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1. Environment, ecology, and potential effectiveness of an area protected from deep-sea mining (Clarion Clipperton Zone, abyssal Pacific)

Author

Jones, Daniel O.B., Simon-Lledó, Erik, Amon, Diva J., Bett, Brian J., Caulle, Clémence, Clément, Louis, Connelly, Douglas P., Dahlgren, Thomas G., Durden, Jennifer M., Drazen, Jeffrey C., Felden, Janine, Gates, Andrew R., Georgieva, Magdalena N., Glover, Adrian G., Gooday, Andrew J., Hollingsworth, Anita L., Horton, Tammy, James, Rachael H., Jeffreys, Rachel M., Laguionie-Marchais, Claire, Leitner, Astrid B., Lichtschlag, Anna, Menendez, Amaya, Paterson, Gordon L.J., Peel, Kate, Robert, Katleen, Schoening, Timm, Shulga, Natalia A., Smith, Craig R., Taboada, Sergio, Thurnherr, Andreas M., Wiklund, Helena, Young, C. Robert, and Huvenne, Veerle A.I.

Published
2021
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2. Polychaete community structure and biodiversity change in space and time at the abyssal seafloor

Author

Laguionie-Marchais, Claire and Ruhl, Henry

Subjects
550, GC Oceanography, QH301 Biology
Abstract

The deep sea is a dynamic environment over various spatio-temporal scales. But, the characteristics of deep-sea natural variations and underlying processes remain poorly understood, which prevents contextualising any anthropogenic impact on this environment. Long-term observations, from which inter-annual variations can be detected, as well as detailed broad-scale spatial observations, are scarce in the deep sea. In this thesis, I examined changes in both spatial (~ 0.1-10s km scale) and temporal (inter-annual scale) domains in abyssal benthic fauna at two abyssal stations in the North East Pacific (Station M, 1991 to 2011) and in the North East Atlantic (Porcupine Abyssal Plain, PAP, 1991 to 2012) using Polychaeta as study organisms. Four main results were found. 1) At intermediate scales (0.1 to 10s km), the macrofauna and polychaete family composition were related to the sediment grain size distribution (Chapter 2). Differences in sediment grain size distribution between and among abyssal hills created habitat heterogeneity. Differences in near-bed current flows, and thus in particle size and food settling conditions, may be the primary factors influencing the sediment particle size distribution and macrofauna. Overall polychaetes and macrofauna may be more spatially variable than previously thought in abyssal areas when considering that abyssal hills might be one of the most common topographic features on Earth. 2) At inter-annual scale, polychaete families and functional groups varied in density, diversity and community structure at Sta. M and PAP (chapter 3). Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Differences may be related to the quantity and quality of the particulate organic carbon reaching the seafloor. Overall, changes in the dominance of functional groups imply changes in abyssal ecosystem functioning. 3) At inter-annual scale, the dynamics of polychaete abundances and body sizes suggested that migration/enhanced survivorship and recruitment events occurred (chapter 4). The densities and median body sizes of the five density-dominant species at Sta. M were analysed over time to help elucidate population dynamics as population parameters such as reproduction or growth rate could not be directly measured. The results indicated that the density dynamics of Paradoneis cf. lyra may have be related to enhanced survivorship or immigration of adult individuals, while the density dynamics of Cossura cf. rostrata may have be linked to individuals shifting between growth and reproduction. 4) At inter-annual scale, Sta. M polychaete changes were detected in standing stocks, rank distributions, species and functional group composition (chapter 5). Although a change in sampling location occurred after 2005, preventing ascribing the assemblage change unequivocally to particular environmental drivers, analyses prior to 2005 showed that the polychaete assemblage composition dynamics were primary driven by food supply variation. Overall, energetic zero-sum dynamics were not clearly observed at polychaete assemblage level, but were evident in the greater macrofauna community that includes the polychaetes. Polychaete displayed stability in body size structure in space and time, following the predictions of the metabolic theory of ecology. In conclusion, this work highlighted that abyssal polychaete communities can change over spatial scales of tens of square kilometres and time scales of months or more; this work found a large but as yet underappreciated variability.

