Global climate change and small mammal populations in north-central Chile

Molecular detection of Cryptosporidium parvum in wild rodents (Phyllotis darwini) inhabiting protected and rural transitional areas in north-central Chile

Wild rodents often harbor Cryptosporidium species that can be transmitted to multiple mammal hosts. In Chile, little is known about Cryptosporidium in wild rodents, and available studies have been focused on morphological findings with no molecular-based evidence. A longitudinal survey was conducted between 2021 and 2022 to investigate the occurrence of Cryptosporidium spp. in populations of the Darwin's leaf-eared mouse (Phyllotis darwini) living in protected and rural transitional areas in north-central Chile, using staining and molecular methods. A total of 247 fecal samples were collected and examined by the modified Ziehl-Neelsen (ZN) staining test, 54 of which were positive for Cryptosporidium-like oocysts. Molecular analyses were carried out by PCR of the partial 18S ribosomal RNA and 60 kDa glycoprotein (gp60) genes. Cryptosporidium infection was confirmed in 34 samples (13.7 %) based on the PCR amplification, and individual (i.e., sex, and body mass index) and ecological variables (i.e., type of site and season) were not statistically significant (p > 0.05). Using the nucleotide sequencing of the partial 18S rRNA gene, Cryptosporidium parvum was identified in nine isolates. Also, C. parvum subgenotype family IIa was determined in seven samples by the partial gp60 gene, including the subtype IIaA17G4R1 in two samples. This is the first molecular evidence of Cryptosporidium parvum IIa in Phyllotis darwini in Chile. These results indicate potential cross-species transmition between wild rodents and domestic-wild animals in north-central Chile. More research is needed to understand better the role of wild rodents in the transmission of Cryptosporidium spp. in Chile.

Environmental drivers of long-term variations in the abundance of the red hocicudo mouse (Oxymycterus rufus) in Pampas agroecosystems

During the 20th century, there has been an ongoing agricultural expansion and global warming, two of the main determinants influencing biodiversity changes in Argentina. The red hocicudo mouse (Oxymycterus rufus) inhabits subtropical grasslands and riparian habitats and has increased its abundance in recent years in central Argentina agroecosystems. This paper describes the long-term temporal changes in O. rufus abundance in Exaltación de la Cruz department, Buenos Aires province, Argentina, in relation to weather fluctuations and landscape features, as well as analyzes the spatio-temporal structure of captures of animals. We used generalized liner models, semivariograms, the Mantel test, and autocorrelation functions for the analysis of rodent data obtained from trappings conducted between 1984 and 2014. O. rufus showed an increase in abundance across the years of study, with its distribution depending on landscape features, such as habitat types and the distance to floodplains. Capture rates showed a spatio-temporal aggregation, suggesting expansion from previously occupied sites. O. rufus was more abundant at lower minimum temperatures in summer, higher precipitation in spring and summer, and lower precipitations in winter. Weather conditions affected O. rufus abundance, but there was local variation that differed from global patterns of climate change.

Decline in small mammal species richness in coastal-central California, 1997-2013

The richness and composition of a small mammal community inhabiting semiarid California oak woodland may be changing in response to climate change, but we know little about the causes or consequence of these changes. We applied a capture-mark-recapture model to 17 years (1997-2013) of live trapping data to estimate species-specific abundances. The big-eared woodrat was the most frequently captured species in the area, contributing 58% of total captures. All small mammal populations exhibited seasonal fluctuations, whereas those of the California mouse, brush mouse, and pinyon mouse declined during the study period. We also applied a multispecies dynamic occupancy model to our small mammal detection history data to estimate species richness, occupancy (ψ ), detection (p), local extinction (ϵ ), and colonization (γ ) probabilities, and to discern factors affecting these parameters. We found that ψ decreased from 0.369 ± 0.088 in 1997 to 0.248 ± 0.054 in 2013; γ was lower during the dry season (May-September) than the wet season (October-April) and was positively influenced by total seasonal rainfall (slope parameter, β  = 0.859 ± 0.371; 95% CI = 0.132-1.587). Mean mammalian species richness decreased from 11.943 ± 0.461 in 1997 to 7.185 ± 0.425 in 2013. With highly variable climatic patterns expected in the future, especially increased frequency and intensity of droughts, it is important to monitor small mammal communities inhabiting threatened California oak woodlands.

Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species' synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world.

Small Mammal Diversity Changes in a Baltic Country, 1975-2021: A Review

The structure and diversity of small mammal (SM) communities over the long term may show the influences of climate change, landscape changes and local disturbances. We review published data regarding SM trapping and owl pellet analysis from Lithuania (the most southerly of the three Baltic States, Northern Europe), covering the period 1975-2021. Over decades, we analysed trends in the diversity of SM communities and the proportions of species and proportions of trophic groups. The large increase in granivores, from 6.9% in 1975-1980 to 45.4% in 2011-2020 and 54.7% in 2021, coincided with a decrease in omnivores and insectivores. The proportion of herbivores increased less notably. At the species level, significant decreases in the proportions of M. arvalis, C. glareolus and S. araneus were accompanied by notable increases in the proportions of A. flavicollis and A. agrarius, the latter from 1.0% in 1975-1980 to 25.3% in 2021. Concluding, two periods were identified, specifically before the 1990s and subsequently. In the second period, in the aftermath of land-use changes within the country in 1990, diversity increased, and dominance decreased, a situation that has not subsequently changed. Not excluding the concomitant effects of climate change, we relate these patterns to the alterations in habitat and anthropogenic impact.

