Davis et al Data Matrix

Davis et al Data Matri

Nexus file of 114 chloroplast genes and gene positions

Nexus file containing the 114 genes data set followed by the position of each gene with the matrix

M1 Langrange combined input and output

Combined Lagrange M1 model input python script followed by the results output. This includes the dispersal constraints, geographic coding for taxa, concatenated 85 genes ML tree, and inferred ancestral areas within two log-likelihoods of the most likely area with relative probabilities

alignments_and_trees

This zip file contains the alignments and trees, as well as a ReadMe file

baits-120-60

The probe sequences to target phytochrome, phototropin and neochrome genes, with a special focus on those of hornworts and ferns

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

Flowchart of our transcriptome-mining pipeline.

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

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

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