Samuel Cushman

University of Oxford | OX · Department of Biology, Wildlife Conservation Research Unit

Understanding habitat selection is critical for the conservation of ungulate species. Our aim was to (1) quantify herd-specific habitat selection for American pronghorn (Antilocapra americana) in the southwestern United States and (2) produce a habitat suitability map that can aid in the prioritization of management actions. We used GPS telemetry l...

The ecological niche and the species-environment relationship are both cornerstones of contemporary ecological science. The realized habitat niche defines the conditions in which a species occurs, is adapted and can thrive, and quantification of the species-environment relationship is a means to describe the realized habitat niche. A frequent, if u...

Protein isoforms (PIs) play pivotal roles in regulating plant growth and development that confer adaptability to diverse environmental conditions. PIs are widely present in plants and generated through alternative splicing (AS), alternative polyadenylation (APA), alternative initiation (AI), and ribosomal frameshifting (RF) events. The widespread p...

CONTEXT: The efficient and effective design of protected areas is a fundamental challenge in landscape ecology, focusing on how spatial patterns of habitat influence conservation outcomes. This has sparked debate about the relative importance of habitat area versus connectivity in maintaining populations across fragmented landscapes. OBJECTIVES: We...

Landscape-scale analysis is an evolving approach to quantify the effects of landscape structure (composition and configuration) on focal species. Bats—a remarkably rich and diverse group—use habitat from fine (< 0.5 km) to broad (> 4 km) scales, and thus identifying their responses to changing landscapes can highlight a variety of management implic...

Hunting, habitat loss and fragmentation have caused a rapid decline in the distribution and abundance of the clouded leopard Neofelis nebulosa across its range, and in several areas, including Taiwan, the species is now extirpated. Taiwan, a former stronghold for the species, is a candidate for its reintroduction, based on increasing prey abundance...

Aim Myanmar, an Indo‐Burmese biodiversity hotspot, lacks baseline data on species occurrence and distribution. This hinders biodiversity monitoring and optimisation of conservation and development plans. We aim to document baseline mammal occupancy, interactions with environmental factors and scale‐dependent responses. Location Hkakaborazi Nationa...

Context There have been few evaluations of how well different connectivity modelling methods are able to predict the spatial genetic structure and genetic diversity of populations residing in complex landscapes. Given the wide application of connectivity modelling tools in applied conservation planning, it is crucial to broadly evaluate how these m...

Habitat fragmentation and loss are major threats to species conservation worldwide. Studying species-habitat relationships is a crucial first step toward understanding species habitat requirements, which is necessary for conservation and management planning. However, some species inhabit a range of habitat types, potentially making the use of range...

Protected areas are an important tool for wildlife conservation; however, research is increasingly revealing both biases and inadequacies in the global protected area network. One common criticism is that protected areas are frequently located in remote, high-elevation regions, which may face fewer threats compared to more accessible locations. To...

Identification of highly biodiverse areas has become a crucial step in protecting species richness, especially considering the rapid collapse of biodiversity and the limited funds available to avert, far less to reverse, these trends. Therefore, we aimed to identify the most important areas for the conservation of specified mammalian groups in Sout...

Recent research, has shown that species-environmental relationships and habitat model predictions are often nonstationary in space, time and ecological context. This calls into question modeling approaches that assume a global, stationary ecological realized niche and use predictive modeling to describe it. This paper explores this issue by compari...

Context Predicting and mapping connectivity between habitats and populations is critical to addressing habitat loss and biodiversity issues. Several strategies in the literature exist to understand, restore, and preserve ecological connectivity. The main issue of the current research is to identify which connectivity modeling strategies are the mos...

Virus spillovers from managed honey bees, Apis mellifera, are thought to contribute to the decline of wild pollinators, including bumble bees. However, data on the impact of such viruses on wild pollinators remain scarce, and the influence of landscape structure on virus dynamics is poorly understood. In this study, we deployed bumble bee colonies...

