Biochemical genetic markers to identify two morphologically similar South African Mastomys species (Rodentia: Muridae)

The two common southern African mice species (Mastomys coucha and M. natalensis) are morphologically almost identical, making field identification impossible at present. Specimens from two localities were collected and tissue and blood samples taken. The habitat type of each locality was studied, and a distribution map compiled. A definite correlation between biome-type and species range was found to be present. Three isozyme markers were identified: glucose phosphate isomerase in liver, and two general (non-specific) protein coding loci in muscle. In addition, we also identified species characteristic haemoglobin components in both species. This is the first study to report genetic variation within, and differentiation between these species. Our results are of medical importance because Mastomys coucha carries bubonic plague and M. natalensis carries Lassa Fever.     

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

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

Host habitat patchiness and the distance decay of similarity among gastro-intestinal nematode communities in two species of <Emphasis Type="Italic">Mastomys</Emphasis> (southeastern Senegal)

Beta-diversity, or how species composition changes with geographical distance, has seldom been studied for different habitats. We present here quantitative estimates of the relationship between geographic distance and similarity of parasitic nematode communities in two closely related rodent host species that live in habitats with very different spatial configurations. In southeastern Senegal Mastomys natalensis lives exclusively inside human villages whereas M. erythroleucus is continuously distributed outside villages. Both host species and their gastro-intestinal nematodes were sampled on the same spatial scale. Beta-diversity was found to be higher in parasite communities of M. erythroleucus than in those of M. natalensis, and significantly related to geographic distance in this first species. Even on the local spatial scale studied, host dispersal limitation, and stochastic events, may affect species turnover in nematode communities of M. erythroleucus. In M. natalensis, no relationship was found between geographic distance and nematode community similarity, however, suggesting low host dispersal rates between habitat patches. Together with previous population genetic results, this study illustrates the need for different approaches with regard to dispersal in natural populations and its effect on biodiversity.     

Hierarchical analysis of population genetic structure in the monogynous ant Cataglyphis cursor using microsatellite and mitochondrial DNA markers

Despite having winged queens, female dispersal in the monogynous ant Cataglyphis cursor is likely to be restricted because colonies reproduce by fission. We investigated the pattern of population genetic structure of this species using eight microsatellite markers and a mitochondrial DNA (mtDNA) sequence, in order to examine the extent of female and nuclear gene flow in two types of habitat. Sampling was carried out at a large spatial scale (16 sites from 2.5 to 120 km apart) as well as at a fine spatial scale (two 4.5-km transects, one in each habitat type). The strong spatial clustering of mtDNA observed at the fine spatial scale strongly supported a restricted effective female dispersal. In agreement, patterns of the mtDNA haplotypes observed at large and fine spatial scales suggested that new sites are colonized by nearby sites. Isolation by distance and significant nuclear genetic structure have been detected at all the spatial scales investigated. The level of local genetic differentiation for mitochondrial marker was 15 times higher than for the nuclear markers, suggesting differences in dispersal pattern between the two sexes. However, male gene flow was not sufficient to prevent significant nuclear genetic differentiation even at short distances (500 m). Isolation-by-distance patterns differed between the two habitat types, with a linear decrease of genetic similarities with distance observed only in the more continuous of the two habitats. Finally, despite these low dispersal capacities and the potential use of parthenogenesis to produce new queens, no signs of reduction of nuclear genetic diversity was detected in C. cursor populations.     

The influence of life history and climate driven diversification on the mtDNA phylogeographic structures of two southern African Mastomys species (Rodentia: Muridae: Murinae)

The phylogeographic patterns of small mammals in southern Africa are frequently disjunct. This pattern is predominately attributed to vicariant geographical barriers coupled to climate driven diversification. To gain further insights into this hypothesis, we embarked on a comparative mtDNA phylogeographic study of two common rodent species in southern Africa, Mastomys natalensis and Mastomys coucha. Parsimony haplotype networks and SplitsTrees of mtDNA cytochrome oxidase I data showed a large degree of haplotype sharing throughout the sampling range. Within southern Africa, we found no conclusive evidence to support geographic vicariance as a contributing factor towards Mastomys speciation. We proposed that the regional phylogeographic structures detected for M. natalensis and M. coucha are the result of weak isolation by distance coupled to repeated expansions and contractions of suitable habitat. Both species probably survived in multiple refugia during unfavourable periods and mismatch distributions show signs of population expansion. Mitochondrial DNA nucleotide diversity values (π) show marked differences between the two species (M. natalensis: 0.003 and M. coucha: 0.468), and M. coucha also shows a higher level of population differentiation in AMOVA analyses. These differences are most likely due to life history discrepancies between the two species. Mastomys coucha is regarded to be more of a habitat specialist when compared to M. natalensis, and this probably places a higher constraint on M. coucha dispersal abilities. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 58–68.     

