Microsatellite genotypes of wild-caught sawfish, including putative parhenogens

Individual sawfish plus their genotypes at 16 microsatellite loci. Locus names are at the top of each column, and each locus is represented by two columns. Numbers represent sizes of PCR products (i.e. alleles). The first seven individuals in the spreadsheet are the putative parthenogens (Saw144, Saw146, Saw147, Saw153, Saw181, Saw008, and Saw169)

Compound character attributes (<i>c</i>CA) for CITES-listed shark species.

<p>Position numbers (bold) are from the beginning of the COI gene.</p><p>Compound character attributes (<i>c</i>CA) for CITES-listed shark species.</p

Feldheim et al. lemon shark morphological and catch data Bimini, Bahamas 1995-2012

The first worksheet of the excel file is entitled "explanation of data." This sheet contains a key for abbreviations and explanations of each subsequent sheet

Nonaplex primer amplification gel profile.

<p>Results of amplification reactions utilizing the nine-primer nonaplex: two shark universal primers and all the seven species-specific primers. Lanes 1–7 show nonaplex-PCR amplification products of target <i>Rhizoprionodon</i> samples: 1- <i>R. acutus</i>; 2- <i>R. porosus</i>; 3- <i>R. longurio</i>; 4- <i>R. terranovae</i>; 5- <i>R. oligolinx</i>; 6- <i>R. taylori</i>; 7- <i>R. lalandei</i>. Lanes 8–17 show nonaplex-PCR amplification products from non-target species: 8- <i>Galeocerdo cuvier</i>; 9- <i>Negaprion acutidens</i>; 10- <i>Carcharhinus porosus</i>; 11- <i>Prionace glauca</i>; 12- <i>Isurus paucus</i>; 13- <i>Alopias superciliosus</i>; 14- <i>Squalus acantias</i>; 15- <i>Nebrius ferrugineus</i>; 16- <i>Squatina californica</i>; 17- <i>Hexanchus griseus</i>. Lines 8–11, Carcharhiniformes; Line 12, Orectolobiformes; Line 13, Squaliformes; Lines 14–15, Lamniformes; Line 16, Squatiformes; Line 17, Hexanchiformes; Line 18 is the negative control. Lanes labeled “M” contain the molecular size-standard 1kb plus. Faint non-specific bands likely correspond to pseudogenes or uncommon variant copies of ribosomal genes rarely amplified by universal and species-specific primers.</p

Species-specific primers designed along with their sequences and expected amplicon sizes for each species.

<p>Rlal: <i>Rhizoprionodon lalandei</i>; Rtay: <i>R. taylori</i>; Rolig: <i>R. oligolinx</i>; Rter: <i>R. terranovae</i>; Rlong: <i>R. longurio</i>; Rpor: <i>R. porosus</i>; Racut: <i>R. acutus</i>.</p

A Novel Mini-DNA Barcoding Assay to Identify Processed Fins from Internationally Protected Shark Species

<div><p>There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, <i>Lamna nasus</i>, oceanic whitetip, <i>Carcharhinus longimanus</i> scalloped hammerhead, <i>Sphyrna lewini</i>, smooth hammerhead, <i>S. zygaena</i> and great hammerhead <i>S. mokarran</i>) in addition to three species listed in the early part of this century (whale, <i>Rhincodon typus</i>, basking, <i>Cetorhinus maximus</i>, and white, <i>Carcharodon carcharias</i>). Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA (“processed fins”). Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples).</p></div

Triplex scheme of ITS2 species-diagnostic primers.

<p>Representation of the shark nuclear 5.8S and 28S ribosomal RNA genes and ITS2 locus showing relative annealing sites and orientation of the shark universal ITS2 primers (Fish 5.8SF and 28SR indicated by gray irregular pentagons). The Brazilian sharpnose (<i>R. lalandei</i>) Rlal293F primer is an example of a species-specific primer used in this study and is shown as a dark gray irregular pentagon. Also represented are the positive control and species-specific amplicons expected to be produced using this combination of three primers when tested against the target species, <i>R.lalandei</i>, DNA (Figure adapted from Shivji et al. 2002).</p

Inventory of sharpnose sharks showing the number of individuals investigated by species and their geographic ocean basin origins.

<p>Inventory of sharpnose sharks showing the number of individuals investigated by species and their geographic ocean basin origins.</p

Sequence matching results in NCBI BLAST and BOLD of unknown processed fins and fin soup samples.

<p># = fin sample identifier, Type = processed fin (P) or soup (S), Loc = Collection location (HK = Hong Kong, USA = United States of America), BOLD = 100% identification at the lowest taxon possible (genus or species) in a Fish Barcode of Life Initiative (FISH-BOL) search, BLAST top hit = closest match in GenBank BLAST search (Coverage, Identity and UNQ (wheter or not the match was unique to that species refer to this search), I.D. = best identification based on the two searches.</p><p>Sequence matching results in NCBI BLAST and BOLD of unknown processed fins and fin soup samples.</p

Nonaplex scheme of ITS2 species-diagnostic primers.

<p>Representation of the shark nuclear 5.8S and 28S ribosomal RNA genes and ITS2 locus showing relative annealing sites and orientation of primers used in the nonaplex-PCR assay. Shark universal primers (Fish 5.8SF and Fish 28SR) are shown as gray irregular pentagons, while the seven sharpnose species-specific primers are shown by dark gray irregular pentagons. Rlal: <i>Rhizoprionodon lalandei</i>; Rtay: <i>R. taylori</i>; Rolig: <i>R. oligolinx</i>; Rter: <i>R. terranovae</i>; Rlong: <i>R. longurio</i>; Rpor: <i>R. porosus</i>; Racut: <i>R. acutus</i>.</p