Astroviruses in terrestrial Malagasy mammals.

Small terrestrial mammals are major hosts of infectious agents responsible for zoonotic diseases. Astroviruses (AstVs)-the cause of non-bacterial gastroenteritis mainly affecting young children-have been detected in a wide array of mammalian and avian host species. However, understanding the factors that influence AstV infection within and across hosts is limited. Here, we investigated the impact of land use changes on AstVs in terrestrial small mammals in rural northeastern Madagascar. We sampled 515 small mammals, representing seven endemic and four introduced species. Twenty-two positive samples were identified, all but one of which were found in the introduced species Mus musculus and Rattus rattus (family Muridae), with a positivity rate of 7.7% (6/78) and 5.6% (15/266), respectively. The non-introduced rodent case was from an endemic shrew-tenrec (family Tenrecidae). We found the highest positivity rate of AstVs infection in brushy regrowth (17.5%, 7/40) as compared to flooded rice fields (4.60%, 8/174), secondary forest (4.1%, 3/74), agroforest (3.6%, 1/28), village (2.61%, 3/115), and semi-intact forest (0%, 0/84). A phylogenetic analysis revealed an association between AstVs and their rodent host species. None of the viruses were phylogenetically related to AstVs previously described in Malagasy bats. This study supports AstV circulation in synanthropic animals in agricultural habitats of Madagascar and highlights the need to assess the spillover risk to human populations in rural areas.

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.

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.

[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.

Broad and flexible stable isotope niches in invasive non-native Rattus spp. in anthropogenic and natural habitats of central eastern Madagascar.

BACKGROUND: Rodents of the genus Rattus are among the most pervasive and successful invasive species, causing major vicissitudes in native ecological communities. A broad and flexible generalist diet has been suggested as key to the invasion success of Rattus spp. Here, we use an indirect approach to better understand foraging niche width, plasticity, and overlap within and between introduced Rattus spp. in anthropogenic habitats and natural humid forests of Madagascar. RESULTS: Based on stable carbon and nitrogen isotope values measured in hair samples of 589 individual rodents, we found that Rattus rattus had an extremely wide foraging niche, encompassing the isotopic space covered by a complete endemic forest-dwelling Malagasy small mammal community. Comparisons of Bayesian standard ellipses, as well as (multivariate) mixed-modeling analyses, revealed that the stable isotope niche of R. rattus tended to change seasonally and differed between natural forests and anthropogenic habitats, indicating plasticity in feeding niches. In co-occurrence, R. rattus and Rattus norvegicus partitioned feeding niches. Isotopic mismatch of signatures of individual R. rattus and the habitat in which they were captured, indicate frequent dispersal movements for this species between natural forest and anthropogenic habitats. CONCLUSIONS: Since R. rattus are known to transmit a number of zoonoses, potentially affecting communities of endemic small mammals, as well as humans, these movements presumably increase transmission potential. Our results suggest that due to their generalist diet and potential movement between natural forest and anthropogenic habitats, Rattus spp. might affect native forest-dependent Malagasy rodents as competitors, predators, and disease vectors. The combination of these effects helps explain the invasion success of Rattus spp. and the detrimental effects of this genus on the endemic Malagasy rodent fauna.

Phylogeography and support vector machine classification of colour variation in panther chameleons.

Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high-resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the whole species distribution. First, mitochondrial and nuclear DNA sequence analyses uncover strong genetic structure among geographically restricted haplogroups, revealing limited gene flow among populations. Bayesian coalescent modelling suggests that most of the mitochondrial haplogroups could be considered as separate species. Second, using a supervised multiclass support vector machine approach on five anatomical components, we identify patterns in 3D colour space that efficiently predict assignment of male individuals to mitochondrial haplogroups. We converted the results of this analysis into a simple visual classification key that can assist trade managers to avoid local population overharvesting.