S_hangoei_AFLP_scores

Documentation to S_hangoei_AFLP_scores This text file contains the scored AFLP data for Fst calculations and Structure runs. A total of 379 loci are included, 106 strains from four different populations. The first row (except column 1 and 2) contain the names of the loci (Loc_01 to Loc_379). The first column (as of row 2) contains the strain designation consisting of 4 letter and 2-3 numbers. SH represents species designation, i.e. Scrippsiella aft. hangoei (Dinophyceae), the next two letters indicate the lake from which the strain originates (AB=Abraxas, HI = Highway, MC = McNeil, VE = Vereteno; all lakes located in the Vestfold Hills, Antarctica), the last 2-3 digits represent the strain number. The third column (as of row 2) indicates lake population from which the strain originates. ABRA = Lake Abraxas, HIGH = Highway Lake, MCNEIL = McNeil Lake, VERE = Lake Vereteno. All subsequent columns give scores for presence of AFLP peaks. 1 = presence, 2 = absence of peak. There are no missing data

Data_Sheet_1_Does filter pore size introduce bias in DNA sequence-based plankton community studies?.docx

The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.</p

ITS r RNA Sequence alignment for Polarella glacialis

Sequence alignment of nine Polarella glacialis strains from the Vestfold Hills, Antarctica; the Antarctic Sea; and the Arctic Sea, based on the ITS region (Logares et al. 2009). All sequences deposited in Genbank (see table 1

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

PGAFLPstructureinput2

AFLP scored data (0,1) from 409 AFLP loci (5 combined primer pairs). Loci listed in row 1. Strain names listed in column 1

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