G. pallidipes microsatellites data - Busia, Rukomeshi, IAEA - Ciosi et al 2014 - PLOS NTD

The file "2013-06-10 BUS+IAEA2012-2013+Zim_ALPHA&BETA.xlsx" contains the genotypes of 121 Glossina pallidipes individuals from two field population samples (Busia and Rukomeshi) and from two samples from the IAEA laboratory colony. These genotypic data have been used in the publication by Ciosi et al. 2014 PLOS Neglected Tropical Diseases untitled "Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes

Loss of genetic diversity in the IAEA colony (2013 sample) with respect to its simulated source population at the Kenya/Uganda border in 1975.

<p>Na; allelic diversity loss and H; expected heterozygosity loss. Both losses are statistically significant (Wilcoson's signed-rank tests over loci, p≤0.05).</p

Effective population sizes (<i>Ne</i>) estimated from the ABC analysis with scenario 4 (Figure 1).

<p>The prior distributions are shown as black lines while the posterior distributions are shown as coloured lines using the same colour code as in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002697#pntd-0002697-g001" target="_blank">Figure 1</a>. The medians of a posterior distribution, considered as point estimate of the parameters, are indicated. Each distribution was obtained from 10000 values. (A) <i>N</i>_Bus.: <i>Ne</i> of the Busia population. <i>N</i>_Ruk.: <i>Ne</i> of the Rukomeshi population. <i>N</i>_IAEA.: <i>Ne</i> of the IAEA colony. The prior distributions for <i>N</i>_Bus. and <i>N</i>_Ruk. are shown as a plain line while the prior distribution for <i>N</i>_IAEA. is shown as a dashed line. (B) <i>NB_col.</i>_Bus.: <i>Ne</i> of the colony of Busia origin (which is at the origin of the current IAEA colony) during the bottleneck associated with its establishment.</p

Genetic differentiation between samples and assignment of the IAEA colony samples into the potential source populations.

<p>Pairwise <i>F</i>_ST are indicated below the diagonal. Significant pairwise genotypic differentiation exact tests are indicated in bold typeface. The mean individual assignment likelihoods of IAEA samples into the potential sources of the colony (<i>L</i>_i→s) are indicated above the diagonal.</p

Estimated number of clusters and population structure from the Structure analysis.

<p>(A) Mean (±SD) natural logarithm of the likelihood of the data [LnP(X|K)] over 10 Structure replicated runs for each value of the putative number of clusters (K). (B) Estimated population structure from the Structure analysis for K = 2 and 3. Each individual is represented by a vertical line divided into K coloured segments that represent the individual's estimated membership fractions in K clusters. Black lines separate individuals from different samples. Each plot, is based on the highest-probability run (among ten) at K = 2 and 3.</p

Posterior probability of the selected scenarios and confidence in scenario choice in the ABC analyses.

<p>Posterior probability of the selected scenarios and confidence in scenario choice in the ABC analyses.</p

Distribution of the allele frequency classes.

<p>(A) in Busia. (B) in the IAEA colony samples from 2012 and 2013. (C) in Rukomeshi. The result of the bottleneck tests (Wilcoxon' tests on heterozygosity excess, and the mode shift tests) are indicated for each panel which correspond to a field population or to the IAEA colony. Heterozygosity excess and/or a shifted mode in the distribution of allele frequency classes indicate a recent reduction in population size.</p

Prior distributions of the parameters used in the ABC analyses.

<p><b>Note:</b><i>N</i>_anc.: effective population size (<i>Ne</i>) of the ancestral population. <i>N</i>_Bus.: <i>Ne</i> of the Busia population. <i>N</i>_Ruk.: <i>Ne</i> of the Rukomeshi population. <i>N</i>_IAEA: <i>Ne</i> of the IAEA colony. <i>N</i>_col.Bus.: <i>Ne</i> of the unsampled colony of Busia origin. <i>N</i>_col.Ruk.: <i>Ne</i> of the unsampled colony of Rukomeshi origin. <i>NB_col.</i>_Bus.: <i>Ne</i> of the colony of Busia origin (IAEA in scenario 4 and unsampled in scenario 6) during the bottleneck associated with its establishment that started in 1975 lasted <i>BD</i>_col.Bus. generations. <i>NB_col.</i>_Ruk.: <i>Ne</i> of the colony of Rukomeshi origin (IAEA in scenario 5 and unsampled in scenario 6) during the bottleneck associated with its establishment that started at <i>T_col.Ruk.</i> and lasted <i>BD</i>_col.Ruk. generations. <i>NB</i>_cont.: <i>Ne</i> of the Busia population during the bottleneck associated with the tsetse control that started in 1991 and lasted <i>BD</i>_cont. generations. <i>T_anc.</i>: number of generations between present and the merge of the two potential source populations an unsampled ancestral population. <i>T_admix.</i>: date of the admixture. <i>ar</i>: admixture rate. GSM: Generalized Stepwise Mutation model. SNI: Single nucleotide indel mutations.</p>*<p>: see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002697#pntd.0002697.s003" target="_blank">Supplementary file S2</a> (Table S7 in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002697#pntd.0002697.s003" target="_blank">Supplementary file S2</a>) for a rationale.</p

Competing scenarios considered in the ABC analysis of IAEA colony past demography (analysis 3).

<p>The demography of the Busia and Rukomeshi populations was determined as described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002697#pntd.0002697.s003" target="_blank">Supplementary file S2</a>. In all scenarios, the two potential source populations merged <i>T_anc.</i> ago into an unsampled ancestral population and a bottleneck started in Busia in 1991 and lasted <i>BD</i>_cont. generations. Scenario 4, 5 and 6 are respectively variations of scenarios 1, 2 and 3 in which a genetic bottleneck (of duration <i>BD</i>_col.Bus. or <i>BD</i>_col.Ruk.) is associated with the laboratory colonisation. In scenarios 1, 2, 4 and 5 the IAEA colony has a single population of origin. In scenarios 1 and 4, the IAEA colony was founded from the Busia population in 1975 while in scenarios 2 and 5, it was founded from the Rukomeshi population <i>T_col.Ruk.</i> generations ago. In scenario 3 and 6 the IAEA colony originates from an admixture between unsampled colonies of Busia and Rukomeshi origin that were respectively founded from the Busia population in 1975 and from the Rukomeshi population <i>T_col.Ruk.</i> generations ago. When admixture occurs, the admixture rate <i>ar</i> is the proportion from unsampled Busia colony that contributed to the admixed IAEA colony.</p

Building Endogenous Capacity for the Management of Neglected Tropical Diseases in Africa: The Pioneering Role of ICIPE

<p>Building Endogenous Capacity for the Management of Neglected Tropical Diseases in Africa: The Pioneering Role of ICIPE</p