Species Distribution Models (SDMs) have been used extensively to understand species-habitat relationships and design conservation strategies. The ability to train these models using a wide variety of datasets and modelling algorithms has led to their wide applicability across systems. However, the ease of modelling also leads to their use as off-th...

Southeast Asia hosts more felid species than any other region and, although smaller (< 30kg) felids have important ecological roles, regional conservation has mainly focused on a few charismatic big cats. Information on the ecology and conservation status of small felids is often lacking or geographically limited. We used empirically derived scale-...

Little is known about the factors that drive nonstationarity and inter-individual differences in realized habitat niches and species-environment relationships. We explored this topic by developing individual habitat selection models for 14 wildcat hybrids distributed across Scotland, and assessed how differences in their predicted probabilities of...

Species distribution modeling is widely used to quantify and predict species-environment relationships. Most past applications and methods in species distribution modeling assume context independent and stationary relationships between patterns of species occurrence and environmental variables. There has been relatively little research investigatin...

Effective conservation management depends on the maintenance of key areas that allow population connectivity across the landscape. However, the lack of knowledge of how habitat conversion affects species movement hinders the identification of these areas. Here, we analyzed the impact of habitat fragmentation on landscape connectivity for Leopardus...

The Arabian leopard (Panthera pardus nimr) has experienced dramatic range and population contractions over the last century. Conservation efforts for this felid focused on captive breeding and identification of suitable conditions for reintroductions. With this study, we unravelled historical collaring and direct observations data to understand the...

Understanding how genetic diversity is spatially structured is a priority to gain insights into populations’ genetic status and to assess their abilities to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, the wide-ranging felid of Central Asia mountains. Focusing on a snow leopard population from...

Successful conservation hinges on the reliable prediction and prioritisation of population core habitats and dispersal corridors. However, reliance on single-species connectivity has produced mixed results and, in most cases, failed to protect other species under the appealing but often unfulfilled guise of umbrella protection. The main objectives...

Models and metrics to measure ecological connectivity are now well-developed and widely used in research and applications to mitigate the ecological impacts of climate change and anthropogenic habitat loss. Despite the prevalent application of connectivity models, however, relatively little is known about the performance of these methods in predict...

The islands of Borneo and Sumatra are strongholds for biodiversity and home for many endemic species. They also have experienced amongst the highest deforestation rates globally. Both islands are undergoing massive, rapid infrastructure development, leading to further deforestation and habitat fragmentation. Here, we identify priority areas for con...

Aim The goal of this study was to evaluate consistency among multiple connectivity models for jaguar and puma across Panama to evaluate the plausible current patterns of habitat connectivity for these and potentially other species in this critical biogeographic linkage zone. Approach We compared 72 different models of landscape connectivity for bo...

Context Evaluating connectivity and identifying corridors for protection is a central challenge in applied ecology and conservation. Rigorous validation and comparison of how approaches perform in capturing biological processes is needed to guide research and conservation action. Objectives We aim to compare the ability of connectivity surfaces op...

Biodiversity-structure relationships (BSRs) describe the correlation between biodiversity and three-dimensional forest structure which have been used to map spatial patterns in biodiversity based on forest structural attributes derived from lidar. However, with the advent of spaceborne lidar like the Global Ecosystem Dynamics Investigation (GEDI),...

The regulation of flowering time is typically governed by transcription factors or epigenetic modifications. Transcript isoforms can play important roles in flowering regulation. Recently, transcript isoforms were discovered in the key genes, OfAP1 and OfTFL1, of the flowering regulatory network in Osmanthus fragrans. OfAP1-b generates a full-lengt...

Virus host shifts from managed honey bees, Apis mellifera, are thought to contribute to the decline of wild pollinators. However, data on the impact of such viruses on wild pollinators remain scarce, and how landscape structure may affect virus transmission is poorly understood. We experimentally deployed bumble bee colonies in an agricultural land...

The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines1. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear2-5. Unregulated hunting can empty PAs of large...

Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-indu...

