Mustelus_spp_genotypes.txt

Mustelus_spp_genotypes.tx

Mustelus_spp_rawdata

Mustelus_spp_rawdat

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

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

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

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

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

Puzzling over spurdogs : molecular taxonomy assessment of the Squalus species in the Strait of Sicily

The actual occurrence of Squalus megalops in the Mediterranean Sea has recently been questioned. Several research works which sought to assess available morphological and meristic features that differentiate S. megalops from other Squalus species in the Mediterranean Sea, revealed poor discriminatory power and high variability of the assessed characters, especially when comparing S. megalops and S. blainville. The application of molecular tools does not support the presence of S. megalops. In the present study, we screened spurdog species from the Strait of Sicily using a molecular taxonomy approach based on two mitochondrial DNA markers and we report the occurrence of two Squalus lineages characterizing specimens collected from the stretch of sea between Tunisia, southern Sicily, Malta and Libya. The results support the hypothesis that a common species, S. blainville, currently inhabits the Mediterranean Sea, while a second and rare species is probably an occasional visitor with high morphological similarity to the S. megalops and S. blainville but is genetically distinct from both. Within this perspective, the occurrence of S. megalops in the Mediterranean Sea is not confirmed and our study highlights the taxonomic uncertainties in relation to the occurrence and distribution of Squalus species in this region. We encourage the establishment of a coordinated international effort to implement a comprehensive and integrated taxonomic assessment on this genus which represents an irreplaceable component of the biodiversity of the area.</p