Modeling Posidonia oceanica shoot density and rhizome primary production.


Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
12 10 2020
Historique:
received: 21 01 2020
accepted: 09 09 2020
entrez: 13 10 2020
pubmed: 14 10 2020
medline: 14 10 2020
Statut: epublish

Résumé

Posidonia oceanica meadows rank among the most important and most productive ecosystems in the Mediterranean basin, due to their ecological role and to the goods and services they provide. Estimations of crucial ecological process such as meadows productivity could play a major role in an environmental management perspective and in the assessment of P. oceanica ecosystem services. In this study, a Machine Learning approach, i.e. Random Forest, was aimed at modeling P. oceanica shoot density and rhizome primary production using as predictive variables only environmental factors retrieved from indirect measurements, such as maps. Our predictive models showed a good level of accuracy in modeling both shoot density and rhizome productivity (R

Identifiants

pubmed: 33046821
doi: 10.1038/s41598-020-73722-9
pii: 10.1038/s41598-020-73722-9
pmc: PMC7550612
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

16978

Références

Boudouresque, C. F., Mayot, N. & Pergent, G. The outstanding traits of the functioning of the Posidonia oceanica seagrass ecosystem. Biol. Mar. Medit. 13, 109–113 (2006).
Boudouresque, C. F. et al. Protection and Conservation of Posidonia oceanica Meadows (RAC/SPA and GIS Posidonie publ, Marseille, 2012).
Pergent-Martini, C. & Pergent, G. Lepidrochronological analysis in the Mediterranean seagrass Posidonia oceanica: state of the art and future developments. Oceanol. Acta 17, 673–682 (1994).
Pergent, G., Romero, J., Pergent-Martini, C., Mateo, M.-A. & Boudouresque, C.-F. Primary production, stocks and fluxes in the Mediterranean seagrass Posidonia oceanica. Mar. Ecol. Prog. Ser. 106, 139–146 (1994).
Pergent, G., Rico-Raimondino, V. & Pergent-Martini, C. Fate of primary production in Posidonia oceanica meadows of the Mediterranean. Aquat. Bot. 59, 307–321 (1997).
doi: 10.1016/S0304-3770(97)00052-1
Pergent, G. Lepidochronological analysis of the seagrass Posidonia oceanica (L.) Delile: a standardized approach. Aquat. Bot. 37, 39–54 (1990).
doi: 10.1016/0304-3770(90)90063-Q
Mateo, M. A., Romero, J., Pérez, M., Littler, M. M. & Littler, D. S. Dynamics of millenary organic deposits resulting from the growth of the Mediterranean seagrass Posidonia oceanica. Estuar. Coast. Shelf Sci. 44, 103–110 (1997).
doi: 10.1006/ecss.1996.0116
Guidetti, P., Buia, M. C. & Mazzella, L. The use of lepidochronology as a tool of analysis of dynamic features in the seagrass Posidonia oceanica of the Adriatic Sea. Bot. Mar. 43, 1–9 (2000).
doi: 10.1515/BOT.2000.001
Montefalcone, M. et al. Multiscale lepidochronological analysis of Posidonia oceanica (L.) Delile rhizome production in a northwestern Mediterranean coastal area. Chem. Ecol. 24, 93–99 (2008).
doi: 10.1080/02757540801970100
Romero, J. Primary production of Posidonia oceanica beds in the Medas Islands (Girona, NE Spain). In International workshop on Posidonia oceanica beds 2, 83–86 (1989).
Libes, M. Productivity-irradiance relationship of Posidonia oceanica and its epiphytes. Aquat. Bot. 26, 285–306 (1986).
doi: 10.1016/0304-3770(86)90028-8
Pergent-Martini, C., Rico-Raimondino, V. & Pergent, G. Primary production of Posidonia oceanica in the Mediterranean Basin. Mar. Biol. 120, 9–15 (1994).
Džeroski, S. Applications of symbolic machine learning to ecological modelling. Ecol. Model. 146, 263–273 (2001).
doi: 10.1016/S0304-3800(01)00312-X
Recknagel, F. Applications of machine learning to ecological modelling. Ecol. Model. 146, 303–310 (2001).
doi: 10.1016/S0304-3800(01)00316-7
Crisci, C., Ghattas, B. & Perera, G. A review of supervised machine learning algorithms and their applications to ecological data. Ecol. Model. 240, 113–122 (2012).
doi: 10.1016/j.ecolmodel.2012.03.001
Fabbrizzi, E. et al. Modeling macroalgal forest distribution at mediterranean scale: present status, drivers of changes and insights for conservation and management. Front. Mar. Sci. 7, 20 (2020).
doi: 10.3389/fmars.2020.00020
