Journal: PLoS ONE
Article Title: Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi
Figure Lengend Snippet: First part of three (Figs. 3, 4 and 5 ): Phylogenetic tree of nifH protein sequences. 50% majority rule consensus tree of 13,500 PhyloBayes  post burn-in trees, unrooted. Black values at internodes = Bayesian Posterior Probability (if > 0.5). Pink values = MEGA5  Maximum Parsimony (MP) bootstrap support (if > 50). Green values = GARLI  Maximum Likelihood bootstrap support (if > 50). Terminal triangles represent monophyletic clades with MOTUs solely of one tree species origin, collapsed but keeping the internal distance (substitutions per site, see scale bar), in light pink = 50–79 MP bootstrap support, dark pink = 80–100 MP bootstrap support. Green color indicates MOTUs solely from Fagus origin, red color Picea origin and dark blue color mixed origin (with bars showing ratio of [green] vs. [red]). Terminal labels with sequences from this study: MOTU ID (SMOTU = singleton MOTU), total number of sequences, FASY = from Fagus , PIAB = from Picea , followed by number of sequences in the same order, then forest management type(s) (AC.Conif = managed spruce forests, AC.Decid = managed beech forests, Extensiv = extensively managed beech forests) and number of sequences in same order. Terminal labels with sequences from other sources: near BLAST hit, summary of ecological data of sequences in that MOTU. MOTUs that contain nucleotide sequences flagged as potential chimeras appear in italics and with the term PotChim (only present in Fig. 3, Supergrade). The width of visible terminal branches represents the number of sequences (size correct up to 10 sequences). To the right, amino acid sequence logos and Kyte-Doolittle hydophobicity alignments for labeled nodes on the tree. The small tree shape (based on screenshot from Archaeopteryx v.0.972  ) shows the position within the complete phylogenetic tree.
Article Snippet: Each composite DNA extract was amplified separately by PCR in triplicate 20 µl reaction mixtures containing 4 µl FIREPol 5x Master Mix (Solis BioDyne, Tartu, Estonia), 10 µM of each primer and approximately 20 ng template DNA.
Techniques: Sequencing, Labeling