This work proposes a new methodological approach for grouping data in taxonomy. Macroalgae of the genus Caulerpa were selected as a study model on basis of their remarkable morphological plasticity, and of the difficulty in identifying those algae using the traditional systematical methods. The results obtained from the application of the hyperbolic smoothing algorithm demonstrate the feasibility of its use in biological taxonomy. The new methodology herein proposed may be used isolatedly or in association with other methodologies already proven, not only in phycology, but also in other areas of biology.
Accepté le :
DOI : 10.1051/ro/2015002
Mots clés : Hyperbolic smoothing, biological taxonomy, macroalgae
@article{RO_2015__49_4_735_0,
author = {Sousa Batista, Maria Gard\^enia and de Lima, Francisca L\'ucia and Santana, Andr\'e Macedo and Xavier, Adilson Elias},
title = {The use of the hyperbolic smoothing clustering algorithm in taxonomy of macroalgae},
journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
pages = {735--751},
publisher = {EDP-Sciences},
volume = {49},
number = {4},
year = {2015},
doi = {10.1051/ro/2015002},
zbl = {1323.92008},
language = {en},
url = {http://www.numdam.org/articles/10.1051/ro/2015002/}
}
TY - JOUR AU - Sousa Batista, Maria Gardênia AU - de Lima, Francisca Lúcia AU - Santana, André Macedo AU - Xavier, Adilson Elias TI - The use of the hyperbolic smoothing clustering algorithm in taxonomy of macroalgae JO - RAIRO - Operations Research - Recherche Opérationnelle PY - 2015 SP - 735 EP - 751 VL - 49 IS - 4 PB - EDP-Sciences UR - http://www.numdam.org/articles/10.1051/ro/2015002/ DO - 10.1051/ro/2015002 LA - en ID - RO_2015__49_4_735_0 ER -
%0 Journal Article %A Sousa Batista, Maria Gardênia %A de Lima, Francisca Lúcia %A Santana, André Macedo %A Xavier, Adilson Elias %T The use of the hyperbolic smoothing clustering algorithm in taxonomy of macroalgae %J RAIRO - Operations Research - Recherche Opérationnelle %D 2015 %P 735-751 %V 49 %N 4 %I EDP-Sciences %U http://www.numdam.org/articles/10.1051/ro/2015002/ %R 10.1051/ro/2015002 %G en %F RO_2015__49_4_735_0
Sousa Batista, Maria Gardênia; de Lima, Francisca Lúcia; Santana, André Macedo; Xavier, Adilson Elias. The use of the hyperbolic smoothing clustering algorithm in taxonomy of macroalgae. RAIRO - Operations Research - Recherche Opérationnelle, Tome 49 (2015) no. 4, pp. 735-751. doi : 10.1051/ro/2015002. http://www.numdam.org/articles/10.1051/ro/2015002/
and , A characterization of linkage-based hierarchical clustering. J. Mach. Learn. Res. 31 (2013) 66–74.
, Performance evaluation of density-based clustering methods. Inform. Sci. 179 (2009) 3583–3602. | DOI
and , The evolution of the Earth. Sci. Am. 271 (1994) 44–51.
Dalton de Souza. Amorim, Fundamentos de sistemática filogenética, in Fundamentos de sistemática filogenética. Holos (2002).
, Modified global k-means algorithm for minimum sum-of-squares clustering problems. Pattern Recognition 41 (2008) 3192–3199. | DOI | Zbl
and . A new nonsmooth optimization algorithm for minimum sum-of-squares clustering problems. Eur. J. Oper. Res. 170 (2006) 578–596. | DOI | Zbl
D. Barata, Taxonomia e filogenia do gênero Caulerpa J.V. Lamour (Bryopsidales, Chlorophyta). Brasil Tese, Instituto de Botânica, São Paulo (2008).
and , Algal phylogeny and the origin of land plants. Plant Physiol. 116 (1998) 9–15. | DOI
, and . Taxonomia e distribuição do gênero Caulerpa Lamouroux. Acta Botanica Brasilica 22 (2008) 914–928. | DOI
, , , and , The seaweed Caulerpa racemosa on Mediterranean rocky reefs: from passenger to driver of ecological change. Ecology 91 (2010) 2205–2212. | DOI
M. do Carmo Calijuri, A. Cordeiro Alves Dos Santos and M. Suely Adriani Alves. Cianobactérias e cianotoxinas em águas continentais. RiMa (2006).
and , Caulerpa section Sedoideae (Chlorophyta, Caulerpales) from the Kenyan coast. Nova Hedwigia 49 (1989) 381–393.
and , Seaweeds of the Snellius-II Expedition (E. Indonesia): the genus Caulerpa (Chlorophyta-Caulerpales). Buil. Séanc. Acad. r. Sei. Outre-Mer 37 (1992) 667–712.
