Plague: Bridging gaps towards better disease control.

After centuries of epidemics and more than a hundred years since the identification of the causative bacterium, very little is known about the plague dynamics in animal reservoirs, vectors and the changing vulnerabilities for humans. The recent plague epidemic in Madagascar in 2017 highlights these gaps existing within the knowledge of the disease dynamics, the factors influencing it, the performance of diagnostic tests and the best recommended treatment. As the eradication of plague will not be possible due to the widespread existence of the bacterium in wildlife, a One Health approach, drawing on animal, human and environmental health disciplines is needed to better control this poverty-related disease. This article focused on the various aspects of the disease for which more tools and better understanding are required to better control the disease in endemic countries.

Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times.

Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.

Invasion genetics of a human commensal rodent: the black rat Rattus rattus in Madagascar.

Studies focusing on geographical genetic patterns of commensal species and on human history complement each other and provide proxies to trace common colonization events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history. In this study, we addressed this question by characterizing the genetic structure of natural populations of R. rattus using both microsatellites and mitochondrial sequences, on an extensive sampling across the island. Such data sets were analysed by a combination of methods using population genetics, phylogeography and approximate Bayesian computation. Our results indicated two introduction events to Madagascar from the same ancestral source of R. rattus, one in the extreme north of the island and the other further south. The latter was the source of a large spatial expansion, which may have initially started from an original point located on the southern coast. The inferred timing of introduction events-several centuries ago-is temporally congruent with the Arabian trade network in the Indian Ocean, which was flourishing from the middle of the first millennium.

Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar.

Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection.

Comparative population genetics of a parasitic nematode and its host community: the trichostrongylid Neoheligmonella granjoni and Mastomys rodents in southeastern Senegal.

Contrasting host and parasite population genetic structures can provide information about the population ecology of each species and the potential for local adaptation. Here, we examined the population genetic structure of the nematode Neoheligmonella granjoni at a regional scale in southeastern Senegal, using 11 microsatellite markers. Using the results previously obtained for the two main rodent species of the host community, Mastomys natalensis and Mastomys erythroleucus, we tested the hypothesis that the parasite population structure was mediated by dispersal levels of the most vagile host. The results showed similar genetic diversity levels between host and parasite populations, and consistently lower levels of genetic differentiation in N. granjoni, with the exception of one outlying locus with a high F(ST). The aberrant pattern at this locus was primarily due to two alleles occurring at markedly different frequencies in one locality, suggesting selection at this locus, or a closely linked one. Genetic differentiation levels and isolation by distance analyses suggested that gene flow was high and random in N. granjoni at the spatial scale examined. The correlation between pair-wise genetic differentiation levels in the parasite and its main host was consistent with the hypothesis tested. Models of local adaptation as a function of the dispersal rates of hosts and parasites suggest that opportunities for local adaptation would be low in this biological system.

Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010.

This article documents the addition of 277 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Ascochyta rabiei, Cambarellus chapalanus, Chionodraco hamatus, Coptis omeiensis, Cynoscion nebulosus, Daphnia magna, Gerbillus nigeriae, Isurus oxyrinchus, Lates calcarifer, Metacarcinus magister, Oplegnathus fasciatus, Pachycondyla verenae, Phaethon lepturus, Pimelodus grosskopfii, Rotylenchulus reniformis, Scomberomorus niphonius, Sepia esculenta, Terapon jarbua, Teratosphaeria cryptica and Thunnus obesus. These loci were cross-tested on the following species: Austropotamobius italicus, Cambarellus montezumae, Cambarellus puer, Cambarellus shufeldtii, Cambarellus texanus, Chionodraco myersi, Chionodraco rastrospinosus, Coptis chinensis, Coptis chinensis var. brevisepala, Coptis deltoidea, Coptis teeta, Orconectes virilis, Pacifastacus leniusculus, Pimelodus bochii, Procambarus clarkii, Pseudopimelodus bufonius, Rhamdia quelen, Sepia andreana, Sepiella maindroni, Thunnus alalunga, Thunnus albacares, Thunnus maccoyii, Thunnus orientalis, Thunnus thynnus and Thunnus tonggol.

AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection.

The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining P-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci.

