Exotic species have had devastating impacts worldwide and are a major threat to native wildlife. Human commensal species (hereafter commensals) are a special class of exotic species that live largely off the resources associated with human activity. The encroachment of commensals from an urban area into surrounding bushland has been frequently overlooked as an important component of urban impacts, even though human-commensals are common to many urban regions globally. In this review, we present theoretical and empirical evidence for the processes and outcomes occurring when exotic commensal species encroach into native bushland. Specifically we ask when, how and why exotic commensal species encroach into bushland, what determines whether they establish, and what are the ecological consequences. We focus on the black rat, Rattus rattus, arguably the archetypal commensal species with a cosmopolitan distribution and the greatest potential for ecological damage of all the commensal rodents. We expect that the processes that we outline apply to other commensal species more broadly. We argue that commensals are in fact natives of the urban milieu and only become alien when they encroach into peri-urban bushland. We propose that the mechanisms of this encroachment will be different from those of other, non-commensal exotic species because urban areas act as dispersal hubs to overcome many of the barriers of invasion that other exotic species face. We suggest that resource supplementation by urban areas creates a great potential for promoting encroachment, invasion as well as impact. However, biotic and abiotic barriers to invasion are still relevant for commensals, highlighting the need to maintain the integrity of ecosystems and wildlife populations in urban edges so as to prevent commensal incursion. We examine how commensal black rats affect wildlife via three fundamental mechanisms, namely, predation, disease transfer and competition for resources, and also consider their possible positive impacts acting as functional replacements for lost natives. We conclude the review with an outline of research priorities and future directions that are essential for progressing our understanding of the ecology of commensal species.

This review aims to synthesise knowledge regarding the taxonomy of South-east Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specialisations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analysed the prevalence of major rodent-borne diseases in South-east Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rain-fed and irrigated landscapes, generally in and around rice fields.

In this review we summarise published knowledge regarding small mammal population recovery following sudden population collapse, regardless as to whether the collapse is caused by natural or man-made events. We determine recovery mechanisms, recovery time and recovery rate, and suggest how to adapt and optimise current methods to regulate small mammal population size, for pest management and/or conservation. It is vital that the principles underlying the recovery mechanisms are known for both pest control and conservation to align management methods to either maintain animal numbers at a permanent minimum level or increase population size. Collapses can be caused naturally, as in the declining phase of multi-annual fluctuations and after natural disasters, or by man-made events, such as pesticide application. In general, there are three ways population recovery can occur: (1) in situ survival and multiplication of a small remaining fraction of the population; (2) immigration; or (3) a combination of the two. The recovery mechanism strongly depends on life history strategy, social behaviour and density-dependent processes in population dynamics of the species in question. In addition, the kind of disturbance, its intensity and spatial scale, as well as environmental circumstances (e.g. the presence and distance of refuge areas) have to be taken into account. Recovery time can vary from a couple of days to several years depending on the reproductive potential of the species and the type of disturbances, regardless of whether the collapse is man made or natural. Ultimately, most populations rebound to levels equal to numbers before the collapse. Based on current knowledge, case-by-case decisions seem appropriate for small-scale conservation. For pest control, a large-scale approach seems necessary. Further investigations are required to make sound, species-specific recommendations.

Context . Protection of natural ecosystems undoubtedly safeguards ecological communities, with positive benefits for ecosystem processes and function. However, ecosystems are under threat from anthropogenic stressors that reduce the resilience both of component species and the system as a whole.

Aims . To determine how anthropogenic stressors (land use and climate change) could impact the diversity and resilience of a small mammal community in the greater Serengeti ecosystem, an East African savanna comprising Serengeti National Park (SNP) and adjacent agro-ecosystems, at local (SNP) and Africa-wide geographic scales.

Methods . We recorded small mammal species in 10 habitats in the greater Serengeti ecosystem, including the agro-ecosystem, over 48 years (1962–2010). We calculated richness and diversity for each habitat type, and used an index of similarity to quantify differences in the community among habitats. Species accumulation curves were also generated for each habitat type.

Key results . We recorded 40 species of small mammals in the greater Serengeti ecosystem. At the local scale, restricted habitat types in SNP (each <1% of the total area) made a disproportionately large contribution to diversity. Agro-ecosystems had lower richness and were less likely to contain specialist species. At regional and Africa-wide scales, local endemics were less likely to be recorded in the agro-ecosystem (57% species loss) compared with those with regional (33% loss) or Africa-wide (31%) geographic distributions.