Species diversity and population density affect genetic structure and gene dispersal in a subtropical understory shrub

Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions, population histories or abiotic conditions. Because gene dispersal is spatially restricted, it will eventually result in the development of spatial genetic structure (SGS), which in turn can allow insights into gene dispersal processes. Here, we assessed the effect of habitat characteristics like population density and community structure on small-scale SGS and estimate historical gene dispersal at different spatial scales.Methods In a set of 12 populations of the subtropical understory shrub Ardisia crenata, we assessed genetic variation at 7 microsatellite loci within and among populations. We investigated small-scale genetic structure with spatial genetic autocorrelation statistics and heterogeneity tests and estimated gene dispersal distances based on population differentiation and on within-population SGS. SGS was related to habitat characteristics by multiple regression.Important findings The populations showed high genetic diversity (H e = 0.64) within populations and rather strong genetic differentiation (F ′ ST = 0.208) among populations, following an isolation-by-distance pattern, which suggests that populations are in gene flow–drift equilibrium. Significant SGS was present within populations (mean Sp = 0.027). Population density and species diversity had a joint effect on SGS with low population density and high species diversity leading to stronger small-scale SGS. Estimates of historical gene dispersal from between-population differentiation and from within-population SGS resulted in similar values between 4.8 and 22.9 m. The results indicate that local-ranged pollen dispersal and inefficient long-distance seed dispersal, both affected by population density and species diversity, contributed to the genetic population structure of the species. We suggest that SGS in shrubs is more similar to that of herbs than to trees and that in communities with high species diversity gene flow is more restricted than at low species diversity. This may represent a process that retards the development of a positive species diversity–genetic diversity relationship.     

Polymorphism and polytypy for pericentric inversions in 38-chromosome Mastomys (Rodentia, Murinae) and possible taxonomic implications.

Chromosome banding analysis (R- and C-bands) of two 38-chromosome Mastomys specimens originating from the Ivory Coast and Uganda revealed different numbers of autosome arms (NFa), equal to 51 and 60, respectively. Comparison of their chromosome banding patterns with those of Mastomys specimens from the Sudan (NFa = 41) and Senegal (NFa = 51-54), studied previously, showed that variation of the NFa from 40 to 60 throughout the species distribution is the result of a pericentric inversion polymorphism involving 3-12 chromosome pairs. At the population level, this variation is much narrower and never results from more than two chromosome pairs involved in inversion polymorphism. Taking into account that the NFa values recorded to date form a well-defined discontinuous row, we presume that introgressive hybridization between populations differing from each other by 3-5 to 11-12 pericentric inversions is interrupted. From there, the hypothesis of the existence of at least three cryptic species (designated provisionally as MER-1, MER-2, and MER-3) within 38-chromosome Mastomys populations previously assigned to M. erythroleucus can be made. It looks likely that one of them, possessing a karyotype with an NFa = 50-56, is widely distributed throughout sub-Saharan Africa and includes karyotyped populations from Senegal, the Ivory Coast, Mali, Benin, Cameroon, Zaire, and the Sudan. The second species (MER-2) includes the specimens karyotyped (NFa = 40-41) from Chad and the Sudan. Finally, a third tentative species (MER-3) corresponds to specimens with NFa = 59-60 found in East Zaire and Uganda, as well as possibly Mali and Chad.     

Distribution of sibling species of the Praomys (Mastomys) natalensis group in Rhodesia (Mammalia: Rodentia)

The taxon Praomys ( Mastomys ) natalensis, the multimammate mouse, comprises at least two biological species in Rhodesia. Species-specific haemoglobin phenotypes which were previously documented for sympatric populations near Salisbury are shown to apply throughout Rhodesia. Several areas of sympatry were revealed which encompassed various habitats. No hybrids for diploid number or haemoglobin phenotype were found.     

