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Evolutionary theory predicts that the lack of recombination and chromosomal re-assortment in strictly asexual organisms results in homologous chromosomes irreversibly accumulating mutations and thus evolving independently of each other, a phenomenon termed the Meselson effect. We apply a population genomics approach to examine this effect in an important human pathogen, Trypanosoma brucei gambiense. We determine that T.b. gambiense is evolving strictly asexually and is derived from a single progenitor, which emerged within the last 10,000 years. We demonstrate the Meselson effect for the first time at the genome-wide level in any organism and show large regions of loss of heterozygosity, which we hypothesise to be a short-term compensatory mechanism for counteracting deleterious mutations. Our study sheds new light on the genomic and evolutionary consequences of strict asexuality, which this pathogen uses as it exploits a new biological niche, the human population. An organism’s genetic ‘blueprint’ is encoded in DNA packaged within structures called chromosomes. Most organisms have two copies of each chromosome and, through sexual reproduction, the DNA within a pair of chromosomes can recombine randomly in a process that could be likened to shuffling a deck of cards. This process generates genetic diversity and means that any undesirable combinations of genes or mutations can be eliminated from the population by natural selection. While these activities are thought to promote the long-term survival of a species, some organisms appear not to have sex at all. Evolutionary theory predicts that ‘asexual’ organisms should face extinction in the long-term and that a lack of sexual recombination should leave a characteristic genetic ‘signature’ in their DNA. The theory also predicts that pairs of chromosomes will evolve independently, a phenomenon that is termed the ‘Meselson effect’. However, while it was first predicted almost twenty years ago, evidence for this signature has been elusive. Now, Weir et al. have used the asexual parasite (Trypanosoma brucei gambiense), which causes African sleeping sickness in humans, to search for signs of the Meselson effect. Sequencing the whole genome of a large number of parasites revealed that the population of this parasite arose from a single individual within the last 10,000 years. Over this time, mutations have built up and the lack of sexual recombination means that the two chromosomes in each pair have evolved independently of the other. These results provide the first demonstration of the Meselson effect at a genome-wide level in any organism. Weir et al. also uncovered evidence that this parasite uses a mechanism called “gene conversion” to compensate for its lack of sex. This mechanism essentially repairs the inferior, or mutated, copy of a gene on a chromosome by ‘copying and pasting’ the superior copy from the chromosome’s partner. The findings also suggest that gene conversion can only go some way to compensating for a lack of sex. A future challenge will be to investigate how effective this mechanism can be in the long term and to predict whether the parasite will ultimately become extinct.

Important control efforts have led to a significant reduction of the prevalence of human African trypanosomiasis (HAT) in Côte d'Ivoire, but the disease is still present in several foci. The existence of an animal reservoir of Trypanosoma brucei gambiense may explain disease persistence in these foci where animal breeding is an important source of income but where the prevalence of animal African trypanosomiasis (AAT) is unknown. The aim of this study was to identify the trypanosome species circulating in domestic animals in both Bonon and Sinfra HAT endemic foci. 552 domestic animals (goats, pigs, cattle and sheep) were included. Blood samples were tested for trypanosomes by microscopic observation, species-specific PCR for T. brucei sl, T. congolense, T. vivax and subspecies-specific PCR for T. b. gambiense and T. b. gambiense immune trypanolysis (TL). Infection rates varied significantly between animal species and were by far the highest in pigs (30%). T. brucei s.l was the most prevalent trypanosome species (13.7%) followed by T. congolense. No T. b. gambiense was identified by PCR while high TL positivity rates were observed using T. b. gambiense specific variants (up to 27.6% for pigs in the Bonon focus). This study shows that domestic animals are highly infected by trypanosomes in the studied foci. This was particularly true for pigs, possibly due to a higher exposure of these animals to tsetse flies. Whereas T. brucei s.l. was the most prevalent species, discordant results were obtained between PCR and TL regarding T. b. gambiense identification. It is therefore crucial to develop better tools to study the epidemiological role of potential animal reservoir for T. b. gambiense. Our study illustrates the importance of \"one health\" approaches to reach HAT elimination and contribute to AAT control in the studied foci.

The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.