, , , and , Discovery of feature-based hot spots using supervised clustering. Comput. Geosci. 35 (2009) 1508–1516. | DOI
, , and , Clustering for mining in large spatial databases. KI 12 (1998) 18–24.
D.E. Fairbrothers, T.J. Mabry, R.L. Scogin and B.L. Turner, The bases of angiosperm phylogeny: chemotaxonomy. Ann. Missouri Bot. Garden (1975) 765–800.
D. Fasulo, An analysis of recent work on clustering algorithms. Department of Computer Science & Engineering, University of Washington (1999).
, The use of multiple measurements in taxonomic problems. Annals Eugenics 7 (1936) 179–188. | DOI
and , A novel genetic algorithm for automatic clustering. Patt. Recog. Lett. 25 (2004) 173–187. | DOI
, , , , , and , In vitro anti-herpetic activity of sulfated polysaccharide fractions from Caulerpa racemosa. Phytochemistry 65 (2004) 3151–3157. | DOI
L.E. Graham and L.W. Wilcox, Algae. Prentice-Hall do Brasil, Rio de Janeiro (2000).
M.D. Guiry and G.M. Guiry. AlgaeBase. AlgaeBase (2008).
J. Han, M. Kamber and K.H. Tung, Spatial clustering methods in data mining: A survey, in Geographic data mining and knowledge discovery, edited by H.J. Miller and J. Han. Taylor and Francis (2001).
and , Megascopic eukaryotic algae from the 2.1-billion-year-old Negaunee Iron-Formation, Michigan. Science 257 (1992) 232–235. | DOI
C.P. Hickman Jr., L.S. Roberts and A. Larson, Princípios integrados de zoologia (2004).
, et al. An algorithmic model for invasive species: Application to Caulerpa taxifolia (Vahl) C. Agardh development in the North-Western Mediterranean Sea. Ecol. Model. 109 (1998) 251–266. | DOI
, Data clustering: 50 years beyond K-means. Patt. Recog. Lett. 31 (2010) 651–666. | DOI
A.K. Jain and R.C. Dubes, Algorithms for clustering data. Prentice-Hall, Inc. (1988). | Zbl
, and , Data clustering: a review. ACM computing surveys (CSUR) 31 (1999) 264–323. | DOI
K. Jajuga, A. Sokolowski and H.H. Bock, Classification, clustering, and data analysis: Recent advances and applications (studies in classification, data analysis, and knowledge organization) (2002). | Zbl
, , , and , Molecular evidence for the aquarium origin of the green alga Caulerpa taxifolia introduced to the Mediterranean Sea. Mar. Ecol. Prog. Ser. 172 (1998) 275–280. | DOI
J.A. Kaandorp and J.E. Kübler, The algorithmic beauty of seaweeds, sponges and corals. Springer (2001). | Zbl
, Nuclear DNA content estimates in multicellular green, red and brown algae: phylogenetic considerations. Ann. Bot. 95 (2005) 7–44. | DOI
and . A novel clustering approach: Artificial Bee Colony (ABC) algorithm. Appl. Soft Comput. 11 (2011) 652–657. | DOI
, Earth’s early atmosphere. Science 259 (1993) 920–926. | DOI
, and . Molecular phylogeny and barcoding of Caulerpa (Bryopsidales) based on the tufA, rbcL, 18S rDNA and ITS rDNA Genes. PloS One 8 (2013) e82438. | DOI
and , Phylogenetic analyses of the Bryopsidales (Ulvophyceae, Chlorophyta) based on Rubisco large subunit gene sequences. J. Phycol. 42 (2006) 669–678. | DOI
and , A genetic algorithm that exchanges neighboring centers for means clustering. Patt. Recog. Lett. 28 (2007) 2359–2366. | DOI
N. Lavesson, Evaluation and analysis of supervised learning algorithms and classifiers. Blekinge Institute of Technology (2006).
G. Lawrence and M. Hill, Taxonomia das plantas vasculares. Fundação Calouste Gulbenkian (1973).
Lee, Robert Edward. Phycology. Cambridge University Press (2008).