Isolation of wildlife populations represents a key conservation challenge in the twenty-first century. This may necessitate consideration of translocations to ensure population viability. We investigated the potential population and genetic trajectory of a small, isolated tiger (Panthera tigris) population in Thailand’s Dong Phayayen-Khao Yai fores...

Today there is increasing investigation of how to succeed in land operations without damaging delicate natural ecosystems. Over the past century, the planning of land interventions operated without following a guideline has led to fragmentation of ecosystems and progressive biodiversity loss. Several strategies have emerged in this regard to identi...

Intensification of human activities is pushing our use of ecosystems beyond thresholds of resiliency. Given the accelerating global crisis of ecological sustainability, there has been enormous growth in research related to ecological security. However, differences in opinions on ecological security have hindered understanding and effective applicat...

Wildlife conservation necessitates understanding spatiotemporal drivers that facilitate disease outbreaks. Wildlife diseases are influenced by population and landscape level factors which affects host species’ persistence through time. Recurrent pneumonia outbreaks in bighorn sheep have impeded population recovery throughout the western US. Recover...

Context Identifying core habitat areas and corridors is a first step to ensuring suitable areas are available to support movement and gene flow. The pygmy rabbit (Brachylagus idahoensis) is a species of concern and a sagebrush obligate of the arid Great Basin, yet a habitat network of core areas and corridors for this species has not been assessed....

Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns. We test the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide S...

Context The accurate estimation of landscape resistance to movement is important for ecological understanding and conservation applications. Rigorous estimation of resistance requires validation and optimization. One approach uses genetic data for the optimization or validation of resistance models. Objectives We used a genetic dataset of snow leo...

Large and severe wildfires, exacerbated by climate change and human behavior, are occurring more frequently in many forests across the western United States. While wildfire is a natural part of most terrestrial ecosystems, rapidly changing fire regimes have the potential to alter habitat beyond the adaptive capabilities of species. Spatial assessme...

Ecological sustainability has recently risen to prominence in scientific research and management applications. Approaches to measuring ecological connectivity and their application to optimize ecological network (EN) design are powerful tools against landscape fragmentation and biodiversity loss. We focused on building an EN by identifying the most...

Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China’s warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To...

Darwin proposed that the capacity of organisms to produce more offspring that can be supported by the environment would lead to a struggle for existence, and individuals that are most fit for survival and reproduction would be selected through natural selection. Ecology is the science that studies the interaction between organisms and their environ...

ContextConservation approaches focussed within protected areas (PAs) have proved successful for tiger (Panthera tigris) conservation in India, but India’s growing tiger population requires a landscape-level approach to ensure protection of both source populations and dispersing individuals. Thus, spatially explicit mapping of corridors to support e...

Many protected areas worldwide increasingly resemble habitat isolates embedded in human-modified landscapes. However, establishing linkages among protected areas could significantly reduce species-loss rates. Here we present a novel method having broad applicability for assessing enhanced regional connectivity on persistence of mammal diversity. We...

Fragmentation of habitat, for example by intensive agricultural practices, can be detrimental to local biodiversity. However, it often remains unclear whether such biodiversity declines are caused by loss of habitat area or increased fragmentation, and how habitat quality factors into it. In our study system, vegetated vineyards are typically small...

Ensemble habitat selection modeling is becoming a popular approach among ecologists to answer different questions. Since we are still in the early stages of development and application of ensemble modeling, there remain many questions regarding performance and parameterization. One important gap, which this paper addresses, is how the number of bac...

Context Recent increases in ecological disturbances driven by climate change and our expanding human footprint make it challenging for natural resource managers to keep apprised of current conditions and adjust management plans accordingly. To effectively conserve species in highly dynamic landscapes requires more timely habitat monitoring and a mo...

Context Understanding habitat dynamics is essential for effective conservation as landscapes rapidly change. In a companion paper in this issue, Shirk et al. (2022) introduced an automated habitat monitoring system using Google Earth Engine and applied this framework to develop a dynamic model of Mexican spotted owl (Strix occidentalis lucida) habi...