Computational protocol: Phylogeography of hydrothermal vent stalked barnacles: a new species fills a gap in the Indian Ocean ‘dispersal corridor’ hypothesis

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Protocol publication

[…] Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) from the adductor muscle of barnacle specimens. Partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene was amplified by polymerase chain reaction (PCR) using universal primer sets (LCO1490 and HCO2198, COI-3 and COI-6 [,]) and the Premix ExTaq Hot Start (TaKaRa). PCR was carried out in the following steps: initial denaturation at 94°C for 3 min and 35 cycles of denature (94°C for 30 s), annealing (50°C for 30 s) and extension (72°C for 90 s). PCR products were purified using Exo-SAP-it (USB, Affimetrix), following standard protocols. After BigDye reaction with BigDye Terminator v. 3.1, the products were sequenced using an ABI3130 automated sequencer (Applied Biosystems, Thermo Fisher). Electrophenograms obtained were checked by eye and assembled by Geneious v. 9 (Biomatters Limited) and registered to DNA Data Bank of Japan, with accession numbers LC350007–LC350015.The sequences obtained were aligned with eolepadid sequences available in the databases of the International Nucleotide Sequence Database Collaboration, using Clustal X included in MEGA v. 6.06 []. A total of 123 sequences from seven eolepadid taxa were used (4--45 individuals per taxa), with one sequence of the pollicipedid barnacle Capitulum mitella (Linnaeus []) as the outgroup. Electronic supplementary material, table S1 shows the full list of sequences used in this study. The model selection programme in the same software was applied to select the best model for the maximum-likelihood algorithm, which was the Tamura three-parameter + Gamma distribution model. MEGA v. 6.06 was also used to reconstruct the phylogenetic trees using the maximum-likelihood algorithm, with 2000 bootstrap replicates. […]

Pipeline specifications

Software tools Geneious, Clustal W, MEGA-V
Databases DDBJ INSDC
Applications Phylogenetics, GWAS