Samuel Cushman

Samuel Cushman
United States Forest Service, Rocky Mountain Research Station · Forest and Woodlands Ecosystem Program

PhD

About

353
Publications
117,696
Reads
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22,286
Citations
Introduction
Samuel Cushman is a Senior Research Landscape Ecologist at the Rocky Mountain Research Station, in Flagstaff, Arizona, USA. He studies a range of topics in spatial ecology and conservation, including landscape pattern analysis, landscape dynamic simulation modeling, landscape genetics, movement and connectivity ecology, species distribution and habitat relationships modeling, and scenario optimization for natural resources management and conservation.
Additional affiliations
March 2019 - present
United States Forest Service
Position
  • Senior Researcher
February 2016 - present
University of Oxford
Position
  • Research Associate
November 2012 - present
Frontiers in genetics
Position
  • Specialty chief editor for evolutionary and population genetics
Education
July 1998 - December 2006
University of Massachusetts Amherst
Field of study
  • Organismic and Evolutionary Biology
September 1995 - December 1997
Western Washington University
Field of study
  • Landscape Ecology
June 1992 - March 1995
The Evergreen State College
Field of study
  • Ecology

Publications

Publications (353)
Article
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...
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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...
Presentation
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...
Presentation
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...
Article
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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...
Article
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...
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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...
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Geography is a fundamentally important discipline that provides a framework for understanding the complex surface of our Earth [...]
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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...
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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...
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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...
Preprint
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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...
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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...
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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...
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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...
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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,...
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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...
Article
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...
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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...
Article
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...
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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...
Article
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...
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ContextUnited Nations outlined 17 Sustainable Development Goals (SDGs), but at the current rate of progress most will not be achieved within the desired timeframe. Since a third of SDGs are directly related to land resources, it is crucial to improve the effectiveness and efficiency of land-use planning. In that regard, there is particular value in...
Article
Oceanographic features such as currents, waves, temperature, and salinity, together with life history traits, control patterns and rates of gene flow and contribute to shaping the population genetic structure of marine organisms. Seascape genetics is an emerging discipline that adopts a spatially‐explicit approach to examine biotic and abiotic fact...
Preprint
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Macrosystems ecology is an emerging science that aims to integrate traditionally distinct disciplines to predict how hierarchical interacting processes influence the emergence of complex patterns across local to regional and global scales. Despite increased focus on cross-scale relationships and cross-disciplinary integration, few macroecology stud...
Article
Sampling bias and autocorrelation can lead to erroneous estimates of habitat selection, model overfitting and elevated omission rates. We developed a multi-scale habitat suitability model of the flammulated owl (Psiloscops flammeolus) in the Northern Rocky Mountains based on extensive but spatially clustered survey data, and then used simulations t...
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Background Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. Results Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological res...
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Southern Iran is a conservation priority area for the endangered Persian onager (Equus hemionus onager), which is threatened by habitat fragmentation and conflict with local communities. To better understand factors that influence onager conservation, we administered a questionnaire in local communities to survey their ecological knowledge, persona...
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The article Optimization of spatial scale, but not functional shape, affects the performance of habitat suitability models: a case study of tigers (Panthera tigris) in Thailand, written by Eric Ash, David W. Macdonald, Samuel A. Cushman, Adisorn Noochdumrong, Tim Redford and Zaneta Kaszta, was originally published online on 12 January 2021 with Ope...
Article
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Habitat loss and fragmentation are increasingly disrupting natural ecosystems across the world, especially in areas that have experienced extensive recent anthropogenic land use change. Evaluating multi-dispersal scenarios of ecological connectivity networks provides an important means to evaluate how dispersal ability influences the prediction of...
Article
An important line of scholarship concludes that stemming the biodiversity crisis requires widespread nonanthropocentric modes of action and decision-making. In this regard, knowing what would even constitute a nonanthropocentric economic decision-making framework is hobbled by failing to recognize a conflation in the taxonomy of capital as supposed...
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Context Understanding the environmental and anthropogenic factors influencing habitat selection of multiple species is a foundation for quantifying human impacts on biodiversity and developing effective conservation measures. Objectives To determine the effect of multiple scales of environmental/topographic and anthropogenic variables and landscap...
Article
