Complete mitochondrial genomes of bivalves and other mollusks were downloaded from GenBank in November 2011 (Additional file 3 ). Summarizing, we included in our dataset 30 bivalves, 23 gastropods, 6 cephalopods, 1 scaphopod, 1 polyplacophoran, 1 chaetodermomorph, and the polychaete outgroup Platynereis dumerilii[70 (link)]. We assessed phylogenetic representativeness of this sample through the AvTD method as in [49 (link)]. We used the software PhyRe [71 (link)] and set the number of splits, merges, and moves to 2, shuffling at the family level. Sequences were managed through CLC Sequence Viewer 6.6.2 (CLC bio A/S), Microsoft Excel® 2007, and MEGA 5.03.
Each gene, with the exception of atp8, was separately translated into amminoacids and aligned with MAFFT 6 [72 (link)] and Muscle 3.8.31 [73 (link),74 (link)], using the M-Coffee merging algorithm [75 (link),76 (link)]. Gblocks [77 (link),78 (link)] was used to select blocks of conserved positions suitable for phylogenetic analysis under default (stringent) conditions.
PartitionFinderProtein 1.0.1 [79 (link)], using the greedy option and Bayesian Information Criterion (BIC), tested the best partitioning scheme of our dataset, which was chosen for subsequent analysis, as well as the concatenated alignment and the completely partitioned model. Best-fitting amminoacid substitutions models were selected with ProtTest 3.2 ([80 (link)]; and reference therein), through Phyml [81 (link)] and BIC for model selection.
The software RAxML 7.2.8 [82 (link),83 (link)] was used for maximum likelihood analyses, using both the fast (−x) and the standard (−b) bootstrap algorithm with 200 replicates. The PROTCAT model [84 ] was implemented for optimization of individual per-site substitution rates, using models suggested by ProtTest 3.2. Trees were graphically edited by PhyloWidget [85 (link)], Dendroscope [86 (link)], and Inkscape softwares.
Each gene, with the exception of atp8, was separately translated into amminoacids and aligned with MAFFT 6 [72 (link)] and Muscle 3.8.31 [73 (link),74 (link)], using the M-Coffee merging algorithm [75 (link),76 (link)]. Gblocks [77 (link),78 (link)] was used to select blocks of conserved positions suitable for phylogenetic analysis under default (stringent) conditions.
PartitionFinderProtein 1.0.1 [79 (link)], using the greedy option and Bayesian Information Criterion (BIC), tested the best partitioning scheme of our dataset, which was chosen for subsequent analysis, as well as the concatenated alignment and the completely partitioned model. Best-fitting amminoacid substitutions models were selected with ProtTest 3.2 ([80 (link)]; and reference therein), through Phyml [81 (link)] and BIC for model selection.
The software RAxML 7.2.8 [82 (link),83 (link)] was used for maximum likelihood analyses, using both the fast (−x) and the standard (−b) bootstrap algorithm with 200 replicates. The PROTCAT model [84 ] was implemented for optimization of individual per-site substitution rates, using models suggested by ProtTest 3.2. Trees were graphically edited by PhyloWidget [85 (link)], Dendroscope [86 (link)], and Inkscape softwares.
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