Published
2015

3. BioTIME: A database of biodiversity time series for the Anthropocene

Author

Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błazewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Collier, Laura Siegwart, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J. Hans C., Cotano, Unai, Crow, Shannan Kyle, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Farah, Fabiano Turini, Fernandes, Luiz Loureiro, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Franco, Geraldo Antonio Daher Correa, Frank, Grace E., Fraser, William R., García, Hernando, Gatti, Roberto Cazzolla, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Ivanauskas, Natália Macedo, Janík, David, Jandt, Ute, Jazdzewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. M., Kang, Jungwon, Kartawijaya, Tasrif, Keeley, Erin C., Kelt, Douglas A., Kinnear, Rebecca, Klanderud, Kari, Knutsen, Halvor, Koenig, Christopher C., Kortz, Alessandra R., Král, Kamil, Kuhnz, Linda A., Kuo, Chao-Yang, Kushner, David J., Laguionie-Marchais, Claire, Lancaster, Lesley T., Lee, Cheol Min, Lefcheck, Jonathan S., Lévesque, Esther, Lightfoot, David, Lloret, Francisco, Lloyd, John D., López-Baucells, Adrià, Louzao, Maite, Madin, Joshua S., Magnússon, Borgþór, Malamud, Shahar, Matthews, Iain, McFarland, Kent P., McGill, Brian, McKnight, Diane, McLarney, William O., Meador, Jason, Meserve, Peter L., Metcalfe, Daniel J., Meyer, Christoph F. J., Michelsen, Anders, Milchakova, Nataliya, Moens, Tom, Moland, Even, Moore, Jon, Moreira, Carolina Mathias, Müller, Jörg, Murphy, Grace, Myers-Smith, Isla H., Myster, Randall W., Naumov, Andrew, Neat, Francis, Nelson, James A., Nelson, Michael Paul, Newton, Stephen F., Norden, Natalia, Oliver, Jeffrey C., Olsen, Esben M., Onipchenko, Vladimir G., Pabis, Krzysztof, Pabst, Robert J., Paquette, Alain, Pardede, Sinta, Paterson, David M., Pélissier, Raphaël, Peñuelas, Josep, Pérez-Matus, Alejandro, Pizarro, Oscar, Pomati, Francesco, Post, Eric, Prins, Herbert H. T., Priscu, John C., Provoost, Pieter, Prudic, Kathleen L., Pulliainen, Erkki, Ramesh, B. R., Ramos, Olivia Mendivil, Rassweiler, Andrew, Remillard, Suzanne M., Richardson, Anthony J., Richardson, J. Paul, van Rijn, Itai, Rocha, Ricardo, Rivera-Monroy, Victor H., Rixen, Christian, Robinson, Kevin P., Rodrigues, Ricardo Ribeiro, de Cerqueira Rossa-Feres, Denise, Rudstam, Lars, Ruhl, Henry, Ruz, Catalina S., Sampaio, Erica M., Rybicki, Nancy, Rypel, Andrew, Sal, Sofia, Salgado, Beatriz, Santos, Flavio A. M., Savassi-Coutinho, Ana Paula, Scanga, Sara, Schmidt, Jochen, Schooley, Robert, Setiawan, Fakhrizal, Shao, Kwang-Tsao, Shaver, Gaius R., Sherman, Sally, Sherry, Thomas W., Siciński, Jacek, Sievers, Caya, da Silva, Ana Carolina, da Silva, Fernando Rodrigues, Silveira, Fabio L., Slingsby, Jasper, Smart, Tracey, Snell, Sara J., Soudzilovskaia, Nadejda A., Souza, Gabriel B. G., Souza, Flaviana Maluf, Souza, Vinícius Castro, Stallings, Christopher D., Stanforth, Rowan, Stanley, Emily H., Sterza, José Mauro, Stevens, Maarten, Stuart-Smith, Rick, Suarez, Yzel Rondon, Supp, Sarah, Tamashiro, Jorge Yoshio, Tarigan, Sukmaraharja, Thiede, Gary P., Thorn, Simon, Tolvanen, Anne, Toniato, Maria Teresa Zugliani, Totland, Ørjan, Twilley, Robert R., Vaitkus, Gediminas, Valdivia, Nelson, Vallejo, Martha Isabel, Valone, Thomas J., Van Colen, Carl, Vanaverbeke, Jan, Venturoli, Fabio, Verheye, Hans M., Vianna, Marcelo, Vieira, Rui P., Vrška, Tomáš, Vu, Con Quang, Van Vu, Lien, Waide, Robert B., Waldock, Conor, Watts, Dave, Webb, Sara, Wesołowski, Tomasz, White, Ethan P., Widdicombe, Claire E., Wilgers, Dustin, Williams, Richard, Williams, Stefan B., Williamson, Mark, Willig, Michael R., Willis, Trevor J., Wipf, Sonja, Woods, Kerry D., Woehler, Eric J., Zawada, Kyle, and Zettler, Michael L.

