PMC

Localization of sampling areas (stars). (Drawing by Fabrice Courtin, Bobo-Dioulasso, Burkina Faso).

Unrooted NJTREE representation of genetic distance between the different subsamples of T. b. brucei in Guinea (Boffa and Dubreka) and in the Ivory Coast (Bonon) in different years (1998, 2002, and 2004) and with different sampling techniques (KIVI, RI, and BS) using Cavalli-Sforza and Edwards' () chord-distance matrix.

F_IS per locus and over all 7 polymorphic loci (All) (Micbg6 and Trbpa1/2 excluded), averaged over the 6 subsamples. The residual variation across the 6 remaining loci is mainly explained (91%) by the corresponding genetic diversity (in clonal populations a positive relationship is indeed expected, see ref. ). For each locus, 95% confidence intervals (CI) of the means are estimated with the jackknife method over the populations' standard error. Over all loci, CI was obtained by bootstrap over loci. Mean F_IS and 95% bootstrap CI were also computed for Bonon 2000–2002 subsamples (Bonon) and compared to the F_IS computed when GPS coordinates of patients are taken into account (i.e., grouping the most proximate isolates into smaller subunits) (Bonon GPS).

Effective population size (N_e) obtained with the F_IS-based method (see Materials and Methods ) (“model”), with u = 10⁻³ and u = 10⁻⁴, and with Waples' method from temporally spaced samples (with MLG as a single locus), using trypanosome's life cycle as the generation time with the shortest (sgt = 37 days) or largest (lgt = 49 days) generation times (see text). Black squares are the means with 95% CIs (small lines) (averaged over 2000–2002, 2000–2004, and 2002–2004 for Bonon). The dotted line corresponds to the estimated number of infected persons in the different areas according to epidemiological surveys. For Waples' method, CI comes from a χ² distribution with a degrees of freedom (a is the number of alleles, in this case of different MLG's) (). For the F_IS-based method, CIs correspond to those of F_IS obtained by bootstrap over loci.