Description of a new species of Heligmonina Baylis, 1928 (Nematoda: Heligmonellidae) a parasite of Mastomys natalensis (Rodentia: Muridae) from Swaziland and new data on the synlophe of Heligmonina chabaudi (Desset, 1966)

A new species of heligmosomoid nematode belonging to the subfamily Nippostrongylinae Durette-Desset, 1970 is described: Heligmonina wakelini n. sp., a parasite from the small intestine of the commensal rodent Mastomys natalensis (Smith, 1834) from Swaziland. It differs from the most closely related species H. boomkeri Durette-Desset & Digiani, 2005 by the number of the cuticular ridges in the female synlophe (10 vs 12), the width of the left ala, larger than the body diameter in the male, and the inclination of the axis of orientation of the ridges in both sexes (53 degrees vs 70 degrees). New morphological data (head and synlophe) on Heligmonina chabaudi (Desset, 1964), also a parasite of Mastomys natalensis in the Republic of Congo, are provided in order to compare with the new species.     

Effects of predation and dispersal on Mastomys natalensis population dynamics in Tanzanian maize fields

1. We investigate the effects of different levels of predation pressure and rodent dispersal on the population dynamics of the African pest rodent Mastomys natalensis in maize fields in Tanzania. 2. Three levels of predation risk were used in an experimental set-up: natural level (control), excluding predators by nets and attracting avian predators by nest boxes and perch poles. Because dispersal of the rodents could mask the predation pressure treatment effects, control and predator exclusion treatments were repeated with enclosed rodent populations. 3. Population growth during the annual population rise period was faster in the absence of predators and peak population size was higher, but otherwise dynamics patterns were similar for populations where predators had access or were attracted, indicating that compensatory mechanisms operate when rodents are exposed to high levels of predation risk. Reducing dispersal of rodents removed the effect of predation on population growth and peak size, suggesting that local predators may play a role in driving rodent dispersal, but have otherwise little direct effect on population dynamics.     

Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation

Different shapes of landscape boundaries can affect the habitat networks within them and consequently the spatial genetic-patterns of a metapopulation. In this study, we used a mechanistic framework to evaluate the effects of landscape shape, through watershed elongation, on genetic divergence among populations at the metapopulation scale. Empirical genetic data from four, sympatric stream-macroinvertebrates having aerial adults were collected from streams in Japan to determine the roles of species-specific dispersal strategies on metapopulation genetics. Simulation results indicated that watershed elongation allows the formation of river networks with fewer branches and larger topographic constraints. This results in decreased interpopulation connectivity but a lower level of spatial isolation of distal populations (e.g. those found in headwaters) occurring in the landscapes examined. Distal populations had higher genetic divergence when their downstream-biased dispersal (relative to upstream- and/or overland-biased dispersal) was high. This underscores the importance of distal populations influencing genetic divergence at the metapopulation scale for species having downstream-biased dispersal. In turn, lower genetic divergence was observed under watershed elongation when the genetic isolation of distal populations was decreased in such species. This strong association between landscape shape and evolutionary processes highlights the importance of natural, spatial architecture in assessing the effectiveness of conservation and management strategies.     

Genetic differentiation among populations of an oceanic island: The case of Metrosideros boninensis, an endangered endemic tree species in the Bonin Islands

Conservation of endemic species on oceanic islands is an essential issue for biodiversity conservation. Metrosideros boninensis (Myrtaceae) is an endangered tree species endemic to the Bonin Islands of the western North Pacific Ocean. This species is considered to be extremely rare with less than 400 adult individuals, a number that has fluctuated between the 1880s and 1980s through human influence. We analyzed the genetic diversity and genetic structure of this species using amplified fragment length polymorphism markers and microsatellite markers. Genetic diversity of M. boninensis was extremely low compared to related taxa and similar endemic species from small islands. This low genetic diversity might be attributed to a stepwise colonization process with repeated founder bottlenecks in the dispersal pathway to the Bonin Islands. Populations of M. boninensis showed significant genetic differentiation and isolation by distance over a small geographical scale, despite the fact that this species should have extensive gene dispersal ability. This genetic differentiation might be caused by limited gene flow via pollen and seed among populations and genetic drift amid a small number of remnant individuals. Taken together, these findings suggest that the genetic diversity and connectivity of tree populations on islands are more vulnerable to habitat fragmentation than previously thought. We offer some recommendations for management to ameliorate habitat fragmentation and biological invasion.     