Declines in rodent abundance and diversity track regional climate variability in North American drylands

Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, regions defined by the scarcity of water that cover 45% of Earth's land surface and face increasingly drier and more variable climates. We analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland ecosystems in the southwestern USA. Two time series (1995-2006 and 2004-2013) coincided with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20%-35%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of 5% of animals captured. During the first time series (wetter climate), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70% of taxa, whereas during the second period (drier climate), climate best explained variation in abundance for 60% of taxa. Temporal dynamics in diversity and abundance differed spatially among ecosystems, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Which species were winners or losers under increasing drought and amplified interannual variability in drought depended on ecosystem type and the phase of the PDO. Fewer taxa were significant winners (18%) than losers (30%) under drought, but the identities of winners and losers differed among ecosystems for 70% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995-2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major PDO cycle.

Predators and dispersers: Context-dependent outcomes of the interactions between rodents and a megafaunal fruit plant

Many plant species bear fruits that suggest adaptation to seed dispersal by extinct megafauna. Present-day seed dispersal of these megafaunal plants is carried out by rodents, which can act as predators or dispersers; whether this interaction is primarily positive or negative can depend on the context. Here, we parameterized a stochastic model using data from the field and experimental arenas to estimate the effect of rodents on the recruitment of Myrcianthes coquimbensis -an Atacama Desert shrub with megafaunal fruits- and examine whether environmental conditions can alter the sign and strength of these rodent-plant interactions. We show that the outcome of these interactions is context-dependent: in wet conditions seed removal by rodents negatively impacts the recruitment probability of M. coquimbensis; in contrast, in dry conditions, the interaction with rodents increases recruitment success. In all cases, the strength of the effect of rodents on the recruitment success was determined mainly by their role as dispersers, which could be positive or negative. This study demonstrates that by caching seeds, rodents can be effective dispersers of a megafaunal fruit plant, but that the sign and magnitude of their effect on recruitment changes as a function of the environmental context in which the interaction occurs.

Helminthic infection in three native rodent species from a semiarid Mediterranean ecosystem

Helminth parasites are still not a well-known component of animal biodiversity. In this study, we describe and compare the endoparasite assemblages of three native rodent species from a semiarid Mediterranean ecosystem. A total of eight species of gastrointestinal helminth parasites were detected. The endoparasitic communities of the rodents Phyllotis darwini (5 species), Octodon degus (4 species), and Abrothrix olivaceus (3 species) were described in terms of their prevalence and mean abundance. In addition, endoparasite records by rodent species were submitted to rarefaction analyses to verify sampling robustness and used to compare richness and similarity among rodent species. O. degus presented the highest prevalence and parasitic load, but was of low diversity, while P. darwini presented the highest diversity, but had a low prevalence rate. Conversely, A. olivaceus presented the lowest prevalence and diversity. This study contributes to the existing knowledge of the endoparasitic fauna of rodent species from semiarid Mediterranean zones.

Foraging strategies of individual silky pocket mice over a boom-bust cycle in a stochastic dryland ecosystem

Small mammals use multiple foraging strategies to compensate for fluctuating resource quality in stochastic environments. These strategies may lead to increased dietary overlap when competition for resources is strong. To quantify temporal contributions of high (C₃) versus low quality (C₄) resources in diets of silky pocket mice (Perognathus flavus), we used stable carbon isotope (δ¹³C) analysis of 1391 plasma samples collected over 2 years. Of these, 695 samples were from 170 individuals sampled ≥ 3 times across seasons or years, allowing us to assess changes in dietary breadth at the population and individual levels across a boom-bust population cycle. In 2014, the P. flavus population increased to 412 captures compared to 8 captures in prior and subsequent years, while populations of co-occurring small mammals remained stable. As intraspecific competition increased, the population-wide dietary niche of P. flavus did not change, but individual specialization increased significantly. During this period, ~ 27% (41/151) of individuals sampled specialized on C₃ resources, which were abundant during the spring and previous fall seasons. Most of the remaining individuals were C₃-C₄ generalists (64%) (96/151), and only 9% (14/151) specialized on C₄ resources. In 2015, P. flavus population density and resource availability declined, individual dietary breadth expanded (84% generalists), no C₃ specialists were found, and specialization on C₄ resources increased (16%). Our results demonstrate a high degree of inter-individual plasticity in P. flavus foraging strategies, which has implications for how this species will respond to environmental change that is predicted to decrease C₃ resources in the future.

