Samuel Cushman

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

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...

ContextReductions in the tiger’s (Panthera tigris) range in Southeast Asia have been concurrent with large infrastructure expansion and landscape change. Thailand’s Dong Phayayen-Khao Yai Forest Complex (DPKY), a landscape of tiger conservation priority, may be particularly vulnerable to such changes, necessitating investigations into effects on po...

Aim The use of landscape resistance maps to model connectivity has become an indispensable tool for species conservation. However, different methods can be used to estimate landscape resistance, but there is no consensus on which is the most reliable one. Therefore, comparing the performance of those methods in predicting resistance can be quite us...

Landscape connectivity, the extent to which a landscape facilitates the flow of ecological processes such as organism movement, has grown to become a central focus of applied ecology and conservation science. Several computational algorithms have been developed to understand and map connectivity, and many studies have validated their predictions us...

Aim Predict empirically the current and recent historical (c1970) landscape connectivity and population size of the African lion as a baseline against which to assess conservation of the species. Location Continental Africa. Methods We compiled historical records of lion distribution to generate a recent historical range for the species. Historic...

Purpose of Review Climate change will continue to alter spatial and temporal variation in fire characteristics, or pyrodiversity. The causes of pyrodiversity and its consequences for biological communities are emerging as a promising research area with great potential for understanding and predicting global change. We reviewed the literature relate...

Landscape connectivity, the extent to which a landscape facilitates the flow of ecological processes such as organism movement, has emerged as a central focus of landscape ecology and conservation science. Connectivity modelling now encompasses an enormous body of work across ecological theory and application. The dominant connectivity models in us...

Multiple studies have used species distribution models to identify human–wildlife conflict drivers. An important application of these models is spatial conflict resolution by accounting for habitat suitability and corridors. We used distribution and connectivity models to identify habitats and corridors for brown bear Ursus arctos in southwestern I...

Climate and land use change are among the main drivers affecting virtually all species on earth. There were extensive studies projecting impacts of climate and land use changes on habitat loss and fragmentation but few on connectivity loss, and those that investigated connectivity did not disentangle the combined effects between climate change and...

Aim The synergy between human land use and climate change is accelerating the global decline of biodiversity. In the fragile Himalayas, this trend has a strong ecological impact on wildlife communities, and a better understanding is needed to discern changes in the mechanisms. This study aims to understand the effects of land use and climate change...

Comparing spatial variations in habitat selection is particularly important for understanding species that exhibit bi-modal or multimodal habitat use. One such species is the federally listed threatened Mexican spotted owl (Strix occidentalis lucida), which specializes in canyonland habitat and forest habitat. To effectively conserve the species ac...

Multi-scale optimization models are often used to compare species-habitat relationships between multiple species. This approach can be especially useful in understanding the nuances between closely-related species that are typically perceived as having similar relationships with their environments. Two threatened subspecies of spotted owl - Norther...

One of the greatest challenges China faces is how to conserve biodiversity during intensive urban and rural development. Ecological connectivity network modelling is a planning strategy that is increasingly used to achieve habitat and biodiversity conservation goals. Often, researchers have not given enough attention to the comparison of different...

As landscape‐scale conservation models grow in prominence, assessments of how wildlife utilise multiple‐use landscapes are required to inform effective conservation and management planning. Such efforts should incorporate multi‐species perspectives to maximise value for conservation, and should account for scale to accurately capture species‐enviro...

Understanding organism movement is at the heart of many ecological disciplines. The study of landscape connectivity—the extent to which a landscape facilitates organism movement—has grown to become a central focus of spatial ecology and conservation science. Several computational algorithms have been developed to model connectivity; however, the ma...

Geography is a fundamentally important discipline that provides a framework for understanding the complex surface of our Earth [...]

ContextArtificial Intelligence (AI) has rapidly developed over the past several decades. Several related AI approaches, such as Machine Learning (ML), have been applied to research on landscape patterns and ecological processes.Objectives Our goal was to review the methods of AI, particularly ML, used in studies related to landscape ecology and the...

In the face of a growing human footprint, understanding interactions among threatened large carnivores is fundamental to effectively mitigating anthro- pogenic threats and managing species. Using data from a large-scale camera trap survey, we investigated the effects of environmental and anthropogenic variables on the interspecific interaction of a...

As ecological data and associated analyses become more widely available, synthesizing results for effective communication with stakeholders is essential. In the case of wildlife corridors, managers in human-dominated landscapes need to identify both the locations of corridors and multiple stakeholders for effective oversight. We synthesized 5 indep...

Context The assessment of landscape-level connectivity patterns is centrally important to the conservation management of wildlife species. This is especially true for highly vagile carnivore species, for which conservation efforts should extend beyond protected areas and link core populations. Objectives We investigated the effectiveness of the Qil...

Species occur in sympatric assemblages, bound together by ecological relationships and interspecific interactions. Borneo and Sumatra host some of the richest assemblages of biota worldwide. The region, however, faces the highest global deforestation rates, which seriously threaten its unique biodiversity. We used a large camera trap dataset that r...

Context Few habitat modeling studies consider multiple spatial or temporal scales; less identify the operative scale of an organism's response to predictor variables. Optimizing habitat suitability models yields robust, reliable inferences about species-habitat relationships that can inform conservation efforts for species, such as jaguars (Panther...

Several methods have been recently proposed to calculate configurational entropy, based on Boltzmann entropy. Some of these methods appear to be fully thermodynamically consistent in their application to landscape patch mosaics, but none have been shown to be fully generalizable to all kinds of landscape patterns, such as point patterns, surfaces,...

The co-occurrence of felid species in Southeast Asia provides an unusual opportunity to investigate guild structure and the factors controlling it. Using camera-trap data, we quantified the space use, temporal activity, and multi-dimensional niche overlap of the tiger, clouded leopard, Asiatic golden cat, marbled cat, and leopard cat in the Htamant...

Understanding the spatial structure of genetic diversity provides insights into a populations’ genetic status and enables assessment of its capacity to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, a conservation flagship species of Central Asia mountains. Focusing on a snow leopard population...

There has been a recent surge of interest in theory and methods for calculating the entropy of landscape patterns, but relatively little is known about the thermodynamic consistency of these approaches. I posit that for any of these methods to be fully thermodynamically consistent, they must meet three conditions. First, the computed entropies must...

This paper presents a multivariate textual analysis of more than 1300 papers on entropy in ecology. There are six main insights that emerged. First, there is a large body of literature that has addressed some aspect of entropy in ecology, most of which has been published in the last 5-10 years. Second, the vast majority of these papers focus on spe...

Climate refugia management is an emerging natural resource sub-discipline but identifying which species would benefit, their climatic requirements, and where both species and suitable conditions are located remains problematic. Land snails have species specific temperature needs and are one of the most imperiled groups of animals. The goal of our s...

How the observed occurrences of a species relate to environmental gradients is a fundamental question in community ecology. In this paper, we present a new approach to address this question, using the smoothing function, a method not previously recruited into this ecological context. Using simulation techniques, we explore its accuracy in recoverin...

Aims In the sagebrush ecosystems of the western United States, identifying and enhancing habitat for large ungulates has become an increased priority for many management agencies, as indicated by Department of Interior Secretarial Order 3362. Estimating and understanding current and future habitat suitability and connectivity is important for succe...