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Marine Population Genomics: Challenges and Opportunities

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Population Genomics: Marine Organisms

Part of the book series: Population Genomics ((POGE))

Abstract

Population genomics is revolutionizing biology and stimulating new research questions and directions. While human health has driven many of the genomics tools and approaches, all other biological fields have benefitted. This is certainly true in the world’s oceans, which encompass a large diversity of species and ecosystems. In the world’s oceans, population genomics approaches are giving us an unprecedented ability to gain a better understanding of the organisms inhabiting these ecosystems. While population genomics approaches are improving our understanding of genetic diversity and population genetic parameters in marine organisms, they also are providing unexpected insights into marine invasions, population connectivity, and how marine organisms are responding to different stimuli and environments. Some examples include identification of connectivity among populations that is not predicted by geography as well as identification of genes and genetic variants under natural selection in response to environment and climate conditions as indicators of genes and pathways responsible for adaption. This knowledge is important because so much of the world’s oceans is understudied. This knowledge also is critical for understanding how marine organisms will respond to environmental change and thus how we can better protect marine biodiversity and marine resources. That is, we can better predict the effects of enhanced migration on mitigating anthropogenic stressors affecting marine populations and whether outcrossing will enhance population survival or result in outbreeding depression. Simply put, population genomics provides the genetic resolution to make better predictions about how environmental change is affecting populations and thus provides insights into how we might address environmental change’s deleterious effects on important marine resources. In this chapter, we provide an overview of the challenges and opportunities for marine population genomics, addressing how population genomics can be used to understand marine biodiversity, population demographics and connectivity, and response to environmental changes as well as assist sustainable management, protection, and conservation of marine biodiversity.

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References

  • Ackerman MW, Habicht C, Seeb LW. Single-nucleotide polymorphisms (SNPs) under diversifying selection provide increased accuracy and precision in mixed-stock analyses of sockeye Salmon from the Copper River, Alaska. Trans Am Fish Soc. 2011;140(3):865–81.

    Google Scholar 

  • Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond biodiversity: can environmental DNA (eDNA) cut it as a population genetics tool? Genes. 2019;10(3):192.

    CAS  PubMed Central  Google Scholar 

  • Akbar MA, Ahmad A, Usup G, Bunawan H. Current knowledge and recent advances in marine dinoflagellate transcriptomic research. J Mar Sci Eng. 2018;6(1):13.

    Google Scholar 

  • Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376.

    PubMed  PubMed Central  Google Scholar 

  • Barber I, Nettleship S. From ‘trash fish’ to supermodel: the rise and rise of the three-spined stickleback in evolution and ecology. Biologist. 2010;57:15–21.

    Google Scholar 

  • Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental epigenomics and its applications in marine organisms. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_28.

    Chapter  Google Scholar 

  • Bell M, Foster S. The evolutionary biology of the threespine stickleback. Oxford: Oxford University Press; 1994.

    Google Scholar 

  • Benestan L. Population genomics applied to fishery management and conservation. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2019. https://doi.org/10.1007/13836_2019_66.

    Chapter  Google Scholar 

  • Benestan L, Gosselin T, Perrier C, Sainte-Marie B, Rochette R, Bernatchez L. RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus). Mol Ecol. 2015;24(13):3299–315.

    PubMed  Google Scholar 

  • Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, Hogle SL, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulston D, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Chisholm SW. Marine microbial metagenomes sampled across space and time (vol 5, 180176, 2018). Scientific Data. 2019; 6.

    Google Scholar 

  • Bilyk KT, Cheng CH. RNA-seq analyses of cellular responses to elevated body temperature in the high Antarctic cryopelagic nototheniid fish Pagothenia borchgrevinki. Mar Genomics. 2014;18(Pt B):163–71.

    PubMed  Google Scholar 

  • Boeuf D, Edwards BR, Eppley JM, Hu SK, Poff KE, Romano AE, Caron DA, Karl DM, DeLong EF. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci U S A. 2019;116(24):11824–32.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bonduriansky R, Day T. Nongenetic inheritance and its evolutionary implications. Annu Rev Ecol Evol Syst. 2009;40:103–25.

    Google Scholar 

  • Bourne SD, Hudson J, Holman LE, Rius M. Marine invasion genomics: revealing ecological and evolutionary consequences of biological invasions. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_21.