Large manipulative experiments reveal complex effects of food supplementation on population dynamics of Brandt's voles

Although food supplementation is well known to increase population density, there is still debate on the causative effects of food supplementation on reproduction, survival, and immigration. Large manipulative experiments, which exclude any confounding effects of dispersal and predation, are essential for clarifying the debate. In this study, we investigated the effects of food supplementation on Brandt's vole population dynamics and plant community in eight large enclosures (0.48 ha each) from 2010 to 2014. Food supplementation showed significant positive effects on population density due to increases in recruitment; however, it showed a complex effect on survival of voles: positive in non-breeding seasons, but negative in breeding seasons. In addition, food supplementation increased the quality of plants (as reflected by increased crude protein content), but decreased the quantity of less preferred plants in experimental enclosures. Thus, food seems to have direct positive effects on small rodents through improvement of food supply and indirect negative effects through food-induced density-dependent effects, and may have long-term effects on rodents through altering plant community composition and abundance.

The role of refuges in the persistence of Australian dryland mammals

Irruptive population dynamics are characteristic of a wide range of fauna in the world's arid (dryland) regions. Recent evidence indicates that regional persistence of irruptive species, particularly small mammals, during the extensive dry periods of unpredictable length that occur between resource pulses in drylands occurs as a result of the presence of refuge habitats or refuge patches into which populations contract during dry (bust) periods. These small dry-period populations act as a source of animals when recolonisation of the surrounding habitat occurs during and after subsequent resource pulses (booms). The refuges used by irruptive dryland fauna differ in temporal and spatial scale from the refugia to which species contract in response to changing climate. Refuges of dryland fauna operate over timescales of months and years, whereas refugia operate on timescales of millennia over which evolutionary divergence may occur. Protection and management of refuge patches and refuge habitats should be a priority for the conservation of dryland-dwelling fauna. This urgency is driven by recognition that disturbance to refuges can lead to the extinction of local populations and, if disturbance is widespread, entire species. Despite the apparent significance of dryland refuges for conservation management, these sites remain poorly understood ecologically. Here, we synthesise available information on the refuges of dryland-dwelling fauna, using Australian mammals as a case study to provide focus, and document a research agenda for increasing this knowledge base. We develop a typology of refuges that recognises two main types of refuge: fixed and shifting. We outline a suite of models of fixed refuges on the basis of stability in occupancy between and within successive bust phases of population cycles. To illustrate the breadth of refuge types we provide case studies of refuge use in three species of dryland mammal: plains mouse (Pseudomys australis), central rock-rat (Zyzomys pedunculatus), and spinifex hopping-mouse (Notomys alexis). We suggest that future research should focus on understanding the species-specific nature of refuge use and the spatial ecology of refuges with a focus on connectivity and potential metapopulation dynamics. Assessing refuge quality and understanding the threats to high-quality refuge patches and habitat should also be a priority. To facilitate this understanding we develop a three-step methodology for determining species-specific refuge location and habitat attributes. This review is necessarily focussed on dryland mammals in continental Australia where most refuge-based research has been undertaken. The applicability of the refuge concept and the importance of refuges for dryland fauna conservation elsewhere in the world should be investigated. We predict that refuge-using mammals will be widespread particularly among dryland areas with unpredictable rainfall patterns.

Anthropogenic stressors influence small mammal communities in tropical East African savanna at multiple spatial scales

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.

Status and challenges for conservation of small mammal assemblages in South America

South America spans about 44° latitude, covers almost 18 million km(2) , and is second only to Africa in continental mammal species richness. In spite of this richness, research on the status of this fauna and on the nature and magnitude of contemporary threats remains limited. Distilling threats to this diverse fauna at a continental scale is challenging, in part because of the limited availability of rigorous studies. Recognizing this constraint, we summarize key threats to small mammals in South America, emphasizing the roles of habitat loss and degradation, direct persecution, and the increasing threat of climate change. We focus on three regional 'case studies': the tropical Andes, Amazonia and adjacent lowland regions, and the southern temperate region. We close with a brief summary of recent findings at our long-term research site in north-central Chile as they pertain to projected threats to this fauna. Habitat alteration is a pervasive threat that has been magnified by market forces and globalization (e.g. extensive agricultural development in Amazonia), and threatens increasing numbers of populations and species. Climate change poses even greater threats, from changes in rainfall and runoff regimes and resulting changes in vegetative structure and composition to secondary influences on fire dynamics. It is likely that many changes have yet to be recognized, but existing threats suggest that the future may bring dramatic changes in the distribution of many mammal taxa, although it is not clear if key habitat elements (vegetation) will respond as rapidly as climatic factors, leading to substantial uncertainty. Climate change is likely to result in 'winners' and 'losers' but available information precludes detailed assessment of which species are likely to fall into which category. In the absence of long-term monitoring and applied research to characterize these threats more accurately, and to develop strategies to reduce their impacts, managers already are being faced with daunting challenges. As the line between 'pure' and 'applied' research blurs in the face of converging interests of scientists and society we hope that solutions to these critical issues will be incorporated in addressing anticipated conservation crises.