Representative Example for the Scenario Described in the Proof of Theorem 1.

<p>T_X is depicted in blue and T_Y-{<i>x</i>} in green. Species (leaves) in Y are represented by filled circles.</p

Supplementary Methods - 3rd Revision

Supplementary Methods - 3rd Revisio

Representative Examples for Two Scenarios in the Proof of the Lemma

<p>In both examples, T_X is in blue and T_Y-{<i>x</i>} in green, and species (leaves) in Y are represented by filled circles. The two scenarios in the proof of the lemma, A and B, are illustrated correspondingly in (A) and (B), respectively.</p

Topologically Distinct Phylogenetic Trees for Two Sets of Species, X and Y, such that |X| = 2 and |Y| = 3.

<p>X and T_X are depicted in dark blue, leaves in Y are denoted with circles, and a possible choice for <i>x</i> (satisfying the requirements in the lemma), with the path from T_X to <i>x,</i> in light blue.</p

Supplementary Figures - 2nd Revision

Supplementary Figures - 2nd Revisio

Phylogenetic Scopes and Divergence of Sets of Species

<div><p>(A) Phylogenetic scope comprising hypothetical species A, B, C, D, and E. Numbers are branch lengths indicating evolutionary distances (not necessarily reflecting temporal distances). The subtree connecting species B, C, and E is shown in red and has divergence 1 + 3 + 1 + 5 + 2 + 4 = 16. Applying the greedy algorithm always produces maximally divergent extensions of the original set. For example, the subsets constructed starting with B—BE (divergence 11), BCE (16), BCDE (19)—have maximum divergence among those obtainable by adding one, two, and three additional species, respectively. The series AE (12), ACE (17), ACDE (20) is optimal among all possible subsets of two, three, and four species.</p><p>(B) Phylogenetic scope comprising placental mammals that have been or are being sequenced (in red) and candidates for future sequencing (derived from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010071#pgen-0010071-b017" target="_blank">17</a>]). If five groups choose the next five targets for sequencing using the greedy strategy described in the text, the following species (in blue) will be selected (in order): (1) tenrec, (2) hedgehog, (3) rock hyrax, (4) tree shrew, (5) dog-faced fruit bat (a megabat). Within the phylogenetic scope shown, this is guaranteed to be the choice of five species that maximises the total resulting divergence. These species have recently been announced amongst targets for future sequencing [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010071#pgen-0010071-b009" target="_blank">9</a>].</p></div

Supplementary_File_2_Nb_of_Quartets

Table containing the number of quartets needed for likelihood and geometric quartet mapping to get below a certain threshold of the final tree-likeness value, under different phylogenetic settings

Supplementary_File_3_Influence_NbBp

Figure detailing the influence of the number of base pairs sampled on the best evolutionary rate

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

<div><p>In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.</p></div

Performance of NG-SAM in simulated experiments.

<p>The hexagons are colored according to the mean of the metrics from all covered simulated experiments. White areas represent unexplored parameter space. <b>A</b>. The percentage of successful simulated experiments in the first simulation setting, as a function of length and number of repetitive units. The black circle [at the point (3813, 3)] marks the repetitive structure of the target region used in the second simulation setting. The dashed line corresponds to target regions with a total size of 10 kb. <b>B</b>. Percentage of correctly reconstructed bases in the successful experiments from the first simulation setting, as a function of length and number of repetitive units in the target sequence (black circle and dashed line as in <b>A</b>). <b>C</b>. The percentage of successful simulated experiments in the second simulation setting, as a function of the dilution factors ( and in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043359#pone-0043359-g002" target="_blank">Figure 2</a>). The black circle corresponds to the dilution factors used in the first simulation setting. <b>D</b>. Percentage of correctly reconstructed bases in the second simulation setting as a function of the dilution factors. Black circle as in <b>C</b>; see text for further details.</p