Comparison between the numbers of reads obtained with various primer pairs and samples.

<p>Different samples (Ia, Ca, Cb, G, H, H1) in five independent replicates (r1 to r5), as well as in the pool of these five replicates (pool) are represented. <b>A</b>. Primer pairs Trich4 and Trich3 that both target <i>Trichuris trichiura</i>. <b>B</b>. Primer pairs Asc4 and Asc2 that target <i>Ascaris lumbricoides</i> and <i>A</i>. <i>suum</i>. <b>C</b>. Primer pairs Dicro22 and Dicro6.1 that target <i>Dicrocoelium dendriticum and D</i>. <i>chinensis</i>. Black: the more efficient of the two primer pairs, Gray: the less efficient.</p

Comparison of performance of the aMPlex Torrent genotyping and the microscopic approaches to identify parasites in archeological samples up to 7,200 years old.

<p>Comparison of performance of the aMPlex Torrent genotyping and the microscopic approaches to identify parasites in archeological samples up to 7,200 years old.</p

Genotyping reveals past genetic diversity of parasites.

<p><b>A.</b> Comparison of ancient and modern genetic diversity of <i>Ascaris lumbricoides</i> and <i>A</i>. <i>suum</i> on the Asc4 PCR fragment. The ancient sequences are highlighted in yellow. When multiple sequences were identical, a single sequence was represented. The variants of the <i>Ascaris</i> sequences were found in samples H and Na, as indicated. <b>B.</b> Comparison of ancient and modern genetic diversity of <i>Trichuris trichiura</i> on the overlapping Trich3 and Trich4 PCR fragments. The variants v1 and v2 of the <i>Trichuris</i> sequences were found in samples Da and Ia, respectively. <b>C.</b> Median joining network [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146230#pone.0146230.ref028" target="_blank">28</a>] showing the genetic distance separating the human and animal <i>Trichuris</i> species, each represented with a different color, and the central position occupied by the sequence of the ancient European human parasite, indicated by a red arrow. The name of the host is indicated in italics. The number of SNPs distinguishing each sequence is indicated in red alongside the corresponding connecting link. The combined sequences, without primers, of the Trich3 and Trich4 fragments were used. <b>D.</b> Maximum likelihood (ML) tree showing the phylogenetic relationships between the human and animal <i>Trichuris</i> sequences. The tree was constructed using PHYML 3.0 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146230#pone.0146230.ref029" target="_blank">29</a>] and the Shimodaira-Hasegawa-like branch test (SH) was used to evaluate the statistical support of the nodes, which are indicated along the corresponding branches of the tree. The most distant animal <i>Trichuris</i> sequences (<i>T</i>. <i>ovis</i> & <i>T</i>. <i>discolor</i>) were used as an outgroup to reveal the relationships between ancient European and modern Asian and American <i>T</i>. <i>trichiura</i> sequences. The other represented items are as described in panel C.</p

Schematic representation of the workflow of the aMPlex Torrent method for the genotyping of ancient gastrointestinal helminth parasites.

<p>Schematic representation of the workflow of the aMPlex Torrent method for the genotyping of ancient gastrointestinal helminth parasites.</p