    Chapter  Google Scholar 

  • Bozinovic G, Oleksiak MF. Embryonic gene expression among pollutant resistant and sensitive Fundulus heteroclitus populations. Aquat Toxicol. 2010;98(3):221–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bozinovic G, Sit TL, Di Giulio R, Wills LF, Oleksiak MF. Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences. BMC Genomics. 2013;14:779.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bravington MV, Grewe PM, Davies CR. Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture. Nat Commun. 2016;7(1):13162.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999;21(Suppl S):33–7.

    CAS  PubMed  Google Scholar 

  • Bucklin A, Steinke D, Blanco-Bercial L. DNA barcoding of marine metazoa. Annu Rev Mar Sci. 2011;3(1):471–508.

    Google Scholar 

  • Bucklin A, DiVito K, Smolina I, Choquet M, Questel JM, Hoarau G, O’Neill RJ. Population genomics of marine zooplankton. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2017. https://doi.org/10.1007/13836_2017_9.

    Chapter  Google Scholar 

  • Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic methods take the plunge: recent advances in high-throughput sequencing of marine mammals. J Hered. 2016;107(6):481–95.

    CAS  PubMed  Google Scholar 

  • Caron DA, Alexander H, Allen AE, Archibald JM, Armbrust EV, Bachy C, Bell CJ, Bharti A, Dyhrman ST, Guida SM, Heidelberg KB, Kaye JZ, Metzner J, Smith SR, Worden AZ. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat Rev Microbiol. 2016;15:6.

    PubMed  Google Scholar 

  • Cary GA, Cheatle Jarvela AM, Francolini RD, Hinman VF. Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. Proc Natl Acad Sci U S A. 2017;114(23):5854–61.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Corander J, Majander KK, Cheng L, Merila J. High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Mol Ecol. 2013;22(11):2931–40.

    CAS  PubMed  Google Scholar 

  • Crawford DL, Oleksiak MF. Ecological population genomics in the marine environment. Brief Funct Genomics. 2016;15(5):342–51.

    CAS  PubMed  Google Scholar 

  • Croucher NJ, Thomson NR. Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol. 2010;13(5):619–24.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2010;11(9):403.

    PubMed  PubMed Central  Google Scholar 

  • Dayan DI. Clinal adaptation in the marine environment. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_62.

    Chapter  Google Scholar 

  • Dayan DI, Crawford DL, Oleksiak MF. Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations of Fundulus heteroclitus. Mol Ecol. 2015;24(13):3345–59.

    PubMed  Google Scholar 

  • Dayan DI, Du X, Baris TZ, Wagner DN, Crawford DL, Oleksiak MF. Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents. BMC Evol Biol. 2019;19(1):61.

    PubMed  PubMed Central  Google Scholar 

  • De Wit P, Palumbi SR. Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation. Mol Ecol. 2013;22(11):2884–97.

    PubMed  Google Scholar 

  • Deans C, Maggert KA. What do you mean, “epigenetic”? Genetics. 2015;199(4):887–96.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dineshram R, Chandramouli K, Ko GW, Zhang H, Qian PY, Ravasi T, Thiyagarajan V. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors. Glob Chang Biol. 2016;22(6):2054–68.

    PubMed  Google Scholar 

  • Drury C, Dale KE, Panlilio JM, Miller SV, Lirman D, Larson EA, Bartels E, Crawford DL, Oleksiak MF. Genomic variation among populations of threatened coral: Acropora cervicornis. BMC Genomics. 2016;17(1):286.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Edwards M, Richardson AJ. Impact of climate change on marine pelagic phenology and trophic mismatch. Nature. 2004;430(7002):881–4.

    CAS  PubMed  Google Scholar 

  • Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The gut microbiota of marine fish. Front Microbiol. 2018;9:873.

    PubMed  PubMed Central  Google Scholar 

  • Eirin-Lopez JM, Putnam HM. Marine environmental epigenetics. Annu Rev Mar Sci. 2019;11:335–68.

    Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Everett MV, Antal CE, Crawford DL. The effect of short-term hypoxic exposure on metabolic gene expression. J Exp Zool A Ecol Genet Physiol. 2012;317A(1):9–23.

