South African Rodent Research Articles

Physiological Adaptations to Arid Conditions in South African Rodents: A Comparative Study of Rhabdomys Species

Physiological Adaptations to Arid Conditions in South African Rodents: A Comparative Study of Rhabdomys Species

Functional and phylogenetic uniqueness of helminth and flea assemblages of two South African rodents

The loss of a particular species from a community may have different effects on its functioning, depending on the presence or absence of functionally similar or phylogenetically close species in that community (redundancy). Redundancy is thus defined as the fraction of species diversity not expressed by functional or phylogenetic diversity. We assessed functional and phylogenetic alpha- and beta-redundancy in helminth and flea assemblages of two species of South African rodents, Rhabdomys dilectus and Rhabdomys pumilio, using community uniqueness as the inverse indicator of redundancy. We asked whether patterns of functional and phylogenetic alpha- and beta-uniqueness differed between (i) parasite groups (endo- versus ectoparasites), (ii) host species within parasite groups, and (iii) biomes within host species. We found differences between the two hosts in the functional and phylogenetic alpha-uniqueness (but not beta-uniqueness) of flea, but not helminth, assemblages. Significant correlations between the alpha-uniqueness of parasite assemblages and the total parasite prevalence were found only for phylogenetic uniqueness and only in helminths. Pairwise site-by-site dissimilarities in uniqueness (beta-uniqueness) and pairwise dissimilarity in prevalence were significantly associated (positively) in helminths but not in fleas. A between-biome difference in functional (but not phylogenetic) alpha-uniqueness was found in both helminth and flea assemblages harboured by R. pumilio. We conclude that the resilience of parasite assemblages in terms of the effect on hosts depends not only on their transmission strategy but also on traits of host species and environmental factors.

Effects of the colour of photophase light on locomotor activity in a nocturnal and a diurnal South African rodent.

Many physiological and behavioural responses to varying qualities of light, particularly during the night (scotophase), have been well documented in rodents. We used varying wavelengths of day-time (photophase) lighting to assess daily responses in locomotor activity in the nocturnal Namaqua rock mouse (Micaelamys namaquensis) and diurnal four-striped field mouse (Rhabdomys pumilio). Animals were exposed to three light-dark cycle regimes: a short-wavelength- (SWLC, blue), a medium-wavelength- (MWLC, green) and a long-wavelength light-dark cycle (LWLC, red). Overall, daily locomotor activity of both species changed according to different wavelengths of light: the diurnal species displayed most activity under the SWLC and the nocturnal species exhibited the highest levels of activity under the LWLC. Both species showed an increase in diurnal activity and a decrease in nocturnal activity under the LWLC. These results indicate an attenuated responsiveness to long-wavelength light in the nocturnal species, but this does not appear to be true for the diurnal species. These results emphasize that the effect of light on the locomotor activity of animals depends on both the properties of the light and the temporal organization of activity of a species.

Beta diversity of gastrointestinal helminths in two closely related South African rodents: species and site contributions.

A fundamental aim of parasite ecology is to understand the mechanisms behind spatial variation in diversity and structure of parasite assemblages. To understand the contribution of individual parasite species and their assemblages to spatial variation in parasite communities, we examined species contributions to beta diversity (SCBD) and local contributions to beta diversity (LCBD) of parasitic gastrointestinal helminths (nematodes and cestodes) in two closely related rodents, Rhabdomys dilectus and Rhabdomys pumilio, from 20 localities across South Africa. Although the two Rhabdomys spp. are morphologically similar, they differ substantially in body size, habitat preference, and sociality. We asked whether the variation in life history traits and infection parameters are associated with SCBD of helminths and whether variation in environmental factors, host population density, and species richness of host communities are associated with LCBD of component assemblages of helminths. We also considered spatial factors to test whether LCBD of helminth assemblages demonstrate geographic structure. We found that the contribution of helminth species parasitic in both hosts to beta diversity significantly increased with characteristic prevalence of these species, whereas mean abundance, type of life cycle, and location in the host's gut had no effect on SCBD. The LCBD of helminth assemblages showed a significant positive correlation with environmental factors in both host species. Our results suggest that predictors of variation in SCBD and LCBD may substantially differ between parasites with different infection parameters and/or parasite communities at different hierarchical scales.

Incisor Enamel Microstructure of Paleogene Caviomorph Rodents from Contamana and Shapaja (Peruvian Amazonia)

Fil: Boivin, Myriam. Institut Des Sciences de L'evolution de Montpellier; Francia. Centre National de la Recherche Scientifique; Francia. Universite de Montpellier; Francia

Community structure of helminth parasites in two closely related South African rodents differing in sociality and spatial behaviour.

