Comparison of partial and full-length 18S rDNA sequences to infer genetic distances.

<p>The three panels show pair-wise genetic distances (Jukes Cantor corrected) of the complete gene against partial regions (V4–V5 in dark grey or V9 in light grey) for sequences within Stramenopiles (A), Alveolata (B), and Rhizaria (C). Slopes (m) and coefficients (R) of the correlations are shown at the top of the graphs.</p

Maximum Likelihood phylogenetic trees for eukaryotic supergroups.

<p>Trees include several taxonomic groups within Alveolata (A), Stramenopiles (B), and are done with sequences representative of each OTU obtained clustering at 0.05 distance (A) and 0.01 distance (B). The number of sequences (about 550 bp in length) per tree is 798 and 523 respectively. Red dots represent bootstrap values above 75 and orange dots values above 50.</p

Clustering pattern of several groups of marine protists.

<p>The graphs show the percentage of OTUs when sequences are clustered at different genetic distances for several Stramenopiles groups (A), CCTH groups plus Choanoflagellatea (B), Rhizaria and Excavata groups plus Dinophyceae (C) and major ribogroups (D).</p

Phylogenetic structure of several groups of marine protists.

<p>Lineage Through Time (LTT) plots are based on the trees shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057170#pone-0057170-g002" target="_blank">Figure 2</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057170#pone-0057170-g003" target="_blank">3</a> and are displayed for groups having γ<0 (A), γ = 0 (B) and γ>0 (C), which indicates early, constant or late cladogenesis events, respectively. The number of lineages is standardized to the maximum number at present and relative time is considered.</p

Classification of environmental 18S rDNA sequences in 42 taxonomic major groups.

<p>Each group is coded according to their taxonomic rank (S: subphylum; C: class; O: order; G: genus; R: ribogroup). The table shows the number of sequences per group (Seq), the average (Avg), maximum (Max) and maximum corrected (Max_c) pair-wise distances, and the number of OTUs at three cut-off levels. *Nassellaria comprises also the order Collodaria.</p

Intragroup phylogenetic distance and trunk length of Stramenopiles groups.

<p>A complementary view of phylogenetic structure of Stramenopiles is shown by displaying the trunk length (vertical lines) and the Mean Phylogenetic Distance (vertical boxes) of each group (based on tree in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057170#pone-0057170-g002" target="_blank">Figure 2B</a>).</p

Maximum Likelihood phylogenetic trees for eukaryotic supergroups.

<p>Trees include several taxonomic groups within CCTH (A), and Rhizaria (B) and are done with sequences representative of each OTU obtained clustering at 0.05 distance. The number of sequences (about 550 bp in length) per tree 218 and 303 respectively. Red dots represent bootstrap values above 75.</p

Phylogenetic affiliation of clones within choanoflagellates.

<p>Maximum-likelihood phylogenetic tree constructed with 54 partial and complete choanoflagellate sequences (733 informative positions). Clades A–I follow the notation of del Campo and Massana <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041970#pone.0041970-delCampo1" target="_blank">[38]</a>. Four additional clades (J–M) are introduced. For further description see legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041970#pone-0041970-g006" target="_blank">Figure 6</a>.</p

Phylogenetic composition in clone libraries constructed from the three incubation experiments.

<p>Upper and middle panels show the composition of clones in the 3-µm filtered initial and final incubation samples, respectively. The unfiltered final incubation samples are represented by the lower panels. For each library, the proportion of clones within the major taxonomic groups is displayed as pie charts. A finer resolution of the taxonomic groups and their contribution to each library is shown in the bar charts.</p

Novelty pattern determined for all clones obtained at the start and end of incubation experiments.

<p>Each circle represents one clone and its percent similarity to the closest environmental clone and the closest cultured species in GenBank. The mean similarity to both is indicated by the squares.</p