Genetic differentiation estimates among the four <i>Cx</i>. <i>quinquefasciatus</i> populations based on allele frequencies at 26 microsatellite markers.

<p>(A) First and second PCs of the Discriminant Analysis of Principal Components (DAPC) to infer population structure. The graph represents the individuals as dots and the groups as coloured ellipses, which model 95% of the corresponding variability plotted. Populations (ellipses) are plotted within the orthogonal space defined by the first two PCA eigenvalues (inserts). (B) Bayesian analysis of population structure performed using STRUCTURE. Diagrammatic representation of population clusters for the most likely <i>K</i> (<i>K</i> = 3) with each coloured segment corresponding to the proportion of individuals assigned to a hypothetical population or cluster. Each vertical bar represents an individual with the height of the column segments showing the probability of assignment of belonging to one of the three clusters. Dark lines correspond to population assignment based on geographic collection-site.</p

<i>F</i>_<i>ST</i> outlier approach for the 26 studied microsatellite loci versus a model of neutral evolution in Ugandan <i>Cx</i>. <i>quinquefasciatus</i>.

<p>Central populations correspond to a cluster of Jinja and Kampala (based on genetic structure analysis, see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0005917#pntd.0005917.g003" target="_blank">Fig 3</a>). Each dot represents a microsatellite marker. The markers located in the grey middle area are assumed to be neutral. The markers located below the neutral area are candidates for being under balancing selection and the markers located above the neutral area are candidates for being under directional selection. <i>X</i>-axis: estimated heterozygosity values. <i>Y</i>-axis: <i>F</i>_<i>ST</i>-values. Analyses were performed assuming an infinite allele model.</p

Relationship between geographic distance versus genetic distance (<i>F</i>_<i>ST</i>/1- <i>F</i>_<i>ST</i>), analysed in parallel for the microsatellite, <i>Vgsc</i>-<i>L1014F</i> and <i>Ace1-G119S</i> loci.

<p>Significance was tested using a Mantel test. Grey shading corresponds to the 95% confidence interval. Geographic distance corresponding to the great-circle distance, which corresponds to the shortest distance over the earth’s surface between two points.</p

Matrix of inferred gene flow between Ugandan <i>Cx</i>. <i>quinquefasciatus</i> populations.

<p>Matrix of inferred gene flow between Ugandan <i>Cx</i>. <i>quinquefasciatus</i> populations.</p

Caputo et al 2016 Data S1

Information on the two Sequenom iPLEX® multiplexes used to genotype the X-centromeric region of An.gambiae and An.coluzzii specimens from Guinea Bissau and Burkina Faso as described in the paper. The two iPLEX assays were designed to genotype a total of 35 X-pericentromeric species-specific SNPs, yielding a density of 1 SNP per 0.12 Mb across the 4 Mb region targeted

Caputo et al. 2016 - Supporting information 5: Sequenom design

Information on the two Sequenom iPLEX® multiplexes used to genotype the X-centromeric region of An.gambiae and An.coluzzii specimens from Guinea Bissau and Burkina Faso as described in the paper. The two iPLEX assays were designed to genotype a total of 35 X-pericentromeric species-specific SNPs, yielding a density of 1 SNP per 0.12 Mb across the 4 Mb region targeted