    Google Scholar 

  • Ferrer M, Mendez-Garcia C, Bargiela R, Chow J, Alonso S, Garcia-Moyano A, Bjerga GEK, Steen IH, Schwabe T, Blom C, Vester J, Weckbecker A, Shahgaldian P, de Carvalho C, Meskys R, Zanaroli G, Glockner FO, Fernandez-Guerra A, Thambisetty S, de la Calle F, Golyshina OV, Yakimov MM, Jaeger KE, Yakunin AF, Streit WR, McMeel O, Calewaert JB, Tonne N, Golyshin PN, I. Consortium. Decoding the ocean’s microbiological secrets for marine enzyme biodiscovery. FEMS Microbiol Lett. 2019;366(1). https://doi.org/10.1093/femsle/fny285.

  • Ficetola GF, Miaud C, Pompanon F, Taberlet P. Species detection using environmental DNA from water samples. Biol Lett. 2008;4(4):423–5.

    PubMed  PubMed Central  Google Scholar 

  • Fisher MA, Oleksiak MF. Convergence and divergence in gene expression among natural populations exposed to pollution. BMC Genomics. 2007;8:108.

    PubMed  PubMed Central  Google Scholar 

  • Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E, Reusch TB. Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species. Proc Natl Acad Sci U S A. 2011;108(48):19276–81.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A. 2008;105(10):3805–10.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gibson G. The synthesis and evolution of a supermodel. Science. 2005;307(5717):1890.

    CAS  PubMed  Google Scholar 

  • Gil MA, Pfaller JB. Oceanic barnacles act as foundation species on plastic debris: implications for marine dispersal. Sci Rep. 2016;6:19987.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27(2):182–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Goncalves P, Jones DB, Thompson EL, Parker LM, Ross PM, Raftos DA. Transcriptomic profiling of adaptive responses to ocean acidification. Mol Ecol. 2017;26(21):5974–88.

    CAS  PubMed  Google Scholar 

  • González AM, Prada CA, Ávila V, Medina M. Ecological speciation in corals. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_35.

    Chapter  Google Scholar 

  • Grunwald NJ, McDonald BA, Milgroom MG. Population genomics of fungal and oomycete pathogens. Annu Rev Phytopathol. 2016;54:323–46.

    CAS  PubMed  Google Scholar 

  • Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans C, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. Plankton networks driving carbon export in the oligotrophic ocean. Nature. 2016;532(7600):465–70.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guzman C, Shinzato C, Lu TM, Conaco C. Transcriptome analysis of the reef-building octocoral, Heliopora coerulea. Sci Rep. 2018;8(1):8397.

    PubMed  PubMed Central  Google Scholar 

  • Hartl DL, Clark AG. Principles of population genetics. Sunderland: Sinauer Associates; 1997.

    Google Scholar 

  • Hauser L, Carvalho GR. Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish. 2008;9(4):333–62.

    Google Scholar 

  • Hedgecock D. Population genetics of marine organisms. In: Cochran JK, Bokuniewicz HJ, Yager PL, editors. Encyclopedia of ocean sciences, vol. 1. 3rd ed. Oxford: Elsevier; 2019. p. 778–83.

    Google Scholar 

  • Hedgecock D, Pudovkin AI. Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull Mar Sci. 2011;87(4):971–1002.

    Google Scholar 

  • Hess JE, Campbell NR, Close DA, Docker MF, Narum SR. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Mol Ecol. 2013;22(11):2898–916.

    CAS  PubMed  Google Scholar 

  • Hofmann GE, Place SP. Genomics-enabled research in marine ecology: challenges, risks and pay-offs. Mar Ecol Prog Ser. 2007;332:249–55.

    CAS  Google Scholar 

  • Hohenlohe PA, Magalhaes IS. The population genomics of parallel adaptation: lessons from threespine stickleback. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2019. https://doi.org/10.1007/13836_2019_67.

    Chapter  Google Scholar 

  • Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 2010;6(2):e1000862.

    PubMed  PubMed Central  Google Scholar 

  • Holliday JA, Hallerman EM, Haak DC. Genotyping and sequencing technologies in population genetics and genomics. In: Rajora OP, editor. Population genomics: concepts, approaches and applications. Cham: Springer Nature Switzerland AG; 2019. p. 83–126.

    Google Scholar 

  • Horricks RA, Herbinger CM, Lillie BN, Taylor P, Lumsden JS. Differential protein abundance during the first month of regeneration of the Caribbean star coral Montastraea cavernosa. Coral Reefs. 2019;38(1):45–61.