Published
2018

6. Not Drug-like, but Like Drugs: Cnidaria Natural Products

Author

Laguionie-Marchais, Claire, primary, Allcock, A. Louise, additional, Baker, Bill J., additional, Conneely, Ellie-Ann, additional, Dietrick, Sarah G., additional, Kearns, Fiona, additional, McKeever, Kate, additional, Young, Ryan M., additional, Sierra, Connor A., additional, Soldatou, Sylvia, additional, Woodcock, H. Lee, additional, and Johnson, Mark P., additional

Published
2021
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7. Environment, ecology, and potential effectiveness of an area protected from deep-sea mining (Clarion Clipperton Zone, abyssal Pacific)

Author

Jones, Daniel, Simon-Lledó, Erik, Amon, Diva J., Bett, Brian J., Caulle, Clémence, Clement, Louis, Connelly, Douglas P., Dahlgren, Thomas G., Durden, Jennifer, Drazen, Jeffrey C., Felden, Janine, Gates, Andrew, Georgieva, Magdalena N., Glover, Adrian G., Gooday, Andrew, Hollingsworth, Anita L., Horton, Tammy, James, Rachael H., Jeffreys, Rachel M., Laguionie-Marchais, Claire, Leitner, Astrid B., Lichtschlag, Anna, Menendez, Amaya, Paterson, Gordon L.J., Peel, Kate, Robert, Katleen, Schoening, Timm, Shulga, Natalia A., Smith, Craig R., Taboada, Sergio, Thurnherr, Andreas M., Wiklund, Helena, Young III, C. Robert, Huvenne, Veerle, Jones, Daniel, Simon-Lledó, Erik, Amon, Diva J., Bett, Brian J., Caulle, Clémence, Clement, Louis, Connelly, Douglas P., Dahlgren, Thomas G., Durden, Jennifer, Drazen, Jeffrey C., Felden, Janine, Gates, Andrew, Georgieva, Magdalena N., Glover, Adrian G., Gooday, Andrew, Hollingsworth, Anita L., Horton, Tammy, James, Rachael H., Jeffreys, Rachel M., Laguionie-Marchais, Claire, Leitner, Astrid B., Lichtschlag, Anna, Menendez, Amaya, Paterson, Gordon L.J., Peel, Kate, Robert, Katleen, Schoening, Timm, Shulga, Natalia A., Smith, Craig R., Taboada, Sergio, Thurnherr, Andreas M., Wiklund, Helena, Young III, C. Robert, and Huvenne, Veerle

Abstract

To protect the range of habitats, species, and ecosystem functions in the Clarion Clipperton Zone (CCZ), a region of interest for deep-sea polymetallic nodule mining in the Pacific, nine Areas of Particular Environmental Interest (APEIs) have been designated by the International Seabed Authority (ISA). The APEIs are remote, rarely visited and poorly understood. Here we present and synthesise all available observations made at APEI-6, the most north eastern APEI in the network, and assess its representativity of mining contract areas in the eastern CCZ. The two studied regions of APEI-6 have a variable morphology, typical of the CCZ, with hills, plains and occasional seamounts. The seafloor is predominantly covered by fine-grained sediments, and includes small but abundant polymetallic nodules, as well as exposed bedrock. The oceanographic parameters investigated appear broadly similar across the region although some differences in deep-water mass separation were evident between APEI-6 and some contract areas. Sediment biogeochemistry is broadly similar across the area in the parameters investigated, except for oxygen penetration depth, which reached >2 m at the study sites within APEI-6, deeper than that found at UK1 and GSR contract areas. The ecology of study sites in APEI-6 differs from that reported from UK1 and TOML-D contract areas, with differences in community composition of microbes, macrofauna, xenophyophores and metazoan megafauna. Some species were shared between areas although connectivity appears limited. We show that, from the available information, APEI-6 is partially representative of the exploration areas to the south yet is distinctly different in several key characteristics. As a result, additional APEIs may be warranted and caution may need to be taken in relying on the APEI network alone for conservation, with other management activities required to help mitigate the impacts of mining in the CCZ.

Published
2021

9. Using metabolic theory to assess structure and function in the deep-sea benthos, including microbial and metazoan dominance

Author

Laguionie Marchais, Claire, Bett, Brian J., Paterson, Gordon L.J., Smith, Kenneth L., Ruhl, Henry A., Laguionie Marchais, Claire, Bett, Brian J., Paterson, Gordon L.J., Smith, Kenneth L., and Ruhl, Henry A.

