Supplementary Figure 1

A. Identical Maximum Parsimony (MP) and Maximum Likelihood B. MP and ML topologies for rpl32-trnL spacer, and C. ML topology for combined dataset, excluding 15 indel character

Data files for Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data."

README for data related to Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data." A note about gene alignment/tree naming: File names refer to the geneID from which baits were designed from. For example, "Elaeis_1007" indicates that this gene matches the exons "Elaeis_1007_*" which we submitted to MySelect for bait design. Some genes are named "Sabal" or "Nypa" because sequences from those species were submitted for the initial bait design. Files in this repository: 1) alignments.zip - folder containing alignments for all 133 nuclear genes used in phylogenetic analyses. Naming as described above. 2) bootstraps.zip - folder containing bootstrap replicates, 500 per each of 133 genes, output from RAxML. Gene names are the same as described above. 3) genetrees.zip - bipartition tree for the 133 nuclear gene trees, output from RAxML. Naming as described above. 4) concat.align.fasta - supermatrix alignment from concatenation of the 133 nuclear genes for all 17 species. 5) plastid.align.fasta - alignment of 89kb of chloroplast sequence for all 17 species. 6) mpest.tre, star.tre, concat.tre, and plastid.tre - newick tree files for each respective phylogenetic analysis (MP-EST, STAR, supermatrix, and plastome). MP-EST and STAR trees are the output of the respective programs, whereas the supermatrix tree and the plastid tree are output of RAxML. 7) binaligns.zip - folder containing alignments (nexus formatted for BEAST) of each of 27 bins. 8) starBEAST.xml - xml run file for *BEAS

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

Loss and pseudogenization of mitochondrial ribosomal protein genes in Alismatales.

<p>Bars represent events of loss or pseudogenization. Black bars mark unique events of gene loss from the mitogenome. Red (pseudogenization) and blue (loss) bars mark homoplasious gene changes.</p

Mitochondrial DNA similarity between pairs of species of Alismatales.

<p>Mitochondrial DNA similarity between pairs of species of Alismatales.</p

Characteristics of mitogenomes of four representatives of the Alismatales.

<p>Characteristics of mitogenomes of four representatives of the Alismatales.</p

Maps of mitogenomes of <i>Zostera marina</i> and <i>Stratiotes aloides</i>.

<p>For <i>Zostera</i> upper genes are transcribed forward; lower genes are transcribed reverse. For <i>Stratiotes</i> inner genes are transcribed clockwise; outer genes are transcribed counter-clockwise. Genes are color coded as indicated in the lower left corner. The names of <i>trans</i>-spliced genes are followed by exon numbers. Only genes assumed to be functional are shown. The figure was created using OGDRAW [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177606#pone.0177606.ref038" target="_blank">38</a>].</p

Intron content (<i>cis-</i> and <i>trans</i>-spliced) in mitogenomes of the Alismatales.

<p>Intron content (<i>cis-</i> and <i>trans</i>-spliced) in mitogenomes of the Alismatales.</p

Distribution of mitochondrial ribosomal protein genes in Alismatales mitogenomes.

<p>Blank boxes indicate absence of a gene from the mitogenome. Dark grey boxes indicate presence of a gene assumed to be functional. Light grey boxes and <b>Ψ</b> indicates a pseudogene or fragment of gene in the mitogenome. <b>N</b> indicates presence of a gene annotated as of mitochondrial origin in the nuclear genome of <i>Zostera marina</i>. (<b>n</b>) indicates likely presence of a gene in the nuclear genome of <i>Zostera marina</i>, though not annotated as of mitochondrial origin. *<i>Zostera noltii</i> has the same mitochondrial genes, but the potential nuclear location of genes is unknown.</p