Mapping of CSBPSs in the Cetacea phylogenetic tree.

<p>CSBPS, change in sequence in a base pair of a stem; FCBC, fully compensatory base change; HCBC, hemi compensatory base change; Mismatch, mismatch in a base pair of a stem; Number of FCBCs, HCBCs, and Mismatches (included their sum CSBPSs) occurring at the nodes of the reference phylogenetic tree. The asterisk associated with some CSBPS values indicates that these CSBPSs were subjected to successive changes in one/some of the taxa downstream of the considered node. For details on the type of FCBCs, HCBCs, and mismatches occurring at a single node, please refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158129#pone.0158129.s008" target="_blank">S7</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158129#pone.0158129.s010" target="_blank">S9</a> Figs.</p

Global distribution of SPICs and CSBPSs in cetacean tRNAs.

<p>CSBPS, change in sequence in a base pair of a stem; FCBC, fully compensatory base change; HCBC, hemi compensatory base change; Mismatch, mismatch in a base pair of a stem; SPIC, stem position involved in base change. (a) Percent of SPICs in the whole set of tRNAs involved in CSBPSs. The extension of the slices determining the percent and type of FCBCs, HCBCs, and Mismatches was scaled assuming that the whole coverage of a Pie graph was reached only when the considered position resulted in an SPIC for the entire set of tRNAs. (b) Percent of CSBPSs occurring in a considered SPIC with respect to the total number of CSBPSs. The cyan arrows point to stem positions known to be interested in species of Mammalia by an editing activity in at least one tRNA.</p

Distribution of CSBPSs in a single tRNA.

<p>CSBPS, change in sequence in a base pair of a stem; FCBC, fully compensatory base change; HCBC, hemi compensatory base change; Mismatch, mismatch in a base pair of a stem; SPIC, stem position involved in base change. The number/percentage of SPICs is provided in cyan. A green background is used to mark the number of FCBCs occurring in a tRNA as well as the percentage that they represent with respect to the total number of FCBCs. The orange and red backgrounds are used for the number/percentage of HCBCs and Mismatches. A purple background is used for number/percentage of CSBPSs.</p

The tRNA nomenclature and the gene order of vertebrate mtDNA.

<p>Ac, pair of the acceptor stem; dh, pair of the DHU stem; an, pair of the anticodon stem; tp, pair of the TΨC stem. The numbering of pairs follows a 5’ → 3’ orientation. The 5’ nucleotide of a pair is marked with a, while the 3’ base is marked with b. The numbering scheme of Sprinzl et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158129#pone.0158129.ref020" target="_blank">20</a>] is provided only for the stems. Base pairings are indicated as follows: –, canonical Watson-Crick base pairing; •, base pairing involving G and T; |, base pairing implying a mismatch. A The gene order of vertebrate mtDNA is depicted at the bottom, linearised starting from <i>cox1</i>. Genes encoded on the α-strand (right to left orientation) are underlined in green, while those encoded on the β-strand are underlined in red (left to right orientation). Gene nomenclature: <i>atp6</i> and <i>atp8</i>: ATP synthase subunits 6 and 8; <i>cob</i>: apocytochrome b; <i>cox1</i>-<i>3</i>: cytochrome c oxidase subunits 1–3; <i>nad1-6</i> and <i>nad4L</i>: NADH dehydrogenase subunits 1–6 and 4L; <i>rrnS</i> and <i>rrnL</i>: small and large subunit ribosomal RNA (rRNA) genes; and X: transfer RNA (tRNA) genes, where X is the one-letter abbreviation of the corresponding amino acid. In particular, L1 identifies the CTN codon family; L2 the TTR codon family, S1 the AGY codon family, and S2 the TCN codon family. CR, Control Region.</p

d-loop dataset

The complete D-loop dataset (334 sequences

Traits of the 334 specimens

A list of all 334 specimens of Periophthalmus argentilineatus, Periophthalmus kalolo and of the outgroup P. malaccensis. For each call number that is used in the nexus files, the species, the sample locality and the population in which the specimen was included by the AMOVA in the paper, are indicated

16S sequences for calibration

The 16S fish sequences used in the 16S molecular cloc

dloop-sequences to be combined with 16s

The 26 d-loop sequences used to build the combined tree in BEAST