publication . Article . 2018

Divide and conquer! Data-mining tools and sequential multivariate analysis to search for diagnostic morphological characters within a plant polyploid complex (Veronica subsect. Pentasepalae, Plantaginaceae).

López-González, Noemí; Andrés-Sánchez, Santiago; Rojas-Andrés, Blanca M.; Martínez-Ortega, M. Montserrat;
Open Access
  • Published: 01 Jan 2018 Journal: PLOS ONE, volume 13, page e0199818 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
  • Country: Spain
Abstract
[EN]This study exhaustively explores leaf features seeking diagnostic characters to aid the classification (assigning cases to groups, i.e. populations to taxa) in a polyploid plant-species complex. A challenging case study was selected: Veronica subsection Pentasepalae, a taxonomically intricate group. The “divide and conquer” approach was implemented—that is, a difficult primary dataset was split into more manageable subsets. Three techniques were explored: two data-mining tools (artificial neural networks and decision trees) and one unsupervised discriminant analysis. However, only the decision trees and discriminant analysis were finally used to select diagn...
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Medicine, R, Science, Q, Polyploidy, Plant taxonomy, Multivariate analysis, Dentition, Artificial neural networks, Decision trees, Taxonomy, Morphometry, Data Mining, Neural Networks (Computer), 2417.20-1 Taxonomía Vegetal. Plantas Vasculares, 1209.03 Análisis de Datos, poliploidía, minería de datos, redes neuronales (ordenador), Research Article, Engineering and Technology, Management Engineering, Decision Analysis, Research and Analysis Methods, Computer and Information Sciences, Artificial Intelligence, Biology and Life Sciences, Computational Biology, Computational Neuroscience, Neuroscience, Data Management, Imaging Techniques, Genetics, Departures from Diploidy, Physiology, Digestive Physiology, Medicine and Health Sciences, Plant Science, Mathematical and Statistical Techniques, Statistical Methods, Physical Sciences, Mathematics, Statistics (Mathematics)
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123 references, page 1 of 9

1 Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, et al Ancestral polyploidy in seed plants and angiosperms. Nature. 2002; 473:97–100.

2 Soltis PS, Marchant DB, Van de Peer Y, Soltis DE. Polyploidy and genome evolution in plants. Curr Opin Genet Dev. 2015; 35:119–125. doi: 10.1016/j.gde.2015.11.003 26656231 [OpenAIRE] [PubMed]

3 Fawcett JA, Van de Peer Y, Maere S. Significance and biological consequences of polyploidization in land plant evolution In: Greilhuber J, Doležel J, Wendel JF, editors. Physical structure, behaviour and evolution of plant genomes. Vienna: Springer; 2013 pp. 277–293.

4 Ramsey J, Ramsey TS. Ecological studies of polypl oidy in the 100 years following its discovery. Phil Trans R Soc B. 2014; 369:20130352 doi: 10.1098/rstb.2013.0352 24958925 [OpenAIRE] [PubMed]

5 Zozomova-Lihova J, Malanova-Krasna I, Vit P, Urfus T, Senko D, Svitok M, et al Cytotype distribution patterns, ecological differentiation, and genetic structure in a diploid–tetraploid contact zone of Cardamine amara. Am J Bot. 2015; 102:1380–1395. doi: 10.3732/ajb.1500052 26290560 [OpenAIRE] [PubMed]

6 Soltis DE, Visger CJ, Marchant DM, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. Am J Bot. 2016; 103:1146–1166. doi: 10.3732/ajb.1500501 27234228 [OpenAIRE] [PubMed]

7 Rieseberg LH. Hybrid origins of plant species. Annu Rev Ecol Syst. 1997; 1:359–389. [OpenAIRE]

8 Seehausen O. Hybridization and adaptive radiation. Trends Ecol Evol. 2004; 19(4):198–207. doi: 10.1016/j.tree.2004.01.003 16701254 [OpenAIRE] [PubMed]

9 Mallet J. Hybridization as an invasion of the genome. Trends Ecol Evol. 2005; 20(5):229–237. doi: 10.1016/j.tree.2005.02.010 16701374 [PubMed]

10 Tovar-Sánchez E, Oyama K. Natural hybridization and hybrid zones between Quercus crassifolia and Quercus crassipes (Fagaceae) in Mexico: Morphological and molecular evidence. Am J Bot. 2004; 91:1352–1663. doi: 10.3732/ajb.91.9.1352 21652368 [PubMed]

11 Suehs CM, Affre L, Médail F. 2004 Invasion dynamics of two alien Carpobrotus (Aizoaceae) taxa on a Mediterranean island: I. Genetic diversity and introgression. Heredity. 2004; 92:31–40. doi: 10.1038/sj.hdy.6800374 14628076 [OpenAIRE] [PubMed]

12 Raudnitschka D, Hensen I, Oberprieler C. Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae, Senecioneae) along an altitudinal gradient in Harz National Park (Germany). Syst Biodivers. 2007; 5(3):333–344. [OpenAIRE]

13 Levin DA. Polyploidy and novelty in flowering plants. Am Nat. 1983; 122(1):1–25.

14 Abbott RJ, Lowe AJ. Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles. Biol J Linn Soc. 2004; 82(4):467–474.

15 Bardy KE, Schönswetter P, Schneeweiss GM, Fischer MA, Albach DC. Extensive gene flow blurs species boundaries among Veronica barrelieri, V. orchidea and V. spicata (Plantaginaceae) in southeastern Europe. Tax on. 2011; 60:108–121. [OpenAIRE]

