Robustness Supplement

The zip file contains all supplemental files, including supplemental figures, a C program (with README.txt file) for computing false positive, false negative, etc. clades for an estimated tree and reference tree, and list of alignment lengths for loci in the 8881-locus great ape dataset

Estimates of time and hybridization probability (when applicable) on the six candidate species phylogenies shown in Figure 3 for the three <i>Drosophila</i> species <i>Dmel</i>, <i>Dere</i>, and <i>Dyak</i>.

<p>Estimates of time and hybridization probability (when applicable) on the six candidate species phylogenies shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen-1002660-g003" target="_blank">Figure 3</a> for the three <i>Drosophila</i> species <i>Dmel</i>, <i>Dere</i>, and <i>Dyak</i>.</p

Six hypotheses for the evolutionary history of a <i>Drosophila</i> data set.

<p>(A–C) The three possible species tree topologies. (D–E) The three possible single-hybridization species network topologies (excluding extinction events).</p

Analysis results for the six phylogenies in Figure 2 using gene tree topologies inferred by maximum parsimony (using PAUP*).

<p>Analysis results for the six phylogenies in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen-1002660-g002" target="_blank">Figure 2</a> using gene tree topologies inferred by maximum parsimony (using PAUP*).</p

Phylogenetic networks, MUL trees, and valid allele mappings.

<p>In this example, single alleles , , and were sampled from each of the three species , , and , respectively, whereas two alleles ( and ) were sampled from species . See text and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660.s001" target="_blank">Text S1</a> for details.</p

Various hypotheses for the evolutionary history of a yeast data set.

<p>(A) The species tree for the five species <i>Sbay</i>, <i>Skud</i>, <i>Smik</i>, <i>Scer</i>, and <i>Spar</i>, as proposed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Rokas1" target="_blank">[35]</a>, and inferred using a Bayesian approach <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Edwards2" target="_blank">[39]</a> and a parsimony approach <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Than4" target="_blank">[36]</a>. (B) A slightly suboptimal tree for the five species, as identified in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Than4" target="_blank">[36]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Edwards2" target="_blank">[39]</a>. (C–E) The three phylogenetic networks that reconcile both trees in (A) and (B), and which we reported as equally optimal evolutionary histories under a parsimony criterion in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002660#pgen.1002660-Yu1" target="_blank">[30]</a>. (F) A phylogenetic network that postulates <i>Smik</i> and <i>Skud</i> as two sister taxa whose divergence followed a hybridization event.</p

Supplementary Figures

Supplementary Figure