Computational protocol: Molecular systematics of the Labeonini inhabiting the karst regions in southwest China (Teleostei, Cypriniformes)

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Protocol publication

[…] Sequences were aligned using ClustalX v1.83 () and manually checked for inconsistencies. To test for the possible saturation of substitution types, the number of transitions (Ti) and transversions (Tv) versus the F84 distance were plotted for our sequences in DAMBE (). The base compositional bias using a chi-square test with the BaseFreq function implemented in PAUP* 4.0b 10 ().transitions transversions [...] Phylogeny reconstruction was carried out with Bayesian (BI) and maximum likelihood (ML) approaches. The most appropriate evolutionary model was selected by Modeltest v3.7 () for BI and ML using Akaike information criterion (AIC, ) before phylogenetic analyses. Bayesian analysis was conducted using MrBayes 3.1.2 (). Four chains (three hot, one cold) were run for 10,000,000 generations, sampling trees every 100 generations and with the first 25,000 generations discarded as burn-in. Convergence was confirmed by ascertaining that the average standard deviation of split frequencies was below 0.01. Six data partitioning strategies were adopted in the Bayesian analysis on the combined data set, with the number of data partitions ranging from 1 (all genes evolve under a single evolutionary model) to 11 (partitions for each of the 2 protein coding genes plus 5 separate partition for 16S rRNA, RAG1, RH, EGR2B and IRBP) (Table ). The program PartitionFinder was used to select the partition scheme and evolutionary models for our sequences (). Partitioning strategies were compared by Bayes factors, which represent the ratio of the harmonic mean likelihoods of the two analyses being tested in MrBayes 3.1.2. For each run, the harmonic mean likelihoods were calculated using the ‘sump’ command. A value greater than 5 for ln Bayes factor was considered as strong evidence against the alternative topology tested (). The optimal partition selected by Bayes factor was used in Maximum Likelihood analysis. Partitioned ML analysis employing separate models was performed using GARLI 2.0 () with model parameters optimized during the run. Nodal support was assessed by 1000 bootstrap replicates and then the resulting bootstrap trees were imported into PAUP* 4.0b 10 () to obtain the bootstrap values and a majority-rule consensus topology.Bayesian maximum likelihood Akaike information criterion BI and ML tree were tested using the Shimodaira–Hasegawa (SH) test () in PAUP* 4.0b 10, using 1000 bootstrap replicates with RELL optimization. The RELL approximation is used to avoid the re-estimation of the parameters in the bootstrap replicates ().Shimodaira–Hasegawa […]

Pipeline specifications

Software tools Clustal W, DAMBE, PAUP*, ModelTest-NG, MrBayes, PartitionFinder, GARLI
Application Phylogenetics
Organisms Parasinilabeo assimilis, Ptychidio jordani