Abstract

Constraining seafloor carbon stocks and flows, and their links to biodiversity, remains a major global challenge, particularly in the deep ocean. We examine the density, biomass, respiration, and species richness size spectra of polychaetes from a time-series study (1991–2011) in the abyssal NE Pacific (Station M, 35°N, 123°W, 4000 m water depth). The spectra met the predictions of the metabolic theory of ecology (MTE) and were consistent with Damuth's rule of energetic equivalence. When combined via MTE, resource supply rate and habitat temperature have valuable predictive power for seafloor standing stocks. Intra-annual comparisons suggested seasonally variable resource acquisition rates and metabolism, consistent with the scope for specific dynamic action in polychaetes. Accepting and applying the assumptions of MTE, Damuth's rule, and 3/4-power mass-scaling of metabolism to the entire benthos, then two thirds of carbon remineralised at the seafloor might be attributable to metazoan invertebrates. This is contrary to the common finding of microbial dominance but may be resolved by considering (1) that only a fraction of microbial biomass may be metabolically active, and (2) that the metabolism of the largest members of the benthos could only be assessed at physical scales very much greater than are usually examined.

Published
2020

11. A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Author

Howell, Kerry L., primary, Davies, Jaime S., additional, Allcock, A. Louise, additional, Braga-Henriques, Andreia, additional, Buhl-Mortensen, Pål, additional, Carreiro-Silva, Marina, additional, Dominguez-Carrió, Carlos, additional, Durden, Jennifer M., additional, Foster, Nicola L., additional, Game, Chloe A., additional, Hitchin, Becky, additional, Horton, Tammy, additional, Hosking, Brett, additional, Jones, Daniel O. B., additional, Mah, Christopher, additional, Laguionie Marchais, Claire, additional, Menot, Lenaick, additional, Morato, Telmo, additional, Pearman, Tabitha R. R., additional, Piechaud, Nils, additional, Ross, Rebecca E., additional, Ruhl, Henry A., additional, Saeedi, Hanieh, additional, Stefanoudis, Paris V., additional, Taranto, Gerald H., additional, Thompson, Michael B., additional, Taylor, James R., additional, Tyler, Paul, additional, Vad, Johanne, additional, Victorero, Lissette, additional, Vieira, Rui P., additional, Woodall, Lucy C., additional, Xavier, Joana R., additional, and Wagner, Daniel, additional

Published
2019
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12. A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Author

Howell, Kerry L., Davies, Jaime S., Allcock, A. Louise, Braga-henriques, Andreia, Buhl-mortensen, Pål, Carreiro-silva, Marina, Dominguez-carrió, Carlos, Durden, Jennifer M., Foster, Nicola L., Game, Chloe A., Hitchin, Becky, Horton, Tammy, Hosking, Brett, Jones, Daniel Ob, Mah, Christopher, Laguionie Marchais, Claire, Menot, Lenaick, Morato, Telmo, Pearman, Tabitha R. R., Piechaud, Nils, Ross, Rebecca E., Ruhl, Henry A., Saeedi, Hanieh, Stefanoudis, Paris V., Taranto, Gerald H., Thompson, Michael B., Taylor, James R., Tyler, Paul, Vad, Johanne, Victorero, Lissette, Vieira, Rui P., Woodall, Lucy C., Xavier, Joana R., Wagner, Daniel, Howell, Kerry L., Davies, Jaime S., Allcock, A. Louise, Braga-henriques, Andreia, Buhl-mortensen, Pål, Carreiro-silva, Marina, Dominguez-carrió, Carlos, Durden, Jennifer M., Foster, Nicola L., Game, Chloe A., Hitchin, Becky, Horton, Tammy, Hosking, Brett, Jones, Daniel Ob, Mah, Christopher, Laguionie Marchais, Claire, Menot, Lenaick, Morato, Telmo, Pearman, Tabitha R. R., Piechaud, Nils, Ross, Rebecca E., Ruhl, Henry A., Saeedi, Hanieh, Stefanoudis, Paris V., Taranto, Gerald H., Thompson, Michael B., Taylor, James R., Tyler, Paul, Vad, Johanne, Victorero, Lissette, Vieira, Rui P., Woodall, Lucy C., Xavier, Joana R., and Wagner, Daniel

Abstract

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

Published
2019
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13. A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Author

