Placement of the 22 samples along the first two PCA axes (GEnALex); samples of <i>P. multistriata</i> gathered at LTER_MC in 2008 are indicated with grey squares; those in 2009 with grey diamonds, those in 2010 with black squares, and the one in 2011 with a white diamond.

<p>Samples 11 (2009), 19, 20, and 21 (2010), which showed a higher abundance of POP_B strains, but contained a minority of strains assigned to POP_A and others assigned as putative hybrids, are enclosed within an ellipse (see text). The two PCA axes capture 73.2% of the variability.</p

Genetic structure of the strains of <i>Pseudo-nitzschia multistriata</i> within each sample, as defined by Structure.

<p>Samples are presented in ranking order (1–22) along the x-axis. Each vertical bar represents one strain. The y-axis indicates the proportion of a strain’s genotype assigned by Structure to a population (i.e., K-cluster); the two populations identified by Structure are indicated POP_A (green), POP_B (red). Strains in each sample are ranked along the x-axis based on their assignment probabilities. Strains not assignable to any of the two populations above the 0.9-probability-level, are indicated to the right side of each sample. Samples have been grouped by year of collection: samples 1–7 in 2008, samples 8–15 in 2009, samples 16–21 in 2010 and sample 22 in 2011.</p

Cell length of <i>Pseudo-nitzschia multistriata</i> strains assigned to A) POP_A (green), B) POP_B (red), and C) putative hybrids (black), as determined by Structure.

<p>The grey dots in the background represent the cell size classes recorded in the natural environment.</p

Relative abundance of NGS V4 Leptocylindraceae sequences at the six stations.

<p>Data for plankton samples were inferred from the surface cDNA results normalised over the total number of sequences obtained for the sample and the average of the three size fractions (mean relative frequency). Data for sediment samples were inferred from cDNA template based sequences (relative frequency).</p

The Gulf of Naples (GoN) and the location of the Long Term Ecological Research station MareChiara (LTER-MC; 40°48.5′N, 14°15′E).

<p>The Gulf of Naples (GoN) and the location of the Long Term Ecological Research station MareChiara (LTER-MC; 40°48.5′N, 14°15′E).</p

Number of single, multiple and shared genotypes in the inferred populations, POP_A, POP_B and the putative hybrids, as identified by Structure over the four years of the present study.

<p>Included in the table are the number of strains that shared a common genotype (Ns) and the number of shared genotypes (Gs). # indicates that genotypes are shared between different years.</p><p>Number of single, multiple and shared genotypes in the inferred populations, POP_A, POP_B and the putative hybrids, as identified by Structure over the four years of the present study.</p

Population genetic structure of <i>Pseudo-nitzschia multistriata</i> parental strains and samples of their F1 offspring [21] as identified by Structure.

<p>For each cross, parental and F1-strains are grouped in boxes, ordered along the x-axis. Each vertical bar in a box represents one strain; the first two bars represent the parental strains, the remainder, the F1 strains. The y-axis indicates the proportion of a strain’s genome assigned by Structure to POP_A (green) and POP_B (red). Strains not assignable to one of these populations at or above the 0.9-probability-level are considered putative hybrids based on the Structure results. Parental strain assignment according to Structure: Cross 1: SY017 (POP_A; green)×SY278 (hybrid); Cross 2: SY017 (POP_A; green)×SY138 (POP_B; red); Cross 3: SY138 (POP_B; red)×SY378 (POP_B; red); and Cross 4: SY138 (POP_B; red)×SY379 (POP_B; red).</p

RAxML tree inferred from the alignment of 165 representative V9 sequences of leptocylindracean OTUs from the BioMarKs data, six leptocylindracean sequences from GenBank, and 96 reference sequences of bolidomonads, leptocylindraceans and other diatoms, utilizing the GTRGAMMA base substitution model and Hill Climbing algorithm.

<p><i>Bolidomonas pacifica</i> and <i>B. mediterranea</i> were designated as outgroups. All non-leptocylindracean sequences were pruned from the tree following tree construction (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103810#pone.0103810.s002" target="_blank">Figure S2</a> for tree with outgroups included). Bootstrap values were inferred from 100 distinct alternative runs and values <50 are deleted. OTU labels follow same principle as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103810#pone-0103810-g001" target="_blank">Figure 1</a>.</p

Genotypic diversity of the inferred <i>Pseudo-nitzschia multistriata</i> populations POP_A, POP_B and the putative hybrids as identified by Structure over the four years of study.

<p>Included in the table are the number of strains (N), the number of genotypes (G) and the genotypic diversity (G/N).</p><p>Genotypic diversity of the inferred <i>Pseudo-nitzschia multistriata</i> populations POP_A, POP_B and the putative hybrids as identified by Structure over the four years of study.</p

Number of reads and OTUs obtained by clustering the BioMarKs sequences at 97% similarity cut-off.

a<p>percentage over all BioMarKs sequences.</p>b<p>percentage over all BioMarKs diatom sequences.</p>c<p>ambiguously distinguishable in V4 sequences.</p>d<p>identified only among V4 sequences.</p