To understand the effect of social and spatial behaviour of a host on parasite community organization, we studied species co-occurrence and nestedness of assemblages of gastrointestinal helminths in two closely related rodents, solitary and mobile Rhabdomys dilectus and social and territorially conservative Rhabdomys pumilio, and asked whether helminth communities of the two hosts are characterized by a non-random pattern and whether the occurrence or degree of this non-randomness (a) differs between hosts and (b) is associated with abundance, prevalence and diversity of helminths. We found that although the general pattern of helminth co-occurrence was similar in the two hosts, helminth infracommunities of R. dilectus and R. pumilio differed in the relative frequency of positive and negative pairwise species co-occurrences (only positive in the former and both positive and negative in the latter). Nestedness-related patterns in helminth infracommunities were found in R. pumilio (predominantly anti-nested) but not R. dilectus (predominantly non-nested), whereas the opposite was the case for their component communities (non-nested versus nested, respectively). The level of infection was generally associated with the manifestation of non-randomness in helminth assemblages. Different infection parameters affected different structure patterns in the two hosts. We concluded that community structure of helminths in Rhabdomys spp. results from complex interactions between parasite- and host-associated factors.

Helminth parasitism in two closely related South African rodents: abundance, prevalence, species richness and impinging factors.

We investigated patterns of helminth infection in two closely related rodents (social Rhabdomys pumilio occurring mainly in xeric habitats and solitary R. dilectus occurring mainly in mesic habitats) at 20 localities in different biomes of South Africa and asked if between-species differences were mainly caused by difference in sociality or difference in environmental conditions of their respective habitats. Helminths recovered from the gastrointestinal tract totalled 11 nematode and 5 cestode species from R. pumilio and 19 nematode and 7 cestode species from R. dilectus. In both hosts, mean abundance and prevalence of nematodes were higher compared to cestodes. Cestode infection as well as nematode abundance, species richness or prevalence did not differ between the two rodents. However, incidence of nematode infection was significantly higher in R. dilectus than in R. pumilio. Moreover, nematode numbers and species richness in infracommunities of R. pumilio inhabiting the relatively more xeric Karoo biome were significantly lower than in those inhabiting the relatively less xeric Fynbos biome. Although we could not unequivocally distinguish between effects of host sociality and environmental factors on the number of individuals and species of helminths in the two hosts, differences in the incidence of nematode infection between R. pumilio and R. dilectus as well as differences in the number of nematode individuals and species between R. pumilio from the Fynbos and the Karoo suggested the effect of environmental conditions on helminth infection to be more important than that of sociality.

Infracommunity dynamics of chiggers (Trombiculidae) parasitic on a rodent

We studied the structure of chigger mite (Trombiculidae) communities parasitic on a South African rodent, Rhabdomys pumilio. We aimed to determine whether: (a) different chigger species differ in preferences for certain body areas of a host and (b) chigger assemblages among body areas of the same host individual, are structured and if so, whether the structure of these assemblages is aggregative or segregative. Rhabdomys pumilio is parasitized by seven chigger species belonging to six genera. The three most abundant species (Leptotrombidium sp. nr. muridium, Schoutedenichia sp. and Neoschoengastia sp. A) displayed a non-random distribution across the host body, with the two most abundant species (L. sp. nr. muridium and Schoutedenichia sp.) significantly associated with the tail area. In addition, whenever non-randomness of chigger co-occurrence in the same body area was recorded, it indicated positive but not negative co-occurrences of different species. This might be due to similarity of chigger species in resource needs and strategies to avoid host defence efforts.

Temporal changes in cranial size in South African vlei rats (Otomys): evidence for the ‘third universal response to warming’

Using museum collections and recently collected specimens we studied geographical and temporal (from 1906 to 2013) changes in skull size of two sibling species of rodents, Otomys auratus and O. angoniensis, in northern South Africa occupying distinct temperate grassland (O. auratus) and subtropical savanna (O. angoniensis) biomes. We hypothesised that cranial size should vary in space and time within species according to Bergmann's Rule, which predicts an inverse relationship between body size and temperature. We used the greatest length of the skull (GLS) as a robust indicator of body size. Cranial size of both O. auratus and O. angoniensis decreased significantly over the past 100 years, as expected given historical evidence of warming across northern South Africa since the 1950s. In terms of geographical patterns, GLS was inversely correlated with both latitude and longitude in O. auratus but these trends were correlated with annual rainfall rather than mean annual temperature. Conversely, cranial size of O. angoniensis was weakly positively correlated with longitude but with no climatic variables. Our results demonstrate rapid morphological changes in two herbivorous South African rodents over the past 100 years. Whilst the general decline in size with time in relation to increased temperature is consistent with Bergmann's Rule, multiple drivers may underlie geographical trends in the two species.

