowledgeable, genetics. Thus, judicious likely well received, carefully tailored policy (Ovenden Moore, S11). onus geneticists end-users reach mutual (Figure I), else perceived sustained. remain. To decisions. All designs. Unhappily, Novel better biosecurity, [19Willette al.So, you want next-generation sequencing systems? Insight Pan-Pacific Advanced Studies Institute.Bull. 2014; 90: 79-122Crossref (45) 20da Fonseca R.R. al.Next-generation biology: analysis non-model organisms.Mar. Genom. 30: 3-13Crossref (97) markers microsatellite DNA), little policies refers relating complete genome organism [21Pearse Saving spandrels? Adaptive management.J. 89: 2697-2716Crossref (37) In term typically shorthand describe applying large datasets; typical, yet arbitrary, threshold >1000s versus 10s–100s distinguish between studies, respectively. decades, low-resolution available pertaining aquaculture. Indeed first sequence key published 2011 [22Star al.The Atlantic reveals unique immune system.Nature. 2011; 477: 207-210Crossref (570) limited incorporation new problem makes situation different. because time development cost-effective traceability supply chain [23Kelley J.L. life aquatic: advances vertebrate genomics.Nat. Rev. Genet. 4: 523-534Crossref (52) Scholar] Specifically defines quantifies extent adaptive divergence connectivity them, allows performing mixed-stock substantially increased resolution. advance means selection resistance, identifying greatest domestication [24Yáñez J.M. al.Genomics accelerate progress.Front. 6https://doi.org/10.3389/fgene.2015.00128Crossref (76) escapees farms. A small moderate number sometimes sufficient hand 25Ovenden (31) necessary step set subsequent surveys. Tools derived environments community level, biological species, instance, provided exponential (eDNA) metabarcoding [26Rees H.C. al.REVIEW: detection – eDNA tool ecology.J. Appl. Ecol. 51: 1450-1459Crossref (596) following outlines representative examples direct aquaculture, quality safety purposes. Details each these case presented 14 short papers (S1–S14) Supplementary Material summarise presentations invited speakers during symposium entitled: "Genomics conservation: promises fulfilled?" Accurate identification mandatory enable proactive Bernatchez (S6) thousands single nucleotide polymorphism (SNP) allowed refinement American lobster, documenting degree overlap while providing evidence adaptation. Regional patterns recruitment eel imposed shown recur every generation dispersal spawning area (Bernatchez, S6). finding influence both restoration strategies. Species practices aided approaches. Lee (S7) neutral considerable discriminate cryptic sympatric fishes Korean peninsula. Similarly, Araneda Larraín (S1) 2).Box 2Genomic Approaches TraceabilityTraceability aquacultured products like shellfish throughout ('from fork ') high certainty origin identity crucial utilisation, prevent fraud [53Stawitz C.C. al.Financial Ecological Implications Global Mislabeling.Conserv. Lett. https://doi.org/10.1111/conl.12328Crossref (28) general, identified external traits; phenotypic tracing becomes unusable once entered processing. resources reproducibility reliability, products; easily combined reference materials [54Martinshohn al.Tracing advanced technologies. Woodhead Publishing, 2011Google authenticity verify labelling information. Traceability applied broad levels: individual identification. Hitherto, levels explored either methods.Two objectives level include preventing substitution valuable lower marketing potentially harmful consumer protected [55Abbadi al.Species bivalve molluscs pyrosequencing.J. Food Agr. Discipl. 97: 512-519Crossref (19) 56Wong E.H.-K. Hanner R.H. detects market seafood.Food Int. 41: 828-837Crossref (351) 57Miller al.Seafood mislabelling: comparisons western assist influencing factors, mechanisms motives.Fish 2012; 13: 345-358Crossref (68) 58Filonzi al.Molecular mislabelling commercial Italy.Food 43: 1383-1388Crossref (151) Many detected through cytochrome oxidase I gene (COI) comparing database (FISH-BOL) [59Ward R.D. campaign barcode all fishes, FISH-BOL.J. 74: 329-356Crossref (656) 60Becker al.Five years FISH-BOL: brief report.Mitochondrial DNA. 22: 3-9Crossref (98) 61Oliveira al.Assembling auditing library fishes.J. 2741-2754Crossref (21) less requires different mitochondrial nuclear SNP panels [62Zbawicka al.Identification validation novel Mytilus mussels.Mar. 159: 1347-1362Crossref (43) depending taxa [63Kijewski T. al.Distribution coastal areas inferred markers.J. Sea 65: 224-234Crossref (53) Examples include, separation mussel, common blue Baltic mussel Chilean accuracy panel 49 SNPs (Larraín preparation) mussels subpanel 19 (Araneda Larraín, S1).The second (population) sale illegal, unreported unregulated protecting consumers collected threats public health (for algal blooms). Assignments non-neutral successful differentiating (Atlantic cod, herring, sole, hake) geographical Europe [31Nielsen E.E. al.Gene-associated tackling illegal false eco-certification.Nat. 851Crossref (178) differentiate [64Araneda al.Adaptive distinguishes (Mytilus chilensis) environments.Ecol. Evol. 6: 3632-3644Crossref (38) red tide 2016, thus permitting physical (records, labels). Such informative usually perform