African trypanosomosis (AT), caused by protozoan parasites of the genus Trypanosoma , has plagued the African continent for centuries, affecting both humans and animals. Its principal vector, tsetse flies, can be found across sub-Saharan Africa. Vector control represents an efficient way to reduce the burden of AT. In Mozambique, control campaigns reshaped tsetse fly distribution to what it is today, with four species presently found: Glossina brevipalpis, G. pallidipes, G. morsitans and, G. austeni . Additionally, G. brevipalpis can be observed in two National parks, Gorongosa National Park in the Centre and Maputo National Park in the South, with an 840 km wide tsetse-free zone between them. In order to improve our knowledge on the genetic diversity in these populations, and their probable isolation, we undertook a population genetics study with 11 microsatellite loci. We found that these two zones behave as strongly isolated subpopulations, only exchanging a few individuals per year. To explain this finding, we suggest the existence of undocumented pocket populations between the two parks, or, in the absence of these, the accidental translocation of tsetse flies during human-driven animal transportation. We suggest that translocation through human-driven animal movement should be explored in future studies investigating Glossina populations. If eradication were to be attempted, re-invasion of the tsetse via motorized human transport should be considered in conjunction with the exploration of other sites within a 30 km radius to validate that no sources of re-invasion exist around these parks.

The existence of an animal reservoir of Trypanosoma brucei gambiense (T. b. gambiense), the agent of human African trypanosomiasis (HAT), may compromise the interruption of transmission targeted by World Health Organization. The aim of this study was to investigate the presence of trypanosomes in pigs and people in the Vavoua HAT historical focus where cases were still diagnosed in the early 2010's. For the human survey, we used the CATT, mini-anion exchange centrifugation technique and immune trypanolysis tests. For the animal survey, the buffy coat technique was also used as well as the PCR using Trypanosoma species specific, including the T. b. gambiense TgsGP detection using single round and nested PCRs, performed from animal blood samples and from strains isolated from subjects positive for parasitological investigations. No HAT cases were detected among 345 people tested. A total of 167 pigs were investigated. Free-ranging pigs appeared significantly more infected than pigs in pen. Over 70% of free-ranging pigs were positive for CATT and parasitological investigations and 27-43% were positive to trypanolysis depending on the antigen used. T. brucei was the most prevalent species (57%) followed by T. congolense (24%). Blood sample extracted DNA of T. brucei positive subjects were negative to single round TgsGP PCR. However, 1/22 and 6/22 isolated strains were positive with single round and nested TgsGP PCRs, respectively. Free-ranging pigs were identified as a multi-reservoir of T. brucei and/or T. congolense with mixed infections of different strains. This trypanosome diversity hinders the easy and direct detection of T. b. gambiense. We highlight the lack of tools to prove or exclude with certainty the presence of T. b. gambiense. This study once more highlights the need of technical improvements to explore the role of animals in the epidemiology of HAT.

Despite their role in Leishmania transmission, little is known about the organization of sand fly populations in their environment. Here, we used 11 previously described microsatellite markers to investigate the population genetic structure of Phlebotomus ariasi , the main vector of Leishmania infantum in the region of Montpellier (South of France). From May to October 2011, we captured 1,253 Ph. ariasi specimens using sticky traps in 17 sites in the North of Montpellier along a 14-km transect, and recorded the relevant environmental data (e.g., altitude and hillside). Among the selected microsatellite markers, we removed five loci because of stutter artifacts, absence of polymorphism, or non-neutral evolution. Multiple regression analyses showed the influence of altitude and hillside (51% and 15%, respectively), and the absence of influence of geographic distance on the genetic data. The observed significant isolation by elevation suggested a population structure of Ph. ariasi organized in altitudinal ecotypes with substantial rates of migration and positive assortative mating. This organization has implications on sand fly ecology and pathogen transmission. Indeed, this structure might favor the global temporal and spatial stability of sand fly populations and the spread and increase of L. infantum cases in France. Our results highlight the necessity to consider sand fly populations at small scales to study their ecology and their impact on pathogens they transmit.

Human African Trypanosomiasis (HAT) in West Africa is a lethal, neglected disease caused by Trypanosoma brucei gambiense transmitted by the tsetse Glossina palpalis gambiensis. Although the littoral part of Guinea with its typical mangrove habitat is the most prevalent area in West Africa, very few data are available on the epidemiology of the disease in such biotopes. As part of a HAT elimination project in Guinea, we carried a cross-sectional study of the distribution and abundance of people, livestock, tsetse and trypanosomes in the focus of Boffa. An exhaustive census of the human population was done, together with spatial mapping of the area. Entomological data were collected, a human medical survey was organized together with a survey in domestic animals. In total, 45 HAT cases were detected out of 14445 people who attended the survey, these latter representing 50.9% of the total population. Potential additional carriers of T. b. gambiense were also identified by the trypanolysis test (14 human subjects and two domestic animals). No trypanosome pathogenic to animals were found, neither in the 874 tsetse dissected nor in the 300 domestic animals sampled. High densities of tsetse were found in places frequented by humans, such as pirogue jetties, narrow mangrove channels and watering points. The prevalence of T. b. gambiense in humans, combined to low attendance of the population at risk to medical surveys, and to an additional proportion of human and animal carriers of T. b. gambiense who are not treated, highlights the limits of strategies targeting HAT patients only. In order to stop T. b. gambiense transmission, vector control should be added to the current strategy of case detection and treatment. Such an integrated strategy will combine medical surveillance to find and treat cases, and vector control activities to protect people from the infective bites of tsetse.