123 references, page 1 of 9
Abstract
[EN]This study exhaustively explores leaf features seeking diagnostic characters to aid the classification (assigning cases to groups, i.e. populations to taxa) in a polyploid plant-species complex. A challenging case study was selected: Veronica subsection Pentasepalae, a taxonomically intricate group. The “divide and conquer” approach was implemented—that is, a difficult primary dataset was split into more manageable subsets. Three techniques were explored: two data-mining tools (artificial neural networks and decision trees) and one unsupervised discriminant analysis. However, only the decision trees and discriminant analysis were finally used to select diagn...
Subjects
ACM Computing Classification System: ComputingMethodologies_PATTERNRECOGNITION
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Medicine, R, Science, Q, Polyploidy, Plant taxonomy, Multivariate analysis, Dentition, Artificial neural networks, Decision trees, Taxonomy, Morphometry, Data Mining, Neural Networks (Computer), 2417.20-1 Taxonomía Vegetal. Plantas Vasculares, 1209.03 Análisis de Datos, poliploidía, minería de datos, redes neuronales (ordenador), Research Article, Engineering and Technology, Management Engineering, Decision Analysis, Research and Analysis Methods, Computer and Information Sciences, Artificial Intelligence, Biology and Life Sciences, Computational Biology, Computational Neuroscience, Neuroscience, Data Management, Imaging Techniques, Genetics, Departures from Diploidy, Physiology, Digestive Physiology, Medicine and Health Sciences, Plant Science, Mathematical and Statistical Techniques, Statistical Methods, Physical Sciences, Mathematics, Statistics (Mathematics)
Related Organizations
Download fromView all 4 versions
PLoS ONE
Article . 2018
Provider: Crossref
PLoS ONE
Article
Provider: UnpayWall
PLoS ONE
Article . 2018
123 references, page 1 of 9

1 Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, et al Ancestral polyploidy in seed plants and angiosperms. Nature. 2002; 473:97–100.

2 Soltis PS, Marchant DB, Van de Peer Y, Soltis DE. Polyploidy and genome evolution in plants. Curr Opin Genet Dev. 2015; 35:119–125. doi: 10.1016/j.gde.2015.11.003 26656231 [OpenAIRE] [PubMed]

3 Fawcett JA, Van de Peer Y, Maere S. Significance and biological consequences of polyploidization in land plant evolution In: Greilhuber J, Doležel J, Wendel JF, editors. Physical structure, behaviour and evolution of plant genomes. Vienna: Springer; 2013 pp. 277–293.

4 Ramsey J, Ramsey TS. Ecological studies of polypl oidy in the 100 years following its discovery. Phil Trans R Soc B. 2014; 369:20130352 doi: 10.1098/rstb.2013.0352 24958925 [OpenAIRE] [PubMed]

5 Zozomova-Lihova J, Malanova-Krasna I, Vit P, Urfus T, Senko D, Svitok M, et al Cytotype distribution patterns, ecological differentiation, and genetic structure in a diploid–tetraploid contact zone of Cardamine amara. Am J Bot. 2015; 102:1380–1395. doi: 10.3732/ajb.1500052 26290560 [OpenAIRE] [PubMed]

6 Soltis DE, Visger CJ, Marchant DM, Soltis PS. Polyploidy: Pitfalls and paths to a paradigm. Am J Bot. 2016; 103:1146–1166. doi: 10.3732/ajb.1500501 27234228 [OpenAIRE] [PubMed]

7 Rieseberg LH. Hybrid origins of plant species. Annu Rev Ecol Syst. 1997; 1:359–389. [OpenAIRE]

8 Seehausen O. Hybridization and adaptive radiation. Trends Ecol Evol. 2004; 19(4):198–207. doi: 10.1016/j.tree.2004.01.003 16701254 [OpenAIRE] [PubMed]

9 Mallet J. Hybridization as an invasion of the genome. Trends Ecol Evol. 2005; 20(5):229–237. doi: 10.1016/j.tree.2005.02.010 16701374 [PubMed]

10 Tovar-Sánchez E, Oyama K. Natural hybridization and hybrid zones between Quercus crassifolia and Quercus crassipes (Fagaceae) in Mexico: Morphological and molecular evidence. Am J Bot. 2004; 91:1352–1663. doi: 10.3732/ajb.91.9.1352 21652368 [PubMed]

11 Suehs CM, Affre L, Médail F. 2004 Invasion dynamics of two alien Carpobrotus (Aizoaceae) taxa on a Mediterranean island: I. Genetic diversity and introgression. Heredity. 2004; 92:31–40. doi: 10.1038/sj.hdy.6800374 14628076 [OpenAIRE] [PubMed]

12 Raudnitschka D, Hensen I, Oberprieler C. Introgressive hybridization of Senecio hercynicus and S. ovatus (Compositae, Senecioneae) along an altitudinal gradient in Harz National Park (Germany). Syst Biodivers. 2007; 5(3):333–344. [OpenAIRE]

13 Levin DA. Polyploidy and novelty in flowering plants. Am Nat. 1983; 122(1):1–25.

14 Abbott RJ, Lowe AJ. Origins, establishment and evolution of new polyploid species: Senecio cambrensis and S. eboracensis in the British Isles. Biol J Linn Soc. 2004; 82(4):467–474.

15 Bardy KE, Schönswetter P, Schneeweiss GM, Fischer MA, Albach DC. Extensive gene flow blurs species boundaries among Veronica barrelieri, V. orchidea and V. spicata (Plantaginaceae) in southeastern Europe. Tax on. 2011; 60:108–121. [OpenAIRE]

123 references, page 1 of 9
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