Genetic analysis of the <i>Trypanosoma brucei</i> population at the Côte d’ivoire focus.

<p><b>a.</b> Dendrogram of multi-locus genotypes (MLG) for the <i>T. brucei</i> isolates collected from several townships in Côte d’Ivoire, over the period of time 1978–1983 in addition to DAL972 and ELIANE. Bootstrap values from 100 iterations are indicated for branch nodes with a bootstrap value above 10. The presence of <i>TgSGP</i> using primers spanning the 5′ and 3′ ends is indicated by *. Isolates that displayed human serum resistance, the classical <i>T. b. gambiense</i> isoenzyme profile and possess <i>TgSGP</i> can be inferred to be group 1 <i>T. b. gambiense</i> (Red). Isolates that display a degree of resistance or were isolated from humans but did not possess the classical isoenzyme profile or <i>TgSGP</i> were determined to be group 2 <i>T. b gambiense</i> (Blue). Strains that exhibited no human serum resistance and were isolated from animals are most likely <i>T. b. brucei</i> (Black). <b>b.</b> Predicted structure of the Côte d'Ivoire <i>T. brucei</i> focus for the most likely population number (K = 2). The proportion of each population that an isolate is a member of is indicated by red and blue in the histogram. <b>c.</b> Principal component analysis (PCA) of the Côte d’Ivoire <i>T. brucei</i> isolates using a pair-wise genetic distance comparison between each isolates MLG. The x-axis explains 56.45% of the variability in the populations and the y-axis 13.98%, for a total of 70.45%. Isolates are colored as outlined in 1a. The circled numbers indicate the centroids of the two clusters identified by <i>k</i>-means analysis. The limits of these clusters are also indicated.</p

Linkage disequilibrium for each genetic marker (statistically significant disequilibrium highlighted in bold) between pair wise polymorphic loci in the combined <i>T. b. brucei</i> and group 2 <i>T. b. gambiense</i> population at the Côte d’Ivoire focus (N = 25).

<p>The data were analyzed using the Genepop 4.0 software package.</p

F_st proportion indicating genetic distance between the populations of group 1 and 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus.

<p>F_st proportion indicating genetic distance between the populations of group 1 and 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus.</p

Hardy-Weinberg analysis of group 1 <i>T. b. gambiense</i> isolates at the Côte d’Ivoire focus (N = 20).

<p>Hardy-Weinberg analysis of group 1 <i>T. b. gambiense</i> isolates at the Côte d’Ivoire focus (N = 20).</p

Details of the isolates used in the study, including the isolate name, the host each strain was isolated from, the serum resistance profile resulting from a 5 rodent BIIT (R = highly resistant, I = intermediate or sub-resistant and S = sensitive) and the geographic location of the isolate when collected within Côte d’Ivoire.

<p>Details of the isolates used in the study, including the isolate name, the host each strain was isolated from, the serum resistance profile resulting from a 5 rodent BIIT (R = highly resistant, I = intermediate or sub-resistant and S = sensitive) and the geographic location of the isolate when collected within Côte d’Ivoire.</p

Hardy-Weinberg analysis for the combined population of group 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus (N = 25).

<p>Hardy-Weinberg analysis for the combined population of group 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus (N = 25).</p

Polymorphisms and heterozygosity of <i>T. brucei</i> at the Côte d’Ivoire focus (N = 45).

<p>Polymorphisms and heterozygosity of <i>T. brucei</i> at the Côte d’Ivoire focus (N = 45).</p

Nei’s genetic distance between the populations of group 1 and 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus.

<p>Nei’s genetic distance between the populations of group 1 and 2 <i>T. b. gambiense</i> and <i>T. b. brucei</i> at the Côte d’Ivoire focus.</p

Basic population genetic parameters of the four <i>T. b. rhodesiense</i> populations.

<p>n = ‘all samples/unique MLGs (n)’, respectively, p = proportion of polymorphic loci, A = mean allele number per locus, He = Expected heterozygosity, Ho = Observed heterozygosity, F_IS = fixation index; the first number in each cell is measurement with all samples, the second number is after removal of repeated genotypes.</p

Linkage equilibrium/disequilibrium in <i>T. b. rhodesiense</i> populations and the frequency of repeated genotypes.

<p>nd = not done, as analysis not appropriate.</p