Variation of <i>F</i>_IS between loci and between subsamples (host species and year) for <i>Trypanosoma congolense</i> (“savannah” type) from The Gambia [7].

<p>95% confidence intervals were obtained by jackknife on subsamples (three host species and two years), except for the average across all loci where the interval was obtained by bootstrapping over loci.</p

Regression between <i>F</i>_IS, inbreeding index of individuals relative to subpopulations per locus, and Nei's unbiased estimator of genetic diversity <i>H</i>_<i>s</i> [52] in <i>Trypanosoma brucei gambiense</i> 1 [19] in West Africa [12] and Central Africa [23].

<p>The proportion of variance explained by the model (<i>R</i>²) and the corresponding <i>p</i>-values are indicated.</p

Neighbor-joining dendrogram based on a Cavalli-Sforza and Edwards [80] distance matrix of different samples of <i>Trypanosoma brucei gambiense</i> type 1 in Western and Central Africa and computed out of eight microsatellite loci [12].

<p>Red, <i>T</i>. <i>b</i>. <i>gambiense</i> reference strains; gold, <i>T</i>. <i>b</i>. <i>gambiense</i> type 2; green, <i>T</i>. <i>b</i>. <i>brucei</i>; blue, <i>T</i>. <i>b</i>. <i>rhodesiense</i>. Isolates suspected of deriving from immigrants are in italics. Major (>50%) bootstrap values are also indicated. Bootstraps were undertaken with the isolate Stib215 as the root (<i>T</i>. <i>b</i>. <i>brucei</i>).</p

Location of different samples of trypanosomes reanalyzed with population genetics tools for estimating population parameters.

<p>1: Boffa and Dubréka (Guinea) HAT foci. Strains were isolated (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref012" target="_blank">12</a>] or directly amplified (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref028" target="_blank">28</a>]. 2: Bonon HAT focus (I) (Ivory Coast) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref012" target="_blank">12</a>]. 3: Campo, Bipindi, and Fontem HAT foci (Cameroon), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref023" target="_blank">23</a>], (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref036" target="_blank">36</a>], 4: Mbini and Kogo HAT foci (Equatorial Guinea), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref023" target="_blank">23</a>]. 5: Batangafo and Obo HAT foci (Central African Republic), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref023" target="_blank">23</a>]. 6: Omougou HAT foci (Uganda), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref023" target="_blank">23</a>]. 7: Nyanza HAT focus (Kenya), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref022" target="_blank">22</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref037" target="_blank">37</a>]. 8: Luangwa HAT focus (Zambia), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref022" target="_blank">22</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref037" target="_blank">37</a>]. 9: Busoga HAT focus (Uganda), (I) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref022" target="_blank">22</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref037" target="_blank">37</a>], (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref038" target="_blank">38</a>]. 10: Soroti HAT focus (Uganda), (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref038" target="_blank">38</a>]; 11. Maluku HAT foci (DRC), (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref036" target="_blank">36</a>]. 12: Nagana area of Central River District (The Gambia), (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref005" target="_blank">5</a>,<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref007" target="_blank">7</a>]. 13: Surra area of Darfour, Kurdofan, Kassala, Halfa and Showak (Sudan), (D) [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref039" target="_blank">39</a>]. μ: Microsatellite genotyping; mini: minisatellite genotyping.</p

Genetic differentiation (<i>F</i>_ST) between <i>Trypanosoma brucei rhodesiense</i> subsamples from the Busoga focus (Uganda) according to hosts (human or cattle) and/or year of sampling and significance testing (<i>p</i>-value).

<p>Data were computed out of three minisatellite loci [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003985#pntd.0003985.ref037" target="_blank">37</a>]. When host species is different, only subsamples not separated by more than three years were compared.</p