Human-dominated Ecosystems Research Articles

To breed or not to breed: Territory occupancy is predicted by reproductive performance and habitat heterogeneity.

Species life history and anthropogenic influence are important drivers of population performance and viability in human-dominated ecosystems. How these factors affect habitat selection and occupancy in long-lived species is an important topic for their conservation. Long-term datasets are needed for establishing the underlying drivers of this process. In this 22 year-long study, we conducted annual surveys of Bonelli's eagle in the east of the Iberian Peninsula. During this period, 42.8% of the known territories remained unoccupied. Territories with a higher likelihood of raising two chicks over time were stable, evidenced by a lower coefficient of variation in productivity, and were more likely to remain occupied. Moreover, territories with lower habitat diversity, dominated by coniferous forest or agricultural fields, and those located further away from the coast and at higher altitudes showed lower rates of occupancy (i.e., unoccupied >3 consecutive years). To validate these associations, we monitored space use of 22 individuals equipped with Global Positioning System/Global System for Mobile (GPS/GSM) transmitters, which confirmed that eagles selected for open habitats (mainly scrublands and transitional woodland-scrubs) intermixed with forest areas within their home ranges. In contrast, individuals avoided areas dominated by agricultural, urban, and continuous forests for breeding in line with the observations for unoccupied territories. Our results highlight the important interplay between natural and anthropogenic factors, which also have important implications for other raptor species. Preservation of the most productive territories and the re-occupancy of unoccupied territories along with reducing threats in the preferred habitats are fundamental actions that should be taken immediately to sustain viable populations. Potential management actions include enhancing natural prey density through habitat restoration and conservation, mitigating threats and reducing mortality risks due to power lines, fences, poisoning, and maintaining habitat heterogeneity important to eagles' hunting activities.

Greening of human-dominated ecosystems in India

Satellite data show the Earth has been greening and identify croplands in India as one of the most prominent greening hotspots. Though India’s agriculture has been dependent on irrigation enhancement to reduce crop water stress and increase production, the spatiotemporal dynamics of how irrigation influenced the satellite observed greenness remains unclear. Here, we use satellite-derived leaf area data and survey-based agricultural statistics together with results from state-of-the-art Land Surface Models (LSM) to investigate the role of irrigation in the greening of India’s croplands. We find that satellite observations provide multiple lines of evidence showing strong contributions of irrigation to significant greening during dry season and in drier environments. The national statistics support irrigation-driven yield enhancement and increased dry season cropping intensity. These suggest a continuous shift in India’s agriculture toward an irrigation-driven dry season cropping system and confirm the importance of land management in the greening phenomenon. However, the LSMs identify CO2 fertilization as a primary driver of greening whereas land use and management have marginal impacts on the simulated leaf area changes. This finding urges a closer collaboration of the modeling, Earth observation, and land system science communities to improve representation of land management in the Earth system modeling.

Biodiversity response to rapid successive land cover conversions in human-dominated landscapes

Much of the world’s formerly “intact” land cover has been modified by humans with major impacts on biodiversity. Extensive areas of already modified land are now being subjected to yet further land cover conversions. Indeed, in many places, land cover and land use are changing repeatedly and frequently. Here, we use ecological theory to develop a new conceptual framework with associated postulates about how biodiversity could respond to repeated and rapid changes in land cover (over timespans of years to decades). Our framework focuses on five drivers: (1) conversion completeness, (2) persistence of biological, chemical, and physical legacies from previous land cover type to a new kind of cover, (3) number of previous land cover conversions, (4) time elapsed since land cover change, and (5) levels of contrast between the previous and new land cover. We predicted that biodiversity responses to repeated conversions in human-generated land cover would be a function of the main effects of these five drivers, as well as complex interactions among them (e.g. each new land cover type may act as a filter for species assemblages and interact in complex spatio-temporal ways with the previous land cover). Biodiversity responses may therefore be species- and land cover type specific, and not be readily predictable from insights provided by studies of single landscape conversions from an intact to a human-dominated ecosystem. Ignoring the impacts of successive land cover conversions on biodiversity could lead to increased biodiversity loss with each land cover conversion. Therefore, impact assessments are needed each time a new land cover conversion is proposed. Policies and management actions need to focus on the maintenance and/or restoration of remnant vegetation and other kinds of natural features (like large trees and wetlands) with each land cover conversion.