Variation in cestode assemblages of Mastomys and Arvicanthis species (rodents: Muridae) from Lake Retba in Western Senegal.

We studied patterns of variation in cestode communities of 3 abundant rodent species that live in sympatry in the Niayes of the Retba Lake, Western Senegal. We evaluated whether the host species have the same parasites and, within host species, whether the variability in parasite community is related to intrinsic (sex, age of the host individual) or extrinsic (habitat, season) factors. Arvicanthis niloticus was parasitized by 2 cestode species, namely Inermicapsifer madagascariensis and the highly dominant Raillietina trapezoïdes . Raillietina baeri was the only cestode species found in Mastomys erythroleucus , and there was no cestode in M. huberti . Prevalence and abundance levels of cestodes were very high in A. niloticus , especially in adults. Seasonal and habitat effects were found in both cestode communities of M. erythroleucus and A. niloticus . Local host specificity and abundance/prevalence levels suggested variations in the interaction between rodents and cestode intermediate host species among habitats and seasons.

Susceptibility to Yersinia pestis experimental infection in wild Rattus rattus, reservoir of plague in Madagascar.

In Madagascar, the black rat, Rattus rattus, is the main reservoir of plague (Yersinia pestis infection), a disease still responsible for hundreds of cases each year in this country. This study used experimental plague challenge to assess susceptibility in wild-caught rats to better understand how R. rattus can act as a plague reservoir. An important difference in plague resistance between rat populations from the plague focus (central highlands) and those from the plague-free zone (low altitude area) was confirmed to be a widespread phenomenon. In rats from the plague focus, we observed that sex influenced plague susceptibility, with males slightly more resistant than females. Other individual factors investigated (weight and habitat of sampling) did not affect plague resistance. When infected at high bacterial dose (more than 105 bacteria injected), rats from the plague focus died mainly within 3-5 days and produced specific antibodies, whereas after low-dose infection (< 5,000 bacteria), delayed mortality was observed and surviving seronegative rats were not uncommon. These results concerning plague resistance level and the course of infection in the black rat would contribute to a better understanding of plague circulation in Madagascar.

Geographic patterns of inversion polymorphisms in a wild African rodent, Mastomys erythroleucus.

By suppressing recombination and reducing gene flow, chromosome inversions favor the capture and protection of advantageous allelic combinations, leading to adaptive polymorphisms. However, studies in non-model species remain scarce. Here we investigate the distribution of inversion polymorphisms in the multimammate rat Mastomys erythroleucus in West Africa. More than 270 individuals from 52 localities were karyotyped using G-bands and showed widespread polymorphisms involving four chromosome pairs. No significant deviations from Hardy-Weinberg equilibrium were observed either through space or time, nor were differences retrieved in viability or sex contribution between cytotypes. The distribution of chromosomal variation, however, showed perfect congruence with that of mtDNA-based phylogeographic clades. Thus, inversion diversity patterns in M. erythroleucus appeared more related to historical and/or demographic processes than to climate-based adaptive features. Using cross-species chromosome painting and G-banding analyses to identify homologous chromosomes in related out-group species, we proposed a phylogenetic scenario that involves ancestral-shared polymorphisms and subsequent lineage sorting during expansion/contraction of West African savannas. Our data suggest that long-standing inversion polymorphisms may act as regions in which adaptation genes may accumulate (nucleation model).

Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010.

This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).

CCR5 polymorphism and plague resistance in natural populations of the black rat in Madagascar.

Madagascar remains one of the world's largest plague foci. The black rat, Rattus rattus, is the main reservoir of plague in rural areas. This species is highly susceptible to plague in plague-free areas (low-altitude regions), whereas rats from the plague focus areas (central highlands) have evolved a disease-resistance polymorphism. We used the candidate gene CCR5 to investigate the genetic basis of plague resistance in R. rattus. We found a unique non-synonymous substitution (H184R) in a functionally important region of the gene. We then compared (i) CCR5 genotypes of dying and surviving plague-challenged rats and (ii) CCR5 allelic frequencies in plague focus and plague-free populations. Our results suggested a higher prevalence of the substitution in resistant animals compared to susceptible individuals, and a tendency for higher frequencies in plague focus areas compared to plague-free areas. Therefore, the CCR5 polymorphism may be involved in Malagasy black rat plague resistance. CCR5 and other undetermined plague resistance markers may provide useful biological information about host evolution and disease dynamics.

Isolation and characterization of microsatellites in Rattus rattus.

We isolated and characterized 10 microsatellite loci in the black rat Rattus rattus (Muridae, Rodentia), a widespread invasive species largely known to cause serious problems in agriculture and human health. Polymorphism was studied in two populations, one from Madagascar and one from Senegal. It ranged from three to 12 alleles in Madagascar, and from two to five alleles in Senegal. Together with the loci previously adapted from Rattus norvegicus, this set of markers should allow the conduct of thorough studies on the genetic structure of natural populations of R. rattus.

Description of two new species of Nippostrongylinae (Nematoda: Heligmonellidae) coparasites in three sympatric species of Mastomys spp. (Rodentia: Muridae) from Senegal.

Two new species of heligmosomoid Trichostrongylina nematodes belonging to the genera Neoheligmonella Durette-Desset, 1970 and Heligmonina Baylis, 1928 are described. They are parasitic in the small intestine of three species of Mastomys from Senegal living in sympatry: M. natalensis (Smith, 1834), M. erythroleucus (Temminck, 1853) and M. huberti (Wroughton, 1909). Neoheligmonella granjoni n. sp. is closely related to three species from Senegal. They concern: N. bai Diouf & Durette-Desset, 2002 and N. dielmensis Diouf, Bâ & Durette-Desset, 1998, both parasitic in Arvicanthis niloticus Geoffroy, 1903 and N. mastomysi Diouf et al., 1998, a parasite of M. erythroleucus. N. granjoni n. sp. differs from these species by having 15 cuticular ridges at mid-body versus 13, a large carene and spicules taking up 10-15% of body length versus 5.3-7.1%. Heligmonina kanei n. sp. differs from the most related species H. kotoensis Diouf, Daouda & Durette-Desset 2005, a parasite of M. natalensis from Benin in the following features: spicules taking up 11.6% of body length on average versus 16.8%; a female tail three times longer than the distance anus-vulva versus a tail of equivalent size to this distance. In N. granjoni n. sp., where the material is abundant in all three hosts, the infra-specific variations observed (morphological or morphometrical) were not related to the host species. This is the first report of the genera Neoheligmonella and Heligmonina in M. huberti. The relevance of the phenomenon of host capture concerning the evolution of these two genera is confirmed.

Population genetic structure of two ecologically distinct multimammate rats: the commensal Mastomys natalensis and the wild Mastomys erythroleucus in southeastern Senegal.

Using the same set of microsatellite markers, we compared the population genetic structure of two Mastomys species, one being exclusively commensal in southeastern Senegal, and the other being continuously distributed outside villages in this region. Both species were sampled in the same landscape context and at the same spatial scale. According to the expectations based on the degree of habitat patchiness (which is higher for commensal populations in this rural area), genetic diversity was lower and genetic differentiation was higher in commensal populations of Mastomys natalensis than in wild populations of Mastomys erythroleucus. Contrasting estimates of effective dispersal and current migration rates corroborates previous data on differences in social structure between the two species. Isolation-by-distance analyses showed that human-mediated dispersal is not a major factor explaining the pattern of genetic differentiation for M. natalensis, and that gene flow is high and random between M. erythroleucus populations at the spatial scale considered.

Host ecology and variation in helminth community structure in Mastomys rodents from Senegal.

We studied patterns of variation in parasite communities of 2 closely related species of Mastomys rodents. These 2 species live in sympatry in South-eastern Senegal, but differ drastically in their habitat choice. We asked (a) whether the host species have the same parasites; (b) whether there is any observable pattern relative to the host species/habitat type in the structure of parasite communities; (c) whether the variability in parasite community for each host species is related to habitat characteristics. We analysed 220 and 264 individuals of each host species, sampled respectively in 10 and 11 trap sites. Twenty parasite taxa were recorded, and the majority were nematodes. Between-host species comparisons showed that helminth communities were slightly more diversified in M. natalensis. Many parasite species were found in both Mastomys. However, various helminth taxa varied in frequency and abundance between host species. Within each host species, helminth diversity, prevalence and/or abundance of some parasites were correlated with habitat or host population factors that may influence parasite life-cycles, such as village structure, or the presence/absence of a pool. Our results suggest that habitat characteristics have a strong impact on helminth community structure.

