Genetic distance within and between the <i>Pomatoschistus microps</i> lineages and the species used as outgroup.

a<p>Genetic distance within lineages (S.E. = standard error).</p>b<p>Genetic distance between lineages (below the diagonal).</p>c<p>Standard error (above the diagonal).</p

Median-joining network of the concatenated control region and cytochrome <i>b</i> gene haplotypes for <i>Pomatoschistus microps</i> of the Mediterranean lineage.

<p>Haplotypes are indicated by numbers as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091576#pone.0091576.s005" target="_blank">Table S1</a>. Line lengths reflect the number of mutational changes (in brackets when >1) between haplotypes.</p

Demographic history of <i>Pomatoschistus microps</i> inferred from concatenated control region and cytochrome <i>b</i> gene sequences.

<p>Observed mismatch distributions (grey line) for each lineage are compared to expected distributions (black line) under a population growth-decline model.</p

Genetic diversity indices for each <i>Pomatoschistus microps</i> lineage.

a<p>Number of sequences.</p>b<p>Number of haplotypes.</p>c<p>Nucleotide diversity (sd = standard deviation).</p>d<p>Haplotype diversity (sd = standard deviation).</p>e<p>Mean number of pairwise differences.</p

Maximum-likelihood tree reconstructed from concatenated control region and cytochrome <i>b</i> gene sequences from <i>Pomatoschistus microps</i>.

<p><b>A</b>. Individual labels are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091576#pone.0091576.s005" target="_blank">Table S1</a>. Individuals with • are from an Atlantic locality, whereas individuals with blue * and red star are, respectively, from northern Europe and Mediterranean localities. Numbers at nodes are for ML bootstrap percentages (≥50%). <b>B</b>. Numbers at nodes are for divergence times (Myr) estimated with PAML and based on a geologic calibration point, 6.05±0.09 Myr (between 6.14 and 5.96 Myr) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091576#pone.0091576-Rouchy1" target="_blank">[7]</a>. For both figures, <i>P. microps</i> lineages are indicated on the right.</p

Locality distribution for the common goby, <i>Pomatoschistus microps</i>, in the Northeastern Atlantic Ocean and Mediterranean Sea.

<p>Details about localities and samples are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091576#pone.0091576.s005" target="_blank">Table S1</a>.</p

Demographic indices for each <i>Pomatoschistus microps</i> lineage.

a<p>Fu’s <i>F</i>s.</p>b<p>Tajima’s <i>D.</i></p>c<p>Ramos-Onsins and Rozas’s <i>R</i>_2.</p>d<p>Sum of squared deviations.</p>e<p>Raggedness index.</p>f<p>Probability of the test: *** <0.001, ** <0.01, * <0.05.</p

COI sequence alignment

DNA sequence alignment containing all 3165 individuals. Sequence labels contain genus, species, drainage system, country of origin, field or museum ID, and sample ID