Twenty-nine years of continuous monthly capture-mark-recapture data of multimammate mice (Mastomys natalensis) in Morogoro, Tanzania.

The multimammate mice (Mastomys natalensis) is the most-studied rodent species in sub-Saharan Africa, where it is an important pest species in agriculture and carrier of zoonotic diseases (e.g. Lassa virus). Here, we provide a unique dataset that consists of twenty-nine years of continuous monthly capture-mark-recapture entries on one 3 ha mosaic field (MOSA) in Morogoro, Tanzania. It is one of the most accurate and long-running capture-recapture time series on a small mammal species worldwide and unique to Africa. The database can be used by ecologists to test hypotheses on the population dynamics of small mammals (e.g. to test the effect of climate change), or to validate new algorithms on real long-term field data (e.g. new survival analyses techniques). It is also useful for both scientists and decision-makers who want to optimize rodent control strategies and predict outbreaks of multimammate mice.

Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity.

Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.

Preliminary investigation and intervention of the suspected plague outbreak in Madunga, Babati District-Tanzania.

BACKGROUND: Rodents are known to be reservoirs of plague bacteria, Yesinia pestis in the sylvatic cycle. A preliminary investigation of the suspected plague outbreak was conducted in Madunga Ward, Babati District Council in Manyara Region December-2019-January 2020 Following reported two cases which were clinically suspected as showing plague disease symptoms. METHOD: The commensal and field rodents were live trapped using Sherman traps in Madunga Ward, where plague suspect cases were reported and, in the Nou-forest reserve areas at Madunga Ward, Babati District Council, to assess plague risk in the area. Fleas were collected inside the houses using light traps and on the rodents 'body after anaesthetizing the captured rodent to determine flea indices which are used to estimate the risk of plague transmission. Lung impression smears were made from sacrificed rodents to examine for possible bipolar stained Yersinia spp bacilli. RESULTS: A total of 86 rodents consisting of ten rodent species were captured and identified from the study sites. Nine forest rodent species were collected. Field/fallow rodent species were dominated by Mastomys natalensis. whereas domestic rodent species captured was Rattus rattus. Overall lung impression smear showed bipolar stain were 14 (16.28%) while House Flea Index (HFI) was 3.1 and Rodent Flea Index (RFI) was 1.8. CONCLUSION: The findings of this study have shown that, the presence of bipolar stained bacilli in lung impression smears of captured species of rodents indicates (not confirmed) possible circulation of Yesrsinia pests in rodents and the high flea indices in the area which included the most common flea species known to be plague vectors in Tanzania could have played transmission role in this suspected outbreak. The study recommends surveillance follow-up in the area and subject collected samples to the standard plague confirmatory diagnosis.

The effects of personality on survival and trappability in a wild mouse during a population cycle.

The pace-of-life syndrome (POLS) theory provides an evolutionary explanation for the existence of consistent among-individual variation in behaviour, or animal personality. Herein, individuals with a fast lifestyle are considered to be bolder and should take more risks resulting in a lower life expectancy compared to shyer individuals with a slower lifestyle. However, this assumption depends on the levels of intra-specific competition that the individuals experience which has rarely been tested in species that experience large changes in competition on a very short time scale. We used the multimammate mice (Mastomys natalensis) as a model system to study the POLS assumption by investigating the effects of two personality traits (exploration and stress-sensitivity) on survival, maturation (a proxy for reproductive investment) and recapture probability during one population cycle (Nindividuals = 201). Such a cycle consists of two phases in which the levels of intra-specific competition vary drastically. We found that only one personality trait, namely stress-sensitivity, had a negative effect on both survival and recapture probability but none of them affected maturation. This suggests that less stress-sensitive individuals take more risks in the wild and have a higher survival probability compared to high stress-sensitive individuals. However, the effect of personality on survival was only present during the population decrease phase, when the levels of intra-specific competition are high due to a scarcity of food. This suggests that seasonal changes in competition might be important in the evolution and maintenance of animal personalities in species whose population dynamics have a clear seasonal component.

Density dependence and persistence of Morogoro arenavirus transmission in a fluctuating population of its reservoir host.

A key aim in wildlife disease ecology is to understand how host and parasite characteristics influence parasite transmission and persistence. Variation in host population density can have strong impacts on transmission and outbreaks, and theory predicts particular transmission-density patterns depending on how parasites are transmitted between individuals. Here, we present the results of a study on the dynamics of Morogoro arenavirus in a population of multimammate mice (Mastomys natalensis). This widespread African rodent, which is also the reservoir host of Lassa arenavirus in West Africa, is known for its strong seasonal density fluctuations driven by food availability. We investigated to what degree virus transmission changes with host population density and how the virus might be able to persist during periods of low host density. A seven-year capture-mark-recapture study was conducted in Tanzania where rodents were trapped monthly and screened for the presence of antibodies against Morogoro virus. Observed seasonal seroprevalence patterns were compared with those generated by mathematical transmission models to test different hypotheses regarding the degree of density dependence and the role of chronically infected individuals. We observed that Morogoro virus seroprevalence correlates positively with host density with a lag of 1-4 months. Model results suggest that the observed seasonal seroprevalence dynamics can be best explained by a combination of vertical and horizontal transmission and that a small number of animals need to be infected chronically to ensure viral persistence. Transmission dynamics and viral persistence were best explained by the existence of both acutely and chronically infected individuals and by seasonally changing transmission rates. Due to the presence of chronically infected rodents, rodent control is unlikely to be a feasible approach for eliminating arenaviruses such as Lassa virus from Mastomys populations.