    Google Scholar 

  • Johannesson K. What can be learnt from a snail? Evol Appl. 2016;9(1):153–65.

    PubMed  Google Scholar 

  • Johannesson K, Tatarenkov A. Allozyme variation in a snail (Littorina saxatilis) – deconfounding the effects of microhabitat and gene flow. Evolution. 1997;51(2):402–9.

    CAS  PubMed  Google Scholar 

  • Johannesson K, Johannesson B, Lundgren U. Strong natural selection causes microscale allozyme variation in a marine snail. Proc Natl Acad Sci U S A. 1995;92(7):2602–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Johannesson K, Butlin RK, Panova M, Anja M, Westram AM. Mechanisms of adaptive divergence and speciation in Littorina saxatilis: integrating knowledge from ecology and genetics with new data emerging from genomic studies. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2017. https://doi.org/10.1007/13836_2017_6.

    Chapter  Google Scholar 

  • Johnston SE, Orell P, Pritchard VL, Kent MP, Lien S, Niemela E, Erkinaro J, Primmer CR. Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar). Mol Ecol. 2014;23(14):3452–68.

    CAS  PubMed  Google Scholar 

  • Kalujnaia S, McWilliam IS, Zaguinaiko VA, Feilen AL, Nicholson J, Hazon N, Cutler CP, Balment RJ, Cossins AR, Hughes M, Cramb G. Salinity adaptation and gene profiling analysis in the European eel (Anguilla anguilla) using microarray technology. Gen Comp Endocrinol. 2007;152(2–3):274–80.

    CAS  PubMed  Google Scholar 

  • Kelly RP, Port JA, Yamahara KM, Martone RG, Lowell N, Thomsen PF, Mach ME, Bennett M, Prahler E, Caldwell MR, Crowder LB. Environmental monitoring. Harnessing DNA to improve environmental management. Science. 2014;344(6191):1455–6.

    CAS  PubMed  Google Scholar 

  • Kronholm I, Collins S. Epigenetic mutations can both help and hinder adaptive evolution. Mol Ecol. 2016;25(8):1856–68.

    CAS  PubMed  Google Scholar 

  • Lester SE, Halpern BS, Grorud-Colvert K, Lubchenco J, Ruttenberg BI, Gaines SD, Airamé S, Warner RR. Biological effects within no-take marine reserves: a global synthesis. Mar Ecol Prog Ser. 2009;384:33–46.

    Google Scholar 

  • Libro S, Kaluziak ST, Vollmer SV. RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease. PLoS One. 2013;8(11):e81821.

    PubMed  PubMed Central  Google Scholar 

  • Liggins L, Treml EA, Riginos C. Seascape genomics: contextualizing adaptive and neutral genomic variation in the ocean environment. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2019. https://doi.org/10.1007/13836_2019_68.

    Chapter  Google Scholar 

  • Luikart G, Kardos M, Hand B, Rajora OP, Aitken S, Hohenlohe PA. Population genomics: advancing understanding of nature. In: Rajora OP, editor. Population genomics: concepts, approaches and applications. Cham: Springer Nature Switzerland AG; 2019. p. 3–79.

    Google Scholar 

  • Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7(2):111–8.

    CAS  PubMed  Google Scholar 

  • Martinsohn JT, Ogden R. FishPopTrace – developing SNP-based population genetic assignment methods to investigate illegal fishing. Forensic Sci Int. 2009;2(1):294–6.

    Google Scholar 

  • Metzger DCH, Schulte PM. Epigenomics in marine fishes. Mar Genomics. 2016;30:43–54.

    PubMed  Google Scholar 

  • Mineta K, Gojobori T. Databases of the marine metagenomics. Gene. 2016;576(2, Part 1):724–8.

    CAS  PubMed  Google Scholar 

  • Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci. 2015;2(7):150088.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moler ERV, Abakir A, Eleftheriou M, Johnson JS, Krutovsky KV, Lewis LC, Ruzov A, Whipple AV, Rajora OP. Population epigenomics: advancing understanding of phenotypic plasticity, acclimation, adaptation and diseases. In: Rajora OP, editor. Population genomics: concepts, approaches and applications. Cham: Springer Nature Switzerland AG; 2019. p. 179–260.

