Computational protocol: Distinct Genetic Lineages of Bactrocera caudata (Insecta: Tephritidae) Revealed by COI and 16S DNA Sequences

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Protocol publication

[…] The COI and 16S rDNA sequences were preliminarily aligned using the CLUSTAL X program and subsequently manually aligned. The sequences of the COI and 16S rDNA were also combined to further understand the systematic relationships among B. caudata and closely related species. Several researchers suggested the need to use the incongruence of length differential (ILD) test or partition homogeneity test to determine whether the sequences contain congruent phylogenetic information , . In this study, partition homogeneity tests – were performed in PAUP* 4.0b10 software with 100 replicates, heuristic search using the tree-bisection-reconnection (TBR) branch swapping algorithm. Due to some recent criticism against the application of the ILD , additional analyses on each gene were conducted for topology comparison.The aligned sequences were subjected to maximum-parsimony (MP) and neighbour-joining (NJ) analyses using PAUP* 4.0b10 . The MP tree was constructed using the heuristic search option, 100 random sequences additions, tree bisection reconnection (TBR) branch swapping, and unordered and unweighted characters. Bootstrap percentage (BP) was computed with 1000 replications. NJ bootstrap values were estimated using 1000 replicates with Kimura's two-parameter model of substitution (K2P distance) evolution model.Maximum likelihood (ML) analysis was performed by Treefinder version October 2008 . Bayesian (BI) analysis was performed using MrBayes 3.1.2 . The best fit nucleotide substitution model was determined using KAKUSAN v.3 , which also generates input files for ML and BI. Best fit models were evaluated using the corrected Akaike Information Criterion , for ML and the Bayesian Information Criterion (BIC) with significance determined by Chi-square analysis.The best selected model for COI marker was general time-reversible (GTR) model of DNA evolution with a gamma shape parameter (G); the best selected model for 16S rDNA was J1 model with a gamma shape parameter (G); while the best selected model for the combined sequences of COI and 16S rDNA was J2 model with a gamma shape parameter (G).ML analyses were performed with 1000 bootstrap replicates. Two parallel runs were performed in MrBayes analysis using four chains of Markov chain Monte Carlo (MCMC). One million Markov chain Monte Carlo (MCMC) generations were run, with convergence diagnostics calculated every 1000th generation for monitoring the stabilization of log likelihood scores. Trees in each chain were sampled every 100th generation. A 50% majority rule consensus tree was generated from the sampled trees after discarding the first 20%. […]

Pipeline specifications

Software tools Clustal W, PAUP*, MrBayes
Application Phylogenetics
Organisms Drosophila melanogaster, Zeugodacus cucurbitae, Zeugodacus scutellatus, Zeugodacus diaphorus