in

Species-specific genetic variation in response to deep-sea environmental variation amongst Vulnerable Marine Ecosystem indicator taxa

  • 1.

    Hilário, A. et al. Estimating dispersal distance in the deep sea: Challenges and applications to marine reserves. Front. Mar. Sci. 2, 6 (2015).

    • Article
    • Google Scholar
  • 2.

    Baco, A. R. et al. A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design. Mol. Ecol. 25, 3276–3298 (2016).

  • 3.

    Zeng, C., Rowden, A. A., Clark, M. R. & Gardner, J. P. A. Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: Implications for the conservation and management of vulnerable marine ecosystems. Evol. Appl. 10, 1040–1054 (2017).

  • 4.

    Amils, R., Ellis-Evans, C., Hinghofer-Szalkay, H., Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001).

  • 5.

    Miller, K. J., Williams, A., Rowden, A. A., Knowles, C. & Dunshea, G. Conflicting estimates of connectivity among deep-sea coral populations. Mar. Ecol. 31, 144–157 (2010).

  • 6.

    Bors, E. K., Rowden, A. A., Maas, E. W., Clark, M. R. & Shank, T. M. Patterns of deep-sea genetic connectivity in the New Zealand region: Implications for management of benthic ecosystems. PLoS One 7, e49474 (2012).

  • 7.

    Miller, K.J. & Gunasekera, R. A comparison of genetic connectivity in two deep sea corals to examine whether seamounts are isolated islands or stepping stones for dispersal. Sci. Rep. 7, (2017).

  • 8.

    Chevaldonné, P., Joilivet, D., Vangriesheim, A. & Desbruyéres, D. Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific. 1. Influence of vent site distribution, bottom currents, and biological patterns. Limnol. Oceanogr. 42, 67–80 (1997).

  • 9.

    Arellano, S. M., Van Gaest, A. L., Johnson, S. B., Vrijenhoek, R. C. & Young, C. M. Larvae from deep-sea methane seeps disperse in surface waters. Proc. R. Soc. B 281, 20133276 (2014).

  • 10.

    Miller, K., Rowden, A., Williams, A. & Häussermann, V. Out of their depth? Isolated deep populations of the cosmopolitan coral Desmophyllum dianthus may be highly vulnerable to environmental change. PLoS One 6, e19004 (2011).

  • 11.

    Baco, A. R. & Cairns, S. D. Comparing molecular variation to morphological species designations in the deep-sea coral narella reveals new insights into seamount coral ranges. PLoS One 7, e45555 (2012).

  • 12.

    Catarino, D. et al. The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis). Mol. Ecol. 24, 6061–6079 (2015).

  • 13.

    Ramirez-Llodra, E. et al. Man and the last great wilderness: Human impact on the deep sea. PLoS One 6, e22588 (2011).

  • 14.

    Zeng, C., Clark, M.R., Rowden, A.A. & Gardner, J. P. A. The use of spatially explicit genetic variation data from four deep-sea sponges to inform the protection of Vulnerable Marine Ecosystems. Sci. Rep. (2019).

  • 15.

    Taylor, M. L. & Roterman, C. N. Invertebrate population genetics across Earth’s largest habitat: The deep-sea floor. Mol. Ecol. 26, 4872–4896 (2017).

  • 16.

    FAO. International guidelines for the management of deep-sea fisheries in the high seas. https://doi.org/10.1007/s13398-014-0173-7.2 (2009).

  • 17.

    Aguilar, R., Perry, A. L. & López, J. Conservation and management of vulnerable marine benthic ecosystems. in Marine animal forests: The ecology of benthic biodiversity hotspots (eds. Rossi, S., Bramanti, L., Gori, A. & Covadonga, O.) 1–43 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-17001-5_34-1.

  • 18.

    Adkins, J. F., Boyle, E. A., Curry, W. B. & Lutringer, A. Stable isotopes in deep-sea corals and a new mechanism for ‘vital effects’. Geochim. Cosmochim. Acta 67, 1129–1143 (2003).

  • 19.

    Kiriakoulakis, K. et al. Lipids and nitrogen isotopes of two deep-water corals from the North-East Atlantic: Initial results and implications for their nutrition. in Cold-water Corals and Ecosystems 715–729, https://doi.org/10.1007/3-540-27673-4_37 (2005).

  • 20.

