Computational protocol: Preliminary Investigation of Species Diversity of Rice Hopper Parasitoids in Southeast Asia

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Protocol publication

[…] Quality control and trimming of the forward and reverse DNA sequences were performed with Gap5 v 1.2.14-r []. DNA sequence alignment was performed using MEGA 6 []. Additional Chalcidoidea (the super family containing all four genera) sequences were used as reference material. They were retrieved by using the National Centre for Biotechnology Information (NCBI) BLAST tool [] and the BOLD Identification System (http://www.boldsystems.org) (). The best model to calculate parasitoid phylogeny was determined assuming partial deletion, site coverage cut-off of 95%, and the branch swap filter set to “very strong”. Maximum likelihood trees were generated under the assumption of the best fitting model with 1000 bootstraps. Finally, median-joining networks were constructed using the software NETWORK v. 4.6.1.2 []. The genetic diversity between and within species was estimated using the reference sequences from the superfamily Chalcidoidea (). The appropriate models for the calculation of the pairwise molecular distances between individuals were determined with MEGA 6. The 28S rRNA distances were calculated based on the K2P + G model. COI distances were calculated based on the T92 + G model. The values were compared using a Kruskal–Wallis test, followed by a Dunn’s post hoc test [] in R version 3.2.3 [].To estimate, whether the genetic diversity of the parasitoids was covered by the sample size used in the analyses, we performed a rarefaction analysis () in R version 3.2.3 using the packages vegan [] and drc []. […]

Pipeline specifications

Software tools MEGA, BLASTN, vegan
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Oryza sativa, Nilaparvata lugens