Seagrass production around artificial reefs is resistant to human stressors.

Primary production underpins most ecosystem services, including carbon sequestration and fisheries. Artificial reefs (ARs) are widely used for fisheries management. Research has shown that a mechanism by which ARs in seagrass beds can support fisheries and carbon sequestration is through increasing primary production via fertilization from aggregating fish excretion. Seagrass beds are heavily affected by anthropogenic nutrient input and fishing that reduces nutrient input by consumers. The effect of these stressors is difficult to predict because impacts of simultaneous stressors are typically non-additive. We used a long-term experiment to identify the mechanisms by which simultaneous impacts of sewage enrichment and fishing alter seagrass production around ARs across non-orthogonal gradients in human-dominated and relatively unimpacted regions in Haiti and The Bahamas. Merging trait-based measures of seagrass and seagrass ecosystem processes, we found that ARs consistently enhanced per capita seagrass production and maintained ecosystem-scale production despite drastic shifts in controls on production from human stressors. Importantly, we also show that coupled human stressors on seagrass production around ARs were additive, contrasting expectations. These findings are encouraging for conservation because they indicate that seagrass ecosystems are highly resistant to coupled human stressors and that ARs promote ecosystem services even in human-dominated ecosystems.

Negative and positive impacts of alien macrofungi: a global scale database

Advances in ecological research during the last decades have led to an improved understanding of the impacts of alien species. Despite that, the effects of alien macrofungi have often received little attention and are still poorly understood. With the aim of reducing this knowledge gap, we compiled a database of the recorded socio-economic and environmental impacts of alien macrofungi. This database was compiled from all relevant sources we could identify, through an exhaustive literature review, considering the identity of known alien taxa and explicit indications of impacts of any kind. In total, 1440 records of both negative and positive impacts were collected for 374 distinct species in different regions of all continents, except Antarctica. The most frequently recorded impacts are related to the mutualistic interactions that these fungi can form with their host plants. In total 47.8% of all records refer to the indirect negative effect of these interactions, by facilitating the colonization of invasive plants, while 38.5% refer to their positive contribution to the growth of forestry species. Less frequently recorded negative impacts included ectomycorrhizal interactions with native plants, plant pathogenicity and human poisoning after ingestion. Additional positive impacts include the use as a food source by native species and human populations and commercial exploitation. Alien macrofungi are an increasingly prevalent component of human-dominated ecosystems, having a diverse array of negative and positive impacts on native biota and human population. Our database provided a first step towards the quantification and mapping of these impacts.

Surprising leopard restoration in fragmented ecosystems reveals connections as the secret to conservation success

The Chinese Loess Plateau has been the cradle of Chinese civilization and the main human settlement in China for thousands of years, where anthropogenic activities are believed to have deeply eroded natural landscapes. After decades of minimal leopard sighting in forests of northern China, due to serious human interference, we recently discovered that the leopard population is recovering. This finding provides hope for successful biodiversity conservation in human-dominated ecosystems. To understand the mechanism of leopard return into such a highly fragmented landscape, we applied the concept of ecological networks (ENs) to identify key factors promoting leopard restoration and quantify the ecological links among habitats. We first determined the existence of a healthy leopard population in the study area based on the size of its home range and presence of breeding individuals. We then innovatively used the relationship between species richness and top predators to generate ENs, and found that the connectivity of ENs had a significant positive interaction with leopard survival. Our study validates the effectiveness of establishing ecologically connected habitats for leopard protection, and highlights the importance of applying ENs for conservation planning in highly fragmented ecosystems. This study provides a successful case for the protection of top predators in human-dominated landscapes.

Effects of Nutrient Level and Growth Rate on the Conjugation Process That Transfers Mobile Antibiotic Resistance Genes in Continuous Cultures.