Lecours, Vincent, Howell, Kerry L., Davies, Jaime S., Allcock, A. Louise, Braga-Henriques, Andreia, Buhl-Mortensen, Pål, Carreiro-Silva, Marina, Dominguez-Carrió, Carlos, Durden, Jennifer M., Foster, Nicola L., Game, Chloe A., Hitchin, Becky, Horton, Tammy, Hosking, Brett, Jones, Daniel O. B., Mah, Christopher, Laguionie Marchais, Claire, Menot, Lenaick, Morato, Telmo, Pearman, Tabitha R. R., Piechaud, Nils, Ross, Rebecca E., Ruhl, Henry A., Saeedi, Hanieh, Stefanoudis, Paris V., Taranto, Gerald H., Thompson, Michael B., Taylor, James R., Tyler, Paul, Vad, Johanne, Victorero, Lissette, Vieira, Rui P., Woodall, Lucy C., Xavier, Joana R., Wagner, Daniel, Lecours, Vincent, Howell, Kerry L., Davies, Jaime S., Allcock, A. Louise, Braga-Henriques, Andreia, Buhl-Mortensen, Pål, Carreiro-Silva, Marina, Dominguez-Carrió, Carlos, Durden, Jennifer M., Foster, Nicola L., Game, Chloe A., Hitchin, Becky, Horton, Tammy, Hosking, Brett, Jones, Daniel O. B., Mah, Christopher, Laguionie Marchais, Claire, Menot, Lenaick, Morato, Telmo, Pearman, Tabitha R. R., Piechaud, Nils, Ross, Rebecca E., Ruhl, Henry A., Saeedi, Hanieh, Stefanoudis, Paris V., Taranto, Gerald H., Thompson, Michael B., Taylor, James R., Tyler, Paul, Vad, Johanne, Victorero, Lissette, Vieira, Rui P., Woodall, Lucy C., Xavier, Joana R., and Wagner, Daniel

Abstract

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

Published
2019

15. Polychaete community structure and biodiversity change in space and time at the abyssal seafloor

Author

Laguionie-Marchais, Claire. and Laguionie-Marchais, Claire.

Abstract

The deep sea is a dynamic environment over various spatio-temporal scales. But, the characteristics of deep-sea natural variations and underlying processes remain poorly understood, which prevents contextualising any anthropogenic impact on this environment. Long-term observations, from which inter-annual variations can be detected, as well as detailed broad-scale spatial observations, are scarce in the deep sea. In this thesis, I examined changes in both spatial (~ 0.1-10s km scale) and temporal (inter-annual scale) domains in abyssal benthic fauna at two abyssal stations in the North East Pacific (Station M, 1991 to 2011) and in the North East Atlantic (Porcupine Abyssal Plain, PAP, 1991 to 2012) using Polychaeta as study organisms. Four main results were found. 1) At intermediate scales (0.1 to 10s km), the macrofauna and polychaete family composition were related to the sediment grain size distribution (Chapter 2). Differences in sediment grain size distribution between and among abyssal hills created habitat heterogeneity. Differences in near-bed current flows, and thus in particle size and food settling conditions, may be the primary factors influencing the sediment particle size distribution and macrofauna. Overall polychaetes and macrofauna may be more spatially variable than previously thought in abyssal areas when considering that abyssal hills might be one of the most common topographic features on Earth. 2) At inter-annual scale, polychaete families and functional groups varied in density, diversity and community structure at Sta. M and PAP (chapter 3). Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Differences may be related to the quantity and quality of the particulate organic carbon reaching the seafloor. Overall, changes in the dominance of functional groups imply changes in abyssal ecosystem functioning. 3) At

Published
2015

19. Not Drug-like, but Like Drugs: Cnidaria Natural Products.

Author

Laguionie-Marchais, Claire, Allcock, A. Louise, Baker, Bill J., Conneely, Ellie-Ann, Dietrick, Sarah G., Kearns, Fiona, McKeever, Kate, Young, Ryan M., Sierra, Connor A., Soldatou, Sylvia, Woodcock, H. Lee, and Johnson, Mark P.

Abstract

Phylum Cnidaria has been an excellent source of natural products, with thousands of metabolites identified. Many of these have not been screened in bioassays. The aim of this study was to explore the potential of 5600 Cnidaria natural products (after excluding those known to derive from microbial symbionts), using a systematic approach based on chemical space, drug-likeness, predicted toxicity, and virtual screens. Previous drug-likeness measures: the rule-of-five, quantitative estimate of drug-likeness (QED), and relative drug likelihoods (RDL) are based on a relatively small number of molecular properties. We augmented this approach using reference drug and toxin data sets defined for 51 predicted molecular properties. Cnidaria natural products overlap with drugs and toxins in this chemical space, although a multivariate test suggests that there are some differences between the groups. In terms of the established drug-likeness measures, Cnidaria natural products have generally lower QED and RDL scores than drugs, with a higher prevalence of metabolites that exceed at least one rule-of-five threshold. An index of drug-likeness that includes predicted toxicity (ADMET-score), however, found that Cnidaria natural products were more favourable than drugs. A measure of the distance of individual Cnidaria natural products to the centre of the drug distribution in multivariate chemical space was related to RDL, ADMET-score, and the number of rule-of-five exceptions. This multivariate similarity measure was negatively correlated with the QED score for the same metabolite, suggesting that the different approaches capture different aspects of the drug-likeness of individual metabolites. The contrasting of different drug similarity measures can help summarise the range of drug potential in the Cnidaria natural product data set. The most favourable metabolites were around 210–265 Da, quite often sesquiterpenes, with a moderate degree of complexity. Virtual screening against cancer-relevant targets found wide evidence of affinities, with Glide scores <−7 in 19% of the Cnidaria natural products. [ABSTRACT FROM AUTHOR]

