Dataset composition, marker size and information.

<p>Dataset composition, marker size and information.</p

A Phylogenetic Re-Analysis of Groupers with Applications for Ciguatera Fish Poisoning

<div><p>Background</p><p>Ciguatera fish poisoning (CFP) is a significant public health problem due to dinoflagellates. It is responsible for one of the highest reported incidence of seafood-borne illness and Groupers are commonly reported as a source of CFP due to their position in the food chain. With the role of recent climate change on harmful algal blooms, CFP cases might become more frequent and more geographically widespread. Since there is no appropriate treatment for CFP, the most efficient solution is to regulate fish consumption. Such a strategy can only work if the fish sold are correctly identified, and it has been repeatedly shown that misidentifications and species substitutions occur in fish markets.</p><p>Methods</p><p>We provide here both a DNA-barcoding reference for groupers, and a new phylogenetic reconstruction based on five genes and a comprehensive taxonomical sampling. We analyse the correlation between geographic range of species and their susceptibility to ciguatera accumulation, and the co-occurrence of ciguatoxins in closely related species, using both character mapping and statistical methods.</p><p>Results</p><p>Misidentifications were encountered in public databases, precluding accurate species identifications. Epinephelinae now includes only twelve genera (vs. 15 previously). Comparisons with the ciguatera incidences show that in some genera most species are ciguateric, but statistical tests display only a moderate correlation with the phylogeny. Atlantic species were rarely contaminated, with ciguatera occurrences being restricted to the South Pacific.</p><p>Conclusions</p><p>The recent changes in classification based on the reanalyses of the relationships within Epinephelidae have an impact on the interpretation of the ciguatera distribution in the genera. In this context and to improve the monitoring of fish trade and safety, we need to obtain extensive data on contamination at the species level. Accurate species identifications through DNA barcoding are thus an essential tool in controlling CFP since meal remnants in CFP cases can be easily identified with molecular tools.</p></div

List of the primers used in this study; T° of hyb: temperature of hybridisation used to amplify the marker.

<p>List of the primers used in this study; T° of hyb: temperature of hybridisation used to amplify the marker.</p

Phylogenetic relationships within the Epinephelidae.

<p>Bayesian inference phylogram obtained from phylogenetic analyses of the dataset 1 (A) based on the concatenation of three genes, COI, 16S and TMO-4C4, and the dataset 2 (B) obtained with the concatenation of five genes, COI, 16S, TMO-4C4, Rhodopsin and Pkd1, both under the GTR + I + Γ model. Epinephelidae are highlighted in colour (pink and blue). Each sub families are shown in alternate blue and pink colours. Values at nodes indicate Bayesian posterior probabilities (PP) and maximum likelihood bootstrap percentages (BP). Black circles indicate nodes supported by posterior probability ≥95% and ML bootstrap probability ≥75%.</p

Mismatch distributions of observed (solid lines) pairwise among-individual comparisons as well as theoretical curves for sudden expansion model (dashed lines)

<p><b>Copyright information:</b></p><p>Taken from "Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes? – Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity"</p><p>http://www.biomedcentral.com/1471-2148/7/220</p><p>BMC Evolutionary Biology 2007;7():220-220.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2222253.</p><p></p> For each species, the mismatch distribution of cyt b sequences is given on the left side, while the mismatch distribution of the S7 sequences is given at the right

Results of the Bayesian phylogeny-trait association.

<p>Association index (AI), parsimony score (PS), and monophyletic clade (MC) and their significance. While AI and PS indices test for the overall phylogeny and all the characters at once, MC is drawn to specifically quantify the phylogenetic signal for each specific character (occurrence of ciguatera contamination). Asterisk indicates significant values (*: p≤0.1; **: p≤0.05).</p

List of fish species, specimen vouchers localities and sequence accession numbers.

<p>(¹) Fish specimen collected at Nouméa fish market or obtained through colleagues, (*) new sequences, (_b) BOLD accession number, (_v) sequence corresponds to voucher indicated in Table.</p

NJ tree of pairwise K2P substitution rates for the barcode option 2 (<i>rpoC1</i>, <i>matK</i> and <i>trnH-psbA</i>) implicating the reduced dataset.

<p>Bootstrap values of 50% and above are shown on the branches. Species that were potentially well-delineated with these sequences are marked by a black vertical line. Individuals marked by asterisks were likely misidentified, and not considered in species delineations. The scale bar represents the substitution rate per 100 sites.</p

NJ tree of pairwise K2P substitution rates for the barcode option 1 (<i>rpoC1</i>, <i>rpoB</i> and <i>matK</i>) implicating the reduced dataset.

<p>Bootstrap values of 50% and above are shown on the branches. Species that were potentially well-delineated with these sequences are marked by a black vertical line. Individuals marked by asterisks were likely misidentified, and not considered in species delineations. The scale bar represents the substitution rate per 100 sites.</p

NJ tree of pairwise K2P substitution rates for the <i>rpl32–trnL</i> dataset implicating the expanded dataset.

<p>Bootstrap values of 50% and above are shown on the branches. Species that were potentially well-delineated with these sequences are marked by a black vertical line. The scale bar represents the substitution rate per 100 sites.</p