Alignments

Alignment

Bayesian_analysis

Bayesian_analysi

ML_analysis

ML_analysi

ML_analysis

ML_analysi

Schematic diagrams of the ten nuclear genes for which we developed fern-specific primers.

<p>(A) <i>ApPEFP_C</i>; (B) <i>CRY2</i>; (C) <i>CRY4</i>; (D) <i>DET1</i>; (E) <i>gapCpSh</i>; (F) <i>IBR3</i>; (G) <i>pgiC</i>; (H) <i>SQD1</i>; (I) <i>TPLATE</i>; (J) <i>transducin</i>. Each subset of the figure represents one protein-coding locus, using the most closely related <i>Arabidopsis thaliana</i> homolog as the template. The coding sequence is measured (in base pairs) along the bottom of the thickened horizontal line, with each locus wrapping onto a new line every 2000 base pairs, when necessary. Intron location, number, and length (in base pairs in <i>Arabidopsis</i>) are given above the line. Also shown below the line are the priming locations for each of the markers we developed. For <i>gapCpSh</i>, intron locations are based on <i>Arabidopsis </i><i>gapCp1</i>: the first two exons of <i>Arabidopsis </i><i>gapCp2</i> are each one codon shorter than in <i>gapCp1</i>.</p

Maximum likelihood phylograms for each region, including only those taxa that were successfully sequenced from our 15-taxon genomic DNA test set.

<p>Bold branches indicate strong support (≥70% bootstrap support). Scale bars are in units of substitutions per site. In the taxon names, “<i>C</i>.” and “<i>P</i>.” refer to <i>Cystopteris</i> and <i>Polypodium</i>, respectively. These phylograms are unrooted, but oriented as if rooted by the Cyatheales (or our best guess, when the Cyatheales accession did not sequence successfully), when space permits.</p

Flowchart of our transcriptome-mining pipeline.

<p>Flowchart of our transcriptome-mining pipeline.</p

Combined data maximum likelihood phylogram of our 15-taxon genomic DNA test set.

<p>Analyses were performed under our best-fitting model (model 3, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076957#pone-0076957-t003" target="_blank">Table 3</a>). Bold branches indicate strong support (≥70% bootstrap support); internal branches are labeled A – L for ease of discussion.</p

Example of our sequence-merging protocol.

<p>(A) In this schematic of a transcriptome alignment, aligned sequence fragments are indicated by the horizontal bars. Included are four fragments (colored) from our focal accession, which group together in the maximum parsimony tree. However, the two fragments from the 5’ end of the protein (in red) have some base pair conflicts with each other, as do the fragments from the 3’ end (in blue). Since the two sets of fragments do not overlap, and they group in the same area of the MP tree, it is not possible to determine which 5’ fragment belongs with which 3’ one. In this case we merged the sequences arbitrarily (B). The resulting alignment retains the full nucleotide data for primer-design purposes, but the relationships at the tips of the tree may be erroneous due to the two potentially chimaeric sequences.</p

append_metadata_tofasta_forSequin

A python script that goes through a single-locus alignment and matches each taxon in that alignment with the corresponding metadata, which it adds in a Sequin block to the alignment file. For automating the production of Sequin submission to GenBank in cases where there are many loci, each with different combinations of taxa