Published
2022
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20. BioTIME: A database of biodiversity time series for the Anthropocene

Author

<p>Funding information available at <a href="https://doi.org/10.1111/geb.12729" target="_blank" title="Link to publication">https://doi.org/10.1111/geb.12729</a></p>, Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błażewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Siegwart Collier, Laura, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J Hans C., Cotano, Unai, Kyle Crow, Shannan, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Turini Farah, Fabiano, Loureiro Fernandes, Luiz, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Daher Correa Franco, Geraldo Antonio, Frank, Grace E., Fraser, William R., García, Hernando, Cazzolla Gatti, Roberto, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-Hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Macedo Ivanauskas, Natália, Janík, David, Jandt, Ute, Jażdżewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. M., Kang, Jungwon, Kartawijaya, Tasrif, Keeley, Erin C., Kelt, Douglas A., Kinnear, Rebecca, Klanderud, Kari, Knutsen, Halvor, Koenig, Christopher C., Kortz, Alessandra R., Král, Kamil, Kuhnz, Linda A., Kuo, Chao-Yang, Kushner, David J., Laguionie-Marchais, Claire, Lancaster, Lesley T., Min Lee, Cheol, Lefcheck, Jonathan S., Lévesque, Esther, Lightfoot, David, Lloret, Francisco, Lloyd, John D., López-Baucells, Adrià, Louzao, Maite, Madin, Joshua S., Magnússon, Borgþór, Malamud, Shahar, Matthews, Iain, McFarland, Kent P., McGill, Brian, McKnight, Diane, McLarney, William O., Meador, Jason, Meserve, Peter L., Metcalfe, Daniel J., Meyer, Christoph F. J., Michelsen, Anders, Milchakova, Nataliya, Moens, Tom, Moland, Even, Moore, Jon, Mathias Moreira, Carolina, Müller, Jörg, Murphy, Grace, Myers-Smith, Isla H., Myster, Randall W., Naumov, Andrew, Neat, Francis, Nelson, James A., Paul Nelson, Michael, Newton, Stephen F., Norden, Natalia, Oliver, Jeffrey C., Olsen, Esben M., Onipchenko, Vladimir G., Pabis, Krzysztof, Pabst, Robert J., Paquette, Alain, Pardede, Sinta, Paterson, David M., Pélissier, Raphaël, Peñuelas, Josep, Pérez-Matus, Alejandro, Pizarro, Oscar, Pomati, Francesco, Post, Eric, Prins, Herbert H. T., Priscu, John C., Provoost, Pieter, Prudic, Kathleen L., Pulliainen, Erkki, Ramesh, B. R., Mendivil Ramos, Olivia, Rassweiler, Andrew, Rebelo, Jose Eduardo, Reed, Daniel C., Reich, Peter B., Remillard, Suzanne M., Richardson, Anthony J., Richardson, J. Paul, van Rijn, Itai, Rocha, Ricardo, Rivera-Monroy, Victor H., Rixen, Christian, Robinson, Kevin P., Ribeiro Rodrigues, Ricardo, de Cerqueira Rossa-Feres, Denise, Rudstam, Lars, Ruhl, Henry, Ruz, Catalina S., Sampaio, Erica M., Rybicki, Nancy, Rypel, Andrew, Sal, Sofia, Salgado, Beatriz, Santos, Flavio A. M., Savassi-Coutinho, Ana Paula, Scanga, Sara, Schmidt, Jochen, Schooley, Robert, Setiawan, Fakhrizal, Shao, Kwang-Tsao, Shaver, Gaius R., Sherman, Sally, Sherry, Thomas W., Siciński, Jacek, Sievers, Caya, da Silva, Ana Carolina, Rodrigues da Silva, Fernando, Silveira, Fabio L., Slingsby, Jasper, Smart, Tracey, Snell, Sara J., Soudzilovskaia, Nadejda A., Souza, Gabriel B. G., Maluf