Species and origin of larvae identified using <i>CO1</i> and <i>ITS1</i> genetic markers, BLAST neighbour-joining reconstruction and character-based assignment.

<p>Species and origin of larvae identified using <i>CO1</i> and <i>ITS1</i> genetic markers, BLAST neighbour-joining reconstruction and character-based assignment.</p

Neighbour-joining phenogram of Mediterranean scombrid reference sequences clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the Kimura 2-parameter model [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref065" target="_blank">65</a>] and are in the units of the number of base differences per site. The analysis involved 280 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Neighbour-joining phenogram of Mediterranean scombrid reference sequences clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the p-distance method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref066" target="_blank">66</a>] and are in the units of the number of base differences per site. The analysis involved 280 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Neighbour-joining phenogram of Mediterranean scombrid reference sequences only.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the p-distance method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref066" target="_blank">66</a>] and are in the units of the number of base differences per site. The analysis involved 91 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.

<p>Map of the Mediterranean Sea and surrounding area with three larvae sampling sites: A) Strait of Sicily, B) Ionian Sea and C) Levantine Sea.</p

Characteristic attributes for capable of distinguishing taxa of scombrids in the Mediterranean Sea.

<p>Position of each variable nucleotide is given in relation to 612bp alignment of all sequences. Diagnostic nucleotides at each locus are given in parentheses.</p><p>Characteristic attributes for capable of distinguishing taxa of scombrids in the Mediterranean Sea.</p

Neighbour-joining phenogram of reference sequences (including non-Mediterranean <i>Thunnus</i> species) clustered with number of unknown larvae in parentheses.

<p>The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref067" target="_blank">67</a>]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The evolutionary distances were computed using the p-distance method [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130407#pone.0130407.ref066" target="_blank">66</a>] and are in the units of the number of base differences per site. The analysis involved 330 nucleotide sequences. All ambiguous positions were removed for each sequence pair. There were a total of 612 nucleotide positions in the final dataset.</p

Puncher et al_Thunnus thynnus_384 SNPs with flanking sequences

"Puncher et al_Thunnus thynnus_384 SNPs with flanking sequences.txt" contains the flanking sequences of 384 SNPs discovered using reduced representation sequence libraries, 221 of which passed quality criteria and 95 that were used for population structure analysis

Puncher et al_Thunnus thynnus_221loci_167individuals_9samples

Puncher et al_Thunnus thynnus_221loci_167individuals_9sample

Puncher et al_Thunnus thynnus_95loci_723individuals_27samples

Puncher et al_Thunnus thynnus_95loci_723individuals_27sample