The distribution, identification, and naming of the Mastomys natalensis species complex in southern Africa (Rodentia: Muridae)

Three hundred and forty seven rats belonging to the Mastomys natalensis complex (Smith, 1834) were live trapped from 60 localities in southern Africa. They were identified as species A, or B using either or both diploid chromosome number and haemoglobin electromorphs. These, and previously published data are presented to give a distribution of the species in southern Africa. It is suggested that workers may safely use the haemoglobin marker for identification purposes in this region as opposed to the more difficult chromosome marker. We suggest that species A can be referred to M. natalensis (Smith, 1834), and species B to M. coucha (Smith, 1836). We consider the two other oldest synonyms, M. caffer (Smith, 1834), and M. marikquensis (Smith, 1836).     

Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans

Outcomes of host-pathogen coevolution are influenced by migration rates of the interacting species. Reduced gene flow with increasing spatial distance between populations leads to spatial genetic structure, as predicted by the isolation by distance (IBD) model. In wind-dispersed plant-pathogenic fungi, a significant spatial genetic structure is theoretically expected if local spore dispersal is more frequent than long-distance dispersal, but this remains to be documented by empirical data. For 29 populations of the oilseed rape fungus Leptosphaeria maculans sampled from two French regions, genetic structure was determined using eight minisatellite markers. Gene diversity (H = 0.62-0.70) and haplotypic richness (R = 0.96-1) were high in all populations. No linkage disequilibrium was detected between loci, suggesting the prevalence of panmictic sexual reproduction. Analysis of molecular variance showed that > 97% of genetic diversity was observed within populations. Genetic differentiation was low among populations (F(st) < 0.05). Although direct methods previously revealed short-distance dispersal for L. maculans, our findings of no correlation between genetic and geographic distances among populations illustrate that the IBD model does not account for dispersal of the fungus at the spatial scale we examined. These results indicate high gene flow among French populations of L. maculans, suggesting high dispersal rates and/or large effective population sizes, two characteristics giving the pathogen high evolutionary potential against the deployment of resistant oilseed rape cultivars.     

Genie differentiation in M. m. domesticus populations from Europe, the Middle East and North Africa: geographic patterns and colonization events

Geographic patterns of genie differentiation were investigated in the commensal house mouse subspecies, M. m. domesticus . The analysis by protein electrophoresis of 40 populations throughout Europe, the Middle East and North Africa indicated that genie differentiation was not highly structured on a macrogeographic scale. Mean genie distances between regions showed, however, that populations fell into three levels of differentiation: a low level in southern Europe within which interregional distances were no larger than intraregional ones, an intermediate level between southern European populations and North European and African ones, and finally, a higher level between all the latter and the Middle Eastern populations.
Gene flow estimates indicated that the homogeneity of southern European populations does not result from present high levels of gene flow, but more likely from a very recent ancestry. These data when argumented with the fossil records of mice from the Mediterranean Basin suggest a two-step colonization process, the most recent of which occurred very rapidly and resulted in the multiple founding of populations in southern Europe. The relationship of M. m. domesticus to other subspecies of mice is discussed in relation to introgression and taxonomy.
Microdifferentiation patterns with low levels of within population substructuring and of gene flow suggest that genie differentiation in the western European house mouse is largely determined by genetic drift and/or founder effects. Although historical factors are determinant in the large scale patterns of genie variation in commensal house mice, dispersal by man no longer seems to be a prominent feature moulding the genetic structure of M. m. domesticus .     