Bacteria in the effluent of wastewater treatment plants (WWTPs) can transfer antibiotic resistance genes (ARGs) to the bacteria in receiving water through conjugation; however, there is a lack of quantitative assessment of this phenomenon in continuous cultures. Our objective was to determine the effects of background nutrient levels in river water column and growth rates of bacteria on the conjugation frequency of ARGs from effluent bacteria to river bacteria, as well as on the resulting resistance level (i.e., MICs) of the river bacteria. Chemostats were employed to simulate the discharge points of WWTPs into rivers, where effluent bacteria (donor cells) meet river bacteria (recipient cells). Both donor and recipient cells were Escherichia coli cells, and the donor cells were constructed by filter mating with bacteria in the effluent of a local WWTP. Results showed that higher bacterial growth rate (0.45 h-1 versus 0.15 h-1) led to higher conjugation frequencies (10-4 versus 10-6 transconjugant per recipient). The nutrient level also significantly affected the conjugation frequency, albeit to a lesser extent than the growth rate. The MIC against tetracycline increased from 2 mg/L in the recipient to 64 to 128 mg/L in transconjugants. In comparison, the MIC only increased to as high as 8 mg/L in mutants. Whole-genome sequencing showed that the tet-containing plasmid in both the donor and the transconjugant cells also occur in other fecal bacterial genera. The quantitative information obtained from this study can inform hazard identification related to the proliferation of wastewater-associated ARGs in surface water. IMPORTANCE WWTPs have been regarded as an important hot spot of ARGs. The discharge point of WWTP effluent, where ARGs may be horizontally transferred from bacteria of treated wastewater to bacteria of receiving water, is an important interface between the human-dominated ecosystem and the natural environment. The use of batch cultures in previous studies cannot adequately simulate the nutrient conditions and growth rates in receiving water. In this study, chemostats were employed to simulate the continuous growth of bacteria in receiving water. Furthermore, the experimental setup allowed for separate investigations on the effects of nutrient levels (i.e., simulating background nutrients in river water) and bacterial growth rates on conjugation frequencies and resulting resistance levels. The study generates statistically sound ecological data that can be used to estimate the risk of wastewater-originated ARGs as part of the One Health framework.

Mammals adjust diel activity across gradients of urbanization.

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hr light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of 8 mammal species across 10 US cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hr cycle to reduce risk, adapt, and therefore persist, and in some cases thrive, in human-dominated ecosystems.

From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches.

With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.

How ecological research on human-dominated ecosystems incorporates agricultural and forestry practices: A literature analysis.

Understanding the nexus between practices and ecosystems is a critical challenge for sustainability, but it is unclear how ecological sciences have explored the question. To bring clarification, we conducted an analysis of ecology literature dealing with agricultural and forestry practices (AF practices), scanning a total of 27556 references. Scientometric analyses showed that AF practices were addressed by 5.5% of ecology literature, and that this proportion increased from 2.5 to 8.1% between 1956 and 2017. Content analyses showed that research has mainly focused on monospecific systems in the Global North, predominantly using plot-level experimental approaches. Temporal monitoring, real-world practices and their social context were poorly investigated. This analysis stresses the need to reinforce research in complex agroecosystems, in particular in non-Western countries. Multilevel and spatio-temporal approaches, as well as participatory research, should also be encouraged to build a social-ecological understanding and formulate more grounded, relevant policy recommendations for sustainability.

"The Sky Is Falling," Government Is Not Responding, What Can Scientists Do?

"The Sky Is Falling," Government Is Not Responding, What Can Scientists Do?

Management Actions Promote Human-Wildlife Coexistence in Highly Anthropized Landscapes: The Case of an Endangered Avian Scavenger

