Algorithm 1: maxSumFrequenciesTree.

<p>Algorithm 1: maxSumFrequenciesTree.</p

The accuracy of strategies for selecting events from NPRs depending on various parameters.

<p>Parameter <i>T</i> denotes the filtering threshold and Δ denotes the noise level for generating sets of NPRs. Columns 3, 5, and 7 report the accuracy as measured by the average symmetric distance to the event set in the true gene history. Note that the bold-faced values indicate the method (among (a)s-median and random NPRs) having the symmetric distances of 1000 gene families being significantly less than that of the other methods, i.e. p-value of the paired <i>t.test</i> being less than 0.05. Columns 4, 6 and 8 report the average numbers of predicted , , and events with or without filtering. On average, the true evolutionary history of a gene family contains 13.7 ,, and events.</p

An example where none of the MPRs contain all highly supported events.

<p>(a) The DTL-graph composed of three canonical MPRs was computed by Algorithm 3 of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073667#pone.0073667-Scornavacca1" target="_blank">[18]</a> given the species tree <i>S</i> whose subdivision is (b), the gene tree <i>G</i> (c), and the costs <i>δ</i> = 0.60205, <i>τ</i> = 0.74818, and <i>λ</i> = 0.24303 respectively for a ,, and event. Events with support higher than 50% are highlighted by yellow squares. Each node of (resp. <i>G</i>) is assigned a unique id. An event node (resp. mapping node) of the graph is labeled as “” (resp. “”), where , and <i>N</i> is the number of parsimonious reconciliations passing through the node. Recall that each parsimonious reconciliation tree can contain only one child of a mapping node.</p

Algorithm 2: backtrack(<i>v</i>).

<p>Algorithm 2: backtrack(<i>v</i>).</p

The accuracy of event prediction strategies when inferring the support of events in MPRs from sets of NPRs.

<p>This table shows the average symmetric distance () between predicted and true event sets when computing event supports from their frequency in optimal and near-optimal reconciliations, and filtering the events with (Column 3), where <i>T</i> is the filtering threshold. The degree of non-optimality in reconciliations is indirectly measured by the noise level Δ introduced in the event elementary costs. Column 4 reports the average number of predicted , , and events, depending on both the filtering threshold and noise level. On average, the true evolutionary history of a gene family contains 13.7 such events.</p

The accuracy of competing strategies to infer events in a gene history.

<p>Curves are plotted from experiments on 990 gene families. Strategies are defined by a considered reconciliation set – most parsimonious reconciliations (MPRs) or near-optimal reconciliations (NPRs), by a way to select one of these reconciliations – at random or through the s-median procedure, by the method to compute event supports –Δ = 0% (i.e. computing supports from MPRs) or 20% (i.e. computing supports from NPRs obtained for a noise level of 20% in event costs), and by the subset of events output depending on their support (≥0%, ≥50% or ≥90%). See main text for a description of the proposed strategies.</p

Impact of event filtering on random MPRs.

<p>This table shows the accuracy of filtering events from a random MPR, when varying the filtering threshold <i>T</i>. The event supports have been computed from MPRs only, <i>i.e.</i> Δ = 0. Thus, for each line, the set contains all events <i>e</i> from the chosen random MPR having . Column 2 (resp. Column 3 and 4) reports the accuracy as measured by the average symmetric distance (resp. FP and FN) between and . A bold-faced value indicates that the accuracy of the corresponding strategy is significantly better than that of the previous row (p-values of the paired <i>t.tests</i> are lower than ). Column 5 reports the average numbers of predicted, , , and events with or without filtering. On average, the true evolutionary history of a gene family contains 13.7 such events.</p

An example of reconciliation.

<p>Two valid reconciliations for the trees depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073667#pone-0073667-g001" target="_blank">Figure 1</a> ( events are not indicated). The reconciliation on the left contains two events, one event, a event and four events, while the one on the right contains one event, one , one event, two events and four events.</p

Distribution of genes with contrasted e_T-ratio interquartile in cultivated and wild compartments (Fig 4) according to the potential functional impact of the alternative isoform.

<p>Distribution of genes with contrasted e_T-ratio interquartile in cultivated and wild compartments (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183454#pone.0183454.g004" target="_blank">Fig 4</a>) according to the potential functional impact of the alternative isoform.</p

Number of clean pairs of reads mapped on the sorghum genome.

<p>The number of clean read pairs of each individual is indicated by a blue bar for cultivated sorghum accessions or an orange bar for wild sorghum accessions. For any given accession, the darker or lighter part of each bar corresponds to mapped or not mapped read pairs on the sorghum genome.</p