The potential role of rodents in the enzootic cycle of Rift Valley fever virus in Senegal

Wild rodents (214) of fourteen species were trapped at seven sites in Senegal. Arvicanthis niloticus and Mastomys erythroleucus were among the most frequently collected species (77.2% of total capture). All rodents were examined for the presence of anti-Rift Valley fever virus (RVFV) antibody; the prevalence over all sampled species was 3.8%, varying widely with respect to species and location. Four of 14 species of rodents were found to have anti-RVFV antibodies: Rattus rattus (one positive of two tested) Mastomys huberti (13.5%), A. niloticus (4.3%), and M. erthroleucus (2.4%). The highest prevalence of anti-RVFV antibody was recorded within the enzootic area of the Senegal River delta, at Richard Toll (9.6%). A. niloticus and M. erythroleucus and a strain of laboratory-bred mice were experimentally inoculated with two strains of RVFV and examined for viremia, illness, seroconversion and mortality. A. niloticus and M. erythroleucus demonstrated a limited resistance to infection, thus potentially allowing for the replication of virus in these animals and making these species possible candidates as hosts in the maintenance cycle of RVFV in nature.     

Spatial genetic structuring in a vagile species, the European wood mouse

We examined the genetic structure of natural populations of the European wood mouse Apodemus sylvaticus at the microgeographic (<3 km) and macrogeographic (>30 km) scales. Ecological and behavioural studies indicate that this species exhibits considerable dispersal relative to its home-range size. Thus, there is potential for high gene flow over larger geographic areas. As levels of population genetic structure are related to gene flow, we hypothesized that population genetic structuring at the microgeographic level should be negligible, increasing only with geographic distance. To test this, four sites were sampled within a microgeographic scale with two additional samples at the macrogeographic level. Individuals ( n =415) were screened and analysed for seven polymorphic microsatellite loci. Contrary to our hypothesis, significant levels of population structuring were detected at both scales. Comparing genetic differentiation with geographic distance suggests increasing genetic isolation with distance. However, this distance effect was non-significant being confounded by surprisingly high levels of differentiation among microgeographic samples. We attribute this pattern of genetic differentiation to the effect of habitat fragmentation, splitting large populations into components with small effective population sizes resulting in enhanced genetic drift. Our results indicate that it is incorrect to assume genetic homogeneity among populations even where there is no evidence of physical barriers and dispersal can occur freely. In the case of A. sylvaticus , it is not clear whether dispersal does not occur across habitat barriers or behavioural dispersal occurs without consequent gene flow.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Gene flow between populations of two invertebrates in springs

1. Using allozymes, we analysed genetic structure of the freshwater gastropod Bythinella dunkeri and the freshwater flatworm Crenobia alpina. The two species are habitat specialists, living almost exclusively in springs. The sampled area in Hesse (Germany) covers a spatial scale of 20 km and includes two river drainages. From the biology of the two species we expected little dispersal along rivers. However, the possibility exists that groundwater provide suitable pathways for dispersal. 2. In B. dunkeri heterozygosity decreased from west to east. For some alleles we found clines in this geographic direction. These clines generated a positive correlation between geographic distance and genetic differentiation. Furthermore patterns of genetic variation within populations suggested that populations may have been faced with bottlenecks and founder effects. If populations are not in population genetic equilibrium, such founder effects would also explain the rather high amount of genetic differentiation between populations (10%). 3. For C. alpina the mean number of alleles decreased with increasing isolation of populations. Genetic differentiation between populations contributed 19% to the total genetic variation. Genetic differentiation was not correlated to geographic distance, but compared with B. dunkeri variability of pairwise differentiation between pairs of populations was higher in C. alpina. 4. Overall B. dunkeri appears to be a fairly good disperser, which may use groundwater as dispersal pathway. Furthermore populations seem to be not in equilibrium. In contrast C. alpina forms rather isolated populations with little dispersal between springs and groundwater seems to play no important role for dispersal.     

A mitochondrial phylogeographic scenario for the most widespread African rodent,Mastomys natalensis

In order to evaluate the contribution of geological, environmental, and climatic changes to the spatial distribution of genetic variation of Mastomys natalensis, we analysed cytochrome b sequences from the whole distribution area of the species to infer its phylogeographic structure and historical demography. Six well‐supported phylogroups, differentiated during the Pleistocene, were evidenced. No significant correlation between genetic and geographic distances was found at the continental scale, and the geographic distributions of the observed phylogroups have resulted from extensive periods of isolation caused by the presence of putative geographic and ecological barriers. The diversification events were probably influenced by habitat contraction/expansion cycles that may have complemented topographic barriers to induce genetic drift and lineage sorting. According to our results, we propose a scenario where climate‐driven processes may have played a primary role in the differentiation among phylogroups. © 2013 The Linnean Society of London