Computational protocol: Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae)

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Protocol publication

[…] The relative peak areas of 59 compounds (as identified by GC×GC/MS in the deconvoluted total ion chromatogram mode) were calculated for each replicate of the entities study. Differences in chemical composition of the samples from study entities were analysed by multiple factor analyses (MFA) and/or principal component analysis (PCA). Prior to MFA and/or PCA, peak areas were transformed logarithmically, intraspecific scaling was performed by dividing each species score by its standard deviation, and the data were centred by species’ scores. In PCA analyses, hierarchical clustering based on Pearson correlation showed that entities with similar chemical profiles cluster together. A heat map was used to visualize compounds organized as matrices []. Dendrograms were created using correlation-based distances and the Ward method of agglomeration was used in the analysis []. To further examine differences between the five female entities, the percentage contribution of each female-specific compound (fatty acid esters) to the average dissimilarity between female entities was calculated with similarity percentage analysis (SIMPER) []. All computations were performed with R 3.1.2 [], and the R packages FactoMineR [] and gplots [] were used. […]

Pipeline specifications

Software tools FactoMineR, gplots
Application Miscellaneous
Organisms Bactrocera dorsalis, Bactrocera carambolae
Chemicals Fatty Acids, Hydrocarbons