Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts

Scheme of the mechanism responsible for the phytoplankton dynamics (modified from original figure by Alexey Ryabov).

<p>Inset: (a) Prochlorococcus PCC 9511 (courtesy of Rippka et al., 2000 (Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066765#pone.0066765-Rippka1" target="_blank">[99]</a>)), (b) Micromonas NOUM17 (courtesy of Augustin Engman, Rory Welsh, and Alexandra Worden). (Color online).</p

Results of , reduced chi-square (), and Kolmogorov-Smirnov goodness-of-fit tests for sites L1129b and L1105, at fixed values of , and (stochastic dynamics - case 2).

<p>Results of , reduced chi-square (), and Kolmogorov-Smirnov goodness-of-fit tests for sites L1129b and L1105, at fixed values of , and (stochastic dynamics - case 2).</p

Results of , reduced chi-square (), and Kolmogorov-Smirnov goodness-of-fit tests for site L1105 at different values of (stochastic dynamics - case 1).

<p>Results of , reduced chi-square (), and Kolmogorov-Smirnov goodness-of-fit tests for site L1105 at different values of (stochastic dynamics - case 1).</p

Theoretical distributions (red line) of the total <i>chl a</i> and <i>Dvchl a</i> concentration (stochastic approach).

<p>The profiles were obtained in stationary regime for a given set of noise intensities (case 2 of the stochastic model) as a function of depth, and are compared with the corresponding experimental distributions (green line) in sites L1129b (panel a) and L1105 (panel b). The theoretical values were obtained averaging over numerical realizations. The values of the parameters are those shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066765#pone-0066765-t001" target="_blank">Table 1</a>. The noise intensities are: (a) , and for site L1129b; (b) , and for site L1105. (Color online).</p

Parameters used in the model.

<p>Parameters used in the model.</p

Magnitude, depth, and width of the DCM as a function of obtained from the model.

<p>The values were obtained in stationary regime for site L1129b (panels a, b, c) and site L1105 (panels d, e, f).</p

Stationary distributions of picoeukaryotes and Prochlorococcus biomass concentrations and light intensity: site L1129b (panels a, b, c) and site L1105 (panels d, e, f) as a function of depth.

<p>Stationary distributions of picoeukaryotes and Prochlorococcus biomass concentrations and light intensity: site L1129b (panels a, b, c) and site L1105 (panels d, e, f) as a function of depth.</p

Profiles of <i>chl a</i> concentration measured in sites L1129b (panel a) and L1105 (panel b).

<p>The black lines have been obtained by connecting the experimental points corresponding to samples distanced of 1 meter along the water column. The total number of samples measured in the two sites is for L1129b, and for L1105. (Courtesy of Denaro et al., 2013 (Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066765#pone.0066765-Denaro1" target="_blank">[28]</a>)).</p

Theoretical distributions (red line) of the total <i>chl a</i> and <i>Dvchl a</i> concentration (stochastic approach).

<p>The profiles were obtained in stationary regime for different values of (case 1 of the stochastic model) as a function of depth. The results are compared with the distributions of the total <i>chl a</i> and <i>Dvchl a</i> concentration measured (green line) in site L1105. The theoretical values were obtained averaging over numerical realizations. The values of the parameters are those shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066765#pone-0066765-t001" target="_blank">Table 1</a>. The noise intensities are: (a) (deterministic case), (b) , (c) , (d) , (e) and (f) . (Color online).</p