    Google Scholar 

  • Molnar JL, Gamboa RL, Revenga C, Spalding MD. Assessing the global threat of invasive species to marine biodiversity. Front Ecol Environ. 2008;6(9):485–92.

    Google Scholar 

  • Mora C, Tittensor DP, Adl S, Simpson AG, Worm B. How many species are there on earth and in the ocean? PLoS Biol. 2011;9(8):e1001127.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nielsen EE, Hemmer-Hansen J, Larsen PF, Bekkevold D. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol. 2009;18(15):3128–50.

    PubMed  Google Scholar 

  • Nielsen EE, Cariani A, Aoidh EM, Maes GE, Milano I, Ogden R, Taylor M, Hemmer-Hansen J, Babbucci M, Bargelloni L, Bekkevold D, Diopere E, Grenfell L, Helyar S, Limborg MT, Martinsohn JT, McEwing R, Panitz F, Patarnello T, Tinti F, Van Houdt JKJ, Volckaert FAM, Waples RS, C. FishPopTrace, Albin JEJ, Vieites Baptista JM, Barmintsev V, Bautista JM, Bendixen C, Bergé J-P, Blohm D, Cardazzo B, Diez A, Espiñeira M, Geffen AJ, Gonzalez E, González-Lavín N, Guarniero I, Jeráme M, Kochzius M, Krey G, Mouchel O, Negrisolo E, Piccinetti C, Puyet A, Rastorguev S, Smith JP, Trentini M, Verrez-Bagnis V, Volkov A, Zanzi A, Carvalho GR. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification. Nat Commun. 2012;3:851.

    PubMed  Google Scholar 

  • Norton WHJ, Gutiérrez HC. The three-spined stickleback as a model for behavioural neuroscience. PLoS One. 2019;14(3):e0213320.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nunez JC, Seale TP, Fraser MA, Burton TL, Fortson TN, Hoover D, Travis J, Oleksiak MF, Crawford DL. Population genomics of the euryhaline teleost Poecilia latipinna. PLoS One. 2015;10(9):e0137077.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nunez JCB, Elyanow RG, Ferranti DA, Rand DM. Population genomics and biogeography of the northern acorn barnacle (Semibalanus balanoides) using pooled sequencing approaches. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_58.

    Chapter  Google Scholar 

  • Oleksiak MF. Genomic approaches with natural fish populations. J Fish Biol. 2010;76(5):1067–93.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Oleksiak MF. Adaptation without boundaries: population genomics in marine systems. In: Rajora OP, editor. Population genomics: concepts, approaches and applications. Cham: Springer Nature Switzerland AG; 2019. p. 587–612.

    Google Scholar 

  • Oleksiak MF, Churchill GA, Crawford DL. Variation in gene expression within and among natural populations. Nat Genet. 2002;32(2):261–6.

    CAS  PubMed  Google Scholar 

  • Oleksiak MF, Roach JL, Crawford DL. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nat Genet. 2005;37(1):67–72.

    CAS  PubMed  Google Scholar 

  • Oleksiak MF, Karchner SI, Jenny MJ, Franks DG, Welch DB, Hahn ME. Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site. BMC Genomics. 2011;12:263.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pace NR, Stahl DA, Lane DJ, Olsen GJ. The analysis of natural microbial-populations by ribosomal-RNA sequences. Adv Microb Ecol. 1986;9:1–55.

    CAS  Google Scholar 

  • Palenik B, Ren Q, Tai V, Paulsen IT. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ Microbiol. 2009;11(2):349–59.

    CAS  PubMed  Google Scholar 

  • Parsons KM, Everett M, Dahlheim M, Park L. Water, water everywhere: environmental DNA can unlock population structure in elusive marine species. R Soc Open Sci. 2018;5(8):180537.

    PubMed  PubMed Central  Google Scholar 

  • Pérez-Portela R, Riesgo A. Population genomics of early-splitting lineages of metazoans. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_13.

    Chapter  Google Scholar 

  • Plough LV, Shin G, Hedgecock D. Genetic inviability is a major driver of type III survivorship in experimental families of a highly fecund marine bivalve. Mol Ecol. 2016;25(4):895–910.

