Similar protocols

Protocol publication

[…] Genomic DNA was extracted from muscle tissue that was preserved in 95% ethanol. DNA samples were obtained for eight specimens (one male, two female, five immature), according to procedures described by . A 655 bp fragment of the mitochondrial COI was amplified by PCR and sequenced using primers and protocols reported by . DNA sequences were aligned using the software Clustal X () and deposited in GenBank (Accession numbers: KY964500-KY964504). The basic local alignment search tool (BLAST) was used to search for similar sequences to confirm species assignment.For phylogenetic tree reconstruction, a subset of the COI sequences of Mugil, previously analyzed by , was considered. Those sequences that showed greater than 90% similarity (i.e., the six sequences of M. brevirostris and the seven sequences of Mugil sp. R) were also included; Agonostomus monticola () (JQ060401) was used as an outgroup.Three types of phylogenetic reconstructions were conducted: neighbour-joining (NJ), maximum-likelihood (ML) and Bayesian inference (BI) analyses. NJ and ML analyses (1000 bootstrap pseudoreplicates) were performed using MEGA7 () and PhyML 3.0 (), respectively. Bayesian analyses were carried out as implemented in MrBayes 3.1.2 (). Two independent runs of four Markov chains, each for 1,000,000 generations were performed. ModelTest 3.7 () and MrModelTest 2.3 () were used to select, according to the Akaike information criterion, the evolutionary models that best fit the data set for the ML (GTR + I + G, with nst = 6, gamma shape = 4.682, and proportion of invariant sites = 0.637) and the BI (GTR + I + G) analyses, respectively. Genetic distances were calculated with MEGA7 using the Kimura-2-parameters substitution model (). […]

Pipeline specifications

Software tools Clustal W, BLASTN, MEGA, PhyML, MrBayes, ModelTest-NG, MrModelTest
Application Phylogenetics
Organisms Microphysogobio brevirostris