Stable isotope evidence for trophic niche partitioning in a South African savanna rodent community

Abstract Species’ partitioning of resources remains one of the most integral components for understanding community assembly. Analysis of stable carbon and nitrogen isotopes in animal tissues has the potential to help resolve patterns of partitioning because these proxies represent the individual’s diet and trophic niche, respectively. Using free-ranging rodents in a southern African savanna as a model community, we find that syntopic species within habitats occupy distinct isotope niches. Moreover, species with strongly overlapping isotope niches did not overlap in their spatial distribution patterns, suggesting an underlying effect of competitive exclusion. Niche conservatism appears to characterize the behaviour of most species in our sample - with little or no observed changes across habitats - with the exception of one species, Mastomys coucha. This species displayed a generalist distribution, being found in similar abundances across a variety of habitats. This spatial pattern was coupled with a generalist isotope niche that shifted across habitats, likely in response to changes in species composition over the same spatial gradient. The case for M. coucha supports contentions that past competition effects played a significant evolutionary role in shaping community structures of today, including the absence of strong interspecific niche overlaps within particular habitats. Our study highlights the value of stable isotope approaches to help resolve key questions in community ecology, and moreover introduces novel analytical approaches to quantifying isotope niche breadths and niche overlaps that are easily comparable with traditional metrices.

Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations

With the introduction of relaxed-clock molecular dating methods, the role of fossil calibration has expanded from providing a timescale, to also informing the models for molecular rate variation across the phylogeny. Here I suggest fossil calibration bounds for four mammal clades, Monotremata (platypus and echidnas), Macropodoidea (kangaroos and potoroos), Caviomorpha-Phiomorpha (South American and African hystricognath rodents), and Chiroptera (bats). In each case I consider sources of uncertainty in the fossil record and provide a molecular dating analysis to examine how the suggested calibration priors are further informed by other mammal fossil calibrations and molecular data.

Cryptic Speciation and Chromosomal Repatterning in the South African Climbing Mice Dendromus (Rodentia, Nesomyidae)

We evaluate the intra- and interspecific diversity in the four South African rodent species of the genus Dendromus. The molecular phylogenetic analysis on twenty-three individuals have been conducted on a combined dataset of nuclear and mitochondrial markers. Moreover, the extent and processes underlying chromosomal variation, have been investigated on three species by mean of G-, C-bands, NORs and Zoo-FISH analysis. The molecular analysis shows the presence of six monophyletic lineages corresponding to D. mesomelas, D. mystacalis and four lineages within D. cfr. melanotis with high divergence values (ranges: 10.6% – 18.3%) that raises the question of the possible presence of cryptic species. The first description of the karyotype for D. mesomelas and D. mystacalis and C- and G- banding for one lineage of D. cfr. melanotis are reported highlighting an extended karyotype reorganization in the genus. Furthermore, the G-banding and Zoo-FISH evidenced an autosome-sex chromosome translocation characterizing all the species and our timing estimates this mutation date back 7.4 mya (Late Miocene). Finally, the molecular clock suggests that cladogenesis took place since the end of Miocene to Plio-Pleistocene, probably due to ecological factors, isolation in refugia followed by differential adaptation to the mesic or dry habitat.

Molecular epidemiology of paramyxoviruses in Zambian wild rodents and shrews

Rodents and shrews are known to harbour various viruses. Paramyxoviruses have been isolated from Asian and Australian rodents, but little is known about them in African rodents. Recently, previously unknown paramyxovirus sequences were found in South African rodents. To date, there have been no reports related to the presence and prevalence of paramyxoviruses in shrews. We found a high prevalence of paramyxoviruses in wild rodents and shrews from Zambia. Semi-nested reverse transcription-PCR assays were used to detect paramyxovirus RNA in 21 % (96/462) of specimens analysed. Phylogenetic analysis revealed that these viruses were novel paramyxoviruses and could be classified as morbillivirus- and henipavirus-related viruses, and previously identified rodent paramyxovirus-related viruses. Our findings suggest the circulation of previously unknown paramyxoviruses in African rodents and shrews, and provide new information regarding the geographical distribution and genetic diversity of paramyxoviruses.