Conclusions . At the local scale, the variety of habitats in SNP contributed to overall diversity. However, the ability to maintain this diversity in the adjacent agro-ecosystem was compromised for localised endemics compared with species with Africa-wide ranges. Land use intensification adjacent to SNP and projected changes in rainfall patterns for East Africa under global climate scenarios may compromise the future resilience of the small mammal community in this tropical savanna ecosystem.

Implications . The loss of rare or specialised species from protected areas and human-modified ecosystems could be mitigated by: (1) increasing habitat complexity and maintaining specialist habitats in the agro-ecosystem; and (2) creating buffers at the boundary of protected natural ecosystems that accommodate regime shifts in response to climatic change. These measures would increase the resilience of this coupled human–natural savanna ecosystem.

Context. Post-harvest losses by rodents have traditionally been calculated by estimates of consumption determined in the laboratory. Methods for assessing storage losses by rodents under smallholder conditions will help farmers and policy makers understand the impact rodents may have on food security, nutrition and health. Stored product loss assessment methods could also be used to monitor the effects of rodent control in villages.

Aims. The present study examined a method to measure the amount of rice eaten by rodents in household granaries. The effects of trapping and better hygiene around granaries to reduce rodent populations were investigated using the post-harvest monitoring method to determine whether the program was successful in lowering rodent numbers sufficiently to reduce post-harvest losses.

Methods. Baskets with known quantities of rice were placed within household granaries and monitored periodically for moisture content, weight loss, faecal contamination and percentage of rodent-damaged grains. Using an empirical treatment–control study, rodent management was performed at the community level through daily trapping in two Bangladesh villages and in Myanmar at the granary storehouse level. Post-harvest losses were monitored in granaries in villages with rodent management and in similar granaries in villages where there was no management.

Key results. Estimates of household losses in the absence of rodent control were 2.5% in Bangladesh and 17% in Myanmar. These losses were reduced when rodent control was implemented, down to 0.5% in Bangladesh and 5% in Myanmar.

Conclusions. The impact of rodents on smallholder storage can be accurately assessed in the field under realistic conditions. Intensive daily trapping at the community level together with improved hygiene practices can successfully reduce rodent numbers, and this can significantly reduce stored grain losses and rodent contamination and damage levels.

Implications. In addition to the threat of rodent pests during crop production, rodents are a major threat to food security after harvest and have, as of yet, unquantified impacts on household nutrition and health through potential transmission of gastroenteric diseases and zoonoses to householders and domestic livestock. Trapping and environmental management are affordable and effective tools to reduce rodent impacts on stored grain within communities and are viable alternatives to rodenticides.

Context. Toe clipping is a widely used method for permanent marking of small mammals, but its effects are not well known, despite the ethical and scientific implications. Most studies do not find any clear effects, but there is some indication that toe clipping can affect survival in specific cases. Although effects on survival are arguably the most important, more subtle effects are also plausible, yet very few studies have included body condition and none has investigated effects on mobility.

Aims. We analysed the effects of toe clipping on free-living Mastomys natalensis, a common, morphologically and behaviourally intermediate small rodent.

Methods. Using a 17-year capture–mark–recapture dataset, we compared movement, body weight and survival between newly and previously clipped animals, and tested whether any of these parameters correlated with the number of clipped toes.

Key results. No evidence for a correlation between total number of clips and any of the variables was found. Newly clipped animals had a slightly smaller weight change and larger travel distance than did those that were already clipped, and we show that this is most likely due to stress caused by being captured, clipped and handled for the first time rather than to the actual clipping.

Conclusions. The combination of trapping, handling and marking has a detectable effect on multimammate mice; however, there is no evidence for a clear effect of toe clipping.

Implications. Our study suggests a re-evaluation of ethical guidelines on small-mammal experiments, so as to reach a rational, fact-based decision on which marking method to use.

Context . Mutualistic interactions between animals and plants shape the structure of plant–animal systems and, subsequently, affect plant-community structure and regeneration.

Aims . To assess the effects of plant and rodent functional traits on the formation of mutualistic and predatory interactions regarding seed dispersal and predation in a warm-temperate forest.

Methods . Seed scatter-hoarding and predation by six sympatric rodent species on seeds belonging to five sympatric tree species were tested under enclosure conditions.

Key results . Functional traits (i.e. rodent body size and seed traits) are important to mutualism/predation in this seed–rodent system. The rodent–seed network is highly nested: large-sized rodents have mutualistic or predatory interactions with both large- and small-sized seed species, but small-sized rodents interacted with small-sized seed species only. Large seeds or seeds with hard coats enhanced mutualism and reduced predation.

