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

DataSheet_1_First evidence of population genetic structure of the deep-water blackmouth catshark Galeus melastomus Rafinesque, 1810.docx

Among the main measures adopted to reduce anthropogenic impacts on elasmobranch communities, understanding the ecology of deep-sea sharks is of paramount importance, especially for potentially vulnerable species highly represented in the bycatch composition of commercial fisheries such as the blackmouth catshark Galeus melastomus. In the present work, we unravelled the first indication of population genetic structure of G. melastomus by using a novel and effective panel of nuclear, and polymorphic DNA markers and compared our results with previous findings supporting high genetic connectivity at large spatial scales. Given the lack of species-specific nuclear markers, a total of 129 microsatellite loci (Simple Sequence Repeats, SSRs) were cross-amplified on blackmouth catshark specimens collected in eight geographically distant areas in the Mediterranean Sea and North-eastern Atlantic Ocean. A total of 13 SSRs were finally selected for genotyping, based on which the species exhibited signs of weak, but tangible genetic structure. The clearcut evidence of genetic differentiation of G. melastomus from Scottish waters from the rest of the population samples was defined, indicating that the species is genetically structured in the Mediterranean Sea and adjacent North-eastern Atlantic. Both individual and frequency-based analyses identified a genetic unit formed by the individuals collected in the Tyrrhenian Sea and the Strait of Sicily, distinguished from the rest of the Mediterranean and Portuguese samples. In addition, Bayesian analyses resolved a certain degree of separation of the easternmost Aegean sample and the admixed nature of the other Mediterranean and the Portuguese samples. Here, our results supported the hypothesis that the interaction between the ecology and biology of the species and abiotic drivers such as water circulations, temperature and bathymetry may affect the dispersion of G. melastomus, adding new information to the current knowledge of the connectivity of this deep-water species and providing powerful tools for estimating its response to anthropogenic impacts.</p

Haplotype parsimony networks of <i>Raja miraletus</i>, <i>Raja asterias</i>, <i>Raja polystigma</i>, <i>Raja radula</i> and <i>Torpedo marmorata</i> reconstructed using ELASMOMED COI barcode sequences.

<p>Each circle represents one haplotype and its size is proportional to frequency. Colours indicate the origin of samples according to FAO fishing divisions. Mutations and positions characterizing each haplotype, as well as the size (bp), and the number of the sequences included in each species network, are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s004" target="_blank">S4 Table</a>.</p

Cases of specimens’ misidentification by FAO fishing division.

<p>The number of misidentified individuals over the total number of barcoded individuals is given in parenthesis.</p

Mean and maximum intraspecific distances and Nearest-Neighbour distance (p-distance values) of the 41 chondrichthyan species barcoded for the ELASMOMED library.

<p>The <i>Dasyatis pastinaca</i> cluster is not separated.</p

Neighbour-Joining tree based on genetic p-distances of COI barcode sequences of 17 shark species.

<p>Numbers near nodes indicate bootstrap values (>50%). The distance scale bar is given. Each species' sample size and geographic origin are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s002" target="_blank">S2 Table</a>.</p

Neighbour-Joining tree based on genetic p-distances of COI barcode sequences of 23 skate species.

<p>Numbers near nodes indicate bootstrap values (>50%). The distance scale bar is given. Each species' sample size and geographic origin are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s002" target="_blank">S2 Table</a>.</p

Species with discordant BINs found by the ‘BIN Discordance Report’ sequence analysis tool on BOLD.

<p>Taxonomic ranks of conflict are reported including species of the same genus up to taxa belonging to different orders. The column BIN Taxon Variation shows the number of records for each taxon in parenthesis.</p