P. Legendre and D.J. Rogers, Characters and clustering in taxonomy: a synthesis of two taximetric procedures. Taxon (1972) 567–606.
P. Legendre and L.F.J. Legendre, Numerical ecology. Elsevier (2012). | Zbl
L.-J., Hermann and C. Weihs, Classification as a Tool for Research: Proceedings of the 11th IFCS Biennial Conference and 33rd Annual Conference of the Gesellschaft Für Klassifikation EV, Dresden, March 13-18, 2009. Springer (2010), Vol. 11. | Zbl
J. MacQueen, Some methods for classification and analysis of multivariate observations. Proceedings of the fifth Berkeley symposium on mathematical statistics and probability (1967), Vol. 1. No. 14. | Zbl
P. Madl and M. Yip, Literature review of Caulerpa taxifolia. HTTP:http://www.sbg.ac.at/ipk/avstudio/pierofun/ct/caulerpa.htm (accessed 12 February 2004) (2003).
L. Margulis and Karlene V. Schwartz, Cinco reinos: um guia ilustrado dos filos da vida na Terra. Editora Guanabara Koogan (2001).
, , , , Analysis of rDNA ITS1 indels in Caulerpa taxifolia (Chlorophyta) supports a derived, incipient species status for the invasive strain. Eur. J. Phycol. 39 (2004) 83–92. | DOI
M.C. Oliveira and D. Milstein, Taxonomia molecular. In Macroalgas: uma introduçã o à axonomia, Technical Books Editora, Rio de Janeiro, edited by A. de G. Pedrini (Og.) (2010) 71–82.
, , , and , Mediterranean Caulerpa taxifolia and C. mexicana (Chlorophyta) are not conspecific. J. Phycology 34 (1998) 850–856. | DOI
N. Papavero, Fundamentos práticos de taxonomia zoológica. Unesp (1994).
and , A simple and fast algorithm for K-medoids clustering. Exp. Syst. Appl. 36 (2009) 3336–3341. | DOI
O.O. Parra and C.E. Bicudo, Introducción a la biología y sistemática de las algas de aguas continentales. Universidad de Concepción (1996).
A. de G. Pedrini, Macroalgas; uma introdução à taxonomia. Rio de Janeiro: Technical Books (2010).
, , , et al. Inter-and intraspecific genetic variation in Caulerpa (Chlorophyta) based on nuclear rDNA ITS sequences. Eur. J. Phycol. 32 (1997) 379–386. | DOI
B. de Reviers, Biologia e filogenia das algas. Artmed (2006).
, et al. Polissacarídeos sulfatados isolados das clorofíceas Caulerpa racemosa e Caulerpa cupressoides-extração, fracionamento e atividade anticoagulante. Acta Sci. Biol. Sci. 32 (2010) 113–120.
, Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260 (1993) 640–646. | DOI
W.R. Taylor, Marine algae of the eastern tropical and subtropical coasts of the Americas (1960).
Teixeira, V.L. Taxonomia química. In Macroalgas: uma introdução à taxonomia, Technical Books Editora, Rio de Janeiro. edited by A. de G. Pedrini (2010) 83–97.
, and , Algas de aquarios ornamentales en Brasil: previsión de las introducciones. Latin Amer. J. Aquat. Res. 41 (2013) 344–350.
and , Diversity of the seaweed flora of the Philippines and its utilization. Hydrobiologia 398 (1999) 1–6. | DOI
A. Weber-van Bosse, Monographie des Caulerpes (1898).
, and , The recognition of Caulerpa integerrima (Zanardini) comb. et stat. nov. (Bryopsidales, Chlorophyta) from the Red Sea. Phycologia 48 (2009) 291–301. | DOI
and , Solving the minimum sum-of-squares clustering problem by hyperbolic smoothing and partition into boundary and gravitational regions. Pattern Recognition 44 (2011) 70–77. | DOI | Zbl
, . The hyperbolic smoothing clustering method. Pattern Recognition 43 (2010) 731–737. | DOI | Zbl
and , Survey of clustering algorithms. Neural Netw. IEEE Trans. 16 (2005) 645–678. | DOI
and , Nuclear rDNA and internal transcribed spacer sequences clarify Caulerpa racemosa vars. from other Caulerpa species. Aq. Bot. 80 (2004) 193–207. | DOI
, and , Ranked medoids: A fast and accurate rank-based partitioning algorithm for clustering large datasets. Knowledge-Based Systems 39 (2013) 133–143. | DOI
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