Mattei, F. & Scardi, M. Embedding ecological knowledge into artificial neural network training: a marine phytoplankton primary production model case study. Ecol. Model. 421, 108985 (2020).
doi: 10.1016/j.ecolmodel.2020.108985
Thessen, A. Adoption of machine learning techniques in ecology and earth science. One Ecosyst. 1, e8621 (2016).
doi: 10.3897/oneeco.1.e8621
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).
doi: 10.1023/A:1010933404324
Liaw, A. & Wiener, M. Classification and regression by randomForest. R News 2, 18–22 (2002).
Cutler, A., Cutler, D. R. & Stevens, J. R. Random forests. In Ensemble Machine Learning (eds. Zhang, C. & Ma, Y.) 157–175 (Springer, New York, 2012). https://doi.org/10.1007/978-1-4419-9326-7_5 .
doi: 10.1007/978-1-4419-9326-7_5
Cutler, D. R. et al. Random forests for classification in ecology. Ecology 88, 2783–2792 (2007).
doi: 10.1890/07-0539.1
Evans, J. S., Murphy, M. A., Holden, Z. A. & Cushman, S. A. Modeling species distribution and change using random forest. In Predictive Species and Habitat Modeling in Landscape Ecology (eds. Drew, C. A. et al.) 139–159 (Springer, New York, 2011). https://doi.org/10.1007/978-1-4419-7390-0_8 .
doi: 10.1007/978-1-4419-7390-0_8
Li, J. et al. Predicting seabed hardness using random forest in R. In Data Mining Applications with R (eds. Zhao, Y. & Cen, Y.) 299–329 (Elsevier, Amsterdam, 2014). https://doi.org/10.1016/B978-0-12-411511-8.00011-6 .
doi: 10.1016/B978-0-12-411511-8.00011-6
Catucci, E. & Scardi, M. A machine learning approach to the assessment of the vulnerability of Posidonia oceanica meadows. Ecol. Ind. 108, 105744 (2020).
doi: 10.1016/j.ecolind.2019.105744
Gislason, P. O., Benediktsson, J. A. & Sveinsson, J. R. Random Forests for land cover classification. Pattern Recogn. Lett. 27, 294–300 (2006).
doi: 10.1016/j.patrec.2005.08.011
Rodriguez-Galiano, V. F., Ghimire, B., Rogan, J., Chica-Olmo, M. & Rigol-Sanchez, J. P. An assessment of the effectiveness of a random forest classifier for land-cover classification. ISPRS J. Photogramm. Remote Sens. 67, 93–104 (2012).
doi: 10.1016/j.isprsjprs.2011.11.002
Scornet, E. Tuning parameters in random forests. ESAIM Proc. Surv. 60, 144–162 (2017).
doi: 10.1051/proc/201760144
Breiman, L. Consistency for a simple model of random forests. Technical Report 670, Berkeley (2004).
Biau, G. & Scornet, E. A random forest guided tour. TEST 25, 197–227 (2016).
doi: 10.1007/s11749-016-0481-7
Kruppa, J., Schwarz, A., Arminger, G. & Ziegler, A. Consumer credit risk: individual probability estimates using machine learning. Expert Syst. Appl. 40, 5125–5131 (2013).
doi: 10.1016/j.eswa.2013.03.019
Boulesteix, A. L., Janitza, S., Kruppa, J. & König, I. R. Overview of random forest methodology and practical guidance with emphasis on computational biology and bioinformatics: random forests in bioinformatics. WIREs Data Min. Knowl. Discov. 2, 493–507 (2012).
doi: 10.1002/widm.1072
Team, R. C. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, Vienna, Austria, 2013).
Louppe, G., Wehenkel, L., Sutera, A. & Geurts, P. Understanding variable importances in forests of randomized trees. In Advances in Neural Information Processing Systems 26 (eds. Burges, C. J. C., Bottou, L., Welling, M., Ghahramani, Z. & Weinberger, K. Q.) 431–439 (2013).
Louppe, G. Understanding Random Forests: From Theory to Practice. arXiv:1407.7502 [stat] (2014).
Duarte, C. M. et al.The limits to models in ecology. In Models in ecosystem science (eds. Canham, C. D. W., Cole, J., & Lauenroth, W. K.) 437–451 (Princeton University Press, 2003).
Reiss, H. et al. Benthos distribution modelling and its relevance for marine ecosystem management. ICES J. Mar. Sci. 72, 297–315 (2014).
doi: 10.1093/icesjms/fsu107
Scardi, M. Advances in neural network modeling of phytoplankton primary production. Ecol. Model. 146, 33–45 (2001).
doi: 10.1016/S0304-3800(01)00294-0

Auteurs

Elena Catucci (E)

Department of Biology, University of Rome "Tor Vergata", via della Ricerca Scientifica, 00133, Rome, Italy. catucci.elena@gmail.com.
CoNISMa, Piazzale Flaminio, 9, 00196, Rome, Italy. catucci.elena@gmail.com.

Michele Scardi (M)

Department of Biology, University of Rome "Tor Vergata", via della Ricerca Scientifica, 00133, Rome, Italy.
CoNISMa, Piazzale Flaminio, 9, 00196, Rome, Italy.

Classifications MeSH