    Davies, A. J., Wisshak, M., Orr, J. C. & Murray Roberts, J. Predicting suitable habitat for the cold-water coral Lophelia pertusa (Scleractinia). Deep. Res. Part I Oceanogr. Res. Pap. 55, 1048–1062 (2008).

  • 21.

    Dullo, W. C., Flögel, S. & Rüggeberg, A. Cold-water coral growth in relation to the hydrography of the Celtic and Nordic European continental margin. Mar. Ecol. Prog. Ser. 371, 165–176 (2008).

  • 22.

    Dodds, L. A., Black, K. D., Orr, H. & Roberts, J. M. Lipid biomarkers reveal geographical differences in food supply to the cold-water coral Lophelia pertusa (Scleractinia). Mar. Ecol. Prog. Ser. 397, 113–124 (2009).

  • 23.

    Guinan, J., Grehan, A. J., Dolan, M. F. J. & Brown, C. Quantifying relationships between video observations of cold-water coral cover and seafloor features in rockall trough, west of Ireland. Mar. Ecol. Prog. Ser. 375, 125–138 (2009).

  • 24.

    Roberts, J. M. et al. Mingulay reef complex: An interdisciplinary study of cold-water coral habitat, hydrography and biodiversity. Mar. Ecol. Prog. Ser. 397, 139–151 (2009).

  • 25.

    Case, D. H., Robinson, L. F., Auro, M. E. & Gagnon, A. C. Environmental and biological controls on Mg and Li in deep-sea scleractinian corals. Earth Planet. Sci. Lett. 300, 215–225 (2010).

  • 26.

    Dolan, M. F. J., Grehan, A. J., Guinan, J. C. & Brown, C. Modelling the local distribution of cold-water corals in relation to bathymetric variables: Adding spatial context to deep-sea video data. Deep. Res. Part I Oceanogr. Res. Pap. 55, 1564–1579 (2008).

  • 27.

    Brooke, S. D., Holmes, M. W. & Young, C. M. Sediment tolerance of two different morphotypes of the deep-sea coral Lophelia pertusa from the Gulf of Mexico. Mar. Ecol. Prog. Ser. 390, 137–144 (2009).

  • 28.

    Frederiksen, R., Jensen, A. & Westerberg, H. The distribution of the scleractinian coral Lophelia pertusa around the Faroe Islands and the relation to internal tidal mixing. Sarsia 77, 157–171 (1992).

    • Article
    • Google Scholar
  • 29.

    McCulloch, M. et al. Resilience of cold-water scleractinian corals to ocean acidification: Boron isotopic systematics of pH and saturation state up-regulation. Geochim. Cosmochim. Acta 87, 21–34 (2012).

  • 30.

    Manel, S., Schwartz, M. K., Luikart, G. & Taberlet, P. Landscape genetics: Combining landscape ecology and population genetics. Trends Ecol. Evol. 18, 189–197 (2003).

    • Article
    • Google Scholar
  • 31.

    Richardson, J. L., Brady, S. P., Wang, I. J. & Spear, S. F. Navigating the pitfalls and promise of landscape genetics. Mol. Ecol. 25, 849–863 (2016).

  • 32.

    Selkoe, K. A., Henzler, C. M. & Gaines, S. D. Seascape genetics and the spatial ecology of marine populations. Fish Fish. 9, 363–377 (2008).

    • Article
    • Google Scholar
  • 33.

    Riginos, C. & Liggins, L. Seascape genetics: Populations, individuals, and genes marooned and adrift. Geogr. Compass 7, 197–216 (2013).

    • Article
    • Google Scholar
  • 34.

    Selkoe, K. A. et al. A decade of seascape genetics: Contributions to basic and applied marine connectivity. Mar. Ecol. Prog. Ser. 554, 1–19 (2016).

  • 35.

    Crandall, E. D., Treml, E. A. & Barber, P. H. Coalescent and biophysical models of stepping-stone gene flow in neritid snails. Mol. Ecol. 21, 5579–5598 (2012).

  • 36.

    Liggins, L., Treml, E. A., Possingham, H. P. & Riginos, C. Seascape features, rather than dispersal traits, predict spatial genetic patterns in co-distributed reef fishes. J. Biogeogr. 43, 256–267 (2016).

    • Article
    • Google Scholar
  • 37.

    Silva, C. N. S. & Gardner, J. P. A. Identifying environmental factors associated with the genetic structure of the New Zealand scallop: Linking seascape genetics and ecophysiological tolerance. ICES J. Mar. Sci. 73, 1925–1934 (2016).