Conclusion . Body size of rodents and seed traits such as handling time and nutritional value are key factors in the formation of mutualistic and predatory interactions within seed–rodent systems.

Implications . To promote seedling establishment in degenerated forests, introducing or protecting large-sized scatter hoarders and reducing the density of pure seed eaters are needed.

Context. Reproduction and survival are two of the most important demographic factors that play a major role in changing population abundances of pest species over time and space, solid understanding of which is a useful input to forecast future population changes for proactive management.

Aims. We investigated the effects of rainfall, crop-development stage and density of stone bunds on reproductive patterns, and the effects of stone-bund density and sex on survival probabilities of two widespread rodent species (Mastomys awashensis and Arvicanthis dembeensis) in Ethiopian highlands.

Methods. Rodent population dynamics were monitored from April 2007 to February 2011, using capture–mark–recapture (CMR) technique in four 60 × 60 m permanent square grids for four consecutive cropping seasons. Two of the grids represented fields with low stone-bund density (LSBD, ∼15 m apart) and the other two represented fields with high stone-bund density (HSBD, ∼10 m apart).

Key results. Reproduction was seasonal, commencing during the wet season following the rain and continuing through the early dry season. We found an increase in the abundance of reproductively active female individuals of both species towards the milky and fruiting crop stages and around harvest period. We found no strong difference in survival probability between the two rodent species with variation in stone-bund density and sex.

Conclusions. Stone bunds play a minor role in the reproduction and survival of the rodent species at the observed abundances.

Implications. In terms of pest management, the high local survival rates estimated for both rodent species matter more than survival differences owing to variations in stone-bund density and sex.

Context. Rattus tanezumi (the Asian house rat) is the principal rodent pest of rice and coconut crops in the Philippines. Little is known about the population and breeding ecology of R. tanezumi in complex agroecosystems; thus, current methods of rodent control may be inappropriate or poorly implemented.

Aims. To investigate the habitat use, population dynamics and breeding biology of R. tanezumi in complex lowland agroecosystems of the Sierra Madre Biodiversity Corridor, Luzon, and to develop ecologically based rodent management (EBRM) strategies that will target specific habitats at specific times to improve cost-efficiency and minimise non-target risks.

Methods. An 18-month trapping study was conducted in rice monoculture, rice adjacent to coconut, coconut groves, coconut-based agroforest and forest habitats. Trapped animals were measured, marked and assessed for breeding condition.

Key results. Five species of rodent were captured across all habitats with R. tanezumi the major pest species in both the rice and coconut crops. The stage of the rice crop was a major factor influencing the habitat use and breeding biology of R. tanezumi. In rice fields, R. tanezumi abundance was highest during the tillering to ripening stages of the rice crop and lowest during the seedling stage, whereas in coconut groves abundance was highest from the seedling to tillering stage of nearby rice crops. Peaks in breeding activity occurred from the booting stage of the rice crop until just after harvest, but >10% of females were in breeding condition at each month of the year.

Conclusions. In contrast with the practices applied by rice farmers in the study region, the most effective time for lethal management based on the breeding ecology of R. tanezumi is likely to be during the early stages of the rice crop, before the booting stage. Farmers generally apply control actions as individuals. We recommend coordinated community action. Continuous breeding throughout the year may necessitate two community campaigns per rice cropping season. To limit population growth, the most effective time to reduce nesting habitat is from the booting stage until harvest.

Implications. By adopting EBRM strategies, we expect a reduction in costs associated with rodent control, as well as improved yield and reduced risk to non-target species.

Context. The arctic ground squirrel (Urocitellus parryii) comprised 17% of the biomass of herbivores in the Yukon boreal forest during the summer months from 1987 to 1996 and was responsible for 23% of the energy flow at the herbivore level. By 2000, ground squirrel populations in this region collapsed to nearly zero and have remained there.

Aims. We summarise the population monitoring (since 1975) and recent experimental work that has been done on this key herbivore in the Kluane area of the southern Yukon to test one mechanistic hypothesis as the possible explanation for this population collapse and subsequent lack of recovery: predation.

Methods. Ground squirrels are the preferred summer prey of bird and mammal predators when snowshoe hare (Lepus americanus) populations are declining. We used translocations into formerly occupied habitat and radiotelemetry to determine movements and causes of death from 2009 to 2014. We surveyed 158 sites between 2008 and 2013 to measure the disappearance of colonies in alpine and forest habitats over 25 000 km².