Souza, Flaviana, Castro Souza, Vinícius, Stallings, Christopher D., Stanforth, Rowan, Stanley, Emily H., Mauro Sterza, José, Stevens, Maarten, Stuart-Smith, Rick, Rondon Suarez, Yzel, Supp, Sarah, Yoshio Tamashiro, Jorge, Tarigan, Sukmaraharja, Thiede, Gary P., Thorn, Simon, Tolvanen, Anne, Teresa Zugliani Toniato, Maria, Totland, Ørjan, Twilley, Robert R., Vaitkus, Gediminas, Valdivia, Nelson, Vallejo, Martha Isabel, Valone, Thomas J., Van Colen, Carl, Vanaverbeke, Jan, Venturoli, Fabio, Verheye, Hans M., Vianna, Marcelo, Vieira, Rui P., Vrška, Tomáš, Quang Vu, Con, Van Vu, Lien, Waide, Robert B., Waldock, Conor, Watts, Dave, Webb, Sara, Wesołowski, Tomasz, White, Ethan P., Widdicombe, Claire E., Wilgers, Dustin, Williams, Richard, Williams, Stefan B., Williamson, Mark, Willig, Michael R., Willis, Trevor J., Wipf, Sonja, Woods, Kerry D., Woehler, Eric J., Zawada, Kyle, Zettler, Michael L., <p>Funding information available at <a href="https://doi.org/10.1111/geb.12729" target="_blank" title="Link to publication">https://doi.org/10.1111/geb.12729</a></p>, Dornelas, Maria, Antão, Laura H., Moyes, Faye, Bates, Amanda E., Magurran, Anne E., Adam, Dušan, Akhmetzhanova, Asem A., Appeltans, Ward, Arcos, José Manuel, Arnold, Haley, Ayyappan, Narayanan, Badihi, Gal, Baird, Andrew H., Barbosa, Miguel, Barreto, Tiago Egydio, Bässler, Claus, Bellgrove, Alecia, Belmaker, Jonathan, Benedetti-Cecchi, Lisandro, Bett, Brian J., Bjorkman, Anne D., Błażewicz, Magdalena, Blowes, Shane A., Bloch, Christopher P., Bonebrake, Timothy C., Boyd, Susan, Bradford, Matt, Brooks, Andrew J., Brown, James H., Bruelheide, Helge, Budy, Phaedra, Carvalho, Fernando, Castañeda-Moya, Edward, Chen, Chaolun Allen, Chamblee, John F., Chase, Tory J., Siegwart Collier, Laura, Collinge, Sharon K., Condit, Richard, Cooper, Elisabeth J., Cornelissen, J Hans C., Cotano, Unai, Kyle Crow, Shannan, Damasceno, Gabriella, Davies, Claire H., Davis, Robert A., Day, Frank P., Degraer, Steven, Doherty, Tim S., Dunn, Timothy E., Durigan, Giselda, Duffy, J. Emmett, Edelist, Dor, Edgar, Graham J., Elahi, Robin, Elmendorf, Sarah C., Enemar, Anders, Ernest, S. K. Morgan, Escribano, Rubén, Estiarte, Marc, Evans, Brian S., Fan, Tung-Yung, Turini Farah, Fabiano, Loureiro Fernandes, Luiz, Farneda, Fábio Z., Fidelis, Alessandra, Fitt, Robert, Fosaa, Anna Maria, Daher Correa Franco, Geraldo Antonio, Frank, Grace E., Fraser, William R., García, Hernando, Cazzolla Gatti, Roberto, Givan, Or, Gorgone-Barbosa, Elizabeth, Gould, William A., Gries, Corinna, Grossman, Gary D., Gutierréz, Julio R., Hale, Stephen, Harmon, Mark E., Harte, John, Haskins, Gary, Henshaw, Donald L., Hermanutz, Luise, Hidalgo, Pamela, Higuchi, Pedro, Hoey, Andrew, Van Hoey, Gert, Hofgaard, Annika, Holeck, Kristen, Hollister, Robert D., Holmes, Richard, Hoogenboom, Mia, Hsieh, Chih-Hao, Hubbell, Stephen P., Huettmann, Falk, Huffard, Christine L., Hurlbert, Allen H., Macedo Ivanauskas, Natália, Janík, David, Jandt, Ute, Jażdżewska, Anna, Johannessen, Tore, Johnstone, Jill, Jones, Julia, Jones, Faith A. M., Kang, Jungwon, Kartawijaya, Tasrif, Keeley, Erin C., Kelt, Douglas A., Kinnear, Rebecca, Klanderud, Kari, Knutsen, Halvor, Koenig, Christopher C., Kortz, Alessandra