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Microsatellite loci still represent valuable resources for the study of the population biology of non-model organisms. Discovering or adapting new suitable microsatellite markers in species of interest still represents a useful task, especially so for non-model organisms as tsetse flies (genus Glossina), which remain a serious threat to the health of humans and animals in sub-Saharan Africa. In this paper, we present the development of new microsatellite loci for four species of Glossina: two from the Morsitans group, G. morsitans morsitans (Gmm) from Zimbabwe, G. pallidipes (Gpalli) from Tanzania; and the other two from the Palpalis group, G. fuscipes fuscipes (Gff) from Chad, and G. palpalis gambiensis (Gpg) from Guinea. We found frequent short allele dominance and null alleles. Stuttering could also be found and amended when possible. Cryptic species seemed to occur frequently in all taxa but Gff. This explains why it may be difficult finding ecumenical primers, which thus need adaptation according to each taxonomic and geographic context. Amplification problems occurred more often in published old markers, and Gmm and Gpg were the most affected (stronger heterozygote deficits). Trinucleotide markers displayed selection signature in some instances (Gmm). Combining old and new loci, for Gmm, eight loci can be safely used (with correction for null alleles); and five seem particularly promising; for Gpalli, only five to three loci worked well, depending on the clade, which means that the use of loci from other species (four morsitans loci seemed to work well), or other new primers will need to be used; for Gff, 14 loci behaved well, but with null alleles, seven of which worked very well; and for G. palpalis sl, only four loci, needing null allele and stuttering corrections seem to work well, and other loci from the literature are thus needed, including X-linked markers, five of which seem to work rather well (in females only), but new markers will probably be needed. Finally, the high proportion of X-linked markers (around 30%) was explained by the non-Y DNA quantity and chromosome structure of tsetse flies studied so far., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Glossina palpalis palpalis remains the major vector of sleeping sickness in Côte d'Ivoire. The disease is still active at low endemic levels in Bonon and Sinfra foci in the western-central part of the country. In this study, we investigated the impact of a control campaign on G. p. palpalis population structure in Bonon and Sinfra foci in order to adapt control strategies. Genetic variation at microsatellite loci was used to examine the population structure of different G. p. palpalis cohorts before and after control campaigns. Isolation by distance was observed in our sampling sites. Before control, effective population size was high (239 individuals) with dispersal at rather short distance (731 m per generation). We found some evidence that some of the flies captured after treatment come from surrounding sites, which increased the genetic variance. One Locus, GPCAG, displayed a 1000% increase of subdivision measure after control while other loci only exhibited a substantial increase in variance of subdivision. Our data suggested a possible trap avoidance behaviour in G. p. palpalis. It is important to take into account and better understand the possible reinvasion from neighboring sites and trap avoidance for the sake of sustainability of control campaigns effects., (Copyright © 2019 IRD. Published by Elsevier B.V. All rights reserved.)

The Cichlid fish Sarotherodon melanotheron is typically found in West and Central African estuaries and lagoons. It represents a good candidate for promoting tilapia farming in brackish waters. Understanding the genetic diversity in its populations from the hydrographical basins of Southern Benin is primordial before designing selective breeding programs. For this purpose, 202 samples collected from four rivers of Southern Benin and were genotyped using 15 polymorphic microsatellite DNA markers. Each river was split up into three sampling sites. We found significant global linkage disequilibrium across the genome of natural populations of this tilapia species overall the loci. However, when the loci that display aberrant Wright's (F IS and F ST ) were removed from the data, a linkage disequilibrium was detected for the remaining 11 loci and became compatible with the null hypothesis. Null alleles explained at least 20.58% of F IS variation. We found a significant isolation by distance across subsamples. Effective population size averaged 210 individuals, with a range from 36 to 517 individuals. Assuming that 79% of heterozygote deficits are explained by sib mating lead to a rough estimate of r sm  = 0.4 of mating rate between full sibs within S. melanotheron subpopulations. The fish size correlated positively and significantly with the observed F IS (r = 0.58; p value = 0.04806). Reproduction system (endogamy) in S. melanotheron could explain the strong heterozygote deficit observed. Our results provide technical guidance for efficient management of this tilapia species' genetic resources for breeding programs in fresh and brackish waters.

Trypanosomatidae are a dangerous family of Euglenobionta parasites that threaten the health and economy of millions of people around the world. More precisely describing the population biology and reproductive mode of such pests is not only a matter of pure science, but can also be useful for understanding parasite adaptation, as well as how parasitism, specialization (parasite specificity), and complex life cycles evolve over time. Studying this parasite's reproductive strategies and population structure can also contribute key information to the understanding of the epidemiology of associated diseases; it can also provide clues for elaborating control programs and predicting the probability of success for control campaigns (such as vaccines and drug therapies), along with emergence or re-emergence risks. Population genetics tools, if appropriately used, can provide precise and useful information in these investigations. In this paper, we revisit recent data collected during population genetics surveys of different Trypanosoma species in sub-Saharan Africa. Reproductive modes and population structure depend not only on the taxon but also on the geographical location and data quality (absence or presence of DNA amplification failures). We conclude on issues regarding future directions of research, in particular vis-à-vis genotyping and sampling strategies, which are still relevant yet, too often, neglected issues.

Background: Pathogens 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., Methods: We 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., Results: We 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., Conclusion: Our 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%).