17 research outputs found
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
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
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
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
GIS file for CFP (DBF)
This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs
GIS file for CFP (PRJ)
This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs
Dynamic decision making via iterations spread in time
This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs
KMZ file defining border of the California Floristic Province
This data file describes the border of the California Floristic Province in western North America. It is openable in Google Earth or other GIS applications
GIS file for CFP (SHX)
This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs