Comparison of similarity coefficients based on RAPD markers in the common bean

Duarte, Jair Moura; Santos, João Bosco dos; Melo, L. C.

doi:10.1590/s1415-47571999000300024

Cited by 97 publications

(103 citation statements)

References 13 publications

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“…Jaccard's similarity coefficient, which excludes negative co-occurrences, has been widely employed for statistical analysis of RAPD markers (Duarte et al, 1999). In the present study, our statistical analyses showed considerable genetic variation among individuals of P. marggravii from collection sites A and C.…”

Section: Discussionsupporting

confidence: 53%

RAPD markers indicate the occurrence of structured populations in a migratory freshwater fish species

Hatanaka

Galetti

2003

Genet. Mol. Biol.

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Many factors have contributed to the destruction of fish habitats. Hydroelectric dams, water pollution and other environmental changes have resulted in the eradication of natural stocks. The aim of this study was to detect the genetic variation in Prochilodus marggravii from three collection sites in the area of influence of the Três Marias dam (MG) on the São Francisco river (Brazil), using the RAPD technique. The results obtained revealed that the fish in the downstream region nearest the dam have a higher similarity coefficient than those from the other sampling sites that may be related to differences in environmental characteristics in these regions. Additionaly, significant differences in the band frequencies were observed from one collection site to another. These both findings suggest the occurrence of a structured population and have important implications for the conservation of the genetic variability of distinct natural P. marggravii stocks.

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Section: Discussionsupporting

confidence: 53%

RAPD markers indicate the occurrence of structured populations in a migratory freshwater fish species

Hatanaka

Galetti

2003

Genet. Mol. Biol.

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“…Studies of divergence among vegetal species of agronomic importance have been receiving greater attention, mainly with the recent adoption of molecular markers (Duarte et al, 1999). In these studies, researchers are interested in clustering similar individuals, so that the greater difference occurs among the formed groups.…”

Section: Introductionmentioning

confidence: 99%

“…The similarity coefficients are specific for dichotomic (binary) variables and their use is suggested for divergency studies based on dominant molecular markers, such as RAPD (Duarte et al, 1999). In general, they are based on comparisons between co-occurring bands (indicated by 'ones' in common in the data matrix) and different bands (indicated by 'one and zero' or 'zero and one') between each genotype pair.…”

Section: Introductionmentioning

confidence: 99%

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Comparison of similarity coefficients used for cluster analysis with dominant markers in maize (Zea mays L)

Meyer¹,

et al. 2004

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The objective of this study was to evaluate whether different similarity coefficients used with dominant markers can influence the results of cluster analysis, using eighteen inbred lines of maize from two different populations, BR-105 and BR-106. These were analyzed by AFLP and RAPD markers and eight similarity coefficients were calculated: Jaccard, Sorensen-Dice, Anderberg, Ochiai, Simple-matching, Rogers and Tanimoto, Ochiai II and Russel and Rao. The similarity matrices obtained were compared by the Spearman correlation, cluster analysis with dendrograms (UPGMA, WPGMA, Single Linkage, Complete Linkage and Neighbour-Joining methods), the consensus fork index between all pairs of dendrograms, groups obtained through the Tocher optimization procedure and projection efficiency in a two-dimensional space. The results showed that for almost all methodologies and marker systems, the Jaccard, Sorensen-Dice, Anderberg and Ochiai coefficient showed close results, due to the fact that all of them exclude negative co-occurrences. Significant alterations in the results for the Simple Matching, Rogers and Tanimoto, and Ochiai II coefficients were not observed either, probably due to the fact that they all include negative co-occurrences. The Russel and Rao coefficient presented very different results from the others in almost all the cases studied and should not be used, because it excludes the negative co-occurrences in the numerator and includes them in the denominator of their expression. Due to the fact that the negative co-occurrences do not necessarily mean that the regions of the DNA are identical, the use of coefficients that do not include negative co-occurrences was suggested.

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“…Sokal-Sneath (Hubalek, 1982) SS3 (Gower and Legendre, 1986) S θ a+d a+d+θ (b+c) , θ > 0 S -Nieddu (Nieddu and Rizzi, 2007) SNR a+αd a+βd+γ (b+c) : (Cheetham and Hazel, 1969) K1 (Duarte et al, 1999) And (Tversky, 1977) ST (Gower and Legendre, 1986) T θ a a+θ (b+c) , θ > 0 T Φ(1, 0, −1) Nieddu (Nieddu and Rizzi, 2007) SNR a+αd a+βd+γ (b+c) : (Cheetham and Hazel, 1969) Y Q ad−bc ad+bc Q -Yulle's ω (Hubalek, 1982) Y ω…”

Section: Group Rrmentioning

confidence: 99%

On the order equivalence relation of binary association measures

Paradowski

2015

International Journal of Applied Mathematics and Computer Science

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Over a century of research has resulted in a set of more than a hundred binary association measures. Many of them share similar properties. An overview of binary association measures is presented, focused on their order equivalences. Association measures are grouped according to their relations. Transformations between these measures are shown, both formally and visually. A generalization coefficient is proposed, based on joint probability and marginal probabilities. Combining association measures is one of recent trends in computer science. Measures are combined in linear and nonlinear discrimination models, automated feature selection or construction. Knowledge about their relations is particularly important to avoid problems of meaningless results, zeroed generalized variances, the curse of dimensionality, or simply to save time.

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Comparison of similarity coefficients based on RAPD markers in the common bean

Cited by 97 publications

References 13 publications

RAPD markers indicate the occurrence of structured populations in a migratory freshwater fish species

RAPD markers indicate the occurrence of structured populations in a migratory freshwater fish species

Comparison of similarity coefficients used for cluster analysis with dominant markers in maize (Zea mays L)

On the order equivalence relation of binary association measures

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