Language: Английский

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Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

Molecular Ecology Resources, Journal Year: 2017, Volume and Issue: 17(3), P. 362 - 365

Published: March 20, 2017

Recently, Lowry et al. addressed the ability of RADseq approaches to detect loci under selection in genome scans. While authors raise important considerations, such as accounting for extent linkage disequilibrium a study system, we strongly disagree with their overall view inform our understanding genetic basis adaptation. The family protocols has radically improved field population genomics, expanding by several orders magnitude number markers available while substantially reducing cost per marker. Researchers whose goal is identify regions must consider LD experimental system; however, there no magical cutoff below which researchers should refuse use RADseq. further made two major arguments: theoretical argument that modeled likelihood detecting selective sweeps RAD markers, and gross summaries based on an anecdotal collection studies. Unfortunately, simulations were off worst case, anecdotes merely showed it possible get widely divergent densities tags any particular experiment, either design or due efficacy. We argue remains powerful efficient approach provides sufficient marker density studying many natural populations. Given limited resources, wide range trade-offs among genomic techniques, light question power different techniques answer it.

Language: Английский

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Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

Science, Journal Year: 2019, Volume and Issue: 365(6452), P. 487 - 490

Published: Aug. 1, 2019

Parallel and idiosyncratic fish adaptation Fish populations respond rapidly to fishing pressure. Within a handful of generations, marked phenotypic change can occur—often smaller body sizes, because it is the big that are usually extracted. Therkildsen et al. examined wild ancestor lineages found polygenic mechanisms underpin this rapid evolutionary capacity (see Perspective by Jørgensen Enberg). Phenotypic happened in two ways: first, multiple small parallel changes hundreds unlinked genes associated with growth variation wild, second, shifts large blocks linked genes, causing allele frequency at some loci. Science , issue p. 487 ; see also 443

Language: Английский

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Improving conservation policy with genomics: a guide to integrating adaptive potential into U.S. Endangered Species Act decisions for conservation practitioners and geneticists

Conservation Genetics, Journal Year: 2018, Volume and Issue: 20(1), P. 115 - 134

Published: Aug. 22, 2018

Language: Английский

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Aquatic Landscape Genomics and Environmental Effects on Genetic Variation

Trends in Ecology & Evolution, Journal Year: 2019, Volume and Issue: 34(7), P. 641 - 654

Published: March 20, 2019

Language: Английский

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Development of the Natural Survivor Method (NSM) for designing an updating mechanism in metaheuristic search algorithms

Engineering Applications of Artificial Intelligence, Journal Year: 2023, Volume and Issue: 122, P. 106121 - 106121

Published: March 15, 2023

Language: Английский

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Genome architecture enables local adaptation of Atlantic cod despite high connectivity

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(17), P. 4452 - 4466

Published: June 19, 2017

Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining adaptation despite high gene flow are still poorly understood. Marine ecosystems provide wide array of diverse habitats that frequently promote ecological even species characterized by strong levels flow. As one example, populations the marine fish Atlantic cod (Gadus morhua) highly connected due immense dispersal capabilities but nevertheless show several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval patterns inferred using biophysical ocean model, we individuals residing sheltered estuarine Scandinavian fjords mainly belong offshore oceanic considerable connectivity between these ecosystems. Nevertheless, also find evidence for discrete fjord genetically differentiated from populations, indicative adaptation, degree which appears be influenced connectivity. Analyses architecture reveal significant overrepresentation large ~5 Mb chromosomal rearrangement cod, previously proposed comprise genes critical survival at low salinities. This suggests environments may enabled suppression recombination rearranged region. Our study provides new insights into potential within fine geographical scales and highlights importance genome adaptation.

Language: Английский

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