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An unweighted pair group method with arithmetic mean (UPGMA) tree of Kimura 2-parameter distances (K2P) amongthe cytochrome oxidase c subunit 1 gene (COI) sequences of Leucothrips collections that are indistinguishable based on adult morphology.
Two methods of analysis in the PAUP included: (1) Neighbor-joining (NJ) using the Kimura 2-parameter (Kimura 1980) model, and (2) Maximum Parsimony (MP) with stepwise addition 1000 replicates in a heuristic search (Swofford 2002).
We constructed the tree with the rrs2 sequences (642 bp) from this study by using the Kimura 2-parameter model with MEGA 7.0 (http://www.megasoftware.net); we calculated bootstrap values with 1,000 replicates.
Phylogenetic trees were generated by the maximum-likelihood method based on the Kimura 2-parameter model using MEGA7 (http://www.
We calculated genetic distances using the Kimura 2-parameter model.
Genetic distances were calculated by using the Kimura 2-parameter method, and the tree was plotted using the by the neighbor-joining method.
The tree was created by using the maximum-likelihood method based on the Kimura 2-parameter model with 500 bootstrap replicates from the whole-genome sequence of the displayed sequences.
Phylogenetic trees were constructed by using MEGA version 6.0 (http://www.megasoftware.net/) and a neighbor-joining algorithm with the Kimura 2-parameter model and 1,000 replications of bootstrap analysis.
To investigate SVA phylogeny, we performed ClustalW (http://www.genome.jp/tools/clustalw/) alignment of P1 nucleotide sequences, followed by maximum-likelihood analysis using the best-fitting Kimura 2-parameter plus gamma distribution model of evolution.
The neighbor-joining method by Kimura 2-parameter distance method was used (1,000 bootstrap replicates).
Neighbor-joining and Kimura 2-parameter methods were implemented by using MEGA version 5.0 software (http:// www.megasoftware.net).