    CAS  PubMed  Google Scholar 

  • Porteus CS, Hubbard PC, Uren Webster TM, van Aerle R, Canário AVM, Santos EM, Wilson RW. Near-future CO2 levels impair the olfactory system of a marine fish. Nat Clim Chang. 2018;8(8):737–43.

    CAS  Google Scholar 

  • Puebla O. Ecological speciation in marine v. freshwater fishes. J Fish Biol. 2009;75(5):960–96.

    CAS  PubMed  Google Scholar 

  • Puritz JB, Lotterhos KE. Expressed exome capture sequencing: a method for cost-effective exome sequencing for all organisms. Mol Ecol Resour. 2018;18(6):1209–22.

    CAS  PubMed  Google Scholar 

  • Qiu ZG, Coleman MA, Provost E, Campbell AH, Kelaher BP, Dalton SJ, Thomas T, Steinberg PD, Marzinelli EM. Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp. Proc R Soc B Biol Sci. 2019;286(1896):20181887.

    Google Scholar 

  • Rajora OP, editor. Population genomics: concepts, approaches and application. Cham: Springer Nature Switzerland AG; 2019. 823 pp. ISBN 978-3-030-04587-6; ISBN 978-3-030-04589-0 (eBook).

    Google Scholar 

  • Ramirez F, Afan I, Tavecchia G, Catalan IA, Oro D, Sanz-Aguilar A. Oceanographic drivers and mistiming processes shape breeding success in a seabird. Proc R Soc B Biol Sci. 2016;283(1826):20152287.

    Google Scholar 

  • Ramsay G. DNA chips: state-of-the art. Nat Biotechnol. 1998;16(1):40–4.

    CAS  PubMed  Google Scholar 

  • Riginos C, Liggins L. Seascape genetics: populations, individuals, and genes marooned and adrift. Geogr Compass. 2013;7(3):197–216.

    Google Scholar 

  • Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool. 2016;62(6):581–601.

    PubMed  PubMed Central  Google Scholar 

  • Roberts SB, Hauser L, Seeb LW, Seeb JE. Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing. PLoS One. 2012;7(2):e30908.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roitman S, Pollock FJ, Medina M. Coral microbiomes as bioindicators of reef health. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_29.

    Chapter  Google Scholar 

  • Sassoubre LM, Yamahara KM, Gardner LD, Block BA, Boehm AB. Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish. Environ Sci Technol. 2016;50(19):10456–64.

    CAS  PubMed  Google Scholar 

  • Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. Microarrays: biotechnology’s discovery platform for functional genomics. Trends Biotechnol. 1998;16(7):301–6.

    CAS  PubMed  Google Scholar 

  • Schlotterer C, Tobler R, Kofler R, Nolte V. Sequencing pools of individuals – mining genome-wide polymorphism data without big funding. Nat Rev Genet. 2014;15(11):749–63.

    PubMed  Google Scholar 

  • Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BS. Targeted capture of complete coding regions across divergent species. Genome Biol Evol. 2017;9(2):398–414.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE. Parallel signatures of selection in temporally isolated lineages of pink salmon. Mol Ecol. 2014;23(10):2473–85.

    CAS  PubMed  Google Scholar 

  • Sigsgaard EE, Nielsen IB, Bach SS, Lorenzen ED, Robinson DP, Knudsen SW, Pedersen MW, Jaidah MA, Orlando L, Willerslev E, Møller PR, Thomsen PF. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nat Ecol Evol. 2016;1:0004.

    Google Scholar 

  • Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. J Nat Prod. 2012;75(10):1833–77.

    CAS  PubMed  Google Scholar 

  • Stat M, Huggett MJ, Bernasconi R, DiBattista JD, Berry TE, Newman SJ, Harvey ES, Bunce M. Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Sci Rep. 2017;7(1):12240.

    PubMed  PubMed Central  Google Scholar 

  • Sussarellu R, Fabioux C, Le Moullac G, Fleury E, Moraga D. Transcriptomic response of the Pacific oyster Crassostrea gigas to hypoxia. Mar Genomics. 2010;3(3–4):133–43.

    PubMed  Google Scholar 

  • Thomsen PF, Willerslev E. Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv. 2015;183:4–18.

    Google Scholar 

  • Thomsen PF, Kielgast J, Iversen LL, Moller PR, Rasmussen M, Willerslev E. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One. 2012;7(8):e41732.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tomanek L. Environmental proteomics: changes in the proteome of marine organisms in response to environmental stress, pollutants, infection, symbiosis, and development. Annu Rev Mar Sci. 2011;3:373–99.

