singlehaps_create

File used to generate program-specific input files for Symbiodinium "singlehaps" dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2). Example files created include those for Genepop and Arlequin

totalmatrix_structure

Data file with presence/absence matrix for multiple alleles in Symbiodinium. Used for analyses with the program STRUCTURE

singlehaps_structure

Data file with alleles for 5 haploid microsatellite markers used to run analyses in the program STRUCTURE for Symbiodinium

Pflex_create

File used to generate program-specific input files for Plexaura flexuosa dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2). Example files created include those for Genepop, Arlequin, and Bayesass

MOESM1 of Development and characterization of 10 microsatellite markers in the Cape horseshoe bat, Rhinolophus capensis (Chiroptera, Rhinolophidae) and cross-amplification in southern African Rhinolophus species

Additional file 1. Geographic information of the individuals used for the cross-amplification tests

Cliona microsatellite file

435 individual Cliona are genotyped at 10 species-specific microsatellite loci. Location site of each individual is also included in the file

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

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

Samples of known species identity tested for amplification (AMP) and sequencing (SEQ) performance with the mini-barcode assay.

<p>* denotes a species identified by Clarke et al. (2006) as making up a large fraction of the fin trade. N = Number of individuals tested. “Tests” denotes whether the samples were used to test for positive amplification (“AMP”) and/or sequencing this amplicon (“SEQ”).</p><p>Samples of known species identity tested for amplification (AMP) and sequencing (SEQ) performance with the mini-barcode assay.</p

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