Computational protocol: Molecular Phylogenetic Analysis of the Stegana ornatipes Species Group (Diptera: Drosophilidae) in China, with Description of a New Species

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Protocol publication

[…] The sequences were aligned by the Clustal W () method implemented in program MEGA 4.0 () with default options. A partition homogeneity test (PHT) between the ND2 and COI sequences was performed with PAUP 4.0b10* (). The program DAMBE 5.0.80 () was used to measure the nucleotide substitution saturation using the method of Xia et al. () as the substitution saturation masked the phylogenetic signal (; ). Base compositions were investigated by means of the software PAUP 4.0b10* (), and a χ2 test was also used to test the nucleotide composition homogeneity. Uncorrected pairwise divergence was estimated by program MEGA 4.0 ().Phylogenetic trees were constructed by using the maximum parsimony (MP) and maximum likelihood (ML) in PAUP 4.0b10* (), the Bayesian inferring (BI) method performed in MrBayes 3.2.1 (; ). The MP and ML trees were searched by the heuristic method, with initial trees obtained by randomly adding taxa, and the TBR algorithm was used in branching swapping. Branch support for each node in the MP and ML trees was assessed by 1000 bootstrap replicates. The nucleotide substitution models of ML and BI analyses were selected by MrModeltest 2.3 () using the hierarchical likelihood ratio test (hLRT) criterion (). In the BI analyses, the site-specific models were assigned to dataset partitioned by locus (2 data partitions) and by codon positions (6 data partitions). Two independent runs with 2,000,000 generations were implemented in parallel, sampling frequency of every 100 generations was employed. When the average deviation of split frequencies fell well below 0.01, the two runs were stopped. For each running, the 5,000 early-phase samples were burn-in, the rest samples were used in summarizing and a majority rule tree showing all the compatible partitions was obtained.Partition Bremer support (PBS) was used to show the contribution of each gene partition to the Bremer support of the simultaneous analysis (). Values can be positive, negative or zero and sum of all the partitioned Bremer support values at a node will equal the Bremer support value for that node. A positive PBS value suggests support for the node by that gene, whereas a negative PBS value indicates that the partition lends conflict to a given node, and zero indicate that the partition lends neither support nor conflict to a given node. The partitioned Bremer support values were calculated using the partitioned constraint file in TreeRot v3 (). […]

Pipeline specifications

Software tools Clustal W, MEGA, PAUP*, DAMBE, MrBayes, MrModelTest
Application Phylogenetics