R., Král, Kamil, Kuhnz, Linda A., Kuo, Chao-Yang, Kushner, David J., Laguionie-Marchais, Claire, Lancaster, Lesley T., Min Lee, Cheol, Lefcheck, Jonathan S., Lévesque, Esther, Lightfoot, David, Lloret, Francisco, Lloyd, John D., López-Baucells, Adrià, Louzao, Maite, Madin, Joshua S., Magnússon, Borgþór, Malamud, Shahar, Matthews, Iain, McFarland, Kent P., McGill, Brian, McKnight, Diane, McLarney, William O., Meador, Jason, Meserve, Peter L., Metcalfe, Daniel J., Meyer, Christoph F. J., Michelsen, Anders, Milchakova, Nataliya, Moens, Tom, Moland, Even, Moore, Jon, Mathias Moreira, Carolina, Müller, Jörg, Murphy, Grace, Myers-Smith, Isla H., Myster, Randall W., Naumov, Andrew, Neat, Francis, Nelson, James A., Paul Nelson, Michael, Newton, Stephen F., Norden, Natalia, Oliver, Jeffrey C., Olsen, Esben M., Onipchenko, Vladimir G., Pabis, Krzysztof, Pabst, Robert J., Paquette, Alain, Pardede, Sinta, Paterson, David M., Pélissier, Raphaël, Peñuelas, Josep, Pérez-Matus, Alejandro, Pizarro, Oscar, Pomati, Francesco, Post, Eric, Prins, Herbert H. T., Priscu, John C., Provoost, Pieter, Prudic, Kathleen L., Pulliainen, Erkki, Ramesh, B. R., Mendivil Ramos, Olivia, Rassweiler, Andrew, Rebelo, Jose Eduardo, Reed, Daniel C., Reich, Peter B., Remillard, Suzanne M., Richardson, Anthony J., Richardson, J. Paul, van Rijn, Itai, Rocha, Ricardo, Rivera-Monroy, Victor H., Rixen, Christian, Robinson, Kevin P., Ribeiro Rodrigues, Ricardo, de Cerqueira Rossa-Feres, Denise, Rudstam, Lars, Ruhl, Henry, Ruz, Catalina S., Sampaio, Erica M., Rybicki, Nancy, Rypel, Andrew, Sal, Sofia, Salgado, Beatriz, Santos, Flavio A. M., Savassi-Coutinho, Ana Paula, Scanga, Sara, Schmidt, Jochen, Schooley, Robert, Setiawan, Fakhrizal, Shao, Kwang-Tsao, Shaver, Gaius R., Sherman, Sally, Sherry, Thomas W., Siciński, Jacek, Sievers, Caya, da Silva, Ana Carolina, Rodrigues da Silva, Fernando, Silveira, Fabio L., Slingsby, Jasper, Smart, Tracey, Snell, Sara J., Soudzilovskaia, Nadejda A., Souza, Gabriel B. G., Maluf Souza, Flaviana, Castro Souza, Vinícius, Stallings, Christopher D., Stanforth, Rowan, Stanley, Emily H., Mauro Sterza, José, Stevens, Maarten, Stuart-Smith, Rick, Rondon Suarez, Yzel, Supp, Sarah, Yoshio Tamashiro, Jorge, Tarigan, Sukmaraharja, Thiede, Gary P., Thorn, Simon, Tolvanen, Anne, Teresa Zugliani Toniato, Maria, Totland, Ørjan, Twilley, Robert R., Vaitkus, Gediminas, Valdivia, Nelson, Vallejo, Martha Isabel, Valone, Thomas J., Van Colen, Carl, Vanaverbeke, Jan, Venturoli, Fabio, Verheye, Hans M., Vianna, Marcelo, Vieira, Rui P., Vrška, Tomáš, Quang Vu, Con, Van Vu, Lien, Waide, Robert B., Waldock, Conor, Watts, Dave, Webb, Sara, Wesołowski, Tomasz, White, Ethan P., Widdicombe, Claire E., Wilgers, Dustin, Williams, Richard, Williams, Stefan B., Williamson, Mark, Willig, Michael R., Willis, Trevor J., Wipf, Sonja, Woods, Kerry D., Woehler, Eric J., Zawada, Kyle, and Zettler, Michael L.

Abstract

Dornelas, M., Antao, L. H., Moyes, F., Bates, A. E., Magurran, A. E., Adam, D., ... Zetter, M. L.. (2018). BioTIME: A database of biodiversity time series for the Anthropocene. Global Ecology and Biogeography, 27(7), 760–786. Available here

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