    Google Scholar 

  • Vasquez MC, Lippert MR, White C, Walter RK, Tomanek L. Proteomic changes across a natural temperature gradient in a marine gastropod. Mar Environ Res. 2019;149:137–47.

    CAS  PubMed  Google Scholar 

  • Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences. Mar Ecol Prog Ser. 2019;610:65–81.

    CAS  Google Scholar 

  • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304(5667):66–74.

    CAS  PubMed  Google Scholar 

  • Wagner DN, Baris TZ, Dayan DI, Du X, Oleksiak MF, Crawford DL. Fine-scale genetic structure due to adaptive divergence among microhabitats. Heredity (Edinb). 2017;118(6):594–604.

    CAS  Google Scholar 

  • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol. 2015;21(3):803–14.

    PubMed  PubMed Central  Google Scholar 

  • Webb TJ, Vanden Berghe E, O’Dor R. Biodiversity’s big wet secret: the global distribution of marine biological records reveals chronic under-exploration of the deep pelagic ocean. PLoS One. 2010;5(8):e10223.

    PubMed  PubMed Central  Google Scholar 

  • Weersing K, Toonen RJ. Population genetics, larval dispersal, and connectivity in marine systems. Mar Ecol Prog Ser. 2009;393:1–12.

    Google Scholar 

  • Williams DR, Li W, Hughes MA, Gonzalez SF, Vernon C, Vidal MC, Jeney Z, Jeney G, Dixon P, McAndrew B, Bartfai R, Orban L, Trudeau V, Rogers J, Matthews L, Fraser EJ, Gracey AY, Cossins AR. Genomic resources and microarrays for the common carp Cyprinus carpio L. J Fish Biol. 2008;72(9):2095–117.

    CAS  Google Scholar 

  • Xuereb A, D’Aloia CC, Daigle RM, Andrello M, Dalongeville A, Manel S, Mouillot D, Guichard F, Côté IM, Curtis JMR, Bernatchez L, Fortin M-J. Marine conservation and marine protected areas. In: Oleksiak MF, Rajora OP, editors. Population genomics: marine organisms. Cham: Springer Nature Switzerland AG; 2018. https://doi.org/10.1007/13836_2018_63.

    Chapter  Google Scholar 

  • Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, Zhu Y, Wu F, Chen Y, Wang J, Peng C, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z, Zhu Q, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y, Domazet-Loso T, Du Y, Sun X, Zhang S, Liu B, Cheng P, Jiang X, Li J, Fan D, Wang W, Fu W, Wang T, Wang B, Zhang J, Peng Z, Li Y, Li N, Wang J, Chen M, He Y, Tan F, Song X, Zheng Q, Huang R, Yang H, Du X, Chen L, Yang M, Gaffney PM, Wang S, Luo L, She Z, Ming Y, Huang W, Zhang S, Huang B, Zhang Y, Qu T, Ni P, Miao G, Wang J, Wang Q, Steinberg CE, Wang H, Li N, Qian L, Zhang G, Li Y, Yang H, Liu X, Wang J, Yin Y, Wang J. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 2012;490(7418):49–54.

    CAS  PubMed  Google Scholar 

  • Zhang X, Wen H, Wang H, Ren Y, Zhao J, Li Y. RNA-Seq analysis of salinity stress-responsive transcriptome in the liver of spotted sea bass (Lateolabrax maculatus). PLoS One. 2017;12(3):e0173238.

    PubMed  PubMed Central  Google Scholar 

  • Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. MBio. 2015;6(1):e02288–14.

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

We thank Douglas L. Crawford for helpful comments and input. MFO was supported in part by funding from US National Science Foundation grants MCB 1434565 and 1158241 and IOS 1147042. OPR received support from a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN 2017-04589.

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  1. Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA

    Marjorie F. Oleksiak

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

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Correspondence to Marjorie F. Oleksiak .

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  1. Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA

    Marjorie F. Oleksiak

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

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Oleksiak, M.F., Rajora, O.P. (2019). Marine Population Genomics: Challenges and Opportunities. In: Oleksiak, M., Rajora, O. (eds) Population Genomics: Marine Organisms. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2019_70

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