    • Article
    • Google Scholar
  • 38.

    Wei, K., Wood, A. R. & Gardner, J. P. A. Seascape genetics of the New Zealand greenshell mussel: Sea surface temperature explains macrogeographic scale genetic variation. Mar. Ecol. Prog. Ser. 477, 107–121 (2013).

  • 39.

    Rousset, F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 154, 1219–1228 (1997).

    • Google Scholar
  • 40.

    Holderegger, R., Kamm, U. & Gugerli, F. Adaptive vs. neutral genetic diversity: Implications for landscape genetics. Landsc. Ecol. 21, 797–807 (2006).

    • Article
    • Google Scholar
  • 41.

    Wei, K., Wood, A. R. & Gardner, J. P. A. Population genetic variation in the New Zealand greenshell mussel: Locus-dependent conflicting signals of weak structure and high gene flow balanced against pronounced structure and high self-recruitment. Mar. Biol. 160, 931–949 (2013).

    • Article
    • Google Scholar
  • 42.

    Watling, L., Guinotte, J., Clark, M. R. & Smith, C. R. A proposed biogeography of the deep ocean floor. Prog. Oceanogr. 111, 91–112 (2013).

  • 43.

    Chiswell, S. M., Bostock, H. C., Sutton, P. J. & Williams, M. J. Physical oceanography of the deep seas around New Zealand: A review. New Zeal. J. Mar. Freshw. Res. 49, 1–32 (2015).

    • Article
    • Google Scholar
  • 44.

    Bucklin, A., Wilson, R. R. & Smith, K. L. Genetic differentiation of seamount and basin populations of the deep-sea amphipod Eurythenes gryllus. Deep Sea Res. Part A, Oceanogr. Res. Pap. 34, 1795–1810 (1987).

  • 45.

    Yang, C. H. et al. Connectivity of the squat lobsters Shinkaia crosnieri (Crustacea: Decapoda: Galatheidae) between cold seep and hydrothermal vent habitats. Bull. Mar. Sci. 32, 257 (2015).

    • Google Scholar
  • 46.

    Waller, R. G. & Tyler, P. A. The reproductive biology of two deep-water, reef-building scleractinians from the NE Atlantic Ocean. Coral Reefs 24, 514–522 (2005).

  • 47.

    Waller, R. G. Deep-water Scleractinia (Cnidaria: Anthozoa): Current knowledge of reproductive processes. Cold-water Corals Ecosyst. 691–700, https://doi.org/10.1007/3-540-27673-4_35 (2005).

  • 48.

    Waller, R. G., Tyler, P. A. & Gage, J. D. Sexual reproduction in three hermaphroditic deep-sea Caryophyllia species (Anthozoa: Scleractinia) from the NE Atlantic Ocean. Coral Reefs 24, 594–602 (2005).

  • 49.

    Pires, D. O., Silva, J. C. & Bastos, N. D. Reproduction of deep-sea reef-building corals from the southwestern. Atlantic. Deep. Res. Part II Top. Stud. Oceanogr. 99, 51–63 (2014).

  • 50.

    Burgess, S. N. & Babcock, R. C. In Cold-water Corals and Ecosystems. (eds Freiwald, A. & Roberts, J. M.) 701–713 (Springer-verlag 2015).

  • 51.

    Galindo, H. M. et al. Seascape genetics along a steep cline: Using genetic patterns to test predictions of marine larval dispersal. Mol. Ecol. https://doi.org/10.1111/j.1365-294X.2010.04694.x (2010).

  • 52.

    Nanninga, G. B., Saenz-Agudelo, P., Manica, A. & Berumen, M. L. Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea. Mol. Ecol. https://doi.org/10.1111/mec.12623 (2014).

  • 53.

    Saha, A. et al. Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms. ICES J. Mar. Sci. 72, 2732–2741 (2015).

    • Article
    • Google Scholar
  • 54.

    Silva, C. N. S. & Gardner, J. P. A. Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae. Mol. Ecol. 24, 5379–5393 (2015).

  • 55.

    Durrant, H. M. S., Barrett, N. S., Edgar, G. J., Coleman, M. A. & Burridge, C. P. Seascape habitat patchiness and hydrodynamics explain genetic structuring of kelp populations. Mar. Ecol. Prog. Ser. 587, 81–92 (2018).

  • 56.

