Computational protocol: Demystifying the Capitella capitata complex (Annelida, Capitellidae) diversity by morphological and molecular data along the Brazilian coast

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Protocol publication

[…] Electropherograms were edited with Sequencher 4.1 (Gene Codes Corporation), and sequences were aligned with MAFFT 7.0 [] using the G-INS-I strategy for COI and Q-INS-I for 16S. COI sequences were checked for translation using the invertebrate mitochondrial genetic code. As saturation was not detected in the saturation test [], all codon positions were used, as implemented in DAMBE5 []. The phylogenetic analysis was performed using the maximum likelihood (ML) algorithm and Bayesian inference (BI). Three datasets were considered, COI, 16S and concatenated (COI+16S). The ML trees were estimated in RAxML 8.2 [] using the substitution models GTR+G for all datasets. The best ML tree was obtained from 20 initial independent trees, and the statistical support was obtained with a rapid bootstrap function (-f a) using 1000 replicates. The BI was conducted in MrBayes 3.2 [] under the HKY+I+G model for COI and 16S, and HKY+G for the concatenated dataset, as selected in the jModelTest 2 [] using Bayesian information criterion (BIC). Tree parameters were sampled every 1000 generations, for a total of 107 samples. Two independent runs and 4 chains were implemented. The final results were checked according to the standard deviations of split frequencies (<0.01). The effective sampling size (ESS>200) was assessed via Tracer 1.5 []. The ML and BI analyses were conducted in CIPRES Science Gateway []. Species from two other Capitellidae genera, Notomastus (16S and COI) and Heteromastus (COI), were considered as outgroups and were used to root the trees. The concatenated dataset used only Notomastus as an outgroup as no 16S sequences are available for Heteromastus. Intra- and interspecific pair-wise genetic distances were estimated under the p-distance and Kimura 2 parameters models with MEGA 6.1 []. GenBank sequences of C. capitata from other localities were taken to compare with our sequences. Data collection of specimens, museum codes and GenBank ( accession numbers are detailed in . […]

Pipeline specifications

Software tools Sequencher, MAFFT, DAMBE, RAxML, MrBayes, jModelTest, MEGA
Application Phylogenetics
Organisms Ceratitis capitata, cellular organisms