Anthropized landscapes are characterized by various human activities related to resource extraction, recreational activities, and urbanization, among others. Conservation of species living in such landscapes is challenging due to the lack of compatibility between wildlife and human needs, which can create win-lose scenarios for target species. Therefore, adequate management practices are necessary to reduce conflicts and promote coexistence between wildlife and human beings. Here, we test the effectiveness of management measures on the productivity of an Egyptian vulture population living in an anthropized region of Northern Spain by using long-term monitoring data (2000–2020). During the first decade, we demonstrated that disturbance events negatively affected the species reproduction. Therefore, in 2010 we started a management plan in which we first established a basis for the species protection, and second we developed management actions to avoid or reduce the impact of potential disturbance events on the Egyptian vulture’ breeding. We observed that almost half of the disturbances detected after the management was related to resource extraction activities such as forestry (40.6%). Management measures effectively increased productivity (84 vs 137, chicks fledged successfully before and after, respectively) and the breeding success of the pairs in which the disturbances were detected and stopped (66.7%) was much higher than those non-managed and non-stopped in time (17.4%). Moreover, we estimated that 44 nestlings (32.1%) would have died without management actions during the second decade. Overall, our work demonstrated that collaborative networks can design and implement effective management measures for endangered territorial species, taking into account all agents involved (policymakers, rangers, stakeholders, general public, and researchers) in the conservation area. Thereby, it alleviates conflicts in human-dominated ecosystems and generates a balanced scenario that favors long-term sustainable human-wildlife coexistence.

Bird species richness across a Northern Andean city: Effects of size, shape, land cover, and vegetation of urban green spaces

Cities are human-dominated ecosystems where landscape transformation decreases biodiversity, a conservation concern when urbanization sprawls into biodiversity hotspots with high endemism. We aimed to evaluate the effects of site-specific features such as size and shape of green spaces, land cover, and vegetation on bird species richness in Medellín, Colombia, a city of Northern Andes (n = 44 urban green spaces sampled from February 2018 to February 2019). We found 255 plant species: 23 % of trees and 41 % of understory were native sensu stricto (local origin); most native species and individuals were in green spaces lacking vegetation management. Bird species richness (25.80 ± 8.05 resident species per sampling point; 83 resident species overall) increased towards larger and more regular-shaped urban green spaces (squared or rounded), with less percentage of impervious surfaces and more of grass–shrubs, and less influence of introduced trees in habitat structure (i.e. less crown coverage, basal area, and average height). Bird species richness also increased when richness or abundance of native understory vegetation sensu lato (local or regional origin) increased, but introduced trees dominance represented higher and most significant effects to explain bird species richness. Increasing edge effects across urban green spaces and human-related habitat transformation favoring non-native vegetation might represent significant constraints for enhancing local biodiversity in highly developed Andean cities.

PROFESSIONAL CONSULTING, PLANNING AND DESIGN OF REGIONAL DEVELOPMENT IN THE FACE OF INCREASING UNCERTAINTIES AND RISKS

The article reveals features of the ongoing transformations in the field of consulting, planning and design in the field of regional development in the face of increasing uncertainties and risks, primarily related to climate change and biodiversity loss. It shows that the very basis of such work is significantly changing, as the world-system becomes more complex, during the transition from the concept of an “empty” world to a “full” world. This change includes increasing emphasis on ensuring the resilience of human-dominated ecosystems, a change in decision-making, using behavioral a “responsible” human model that best meets the needs of inclusive sustainable development.The authors define features of consulting, planning and design of regional development in the face of increasing uncertainties and risks, as a special type of thinking activity, in a situation of approaching radical uncertainty. The article shows the necessity of supplementing natural science approaches with the tools and practices of post-normal science and the narrative theory of beliefs, as well as the ideas of K. Friston, implemented within his dynamic causal model.Such an approach is based on a systematic approach to decision-making in regional development and pays special attention to the adaptation of individuals and communities to high risks and uncertainties, primarily climatic and natural. It helps to better reflect the diversity of geographical conditions, to clarify the range of effective solutions for sustainable development of regions and increase the long-term resilience of business.