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.

Tsetse flies, the vectors of African trypanosomes are of key medical and economic importance and one of the constraints for the development of Africa. Tsetse fly control is one of the most effective and sustainable strategies used for controlling the disease. Knowledge about population structure and level of gene flow between neighbouring populations of the target vector is of high importance to develop appropriate strategies for implementing effective management programmes. Microsatellites are commonly used to identify population structure and assess dispersal of the target populations and have been developed for several tsetse species but were lacking for Glossina brevipalpis. In this study, we screened the genome of G. brevipalpis to search for suitable microsatellite markers and nine were found to be efficient enough to distinguish between different tsetse populations. The availability of these novel microsatellite loci will help to better understand the population biology of G. brevipalpis and to assess the level of gene flow between different populations. Such information will help with the development of appropriate strategies to implement the sterile insect technique (SIT) in the framework of an area-wide integrated pest management (AW-IPM) approach to manage tsetse populations and ultimately address the trypanosomoses problem in these targeted areas.

African trypanosomoses, whose pathogens are transmitted by tsetse flies, are a threat to animal and human health. Tsetse flies observed at the military base of the French Forces in Côte d’Ivoire (FFCI base) were probably involved in the infection and death of military working dogs. Entomological and parasitological surveys were carried out during the rainy and dry seasons using “Vavoua” traps to identify tsetse fly species, their distribution, favorable biotopes and food sources, as well as the trypanosomes they harbor. A total of 1185 Glossina palpalis palpalis tsetse flies were caught, corresponding to a high average apparent density of 2.26 tsetse/trap/day. The results showed a heterogeneous distribution of tsetse at the FFCI base, linked to more or less favorable biotopes. No significant variation in tsetse densities was observed according to the season. The overall trypanosomes infection rate according to microscopic observation was 13.5%. Polymerase chain reaction (PCR) analyses confirmed the presence of Trypanosoma vivax and T. congolense forest type, responsible for African animal trypanosomosis. Our findings suggest that there is a risk of introduction and transmission of T. brucei gambiense , responsible for human African trypanosomiasis, on the study site. This risk of transmission of African trypanosomes concerns not only the FFCI base, but also inhabited peripheral areas. Our study confirmed the need for vector control adapted to the eco-epidemiological context of the FFCI base. Les trypanosomoses africaines, dont les agents pathogènes sont transmis par les mouches tsé-tsé, constituent une contrainte pour la santé animale et humaine. Des mouches tsé-tsé observées dans la base militaire des Forces françaises en Côte d’Ivoire (base FFCI) ont probablement été impliquées dans l’infection et la mort de chiens militaires. Des enquêtes entomologiques et parasitologiques ont été menées pendant la saison pluvieuse et la saison sèche à l’aide de pièges “Vavoua” afin d’identifier les espèces de mouches tsé-tsé, leur distribution, les biotopes favorables et leur source de nourriture ainsi que les trypanosomes qu’elles hébergent. Au total 1185 mouches tsé-tsé de l’espèce Glossina palpalis palpalis ont été capturées, ce qui correspond à une densité apparente moyenne élevée de 2,26 tsé-tsé/piège/jour. Les résultats ont montré une distribution hétérogène des tsé-tsé dans la base FFCI en lien avec des biotopes plus ou moins favorables. Aucune variation significative des densités de tsé-tsé n’a été observée en fonction de la saison. Le taux d’infection global par les trypanosomes était de 13,5 % selon l’observation microscopique. Les analyses PCR ont confirmé la présence de Trypanosoma vivax et T. congolense type forêt, responsable de la trypanosomose animale africaine. Nos résultats suggèrent qu’il existe un risque potentiel d’introduction et de transmission de T. brucei gambiense responsable de la trypanosomiase humaine africaine dans la zone d’étude. Ce risque de transmission des trypanosomes africains concerne non seulement l’intérieur de la base FFCI, mais aussi les espaces périphériques habités. Notre étude a confirmé la nécessité de mener une lutte antivectorielle adaptée au contexte éco-épidémiologique de la base FFCI.