A Geographic Information Systems (GIS)-based analysis of modern South African rodent distributions, habitat use, and environmental tolerances

Goals of this study were to: (1) develop distributional maps of modern rodent genera throughout the countries of South Africa, Lesotho, and Swaziland by georeferencing museum specimens; (2) assess habitat preferences for genera by cross-referencing locality position with South African vegetation; and (3) identify mean annual precipitation and temperature range where the genera are located. Conterminous South Africa including the countries of Lesotho and Swaziland Digital databases of rodent museum specimens housed in the Ditsong National Museum of Natural History, South Africa (DM), and the Division of Mammals, National Museum of Natural History, Smithsonian Institution, United States (NMNH), were acquired and then sorted into a subset of specimens with associated coordinate data. The coordinate data were then used to develop distributional maps for the rodent genera present within the study area. Percent habitat occupation and descriptive statistics for six climatic variables were then determined for each genus by cross-referencing locality positions with vegetation and climatic maps. This report presents a series of maps illustrating the distribution of 35 rodent genera based on 19,471 geo-referenced specimens obtained from two major collections. Inferred habitat use by taxon is provided for both locality and specimen percent occurrence at three hierarchical habitat levels: biome, bioregion, and vegetation unit. Descriptive statistics for six climatic variables are also provided for each genus based on locality and specimen percent incidence. As rodent faunas are commonly used in paleoenvironmental reconstructions, an accurate assessment of rodent environmental tolerance ranges is necessary before confidence can be placed in an actualistic model. While the data presented here represent only a subset of the modern geographic distributions for many of the taxa examined, a wide range of environmental regimes are observed, suggesting that more research is necessary in order to accurately reconstruct an environmental signature when these taxa are found in the fossil record.

Male hosts drive infracommunity structure of ectoparasites

We studied the co-occurrence of flea species in infracommunities of 16 rodents from four regions (South Africa, Tanzania, central Europe and western Siberia) using null models, and predicted that flea co-occurrences will be expressed more strongly in male than in female hosts. We examined patterns of co-occurrence (measured as the C score) in infracommunities of fleas that are parasitic on male and female hosts by comparing co-occurrence frequencies with those expected by chance. When a significant degree of nonrandomness in flea co-occurrences was detected, it indicated aggregative infracommunity structure. In Tanzanian rodents, no significant flea co-occurrences were detected in either male or female hosts. In a South African rodent, significant flea co-occurrences were not detected in males, but were found in females in some localities. In Palaearctic rodents, significant nonrandomness was detected either equally for males and females or more frequently in males than in females. Meta-analyses demonstrated that the frequency of the detection of nonrandomness in flea co-occurrences was significantly higher in male than in female hosts. The values of the standardized effect size (SES) for the C score differed significantly among host species, but not between host genders. When the Palaearctic hosts were analyzed separately, the effects of both host gender and species appeared to be significant, with the SES values for the C score in males being smaller than those in females. The strength of the gender difference in the manifestation of flea community structure increased with increasing gender difference in flea species richness, and with decreasing gender difference in flea prevalence for the Palaearctic hosts. We conclude that male hosts are the main drivers of flea infracommunity structure. However, the manifestation of gender bias in flea community structure varies among host species, and is likely determined by the pattern of species-specific spatial behavior.

Spatial variation in gender-biased parasitism: host-related, parasite-related and environment-related effects

The gender-biased pattern of parasite infestation has been shown to be a complicated phenomenon that cannot be explained by a single mechanism but rather involves several different mechanisms. We asked what are the factors that affect the manifestation and extent of gender-biased parasitism and studied the relationship between parasite-related (mean abundance, mean species richness and total species richness of all parasites), host-related (rodent density and proportion of reproductive males and females both separately and together) and environment-related (mean daily maximal and minimal temperatures, rainfall and relative humidity) factors and the magnitude of gender-biased infestation of a South African rodent Rhabdomys pumilio by ixodid ticks, gamasid mites, lice and fleas. We found that spatial variation in gender differences in parasite infestation was affected by parasite-, host- and environment-related factors, although the set of factors affecting gender differences in infestation differed among higher taxa of ectoparasites. Gender differences in infestation by fleas and lice were affected mainly by parasite-related factors, whereas gender differences in infestation by ticks and, in part, by mites were affected mainly by host-related and environmental factors. In addition, spatial variation in most measures of gender difference in mite infestation remained unexplained.