The return of large carnivores: Using hunter observation data to understand the role of predators on ungulate populations

Large carnivores play a key ecological role in nature, yet quantifying the effects of predation at large spatiotemporal scales remains challenging. Wolves and brown bears have recovered in Sweden, where they share the same staple prey, moose. This ecosystem is representative of the Eurasian boreal realm, and makes an interesting case study for exploring the use of hunter-collected observation data to understand the ecological effects of large carnivore recovery in human-dominated ecosystems. We used over 50 million hours of moose observation data collected by “citizen scientists” (i.e., moose hunters) between 2000 and 2017 to evaluate the role of recovering bear and wolf populations on an important ungulate vital rate, calf/cow ratio (the number of observed calves per female in fall). Calf/cow ratios were negatively correlated with both wolf and bear densities, suggesting that summer calf survival decreased via predation. Calf/cow ratios decreased by 7% and 17% in the northern and southern areas where bears and wolves were allopatric, respectively. Where wolves and bears were sympatric, the effect of predator densities was additive; calf/cow ratios decreased by 18%. However, both calf/cow ratios and moose densities declined over the last ~20 years across Sweden, including areas where wolves and bears were absent. While recolonizing large carnivores affected ungulate vital rates in Sweden’s human-dominated landscape, they were likely not the primary driver of long-term moose population trends. Our results reinforce that citizen-collected data are a useful wildlife monitoring tool that help understand ecological processes, including the effects of recovering carnivores on prey populations.

Historical and future global burned area with changing climate and human demography

Summary Wildfires influence terrestrial carbon cycling and represent a safety risk, and yet a process-based understanding of their frequency and spatial distributions remains elusive. We combine satellite-based observations with an enhanced dynamic global vegetation model to make regionally resolved global assessments of burned area (BA) responses to changing climate, derived from 34 Earth system models and human demographics for 1860–2100. Limited by climate and socioeconomics, recent BA has decreased, especially in central South America and mesic African savannas. However, future simulations predict increasing BA due to changing climate, rapid population density growth, and urbanization. BA increases are especially notable at high latitudes, due to accelerated warming, and over the tropics and subtropics, due to drying and human ignitions. Conversely, rapid urbanization also limits BA via enhanced fire suppression in the immediate vicinity of settlements, offsetting the potential for dramatic future increases, depending on warming extent. Our analysis provides further insight into regional and global BA trends, highlighting the importance of including human demographic change in models for wildfire under changing climate.

Zoonotic host diversity increases in human-dominated ecosystems.

Land use change-for example, the conversion of natural habitats to agricultural or urban ecosystems-is widely recognized to influence the risk and emergence of zoonotic disease in humans1,2. However, whether such changes in risk are underpinned by predictable ecological changes remains unclear. It has been suggested that habitat disturbance might cause predictable changes in the local diversity and taxonomic composition of potential reservoir hosts, owing to systematic, trait-mediated differences in species resilience to human pressures3,4. Here we analyse 6,801 ecological assemblages and 376 host species worldwide, controlling for research effort, and show that land use has global and systematic effects on local zoonotic host communities. Known wildlife hosts of human-shared pathogens and parasites overall comprise a greater proportion of local species richness (18-72% higher) and total abundance (21-144% higher) in sites under substantial human use (secondary, agricultural and urban ecosystems) compared with nearby undisturbed habitats. The magnitude of this effect varies taxonomically and is strongest for rodent, bat and passerine bird zoonotic host species, which may be one factor that underpins the global importance of these taxa as zoonotic reservoirs. We further show that mammal species that harbour more pathogens overall (either human-shared or non-human-shared) are more likely to occur in human-managed ecosystems, suggesting that these trends may be mediated by ecological or life-history traits that influence both host status and tolerance to human disturbance5,6. Our results suggest that global changes in the mode and the intensity of land use are creating expanding hazardous interfaces between people, livestock and wildlife reservoirs of zoonotic disease.

Can landscape heterogeneity promote carnivore coexistence in human-dominated landscapes?

