Computational protocol: Discovering Hidden Diversity of Characins (Teleostei: Characiformes) in Ecuador’s Yasuní National Park

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Protocol publication

[…] We generated sequences for 56 characiform samples. We combined them with 176 sequences from GenBank. We chose as outgroup Carassius auratus (Cypriniformes). Sequences were edited in Geneious Pro 5.3.4 (Biomatters Ltd). A preliminary alignment was carried out with MAFFT []. The alignment was visually inspected and manually adjusted with Mesquite 2.74 []. Uncorrected genetic distances were obtained with Mesquite excluding ambiguous sites.Phylogenies were inferred using maximum-likelihood (ML) and Bayesian approaches. For both analyses, evolutionary models for one or two partitions (the whole 16S gene, or stems and loops separately) were estimated with jModelTest []. Bayes factors were used to choose the best partition scheme. ML analyses were performed in GARLI v.2.0 [] with 22 replicate analyses. To assess nodal support, non-parametric bootstrap values were calculated with 100 pseudoreplicates.Bayesian analyses were conducted in MrBayes v.3.2.1 [] with two replicate searches of 2 x 106 generations each with four Markov chains. Trees were sampled every 1000 generations. We used TRACER, v.1.3 [] to verify adequate, effective sample sizes for the search (values > 200). We removed 10% of sampled generations as burn-in before summarizing trees. […]

Pipeline specifications

Software tools Geneious, MAFFT, Mesquite, jModelTest, GARLI, MrBayes
Application Phylogenetics
Organisms Danio rerio