Relationship between population density and viral infection: A role for personality?

Conspecific density and animal personality (consistent among-individual differences in behavior) may both play an important role in disease ecology. Nevertheless, both factors have rarely been studied together but may provide insightful information in understanding pathogen transmission dynamics. In this study, we investigated how both personality and density affect viral infections both direct and indirectly, using the multimammate mice (Mastomys natalensis) and Morogoro arenavirus (MORV) as a model system. Using a replicated semi-natural experiment, we found a positive correlation between MORV antibody presence and density, suggesting that MORV infection is density-dependent. Surprisingly, slower explorers were more likely to have antibodies against MORV compared to highly explorative individuals. However, exploration was positively correlated with density which may suggest a negative, indirect effect of density on MORV infection. We have shown here that in order to better understand disease ecology, both personality and density should be taken into account.

Evolutionary history of Pneumocystis fungi in their African rodent hosts.

Pneumocystis is a genus of parasitic fungi infecting lung tissues in a wide range of mammal species, displaying a strong host specificity and patterns of co-speciation with their hosts. However, a recent study on Asiatic murids challenged these patterns reporting several Pneumocystis lineages/species shared by different host species or even genera in the Rattini and Murini tribes. Here we screened lung samples of 27 species of African rodents from five families for the presence of Pneumocystis DNA. Using reconstructed multi-locus phylogenies of both hosts and parasites, we tested the hypothesis of their co-evolution. We found that Pneumocystis is widespread in African rodents, detected in all but seven screened host species, with species-level prevalence ranging from 5.9 to 100%. Several host species carry pairs of highly divergent Pneumocystis lineages/species. The retrieved co-phylogenetic signal was highly significant (p = .0017). We found multiple co-speciations, sorting events and two host-shift events, which occurred between Murinae and Deomyinae hosts. Comparison of genetic distances suggests higher substitution rates for Pneumocystis relative to the rodent hosts on neutral loci and slower rates on selected ones. We discuss life-history traits and population dynamics factors which could explain the observed results.

Arenavirus infection correlates with lower survival of its natural rodent host in a long-term capture-mark-recapture study.

BACKGROUND: Parasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations. RESULTS: Antibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%). CONCLUSIONS: The small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.

Reconstructing the molecular phylogeny of giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon).

Giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon), also known as giant elephant-shrews, are small-bodied mammals that range from central through eastern Africa. Previous research on giant sengi systematics has relied primarily on pelage color and geographic distribution. Because some species have complex phenotypic variation and large geographic ranges, we used molecular markers to evaluate the phylogeny and taxonomy of the genus, which currently includes four species: R. chrysopygus, R. cirnei (six subspecies), R. petersi (two subspecies), and R. udzungwensis. We extracted DNA from fresh and historical museum samples from all taxa except one R. cirnei subspecies, and we generated and analyzed approximately 4700 aligned nucleotides (2685 bases of mitochondrial DNA and 2019 bases of nuclear DNA) to reconstruct a molecular phylogeny. We genetically evaluate Rhynchocyon spp. sequences previously published on GenBank, propose that the captive R. petersi population in North American zoos is likely R. p. adersi, and suggest that hybridization among taxa is not widespread in Rhynchocyon. The DNA sample we have from the distinctive but undescribed giant sengi from the Boni forest of northern coastal Kenya is unexpectedly nearly identical to R. chrysopygus, which will require further study. Our analyses support the current morphology-based taxonomy, with each recognized species forming a monophyletic clade, but we propose elevating R. c. stuhlmanni to a full species.

Distribution and ecology of lesser pouched rat, Beamys hindei, in Tanzanian coastal forests.

The lesser pouched rat, Beamys hindei, is a small rodent that is patchily distributed in the Eastern Arc Mountains and coastal forests in East Africa. The ecology of this species and its current distribution in coastal forests is not well known. Therefore, we conducted a study in selected coastal forests to assess the current distribution of the species and to investigate the population ecology in terms of abundance fluctuations and demographic patterns. Assessments of the species distribution were conducted in 5 forests through trapping with Sherman live traps. Data on ecology were obtained from monthly capture-mark-recapture studies conducted for 5 consecutive nights per month in two 1 ha grids set in Zaraninge Forest over a 2-year period. The results indicate the presence of B. hindei in 3 forests where it was not previously recorded. The population abundance estimates ranged from 1 to 40 animals per month, with high numbers recorded during rainy seasons. Reproduction patterns and sex ratios did not differ between months. Survival estimates were not influenced by season, and recruitment was low, with growth rate estimates of 1 animal per month. These estimates suggest a stable population of B. hindei in Zaraninge Forest. Further studies are recommended to establish the home range, diet and burrowing behavior of the species in coastal forests in East Africa.

Mopeia virus-related arenavirus in natal multimammate mice, Morogoro, Tanzania.

A serosurvey involving 2,520 small mammals from Tanzania identified a hot spot of arenavirus circulation in Morogoro. Molecular screening detected a new arenavirus in Natal multimammate mice (Mastomys natalensis), Morogoro virus, related to Mopeia virus. Only a small percentage of mice carry Morogoro virus, although a large proportion shows specific antibodies.