Statistical parsimony haplotype networks based on the 16S rDNA sequences of <i>Eurythenes gryllus</i>.

<p>The dataset includes sequences from this study, that of France and Kocher <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-France2" target="_blank">[12]</a> and Escobar-Briones <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-EscobarBriones1" target="_blank">[36]</a>. The area of each circle is proportional to the frequency of the haplotype in our sampling (a scale is presented). Each line represents a single substitution, nodes represent hypothetical haplotypes and colors refer to the sampling localities. Haplotype networks (95% probability threshold) are numbered (Eg1–9) according to the different clusters identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone-0074218-g002" target="_blank">Figures 2</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone-0074218-g003" target="_blank">3</a>.</p

Tree constructions on the three-gene dataset.

<p>Bayesian (BI) and Maximum Parsimony (MP) trees inferred for specimens of <i>Eurythenes gryllus</i> sampled in this study, based on the combined dataset of three genes (COI, 16S rDNA, 28S rDNA), showing posterior probabilities (>0.5) and bootstrap values (>50%; number of bootstrap replicates = 2,000), respectively. Two bootstrap values are shown at each node, the upper one represents the value when gaps were treated as fifth characters whilst the lower one represents the value when gaps were treated as missing data. The different clusters are assigned with the codes Eg1–5. For each cluster, distributional ranges (ocean basin, bathyal vs. abyssal, depth) are indicated. The colored squares refer to the sample localities of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone-0074218-g001" target="_blank">Figure 1</a>.</p

Sample localities of <i>Eurythenes gryllus sensu lato</i>.

<p>Abbreviations refer to samples from this study, that of France and Kocher <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-France2" target="_blank">[12]</a> and Escobar-Briones <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-EscobarBriones1" target="_blank">[36]</a> (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone-0074218-t001" target="_blank">Table 1</a>). The sampling region in the Southern Ocean is shown as an enlargement. Color codes are provided for each sampling locality and are used consistently in the other figures.</p

Bayesian tree inferred for the 16S rDNA dataset of <i>Eurythenes gryllus</i>.

<p>Posterior probabilities (>0.5) are shown at each node. In the case of identical sequences, all specimens are listed with corresponding abbreviations. For the sequences retrieved from GenBank <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-France2" target="_blank">[12]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-EscobarBriones1" target="_blank">[36]</a>, the accession number of the haplotype as well as the number of specimens per haplotype is indicated (when higher than 1). The different clusters are assigned with the codes Eg1–9. For each cluster, distributional ranges (ocean basin, bathyal vs. abyssal, depth) are indicated.</p

Results of the GMYC species delimitation test for <i>Eurythenes gryllus sensu lato</i> on the 16S dataset using single and multiple threshold methods.

<p>Statistical probabilities **P<0.01 and ***P<<0.0001.</p

Data of specimens of <i>Eurythenes gryllus sensu lato</i> (EG) and <i>Eurythenes</i> sp. (ES) obtained for this study and available on GenBank from France and Kocher [12] and Escobar-Briones <i>et al.</i>[36].

<p>For the specimens sequenced by France and Kocher <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-France2" target="_blank">[12]</a>, the number of specimens is added between parentheses. Abbreviations: n.d. – no data, BT – baited traps, FT – fish traps.</p

Range and mean of pairwise K2P intraclade and interclade distances for COI, 28S rDNA and 16S rDNA for each clade identified within <i>Eurythenes gryllus</i> (sequence data from this study, France and Kocher [12], Escobar-Briones <i>et al.</i>[36]).

<p>Range and mean of pairwise K2P intraclade and interclade distances for COI, 28S rDNA and 16S rDNA for each clade identified within <i>Eurythenes gryllus</i> (sequence data from this study, France and Kocher <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-France2" target="_blank">[12]</a>, Escobar-Briones <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074218#pone.0074218-EscobarBriones1" target="_blank">[36]</a>).</p