Interspecific competition can limit species distributions unless competitors partition niche space to enable coexistence. Landscape heterogeneity can facilitate niche partitioning and enable coexistence, but land-use change is restructuring terrestrial ecosystems globally with unknown consequences for species interactions. We tested the relationship between landscape heterogeneity and carnivore co-occurrence in natural and human-dominated ecosystems to assess the landscape-mediated impacts of anthropogenic change on coexistence. We used boosted regression trees to model the distributions and co-occurrence of two competing forest carnivores, American martens and fishers, at two contrasting sites in the Great Lakes region, USA: a “natural” site largely devoid of human impacts and a “human-dominated” site with substantial development and a history of land-use change. We assessed the importance of climate and habitat variables for each species, measured spatial niche overlap, and quantified co-occurrence as a function of compositional (patch richness), configurational (landscape shape), and topographical (elevation range) heterogeneity per site. We observed significant differences in the effect of heterogeneity on co-occurrence between sites. The natural landscape exhibited little niche overlap and co-occurrence had a significant, positive relationship with heterogeneity. Conversely, the human-dominated site exhibited high niche overlap with variable effects of heterogeneity on co-occurrence. Elevation, snowpack, and development had strong, contrasting effects on marten and fisher distributions, suggesting that differential use of habitat and anthropogenic features facilitates coexistence. Heterogeneity can facilitate coexistence, but too much may undermine carnivore coexistence in human-dominated landscapes where habitat and space are limited. Moreover, future climate change will likely erode niche partitioning among martens and fishers, with particularly strong consequences for coexistence in human-dominated landscapes and at range boundaries.

Fear of the dark? Contrasting impacts of humans versus lynx on diel activity of roe deer across Europe.

Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human-modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human-dominated landscapes. We investigated the influence of the density of lynx Lynx lynx, a nocturnal predator, on the diel activity patterns of their main prey, the roe deer Capreolus capreolus, across a gradient of human disturbance and hunting at the European scale. Based on 11 million activity records from 431 individually GPS-monitored roe deer in 12 populations within the EURODEER network (http://eurodeer.org), we investigated how lynx predation risk in combination with both lethal and non-lethal human activities affected the diurnality of deer. We demonstrated marked plasticity in roe deer diel activity patterns in response to spatio-temporal variations in risk, mostly due to human activities. In particular, roe deer decreased their level of diurnality by a factor of 1.37 when the background level of general human disturbance was high. Hunting exacerbated this effect, as during the hunting season deer switched most of their activity to night-time and, to a lesser extent, to dawn, although this pattern varied noticeably in relation to lynx density. Indeed, in the presence of lynx, their main natural predator, roe deer were relatively more diurnal. Overall, our results revealed a strong influence of human activities and the presence of lynx on diel shifts in roe deer activity. In the context of the recovery of large carnivores across Europe, we provide important insights about the effects of predators on the behavioural responses of their prey in human-dominated ecosystems. Modifications in the temporal partitioning of ungulate activity as a response to human activities may facilitate human-wildlife coexistence, but likely also have knock-on effects for predator-prey interactions, with cascading effects on ecosystem functioning.

Influence of microhabitat and landscape-scale factors on the richness and occupancy of small mammals in the northern Western Ghats: A multi-species occupancy modeling approach

Human-dominated ecosystems are characterized by three main processes, viz., habitat degradation, habitat loss and habitat fragmentation, these posing a great threat to biodiversity. However, the relationships between these processes are not clearly understood. Moreover, habitat loss and habitat fragmentation occur at landscape-scale and their effects depend on the spatial scale. We trapped small mammals in a human-dominated area in the northern Western Ghats, India, at 23 sites in three habitats, capturing 479 individuals of 17 species. We adopted the multi-species occupancy model (MSOM) approach within a Bayesian framework to assess species site occupancy using microhabitat-scale and landscape-scale variables measured at five spatial scales. We found that species richness had a hump-shaped relationship with landscape complexity, and it can be best explained at a spatial scale of 300 m. The findings suggest that both microhabitat-scale and landscape-scale variables influence small mammal occupancy. Overall, shrub density had a positive effect on species occurrence with high certainty, which could be related to the protection provided by shrubs from predators and harsh weather conditions. Shrub density was largely influenced small mammal richness and occupancy and thus should be managed appropriately for their conservation. Considering the negative impact of landscape complexity on endemic rodents, especially on the Critically Endangered Millardia kondana, further fragmentation of grasslands and forest habitats and their conversion into unsuitable habitats in the area should be minimized. All high-elevation grasslands important for M. kondana should be strictly protected and managed. We recommend adoption of the MSOM approach in similar studies, as it allows estimation of occupancy even for species with low detectability.