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The effective population size is an important concept in population genetics. It corresponds to a measure of the speed at which genetic drift affects a given population. Moreover, this is most of the time the only kind of population size that empirical population genetics can give access to. Dioecious populations are expected to display excesses of heterozygosity as compared to monoecious panmictic populations, as measured by Wright's FIS. It can be shown that these excesses are negatively correlated with the population size. This is why FIS can be used to estimate the eigenvalue effective population size of dioecious populations. In this paper, we propose a new approximation that provides a very accurate estimate of the eigenvalue effective population size of a dioecious population as a function of the real population size. We then explore the accuracy of different FIS-based methods using the leading eigenvalue of transition matrices or coalescence. It appears that the eigenvalue-based method provides more accurate results in very small populations, probably due to approximations made by the coalescence approach that are less valid in such situations. We also discuss the applicability of this method in the field.

In Subsaharan Africa, tsetse flies (genus Glossina) are vectors of trypanosomes causing Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). Some foci of HAT persist in Southern Chad, where a program of tsetse control was started against the local vector Glossina fuscipes fuscipes in the Mandoul focus in 2014, and in Maro in 2018. Flies were also sampled in 2018 in Timbéri and Dokoutou. We analyzed the population genetics of G. fuscipes fuscipes from the four tsetse-infested zones. The trapping samples were characterized by a strong female biased sex-ratio, except in Timbéri and Dokoutou that had high tsetse densities. Apparent density and effective population density appeared smaller in the main foci of Mandoul and Maro and the average dispersal distance (within the spatial scale of each zone) was as large as or larger than the total length of each respective zone. The genetic signature of a population bottleneck was found in the Mandoul and Timbéri area, suggesting a large ancient interconnected metapopulation that underwent genetic subdivision into small, isolated pockets due to adverse environmental conditions. The long-range dispersal and the existence of genetic outliers suggest a possibility of migration from remote sites such as the Central African Republic in the south (although the fly situation remains unknown there) and/or a genetic signature of recent exchanges. Due to likely isolation, an eradication strategy may be considered for sustainable HAT control in Mandoul focus. Another strategy will probably be required in Maro focus, which probably experiences much more exchanges with its neighbors.

Trypanosoma lewisi belongs to the so-called atypical trypanosomes that occasionally affect humans. It shares the same hosts and flea vector of other medically relevant pathogenic agents as Yersinia pestis, the agent of plague. Increasing knowledge on the population structure (reproductive mode, population size, dispersal) of this parasite thus represents a challenging but important issue. The use of polymorphic genetic markers, together with suitable population genetics tools, is a convenient way to achieve such objectives. To date, the population biology of T. lewisi is poorly known and, to our knowledge, no population genetics studies have ever been conducted. Here, we present the development of nine microsatellite markers of this species. We investigated their polymorphism in different countries from Africa and South-East Asia from DNAs extracted from the spleen of their rodent reservoirs (essentially rat species). Several amplification problems arose, especially with South-East Asian individuals. This led to retain only those individuals with complete genotypes (most of them originating from West Africa, notably Cotonou, Benin) to ensure an optimal estimate of heterozygosity. Our results pointed towards a mainly (at least 95-99%) clonal mode of propagation, a strong subdivision at the smallest scale available (i.e., urban neighborhoods, i.e. 0.250 km²), and a generation time most probably shorter than 4 months. In future studies, more extensive sampling at smaller geographic scales (i.e., households), within a one- or two-months window and with improved amplification conditions, should lead to a more precise picture of the fine population structure of this parasite.

Microsatellites are powerful markers for empirical population genetics, but may be affected by amplification problems like stuttering that produces heterozygote deficits between alleles with one repeat difference. In this paper, we present a simple procedure that aims at detecting stuttering for each locus overall subsamples and only requires the use of a spreadsheet interactive application on any operating system. We compare the performances of this procedure with the one of MicroChecker on simulations of dioecious pangamic populations, monoecious selfing populations and clonal populations with or without stuttering, and on real data of vectors and parasites. We also propose a cure for loci affected and compare the results with those expected without stuttering. In sexual populations (dioecious or selfers), the new procedure appeared more than three times more efficient than MicroChecker. Cure was able to restore Wright's FIS of stuttered data to the expected value, and particularly so in selfing simulations. In clones, lack of segregation artificially increased false stuttering detection, and only highly significant stuttering tests and loci strongly deviating from others, could be usefully cured, in which case FIS estimate could be much improved. In doubt, and whenever possible, removal of affected and not curable loci may help to shift population genetics parameter estimates towards more reliable values.

Null alleles, short allele dominance (SAD), and stuttering increase the perceived relative inbreeding of individuals and subpopulations as measured by Wrights F_IS and F_ST. Ascertainment bias, due to such amplifying problems are usually caused by inaccurate primer design (if developed from a different species or a distant population), poor DNA quality, low DNA concentration, or a combination of some or all these sources of inaccuracy. When combined, these issues can increase the correlation between polymorphism at concerned loci and, consequently, of linkage disequilibrium (LD) between those. In this note, we studied an original microsatellite data set generated by analyzing nine loci in Ixodes scapularis ticks from the eastern U.S.A. To detect null alleles and SAD we used correlation methods and variation measures. To detect stuttering, we evaluated heterozygote deficit between alleles displaying a single repeat difference. We demonstrated that an important proportion of loci affected by amplification problems (one with null alleles, two with SAD and three with stuttering) lead to highly significant heterozygote deficits (F_IS=0.1, p-value

BackgroundPathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright's FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright's FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex.MethodsWe have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright's FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles.ResultsWe show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents.ConclusionOur criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%).

Leishmania species of the subgenus Viannia and especially Leishmania braziliensis are responsible for a large proportion of New World leishmaniasis cases. The reproductive mode of Leishmania species has often been assumed to be predominantly clonal, but remains unsettled. We have investigated the genetic polymorphism at 12 microsatellite loci on 124 human strains of Leishmania braziliensis from 2 countries, Peru and Bolivia. There is substantial genetic diversity, with an average of 12.4 +/- 4.4 alleles per locus. There is linkage disequilibrium at a genome-wide scale, as well as a substantial heterozygote deficit (more than 50% the expected value from Hardy-Weinberg equilibrium), which indicates high levels of inbreeding. These observations are inconsistent with a strictly clonal model of reproduction, which implies excess heterozygosity. Moreover, there is large genetic heterogeneity between populations within countries (Wahlund effect), which evinces a strong population structure at a microgeographic scale. Our findings are compatible with the existence of population foci at a microgeographic scale, where clonality alternates with sexuality of an endogamic nature, with possible occasional recombination events between individuals of different genotypes. These findings provide key clues on the ecology and transmission patterns of Leishmania parasites.

Human African trypanosomiasis, or sleeping sickness caused by Trypanosoma brucei gambiense, occurs in Western and Central Africa. T. brucei s.l. displays a huge diversity of adaptations and host specificities, and questions about its reproductive mode, dispersal abilities, and effective size remain under debate. We have investigated genetic variation at 8 microsatellite loci of T. b. gambiense strains isolated from human African trypanosomiasis patients in the Ivory Coast and Guinea, with the aim of knowing how genetic information was partitioned within and between individuals in both temporal and spatial scales. The results indicate that (i) migration of T. b. gambiense group 1 strains does not occur at the scale of West Africa, and that even at a finer scale (e.g., within Guinea) migration is restricted; (ii) effective population sizes of trypanosomes, as reflected by infected hosts, are probably higher than what the epidemiological surveys suggest; and (iii) T. b. gambiense group 1 is most likely a strictly clonally reproducing organism.