Predicted prevalences, probabilities and Log-Likelihoods for different fitted models.

<p>Predicted prevalences, probabilities and Log-Likelihoods for different fitted models.</p

Frequency of re-inoculations and reinfections based on the best model (<i>PF)</i>.

<p>(A) Distribution of the number of effective re-inoculations per individual one-year (black bars), five-years (dashed bars) and thirty-years (white bars) after the primary infection. (B and C) Distribution of probability of reinfection one-year (black bars), five-years (dashed bars) and thirty-years (white bars) after the primary infection considering (B) <i>F</i> = 0.2 and (C) <i>F</i> = 0.77.</p

Significance of different near-clades in distance matrices of the 60 STs dataset of <i>Candida albicans</i>.

1<p>Distance matrix for concatenated dataset.</p>2<p>Bonferroni corrected p value for Mantel test with 5,000 random permutation. A significant value (p<0.05) means congruence between the distance matrix and a binary distance matrix that discriminate just one of the proposed near-clades.</p>3<p>Significant p values before Bonferroni correction.</p

Summary of dataset structure types found in our comparative analyses.

1<p>Consensus support was arbitrarily considered moderate for datasets with 30–60% of branches supported by at least two fragments and High for datasets with more than 60%.</p>2<p>Bootstrap support was arbitrarily considered moderate for datasets with 40%–60% of branches supported by bootstrap higher than 80% and High for datasets with more than 60% with bootrstrap value higher than 80%.</p>3<p>Topological incongruence was considered moderate for datasets with 20–40% of branches with n-1 fragments topologically incompatible with the validity of the near-clade in the concatenated tree and high incongruence was considered for datasets with more than 40% of branches with n-1 fragments topologically incompatible.</p>4<p>Significant NJ-LILD after Bonferroni correction.</p><p>*Thresholds are only used to define limits to different genetic structure types, which clearly emerge from a visual comparison of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone-0103131-g001" target="_blank">Figures 1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone-0103131-g002" target="_blank">2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone-0103131-g003" target="_blank">3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone.0103131.s002" target="_blank">S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone.0103131.s003" target="_blank">S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103131#pone.0103131.s004" target="_blank">S4</a>. It is important to note that the used thresholds are applicable to define structure types when only datasets around 24 STs are used.</p

Summary of main features of analyzed datasets.

1<p><i>Tc, Trypanosoma cruzi; Fs, Fusarium solani complex; Af, Aspergillus fumigatus; B3, Blastocystis spp ST3; Ld, Leishmania donovani complex; Ca, Candida albicans; Cg, Candida glabrata.</i></p>2<p>Typing efficiency: defined as the number of STs per polymorphic site.</p

Approximated profile likelihood for the rate of protection failure (<i>F</i>) in the model <i>PF</i>.

<p>Dashed lines represent the lower and upper limit of the range of F values providing a good fit to the data.</p

Rules of <i>T</i>. <i>cruzi</i> transmission according to the four hypotheses on reinfections.

<p>(A) Transmission from vector to uninfected humans with probability <i>T</i>_<i>V→H</i>. (B) Definition of the four rules of reinfections. Full Protection <i>(FP</i>); Acute Phase Window (<i>APW</i>); Protection Failure <i>(PF</i>); Acute Phase Window and Protection Failure (<i>APW + PF</i>); <i>A</i>, acute phase window duration; <i>F</i>, protection failure rate. (C) Transmission from human to vectors with probability <i>T</i>_<i>H→V</i>. (D) Transmission of mixed infections. <i>T</i>_<i>mix</i> is the probability of transmission of a mixed infection and <i>z</i> a random number uniformly distributed between 0 and 1. The transmission of the mixed infection occurs when z < <i>T</i>_<i>mix</i>, and a single randomly selected DTU is transmitted otherwise.</p

Consensus support distribution for standardized datasets.

<p>The color scale-bar represents the level of consensus support that varies from 0 fragment trees (white bars) to ≥3 fragment trees (black bars) supporting the branch in the tree for concatenated alignments. The values are calculated as the mean of 10 replications.</p

Topological incongruence distribution for standardized datasets.

<p>The color scale-bar represents the number of fragments topologically incompatible with certain branch. It varies from n incongruent fragments (black bars) to less than n-3 (white bars), where n is the number of fragments of the dataset. The values are calculated as the mean of 10 replications.</p

Prevalence of infection in humans, dogs and vectors.

<p>Prevalence of infection in humans, dogs and vectors.</p