Jennings_POC_PrimerSeqs

This comma-delimited file provides information for 144 primers that were screened the Port-Orford populations. Included are the primer name, forward and reverse primer sequence, the original sequence name from Illumina sequencing, and the nucleotide sequence of the microread (2 x 80 bp, with read 1 and read 2 separated by 8 N's)

Jennings_Nootkacypress_PopInfo

This comma-delimited file provides location and genotype data for individuals from three populations of Alaska and one population of Oregon Nootka cypress that were surveyed with 11 microsatellite loci. The file shows individual numbers, population names, population latitudes, population longitudes, and the microsatellite allele length for diploid loci. Missing genotypes are indicated by the value "0, 0"

Marker <i>trn</i>DT visualized on a polyacrylamide gel.

<p>Lane 1: 50 bp ladder, lane 8: zero control, lane 2–7 and 13–14: analysis of wood-derived DNA, its location is inferred from genotypes, lane 9–12: references from North America (US), Europe (EU) or Asia (AS), respectively.</p

Details for used species, individuals and markers.

<p>Given are number of individuals per species and continent tested with the five markers, and fragment length based on sequencing for each marker and species. Consensus sequences of the five markers are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158221#pone.0158221.s001" target="_blank">S1 Fig</a>.</p

List of primers for the amplification and resequencing of the newly developed markers.

<p>Fluorescent-labeling of the primers is given in column “sequences”: FAM = blue, VIC = green, PET = red. In the last column, the accession numbers of the related markers for the three species <i>Q</i>. <i>robur</i>, <i>Q</i>. <i>mongolica</i> and <i>Q</i>. <i>alba</i> are given. “Length” means sequence length.</p

Weitemier et al. Hyb-Seq for phylogenomics in plants

<p>Hyb-Seq data matrices used by Weitemier et al. for phylogenomic analyses of <em>Asclepias. </em> </p> <p> </p> <p>Weitemier_et_al_Asclepias_syriaca_single_copy_gene_exons.fasta contains the sequences of the targeted exons used for probe design. </p> <p> </p> <p>Weitemier_et_al_plastome.phy contains the whole plastome matrix.</p> <p> </p> <p>Weitemier_et_al_nuclear_concatenated.phy contains a concatenation of all 768 putatively single-copy gene matrices.</p> <p> </p> <p>Weitemier_et_al_nuclear_gene_matrices.tgz is a gzipped tarball of the 768 individual matrices for the putatively single-copy genes. Note that the exons of each gene are concatenated in no particular order.</p> <p> </p> <p>Weitemier_et_al_nuclear_concatenated.tre contains the best ML tree for the concatenation matrix with bootstrap support values.</p> <p> </p> <p>Weitemier_et_al_plastome.tre contains the best ML tree for the plastome matrix with bootstrap support values.</p> <p> </p> <p>Weitemier_et_al_nuclear_gene_trees.tgz contains the bootstrap trees from the ML analysis of each nuclear gene.</p> <p> </p> <p> Weitemier_et_al_MP-EST_species_tree.tre contains the MP-EST species tree with bootstrap values.</p

Results of next-generation sequencing for oak reference assembly and polymorphism screening.

<p>Indexed individuals of oaks were sequenced using 150 bp paired-end reads and evaluated using <i>de novo</i> assembly (reference assembly). Pooled individuals were sequenced using 300 bp paired-end reads and evaluated using reference-guided assembly (polymorphism screen).</p

Jennings_Nootkacypress_PrimerSeqs

This comma-delimited file provides information for 144 primers that were screened on four Nootka cypress populations. Included are the primer name, forward and reverse primer sequence, the original sequence name from Illumina sequencing, and the nucleotide sequence of the microread (2 x 80 bp, with read 1 and read 2 separated by 8 N's)

Phylogenetic relationship among chloroplast genomes of white oak species representing Old World and New World lineages.

<p>The best maximum likelihood tree is shown for four white oak chloroplast genomes (<i>Q</i>. <i>mongolica</i>; <i>Q</i>. <i>robur</i>; <i>Q</i>. <i>petraea</i>; <i>Q</i>. <i>alba</i>) and one outgroup genome (<i>Q</i>. <i>rubra</i>). Inferred branch lengths in maximum likelihood substitutions are shown in bold, and bootstrap support values are show in italics. The phylogenetic resolution of informative indel markers are shown in black inverted triangles, and the resolution of the diagnostic PCR-RFLP marker is shown as a grey triangle.</p

PCR conditions compared for leaf and timber.

<p>Only the differences are shown, all other parameters are as given in material and methods.</p