    Boschen, R. E., Rowden, A. A., Clark, M. R. & Gardner, J. P. A. Limitations in the use of archived vent mussel samples to assess genetic connectivity among seafloor massive sulfide deposits: A case study with implications for environmental management. Front. Mar. Sci. 2, 1–14 (2015).

    • Article
    • Google Scholar
  • 57.

    Bryan, T. L. & Metaxas, A. Distribution of deep-water corals along the North American continental margins: Relationships with environmental factors. Deep. Res. Part I Oceanogr. Res. Pap. 53, 1865–1879 (2006).

  • 58.

    Tittensor, D. P. et al. Predicting global habitat suitability for stony corals on seamounts. J. Biogeogr. 36, 1111–1128 (2009).

    • Article
    • Google Scholar
  • 59.

    Woodby, D., Carlile, D. & Hulbert, L. Predictive modeling of coral distribution in the central Aleutian Islands, USA. Mar. Ecol. Prog. Ser. 397, 227–240 (2009).

  • 60.

    Fisher, C. R. et al. Footprint of deepwater horizon blowout impact to deep-water coral communities. Proc. Natl. Acad. Sci. USA 111, 11744–9 (2014).

  • 61.

    Tracey, D. M., Rowden, A. A., Mackay, K. A. & Compton, T. Habitat-forming cold-water corals show affinity for seamounts in the New Zealand region. Mar. Ecol. Prog. Ser. 430, 1–22 (2011).

  • 62.

    Thiem, Ø., Ravagnan, E., Fosså, J. H. & Berntsen, J. Food supply mechanisms for cold-water corals along a continental shelf edge. J. Mar. Syst. https://doi.org/10.1016/j.jmarsys.2005.12.004 (2006).

    • Article
    • Google Scholar
  • 63.

    White, M., Bashmachnikov, I., Arístegui, J. & Martins, A. Physical processes and seamount productivity. in Seamounts: Ecology, fisheries & conservation (eds. Pitcher, T. J. et al.) 10.1002/9780470691953.ch4. (Blackwell Publishing Ltd, 2008).

  • 64.

    Guinotte, J. M. et al. Will human-induced changes in seawater chemistry alter the distribution of deep-sea scleractinian corals? Front. Ecol. Environ. 4, 141–146 (2006).

    • Article
    • Google Scholar
  • 65.

    Davies, A. J. & Guinotte, J. M. Global habitat suitability for framework-forming cold-water corals. PLoS One 6, e18483 (2011).

  • 66.

    Hurst, R., Renwick, J., Uddstrom, M., Kennan, S. & Rickard, G. J. Climate and ocean trends of potential relevance to fisheries in the New Zealand region.New Zealand Aquatic Environment and Biodiversity Report No. 90. (2012).

  • 67.

    Abelson, A., Miloh, T. & Loya, Y. Flow patterns induced by substrata and body morphologies of benthic organisms, and their roles in determining availability of food particles. Limnol. Oceanogr. 38, 1116–1124 (1993).

  • 68.

    Kaiser, M. J. et al. Marine ecology: Processes, systems and impacts. Marine Ecology vol. 0 (Oxford University Press, 2011).

  • 69.

    Thorson, G. Reproductive and larval ecology of marine bottom invertebrates. Biol. Rev. 25, 1–45 (1950).

  • 70.

    Buss, L. W. & Jackson, J. B. C. Planktonic food availability and suspension-feeder abundance: Evidence of in situ depletion. J. Exp. Mar. Bio. Ecol. 49, 151–161 (1981).

    • Article
    • Google Scholar
  • 71.

    Bertness, M. D. & Gaines, S. D. Larval dispersal and local adaptation in acorn barnacles. Evolution (N. Y). 47, 316–320 (1993).

    • Google Scholar
  • 72.

    Qian, P. Y. Effect of food quantity on growth and reproductive characteristics of Capitella sp (Annelida: Polychaeta). Invertebr. Reprod. Dev. 26, 175–185 (1994).

    • Article
    • Google Scholar
  • 73.

    Pechenik, J. A., Estrella, M. S. & Hammer, K. Food limitation stimulates metamorphosis of competent larvae and alters postmetamorphic growth rate in the marine prosobranch gastropod Crepidula fornicata. Mar. Biol. 127, 267–275 (1996).

    • Article
    • Google Scholar
  • 74.

    Fouzai, N., Opdal, A., Jørgensen, C. & Fiksen, Ø. Effects of temperature and food availability on larval cod survival: A model for behaviour in vertical gradients. Mar. Ecol. Prog. Ser. 529, 199–212 (2015).

  • 75.

    Seibel, B. A. & Drazen, J. C. The rate of metabolism in marine animals: Environmental constraints, ecological demands and energetic opportunities. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 362, 2061–78 (2007).

  • 76.

    Giles, E. C., Saenz-Agudelo, P., Hussey, N. E., Ravasi, T. & Berumen, M. L. Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea. Ecol. Evol. 5, 2487–2502 (2015).

  • 77.

    Hadas, E., Shpigel, M. & Ilan, M. Particulate organic matter as a food source for a coral reef sponge. J. Exp. Biol. 212, 3643–3650 (2009).

  • 78.

    Knudby, A., Kenchington, E. & Murillo, F. J. Modeling the distribution of Geodia sponges and sponge grounds in the Northwest Atlantic. PLoS One 8, e82306 (2013).

  • 79.

    Rooper, C. N., Zimmermann, M., Prescott, M. M. & Hermann, A. J. Predictive models of coral and sponge distribution, abundance and diversity in bottom trawl surveys of the Aleutian Islands, Alaska. Mar. Ecol. Prog. Ser. 503, 157–176 (2014).

  • 80.

    Waples, R. S. & Do, C. ldne: A program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8, 753–6 (2008).

  • 81.

    McCook, L. J. et al. Management under uncertainty: Guide-lines for incorporating connectivity into the protection of coral reefs. Coral Reefs 28, 353–366 (2009).

  • 82.

    Haig, S. M. et al. The conservation genetics juggling act: Integrating genetics and ecology, science and policy. Evol. Appl. 9, 181–195 (2016).

  • 83.

    Selkoe, K. A. et al. The DNA of coral reef biodiversity: Predicting and protecting genetic diversity of reef assemblages. Proc. R. Soc. B Biol. Sci. 283, 20160354 (2016).

  • 84.

    Anderson, O. F. et al. Field validation of habitat suitability models for vulnerable marine ecosystems in the South Pacific Ocean: Implications for the use of broad-scale models in fisheries management. Ocean Coast. Manag. 120, 110–126 (2016).

    • Article
    • Google Scholar
  • 85.

    Anderson, O. F. et al. Habitat suitability models for predicting the occurrence of vulnerable marine ecosystems in the seas around New Zealand. Deep. Res. Part I Oceanogr. Res. Pap. 115, 265–292 (2016).

  • 86.

    Boschen, R. E. et al. A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities. Ocean Coast. Manag. 122, 37–48 (2016).

    • Article
    • Google Scholar
  • 87.

    Prunier, J. G. et al. Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: Towards a better assessment of functional connectivity using an individual-based sampling scheme. Mol. Ecol. 22, 5516–5530 (2013).

  • 88.

    Hall, L. A. & Beissinger, S. R. A practical toolbox for design and analysis of landscape genetics studies. Landsc. Ecol. 29, 1487–1504 (2014).

    • Article
    • Google Scholar
  • 89.

    Luximon, N., Petit, E. J. & Broquet, T. Performance of individual vs. group sampling for inferring dispersal under isolation-by-distance. Mol. Ecol. Resour. 14, 745–752 (2014).

  • 90.

    Gebremedhin, B. et al. Frontiers in identifying conservation units: From neutral markers to adaptive genetic variation. Anim. Conserv. 12, 107–109 (2009).

    • Article
    • Google Scholar
  • 91.

    Antao, T., Lopes, A., Lopes, R. J., Beja-Pereira, A. & Luikart, G. LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9, 1–5 (2008).

  • 92.

    van Oosterhout, C., Hutchinson, W. F., Wills, D. P. M. & Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4, 535–538 (2004).

  • 93.

    Gagnaire, P. A. et al. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol. Appl. 8, 769–786 (2015).

  • 94.

    Graham, M. H. Confronting multicollinearity in ecological multiple regression. Ecology 84, 2809–2815 (2003).

    • Article
    • Google Scholar
  • 95.

    Team, R. C. R. A Language and Environment for Statistical Computing. Vienna, Austria (2019).

  • 96.

    Peakall, R. & Smouse, P. E. GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537–2539 (2012).

  • 97.

    Anderson, M. J., Gorley, R. N. & Clarke, K. R. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods. (primer-E Limited, 2008).


  • Source: Ecology - nature.com

    What is the future of lithium battery waste?

    Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms