Reproductive ecology of the black rat (Rattus rattus) in Madagascar: the influence of density-dependent and -independent effects.

The black rat (Rattus rattus) poses a severe threat to food security and public health in Madagascar, where it is a major cause of pre- and post-harvest crop losses and an important reservoir for many zoonotic diseases, including plague. Elsewhere, ecologically based rodent management (EBRM) strategies have been developed using ecological information to inform decisions on where and when to target control. EBRM could deliver improved health and well-being outcomes in Madagascar if adapted to the local ecological context. Using data collected from removal studies, we explored spatio-temporal patterns in the breeding activity of the black rat (R. rattus) in domestic and agricultural habitats across Madagascar and investigated to what extent these trends are influenced by rainfall and rat density. We identified clear spatio-temporal variation in the seasonality of R. rattus reproduction. Reproduction was highly seasonal both inside and outside of houses, but seasonal trends varied between these two habitats. Seasonal trends were explained, in part, by variation in rainfall; however, the effect of rainfall on reproductive rates did itself vary by season and habitat type. A decline in breeding intensity with increasing rat density was recorded outside of houses. This has important implications for control, as populations may compensate for removal through increased reproduction. We recommend that sustained control initiated before the main breeding season, combined with improved hygiene and adequate rodent-proofing in homes and grain stores, could curtail population growth and reduce pre- and post-harvest losses provided that these measures overcome the compensatory response of rodent populations.

Sociodemographic Variables Can Guide Prioritized Testing Strategies for Epidemic Control in Resource-Limited Contexts.

BACKGROUND: Targeted surveillance allows public health authorities to implement testing and isolation strategies when diagnostic resources are limited, and can be implemented via the consideration of social network topologies. However, it remains unclear how to implement such surveillance and control when network data are unavailable. METHODS: We evaluated the ability of sociodemographic proxies of degree centrality to guide prioritized testing of infected individuals compared to known degree centrality. Proxies were estimated via readily available sociodemographic variables (age, gender, marital status, educational attainment, household size). We simulated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics via a susceptible-exposed-infected-recovered individual-based model on 2 contact networks from rural Madagascar to test applicability of these findings to low-resource contexts. RESULTS: Targeted testing using sociodemographic proxies performed similarly to targeted testing using known degree centralities. At low testing capacity, using proxies reduced infection burden by 22%-33% while using 20% fewer tests, compared to random testing. By comparison, using known degree centrality reduced the infection burden by 31%-44% while using 26%-29% fewer tests. CONCLUSIONS: We demonstrate that incorporating social network information into epidemic control strategies is an effective countermeasure to low testing capacity and can be implemented via sociodemographic proxies when social network data are unavailable.

The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar.

Many of Madagascar's unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar's mammalian biodiversity under these rates, the "evolutionary return time" (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.

Effect of habitat degradation on hantavirus infection among introduced and endemic small mammals of Madagascar.

Hantaviruses are globally distributed zoonotic pathogens capable of causing fatal disease in humans. Rodents and other small mammals are the typical reservoirs of hantaviruses, though the particular host varies regionally. Addressing the risk of hantavirus spillover from animal reservoirs to humans requires identifying the local mammal reservoirs and the predictors of infection in those animals, such as their population density and habitat characteristics. We screened native and non-native small mammals and bats in northeastern Madagascar for hantavirus infection to investigate the influence of habitat, including effects of human land use on viral prevalence. We trapped 227 bats and 1663 small mammals over 5 successive years in and around Marojejy National Park across a range of habitat types including villages, agricultural fields, regrowth areas, and secondary and semi-intact forests. Animals sampled included endemic tenrecs (Tenrecidae), rodents (Nesomyidae) and bats (6 families), along with non-native rodents (Muridae) and shrews (Soricidae). A hantavirus closely related to the previously described Anjozorobe virus infected 9.5% of Rattus rattus sampled. We did not detect hantaviruses in any other species. Habitat degradation had a complex impact on hantavirus prevalence in our study system: more intensive land use increase the abundance of R. rattus. The average body size of individuals varied between agricultural and nonagricultural land-use types, which in turn affected infection prevalence. Smaller R.rattus had lower probability of infection and were captured more commonly in villages and forests. Thus, infection prevalence was highest in agricultural areas. These findings provide new insights to the gradients of hantavirus exposure risk for humans in areas undergoing rapid land use transformations associated with agricultural practices.

Co-Radiation of Leptospira and Tenrecidae (Afrotheria) on Madagascar.

Leptospirosis is a bacterial zoonosis caused by pathogenic Leptospira that are maintained in the kidney lumen of infected animals acting as reservoirs and contaminating the environment via infected urine. The investigation of leptospirosis through a One Health framework has been stimulated by notable genetic diversity of pathogenic Leptospira combined with a high infection prevalence in certain animal reservoirs. Studies of Madagascar's native mammal fauna have revealed a diversity of Leptospira with high levels of host-specificity. Native rodents, tenrecids, and bats shelter several distinct lineages and species of Leptospira, some of which have also been detected in acute human cases. Specifically, L. mayottensis, first discovered in humans on Mayotte, an island neighboring Madagascar, was subsequently identified in a few species of tenrecids on the latter island, which comprise an endemic family of small mammals. Distinct L. mayottensis lineages were identified in shrew tenrecs (Microgale cowani and Nesogale dobsoni) on Madagascar, and later in an introduced population of spiny tenrecs (Tenrec ecaudatus) on Mayotte. These findings suggest that L. mayottensis (i) has co-radiated with tenrecids on Madagascar, and (ii) has recently emerged in human populations on Mayotte following the introduction of T. ecaudatus from Madagascar. Hitherto, L. mayottensis has not been detected in spiny tenrecs on Madagascar. In the present study, we broaden the investigation of Malagasy tenrecids and test the emergence of L. mayottensis in humans as a result of the introduction of T. ecaudatus on Mayotte. We screened by PCR 55 tenrecid samples from Madagascar, including kidney tissues from 24 individual T. ecaudatus. We describe the presence of L. mayottensis in Malagasy T. ecaudatus in agreement with the aforementioned hypothesis, as well as in M. thomasi, a tenrecid species that has not been explored thus far for Leptospira carriage.

Skull morphological evolution in Malagasy endemic Nesomyinae rodents.

Madagascar is a large island to the south-east of Africa and in many ways continental in size and ecological complexity. Here we aim to define how skull morphology of an endemic and monophyletic clade of rodents (sub-family Nesomyinae), that show considerable morphological variation, have evolved and how their disparity is characterized in context of the geographical and ecological complexity of the island. We performed a two-dimensional geometric morphometric analysis on 370 dorsal and 399 ventral skull images of 19 species (comprising all nine extant endemic genera) and tested the influence of three ecological parameters (climate, locomotor habitat and nychthemeral cycle) in a phylogenetic context on size and shape. The results indicate that skull shape appears to importantly reflect phylogeny, whereas skull size does not carry a significant phylogenetic signal. Skull shape is significantly influenced by climate while, skull size is not impacted by any of the ecological factors tested, which is controversial to expectations in an insular context. In conclusion, Nesomyinae must have evolved under unusual types of local constraints, preventing this radiation from demonstrating strong ecological release.

Comparing transmission potential networks based on social network surveys, close contacts and environmental overlap in rural Madagascar.

Social and spatial network analysis is an important approach for investigating infectious disease transmission, especially for pathogens transmitted directly between individuals or via environmental reservoirs. Given the diversity of ways to construct networks, however, it remains unclear how well networks constructed from different data types effectively capture transmission potential. We used empirical networks from a population in rural Madagascar to compare social network survey and spatial data-based networks of the same individuals. Close contact and environmental pathogen transmission pathways were modelled with the spatial data. We found that naming social partners during the surveys predicted higher close-contact rates and the proportion of environmental overlap on the spatial data-based networks. The spatial networks captured many strong and weak connections that were missed using social network surveys alone. Across networks, we found weak correlations among centrality measures (a proxy for superspreading potential). We conclude that social network surveys provide important scaffolding for understanding disease transmission pathways but miss contact-specific heterogeneities revealed by spatial data. Our analyses also highlight that the superspreading potential of individuals may vary across transmission modes. We provide detailed methods to construct networks for close-contact transmission pathogens when not all individuals simultaneously wear GPS trackers.

High Rickettsial Diversity in Rodents and Their Ectoparasites From the Central Highlands of Madagascar.

Rickettsioses are among emerging infectious diseases around the world. In Madagascar, little information is available regarding Rickettsia (Rickettsiales: Rickettsiaceae) diversity and their potential impacts on public health. In fact, molecular screening of ectoparasites of mammals reported the presence of three species, Rickettsia africae, Rickettsia typhi, and Rickettsia felis. The present study aims to investigate the diversity of Rickettsia in small mammals and associated ectoparasites (fleas and ticks) using a molecular approach. In September and December 2016, fieldworks were undertaken in two districts of Madagascar to capture small mammals using standard traps (Tomahawk and Sherman traps) and collect associated ectoparasites. In total, 12 taxa of ectoparasites (5 flea and 7 tick species) were collected from 89 individuals of four species of terrestrial small mammals. Rickettsia spp. were molecularly identified in one specimen of Rattus rattus (Rodentia: Muridae), one specimen of Pulex irritans (Siphonaptera: Pulicidae) as well as four specimens of Ixodes cf. colasbelcouri (Ixodida: Ixodidae). This study showed the presence of three phylogenetically distinct taxa of Rickettsia in small mammals and their ectoparasites. The current study broadens our knowledge on the diversity of Rickettsia in the Central Highlands of Madagascar and highlights for the first time the presence of Ri. felis in R. rattus and in tick, I. cf. colasbelcouri in Madagascar. Additional studies are needed to have exhaustive information on Rickettsia in small mammals and their ectoparasites, to determine their pathogenicity as well as their potential effects on public health in order to update the national policy for the control of emerging infectious diseases in Madagascar.

[Breeding ecology of Microgale brevicaudata (Tenrecidae) in northeastern Madagascar]. / Écologie de la reproduction de Microgale brevicaudata (Tenrecidae) dans le Nord-Est de Madagascar.

With the aim of providing additional information on the reproductive ecology of Microgale brevicaudata G. Grandidier, 1899, the present study examines the breeding season of this species and other related aspects across a range of native forest areas and human modified habitats. This poorly known species occurs in the lowland moist evergreen forest of the Marojejy National Park and the surrounding anthropic zones. Three areas of Marojejy were visited, two of which (Antsahabe and Sarahandrano) during a range of seasons and one (Marojejy NP) during the hot and humid season. Information on the sex, age, and sexual maturity of each captured individual of M. brevicaudata during small mammal surveys and different associated extrapolations indicates that it mates towards the end of the cold and dry season (September-October), and parturition and lactation commence towards the start of the hot and humid season (November-December). Each captured pregnant female had one or two embryos (n = 22). The comparison of reproductive status (X2 = 0.91; df = 2; p > 0.05) and breeding season (X2 = 8.53; df = 7; p > 0.05) of trapped M. brevicaudata indicate that there is no significant difference in the annual breeding cycle between the types of habitats where the species is found on Marojejy, ranging from natural forest to human-disturbed habitats.

Morphological variation of Rattus rattus Linnaeus, 1758 (Rodentia: Muridae) in forest and anthropogenic habitats of a watershed in northeastern Madagascar.

De par sa haute capacité d'adaptation et la plasticité de son alimentation, reflétée par une variation morphologique des individus, Rattus rattus s'est dispersé et a occupé un large éventail d'habitats à Madagascar après son introduction qui date du Xe siècle environ. Cette étude s'intéresse à la variation morphologique de cette espèce superposée à différents modes d'utilisation du paysage. Nous avons analysé des données morphométriques crânio-dentaires recueillies à partir de 333 spécimens capturés dans le bassin-versant de la rivière Manantenina sur la partie orientale du Massif de Marojejy. Les résultats des tests MANOVA comparant la morphologie crânio-dentaire et la taille des individus par sexe, classe d'âge et type d'habitat ont montré qu'il existe des différences significatives entre la forme du crâne et la taille des individus parmi les types d'habitat et la classe d'âge. Aucun dimorphisme sexuel n'a été trouvé sur la morphologie du crâne, par contre la taille des mâles est significativement plus grande par rapport à celle des femelles. Les individus vivant en dehors de l'habitat forestier ont des crânes nettement plus gros (Tukey HSD, p = 0,004). Comme anticipé, les jeunes individus ont un crâne plus petit que les adultes et les adultes plus âgés, mais la largeur de leur première molaire, la longueur de la rangée de dents de la mandibule et la longueur de la couronne de la rangée de molaire maxillaire sont plus grandes. Due to their high adaptability and dietary plasticity, reflected by individual morphological variation, Rattus rattus has dispersed to and occupies a broad range of habitats on Madagascar after its introduction to the island, which dates towards the 10th century. This study focuses on morphological variation of this species overlaid on different human land use patterns.We analyzed cranio-dental morphometric data collected from 333 specimens captured in the Manantenina River valley on the eastern side of the Marojejy Massif.The results of the MANOVA tests comparing cranio-dental morphology and size of individuals by sex, age class, and habitat type showed that there are significant differences between skull shape and size of individuals among the habitat types and age classes. No sexual dimorphism based on cranio-dental morphology was found but we noted a significant difference between male and female body size between different habitats. Individuals living outside of native forest have distinctly larger skulls (Tukey HSD, p = 0,004). As anticipated, young individuals have a smaller skull than adults and old adults, however the breadth of their first molar, length of mandible toothrow, and crown length of maxillary molar row are proportionally larger.

[Diet of Microgale brevicaudata (Tenrecidae) in northeast Madagascar]. / Régime alimentaire de Microgale brevicaudata (Tenrecidae), Nord-Est de Madagascar.

Herein we provide a dietary analysis using stomach contents of Microgale brevicaudata (G. Grandidier, 1899), a poorly known species of shrew tenrec, in the dense lowland moist evergreen forest of the Marojejy National Park and human modified habitats in the peripheral zones. We specifically examine the arthropods consumed by this species and variation related to season, habitat type, sex and age of individuals. Analysis of stomach contents shows that the principal prey types of this species in order of importance are Coleoptera and followed by Hemiptera, Hymenoptera, and Araneae. No differences in prey consumed were found between age and sex classes, nor season, but the percentage of the different arthropod groups varies with the type of habitat.

Effects of land use, habitat characteristics, and small mammal community composition on Leptospira prevalence in northeast Madagascar.

Human activities can increase or decrease risks of acquiring a zoonotic disease, notably by affecting the composition and abundance of hosts. This study investigated the links between land use and infectious disease risk in northeast Madagascar, where human subsistence activities and population growth are encroaching on native habitats and the associated biota. We collected new data on pathogenic Leptospira, which are bacteria maintained in small mammal reservoirs. Transmission can occur through close contact, but most frequently through indirect contact with water contaminated by the urine of infected hosts. The probability of infection and prevalence was compared across a gradient of natural moist evergreen forest, nearby forest fragments, flooded rice and other types of agricultural fields, and in homes in a rural village. Using these data, we tested specific hypotheses for how land use alters ecological communities and influences disease transmission. The relative abundance and proportion of exotic species was highest in the anthropogenic habitats, while the relative abundance of native species was highest in the forested habitats. Prevalence of Leptospira was significantly higher in introduced compared to endemic species. Lastly, the probability of infection with Leptospira was highest in introduced small mammal species, and lower in forest fragments compared to other habitat types. Our results highlight how human land use affects the small mammal community composition and in turn disease dynamics. Introduced species likely transmit Leptospira to native species where they co-occur, and may displace the Leptospira species naturally occurring in Madagascar. The frequent spatial overlap of people and introduced species likely also has consequences for public health.

Comparative assessment on rodent impacts and cultural perceptions of ecologically based rodent management in 3 Afro-Malagasy farming regions.

Rodents generate negative consequences for smallholder farmers in Africa that directly impact household and livestock damage, food security, and public health. Ecologically Based Rodent Management (EBRM) seeks sustainable solutions for the mitigation of rodent damage through assessments of rodent population dynamics, agro-ecosystems, and socio-cultural contexts. We adopt a comparative approach across 3 rural Afro-Malagasy smallholder farming regions in South Africa, Tanzania, and Madagascar to assess the household impacts of rodent pests and current perceptions and preferences associated with several rodent control measures. We conducted focus group questionnaires and interviews in different study site locations. Rodents assert multiple impacts on Afro-Malagasy farmers demonstrating recurrent and emerging agricultural and household costs, and public health impacts. We identify a significant knowledge gap in educating communities about the application of different EBRM approaches in favor of acute poisons that are perceived to be more effective. Cultural issues and taboos also have a significant impact on the social acceptance of rodent hunting as well as biological control using indigenous predators. We advocate for an enhanced investigation of the socio-cultural beliefs associated with different rodent practices to understand the factors underlying social acceptance. A collaborative approach that integrates the perspectives of target communities to inform the design of EBRM initiatives according to the specific agro-ecosystem and socio-cultural context is necessary to ensure programmatic success.

Isotopic evidence for niche partitioning and the influence of anthropogenic disturbance on endemic and introduced rodents in central Madagascar.

We applied a multi-isotope approach to examine aspects of niche partitioning, competition, and mobility for rodents in the Central Highlands of Madagascar. Specifically, we used carbon (δ13C), nitrogen (δ15N), and strontium (87Sr/86Sr) isotope ratios in bone to investigate diet and mobility for endemic tufted tail rats (Eliurus spp.), and introduced black rats (Rattus rattus) and house mice (Mus musculus) within and outside a fragment of montane humid forest in the Ambohitantely Special Reserve. There was a clear spatial segregation in trapping success for different species: Eliurus was only in the forest interior and edge, Mus only outside of the fragment in a marsh and park housing complex, and Rattus in all habitats except the housing complex. We find only moderate support for mobility of rodents among habitats. Mus may routinely move between the marsh and housing complex. However, regular movement between the forest edge and interior, or between the forest fragment and surrounding grassland is not supported. Taxa appear to target different foods: Rattus tends to feed at a higher trophic level than Eliurus, and Mus consumes some C4 resources. To date, strontium isotopes have been underutilized in ecological research. Here, we show that they are highly complementary to carbon and nitrogen isotope data. Even in localities with relatively uniform underlying geology, it may be possible to distinguish individuals that regularly forage in different habitats.

Correction: A systematic review of rodent pest research in Afro-Malagasy small-holder farming systems: Are we asking the right questions?

[This corrects the article DOI: 10.1371/journal.pone.0174554.].

A systematic review of rodent pest research in Afro-Malagasy small-holder farming systems: Are we asking the right questions?

Rodent pests are especially problematic in terms of agriculture and public health since they can inflict considerable economic damage associated with their abundance, diversity, generalist feeding habits and high reproductive rates. To quantify rodent pest impacts and identify trends in rodent pest research impacting on small-holder agriculture in the Afro-Malagasy region we did a systematic review of research outputs from 1910 to 2015, by developing an a priori defined set of criteria to allow for replication of the review process. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We reviewed 162 publications, and while rodent pest research was spatially distributed across Africa (32 countries, including Madagascar), there was a disparity in number of studies per country with research biased towards four countries (Tanzania [25%], Nigeria [9%], Ethiopia [9%], Kenya [8%]) accounting for 51% of all rodent pest research in the Afro-Malagasy region. There was a disparity in the research themes addressed by Tanzanian publications compared to publications from the rest of the Afro-Malagasy region where research in Tanzania had a much more applied focus (50%) compared to a more basic research approach (92%) in the rest of the Afro-Malagasy region. We found that pest rodents have a significant negative effect on the Afro-Malagasy small-holder farming communities. Crop losses varied between cropping stages, storage and crops and the highest losses occurred during early cropping stages (46% median loss during seedling stage) and the mature stage (15% median loss). There was a scarcity of studies investigating the effectiveness of various management actions on rodent pest damage and population abundance. Our analysis highlights that there are inadequate empirical studies focused on developing sustainable control methods for rodent pests and rodent pests in the Africa-Malagasy context is generally ignored as a research topic.

Multiple Loci and Complete Taxonomic Sampling Resolve the Phylogeny and Biogeographic History of Tenrecs (Mammalia: Tenrecidae) and Reveal Higher Speciation Rates in Madagascar's Humid Forests.

The family Tenrecidae (tenrecs) is one of only four extant terrestrial mammal lineages to have colonized and diversified on Madagascar. Over the last 15 years, several studies have disagreed on relationships among major tenrec lineages, resulting in multiple reinterpretations of the number and timing of historical transoceanic dispersal events between Africa and Madagascar. We reconstructed the phylogeny of Tenrecidae using multiple loci from all recognized extant species and estimated divergence timing using six fossil calibrations within Afrotheria. All phylogenetic analyses strongly support monophyly of the Malagasy tenrecs, and our divergence timing analysis places their colonization of the island at 30-56 Ma. Our comprehensive phylogeny supports three important taxonomic revisions that reflect the evolutionary history of tenrecs: (1) we formally elevate the African otter shrews to their own family Potamogalidae, thereby rendering extant Tenrecidae entirely endemic to Madagascar; (2) we subsume the semiaquatic genus Limnogale within the shrew tenrec genus Microgale; and (3) we re-elevate the two largest-bodied shrew tenrecs, Microgale dobsoni and Microgale talazaci, to the genus Nesogale Thomas (1918) Finally, we use recently summarized habitat data to test the hypothesis that diversification rates differ between humid and arid habitats on Madagascar, and we compare three common methods for ancestral biogeographic reconstruction. These analyses suggest higher speciation rates in humid habitats and reveal a minimum of three and more likely five independent transitions to arid habitats. Our results resolve the relationships among previously recalcitrant taxa, illuminate the timing and mechanisms of major biogeographic patterns in an extraordinary example of an island radiation, and permit the first comprehensive, phylogenetically consistent taxonomy of Madagascar's tenrecs.

The Fleas of Endemic and Introduced Small Mammals in Central Highland Forests of Madagascar: Faunistics, Species Diversity, and Absence of Host Specificity.

Data are presented on the flea species of the genera Paractenopsyllus (Ceratophyllidae, Leptopsyllinae) and Synopsyllus (Pulicidae, Xenopsyllinae) obtained from small mammals during two 2014 seasonal surveys at a montane humid forest site (Ambohitantely) in the Central Highlands of Madagascar. The mammal groups included the endemic family Tenrecidae (tenrecs) and subfamily Nesomyinae (rodents) and two introduced families Muridae (rodents) and Soricidae (shrews); no fleas were recovered from the latter family. The surveys were conducted at the end of the wet and dry seasons with 288 individual small mammals captured, including 12 endemic and four introduced species. These animals yielded 344 fleas, representing nine species endemic to Madagascar; no introduced species was collected. Some seasonal variation was found in the number of trapped small mammals, but no marked difference was found in species richness. For flea species represented by sufficient samples, no parasite-host specificity was found, and there is evidence for considerable lateral exchange in the local flea fauna between species of tenrecs and the two rodent families (endemic and introduced). The implications of these results are discussed with regards to small mammal species richness and community structure, as well as a possible mechanism for the maintenance of sylvatic cycles of bubonic plague in the montane forests of Madagascar.

Highly diverse morbillivirus-related paramyxoviruses in wild fauna of the southwestern Indian Ocean Islands: evidence of exchange between introduced and endemic small mammals.

UNLABELLED: The Paramyxoviridae form an increasingly diverse viral family, infecting a wide variety of different hosts. In recent years, they have been linked to disease emergence in many different animal populations and in humans. Bats and rodents have been identified as major animal populations capable of harboring paramyxoviruses, and host shifting between these animals is likely to be an important driving factor in the underlying evolutionary processes that eventually lead to disease emergence. Here, we have studied paramyxovirus circulation within populations of endemic and introduced wild small mammals of the southwestern Indian Ocean region and belonging to four taxonomic orders: Rodentia, Afrosoricida, Soricomorpha, and Chiroptera. We report elevated infection levels as well as widespread paramyxovirus dispersal and frequent host exchange of a newly emerging genus of the Paramyxoviridae, currently referred to as the unclassified morbillivirus-related viruses (UMRVs). In contrast to other genera of the Paramyxoviridae, where bats have been shown to be a key host species, we show that rodents (and, in particular, Rattus rattus) are significant spreaders of UMRVs. We predict that the ecological particularities of the southwestern Indian Ocean, where small mammal species often live in densely packed, multispecies communities, in combination with the increasing invasion of R. rattus and perturbations of endemic animal communities by active anthropological development, will have a major influence on the dynamics of UMRV infection. IMPORTANCE: Identification of the infectious agents that circulate within wild animal reservoirs is essential for several reasons: (i) infectious disease outbreaks often originate from wild fauna; (ii) anthropological expansion increases the risk of contact between human and animal populations and, as a result, the risk of disease emergence; (iii) evaluation of pathogen reservoirs helps in elaborating preventive measures to limit the risk of disease emergence. Many paramyxoviruses for which bats and rodents serve as major reservoirs have demonstrated their potential to cause disease in humans and animals. In the context of the biodiversity hot spot of southwestern Indian Ocean islands and their rich endemic fauna, we show that highly diverse UMRVs exchange between various endemic animal species, and their dissemination likely is facilitated by the introduced Rattus rattus. Hence, many members of the Paramyxoviridae appear well adapted for the study of the viral phylodynamics that may be associated with disease emergence.

Diversification of an emerging pathogen in a biodiversity hotspot: Leptospira in endemic small mammals of Madagascar.

Biodiversity hotspots and associated endemism are ideal systems for the study of parasite diversity within host communities. Here, we investigated the ecological and evolutionary forces acting on the diversification of an emerging bacterial pathogen, Leptospira spp., in communities of endemic Malagasy small mammals. We determined the infection rate with pathogenic Leptospira in 20 species of sympatric rodents (subfamily Nesomyinae) and tenrecids (family Tenrecidae) at two eastern humid forest localities. A multilocus genotyping analysis allowed the characterization of bacterial diversity within small mammals and gave insights into their genetic relationships with Leptospira infecting endemic Malagasy bats (family Miniopteridae and Vespertilionidae). We report for the first time the presence of pathogenic Leptospira in Malagasy endemic small mammals, with an overall prevalence of 13%. In addition, these hosts harbour species of Leptospira (L. kirschneri, L. borgpetersenii and L. borgpetersenii group B) which are different from those reported in introduced rats (L. interrogans) on Madagascar. The diversification of Leptospira on Madagascar can be traced millions of years into evolutionary history, resulting in the divergence of endemic lineages and strong host specificity. These observations are discussed in relation to the relative roles of endemic vs. introduced mammal species in the evolution and epidemiology of Leptospira on Madagascar, specifically how biodiversity and biogeographical processes can shape community ecology of an emerging pathogen and lead to its diversification within native animal communities.