Computational protocol: Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage

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Protocol publication

[…] For all sequence analyses (COI, 12S rRNA, and ND1), genetic similarities were evaluated using BLAST (http://www.ncbi.nlm.nih.gov/BLAST) to identify M. multifarius sequences. Then, the sequences were aligned using Clustal W [], and individual consensus sequences were retrieved using both alignment and manual checks. The aligned DNA sequences were imported into MEGA version 5.0 [] for sequence comparisons and variation analysis. Standard genetic diversity indices, such as the number of haplotypes, polymorphic sites, haplotype diversity (h), and nucleotide diversity (p), were calculated with DnaSP 4.0 []. Tajima’s D [] and Fu’s Fs [] neutrality tests were performed using Arlequin version 3.11 [] and 10,000 random permutations to infer population expansion events and check for deviations from a strictly neutral model of evolution.Phylogenetic trees were constructed using the unweighted pair group method with arithmetic mean (UPGMA) [] based on a matrix of the Kimura two-parameters (K2P) distance method [] in MEGA 5.0 []. Statistical robustness in the nodes of the resulting tree was determined by 1000 bootstrap replicates []. To depict phylogenetic and geographical relationships of the haplotypic sequences, 3 haplotype networks of COI, 12S rRNA, and ND1 were created using the median-joining method in Network 4.6 software []. Population structures based on COI, 12S rRNA, and ND1 genes were investigated using analysis of molecular variance (AMOVA) [] in Arlequin version 3.11 []. Genetic differentiation, genetic distance, and migration rate among the populations were estimated by calculating the F statistic (F ST) between the populations and testing their significance with 1000 permutations. […]

Pipeline specifications

Software tools Clustal W, MEGA, DnaSP, Arlequin
Applications Phylogenetics, Population genetic analysis
Organisms Drosophila melanogaster
Diseases Coloboma, Zellweger Syndrome