Introgression in natural populations of bioindicators: a case study of Carabus splendens and Carabus punctatoauratus.

The evolutionary importance of hybridization in wild plants and animals has become increasingly widely recognized in the last decade. In practical terms, hybridization provides an exceptionally tough set of problems for conservation biologists. We illustrate this in a case study of two Carabidae species widely used to evaluate the impact of human activities on biodiversity. These two species live in a complex mosaic of sympatry/allopatry and are known to hybridize in controlled conditions. Hybridization has not been quantified in natural populations to date due to the lack of a simple set of phenotypic traits for identifying hybrids. We thus screened for hybrids in natural populations, by multilocus genotyping at nine microsatellite loci. A high level of genetic differentiation between these two taxa was observed, as shown by allelic frequency distributions. Two Bayesian assignment procedures without obligatory pure taxon references were used to infer different classes of hybrids (F(1), F(2) and backcrosses) and mixture proportions between the two species. A low level of hybridization (F(1) genotypes) was observed in natural populations, contrasting with results obtained in controlled conditions. A high level of introgression was, however, detected at three of 12 sites, as revealed by the detection of backcrossed genotypes. This interspecific gene flow was detected in a limited zone of the common geographical range of the two species and was not related to the pattern of sympatry/allopatry. We then considered the origin and repercussions of this introgression, based on intraspecific genetic diversity and geographical structure.

Specialization and habitat: spatial and environmental effects on abundance and genetic diversity of forest generalist and specialist Carabus species.

Habitat specialist species are supposed to be more susceptible to variations in local environmental characteristics than generalists. To test this hypothesis, we conducted a comparative analysis on abundance and genetic diversity of forest carabids differing in their habitat requirements. Four species were sampled in forests characterized by abiotic, landscape and biotic environmental variables. A statistical framework based on canonical correspondence analysis was used for one habitat generalist and one habitat specialist species to determine the relative contribution of environmental variables in structuring inter- and intrapopulational genetic diversity depicted by microsatellites. Our results showed that sympatric species differed in their sensitivity to environmental variables. The same variables were found to be important in analyses of abundance and genetic data. However, specialization was not related to a greater sensitivity to local environmental characteristics. The strong impact of spatial variables on genetic data suggested that genetic variation among populations would largely reflect the response of individual species to dispersal opportunities more than the effect of habitat quality.

Differentiation in a geographical mosaic of plants coevolving with ants: phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers.

Comprising four allopatric subspecies that exhibit various grades of ant-plant interactions, from diffuse to obligate and symbiotic associations, the Leonardoxa africana complex (Fabaceae, Caesalpinioideae) provides a good opportunity to investigate the evolutionary history of ant-plant mutualisms. A previous study of the L. africana complex based on chloroplast DNA noncoding sequences revealed a lack of congruence between clades suggested by morphological and plastid characters. In this study, we analysed phylogenetic relationships within the L. africana complex using a Bayesian probability approach on amplified fragment length polymorphism markers. The results reported permit partial validation of the four subspecies of L. africana previously defined by morphological and ecological markers. Incongruences between phylogenies based on chloroplast DNA and amplified fragment length polymorphism markers are discussed in the light of morphological and ecological data, and confronted with hypotheses of convergence, lineage sorting and introgression.

Fine-scale genetic structure of two carabid species with contrasted levels of habitat specialization.

Using microsatellite markers, we compared the genetic structure of populations of two carabid species, one described as a generalist (commonly found in forest and in open habitats) and the other known as a forest specialist. Both species were sampled in the same forest plots, which were separated from each other by either open or forested areas. At the local scale considered (13.6 km separating the most distant plots), genetic differentiation was substantial for both species studied, but populations of the forest specialist Carabus punctatoauratus appeared to be more spatially structured than those of C. nemoralis. Isolation by distance analyses showed that nonforested areas are partial barriers to gene flow for both species studied, although more clearly for the forest specialist. Between and within forests, dispersal capacity of the generalist C. nemoralis was shown to be higher than that of the specialist C. punctatoauratus.