Key results. Ground squirrels from 2000 to 2013 comprised a small fraction of the herbivore biomass in the boreal forest zone, down from 17% earlier. Most forest populations (∼95%) are currently extinct, whereas just over half (65%) of low-elevation meadow populations are locally extinct. One hypothesis is that ground squirrels in the forest have been driven into a predator pit from which they cannot recover. They remain abundant in alpine tundra (93% occupancy rate) and around airport runways and human habitations (97% occupancy), but there is no apparent dispersal from alpine areas down into the boreal forest.

Conclusion. The predator pit hypothesis is a likely explanation for the initial collapse and sustained decline in population size from 2000 to 2013. Recent attenuation of the hare cycle and milder winter climate have allowed shrubs to expand throughout the forest, thereby reducing visibility and increasing predation risk. This conclusion will be tested in further research using reintroductions to formerly occupied sites.

Implication. If the loss of this herbivore from the boreal forest is not reversed, predator pressure on the other major herbivores of the montane forest zone is likely to change significantly.

Bird conservation is nowadays a strong driving force for prioritising rodent eradications, but robust quantitative estimates of impacts are needed to ensure cost-effectiveness of management operations. Here, we review the published literature to investigate on what methodological basis rodent effects on island bird communities have been evaluated for the past six decades. We then discuss the advantages and limitations of each category of methods for the detection and quantification of impacts, and end with some recommendations on how to strengthen current approaches and extend our knowledge on the mechanisms of impacts. Impact studies (152 studies considered) emphasised seabirds (67%), black rats (63%) and the Pacific Ocean (57%). Among the most commonly used methods to study rodent impacts on birds were the observation of dead eggs or empty nests while monitoring bird breeding success, and the analyses of rodent diets, which can both lead to misleading conclusions if the data are not supported by direct field evidence of rodent predation. Direct observations of rodent–bird interactions (19% of studies) are still poorly considered despite their potential to reveal cryptic behaviours and shed light on the mechanisms of impacts. Rodent effects on birds were most often measured as a change or difference in bird breeding parameters (74% of studies), while estimates of bird population growth rates (4%) are lacking. Based on the outcomes of this literature review, we highlight the need for collecting unbiased population-level estimates of rodent impacts, which are essential prerequisites for predicting bird population growth scenarios and prioritising their conservation needs. This could be achieved by a more systematic integration of long-term monitoring of bird populations into rodent management operations and modelling bird population dynamics. We also strongly recommend including various complementary methods in impact assessment strategies to unravel complex interactions between rodents and birds and avoid faulty evidence. Finally, more research should be devoted to a better understanding of the cases of non-impacts (i.e. long-term coexistence) and those impacts mediated by mechanisms other than predation and ecosystem-level processes.

Context. Plague is a serious health problem in northern Tanzania, with outbreaks since 2008 in two districts located in Rift Valley. There is dearth of knowledge on diversity of small mammal and flea fauna occurring in this plague focus. Knowledge on interactions between fleas and rodent species that harbour the plague bacterium, Yersinia pestis, is important for developing strategies for control and prevention of plague.

Aims. This study aims to show how rodents and fleas are associated with each other in the plague focus.

Methods. Animals were trapped bimonthly from 2009 to 2012 in different habitats. The fur of animals was brushed to collect fleas, which were identified and quantified. Network analysis methods, randomisation and rarefaction curves were used to show how hosts and fleas are associated.

Key results. Thirteen species of rodents were associated with 26 species of fleas of which Dinopsyllus lypusus, Xenopsylla brasiliensis and X. cheopis are confirmed efficient vectors of Y. pestis. Randomisation and rarefaction curves established that Lophuromys flavopunctatus had significantly higher flea species richness (n = 9) than did all other hosts, whereas Xenopsylla cheopis and Dinopsyllus spp. showed greater host species richness than did other species of fleas. There was no significant correlation between host sex and flea abundance (χ² = 0.8, d.f. = 6, P = 0.371), but significant differences between reproductive states (adults had more fleas than did subadults) were observed, which probably reflected typical positive correlation between size and flea abundance (χ² = 4.1955, d.f. = 1, P = 0.040).

Conclusions. The plague outbreak focus in northern Tanzania has a diverse fauna of rodents and fleas with multiple patterns of association and connectivity.

Implications. Existence of diverse populations of rodents associated with a large number of flea species, some of which are efficient plague vectors, increases the potential for persistence and transmission of plague to humans in northern Tanzania.