Parasite-specific variation and the extent of male-biased parasitism; an example with a South African rodent and ectoparasitic arthropods

We asked whether the occurrence and the extent of host gender-biased parasitism vary among higher parasite taxa, among individual species within these taxa and within parasite species among localities. To answer this question, we studied prevalence, abundance, species richness and the level of aggregation of ectoparasites (ticks, mites, lice and fleas) collected from male and female striped mice (Rhabdomys pumilio) in 9 localities of the Western Cape Province of South Africa. We used meta-analyses to compare parasitological variables between male and female hosts across localities for individual parasite species and higher taxa as well as across parasite species within a higher taxon. Whenever gender-biased parasitism was found, it indicated higher infestation of male than female hosts (except 1 low abundant mite species). We found that the occurrence and extent of gender-biased infestation varied mainly within a parasite species among localities and among parasite species within a higher taxon but not among parasite taxa. Our results suggest that the extent of a gender-biased pattern of parasite infestation of the same host may not only involve host-related mechanisms but also depends on biological features of a particular parasite species.

Searching for generality in the patterns of parasite abundance and distribution: Ectoparasites of a South African rodent, Rhabdomys pumilio

We studied abundance and distribution of seven ectoparasite species (fleas Chiastopsylla rossi and Dynopsyllus ellobius, a louse Polyplax arvicanthis, mites Androlaelaps fahrenholzi and Laelaps giganteus and two ticks Haemaphysalis elliptica and Hyalomma truncatum) exploiting the same populations of the rodent host Rhabdomys pumilio in South Africa. We considered three general patterns of abundance and distribution, namely (i) aggregated distribution of parasites amongst individual hosts; (ii) positive relationships between mean parasite abundance and their prevalence; and (iii) applicability of a simple epidemiological model based on mean parasite abundance and its variance to predict the observed patterns of prevalence. Our aims were to evaluate the relative role of host- versus parasite-associated factors by looking at similarity amongst different parasites in these patterns. In general, all parasites demonstrated strong similarity in each of the three patterns of abundance and distribution. However, the strength of these patterns differed amongst parasite species. We conclude that these patterns are driven mainly by hosts, but differences are caused by differences between various life-history traits of parasite species. Our results support the idea that general laws apply to parasite population ecology.

Genetic structure and dispersal in a small South African rodent. Is dispersal female-biased?

Dispersal greatly determines genetic structure of populations, although it is influenced by landscape heterogeneity, quality of the matrix, resource distribution and local population densities and dynamics. To get insights into some of those processes we analysed the genetic structure of the hairy-footed gerbil Gerbillurus paeba (Rodentia, Murinae, Gerbillinae) in the southern Kalahari (South Africa). Samples were taken from 20 populations covering an area of about 2200 km 2. Genetic data were related to landscape characters and population dynamics. We used newly developed microsatellites and found at all loci some indication for the presence of null alleles. However, null alleles seem to have little influence on the general results of our analyses. Altogether we found even nearby populations of G. paeba to be significantly differentiated, although assignment tests revealed 24% of individuals as immigrants. Genetic structure was independent of landscape heterogeneities at all spatial scales. Autocorrelation analyses (range 50–90 km) revealed significant genetic structure within populations on distances <3 km. We found some indication for female-biased dispersal. Our study suggests that dispersing individuals have little influence on the long-term genetic structure and that drift is the major cause of genetic diversity. The observed genetic pattern likely derives from strong population fluctuations of G. paeba. The landscape structure has little influence on the genetic differentiation between populations.

Diversity of bartonellae associated with small mammals inhabiting Free State province, South Africa

The prevalence and diversity of bartonellae infecting the blood of 10 small mammal species inhabiting nine Nature Reserves of the Free State province, South Africa, was assessed using phenotypic, genotypic and phylogenetic methods. Of 86 small mammals sampled, 38 animals belonging to five different species yielded putative bartonellae. Thirty-two isolates were confirmed as bartonellae and were characterized by comparison of partial citrate synthase gene (gltA) sequences. Phylogenetic reconstructions derived from alignment of these sequences with those available for other bartonellae indicated that the South African rodent-associated isolates formed two distinct clades within the radius of the genus Bartonella. One of these clades also included recognized Bartonella species associated with rodents native to Eurasia but not to the New World, whereas the second clade contained exclusively isolates associated with South African rodents. Comparison of gltA sequences delineated the isolates into a number of ecologically distinct populations and provided an indication that a combination of phylogenetics and the identification of sequence clusters in housekeeping protein-encoding genes could be developed as a key criterion in the classification of bartonellae. This study is the first to investigate wildlife-associated bartonellae in Africa, adding support to their ubiquity and broad diversity and to the paradigm that the phylogenetic positions of the Bartonella species encountered today have been influenced by the geographical distribution of their hosts.