Genetic mechanisms of species local adaptation are an emerging topic of great interest in evolutionary biology and molecular ecology. In this study, we compared the changes of physiological and phenotypic indexes and gene expression of four weeping forsythia populations under cold stress through a common garden experiment. Physiological and phenoty...
Article
The encroachment of pinyon-juniper woodlands into sagebrush habitat in the Great Basin Ecoregion of the western USA, represents a potential source of habitat degradation for sagebrush-associated wildlife species. To restore sagebrush habitat, managers are conducting large-scale conifer removal efforts within the Great Basin, particularly within Gre...
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Effective conservation and land management require robust understanding of how landscape features spatially and temporally affect population distribution, abundance and connectivity. This is especially important for keystone species known to shape ecosystems, such as the African elephant (Loxodonta africana). This work investigates monthly patterns...
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The community–continuum concept subsumes two contrasting yet complementary approaches to characterizing ecological communities (i.e., species assemblages) that simultaneously embrace communities as distinct and repeatable units while recognizing the continuous nature of their compositional variation. While both terms reference physical entities pop...
Article
Species distribution models (SDMs) are the primary tools currently available for assessing vulnerability to climatic change. Most past projections of the effects of climate change on species distribution have ignored biological interactions. We evaluated to what degree incorporating prey availability into climatic-based SDMs would change the predic...
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Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our s...
Chapter
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Mean surface temperatures have increased globally by ~0.7 °C per century since 1900 and 0.16 °C per decade since 1970 (Levinson and Fettig 2014). Most of this warming is believed to result from increases in atmospheric concentrations of greenhouse gases produced by human activity. Temperature increases have been greater in winter than in summer, an...
Article
Climate change and land use change jointly are the largest drivers of population declines, range contraction and extinction for many species across the globe. Wide‐ranging and large‐bodied species are especially vulnerable to habitat loss and fragmentation due to their typically low population densities, reflecting their need for extensive and conn...
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Habitat loss and fragmentation are key drivers of biodiversity loss. However, they are usually confounded, making it difficult to separate fragmentation effects from those of habitat loss. In addition, it has been shown that often fragmentation negatively affects biodiversity only below a certain threshold of habitat amount. We investigated the sep...
Article
Context Species habitat suitability models rarely incorporate multiple spatial scales or functional shapes of a species’ response to covariates. Optimizing models for these factors may produce more robust, reliable, and informative habitat suitability models, which can be beneficial for the conservation of rare and endangered species, such as tiger...
Preprint
Central Iran supports a diversity of carnivores, most of which are threatened by habitat loss and fragmentation. Carnivore conservation requires the identification and preservation of core habitats and ensuring connectivity between them. In the present study, we applied species distribution modeling to predict habitat suitability and used connectiv...
Article
Identifying factors that create and maintain a hybrid zone is of great interest to ecology, evolution and, more recently, conservation biology. Here, we investigated the role of environmental features in shaping the spatial dynamics of a hybrid zone between the southern tigrina, Leopardus guttulus, and Geoffroy’s cat, L. geoffroyi, testing for exog...
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Iran lies at the southernmost range limit of brown bears globally. Therefore, understanding the habitat associations and patterns of population connectivity for brown bears in Iran is relevant for the species’ conservation. We applied species distribution modeling to predict habitat suitability and connectivity modeling to identify population core...
Article
Jaguars (Panthera onca), like other apex predators, are highly susceptible to habitat loss and fragmentation given their low demographic potential and large habitat area requirements. Across their range, the Pantanal is considered critical for the jaguar's long-term conservation. Here we provide the first multi-scale path selection function model f...
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Western North American forest ecosystems are experiencing rapid changes in disturbance regimes because of climate change and land use legacies (Littell et al. 2018). In many of these forests, the accumulation of surface and ladder fuels from a century of fire suppression, coupled with a warming and drying climate, has led to increases in the number...
Preprint
Full-text available
At least nine felid species can co-occur in Southeast Asia, thus providing an unusual opportunity to investigate poorly known guild structure and the factors controlling it. Using camera-trap data, we quantified space use, temporal activity, and multi-dimensional niche overlap of tiger, clouded leopard, marbled cat, leopard cat, and Asiatic golden...
Article
Full-text available
Scientists at the Rocky Mountain Research Station are helping managers better understand how climate change, wildfire, and forest management interact to drive forest changes. It is important to define what those changes mean for the ecology and conservation of the Mexican spotted owl. In the Southwest, scientists and managers are working together t...
Article
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Background Fire size and severity have increased in the western United States in recent decades, and are expected to continue to increase with warming climate. Habitats for many species are threatened by large and high-severity fires, but the effect of spatial scale on the relationship between fires and habitat modifications is poorly understood. W...
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Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled...
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Rates of biodiversity loss in Southeast Asia are among the highest in the world, and the Indo-Burma and South-Central China Biodiversity Hotspots rank among the world's most threatened. Developing robust multi-species conservation models is critical for stemming biodiversity loss both here and globally. We used a large and geographically extensive...
Article
Full-text available
Rates of biodiversity loss in Southeast Asia are among the highest in the world, and the Indo-Burma and South-Central China Biodiversity Hotspots rank among the world’s most threatened. Developing robust multi-species conservation models is critical for stemming biodiversity loss both here and globally. We used a large and geographically extensive...
Article
Full-text available
1.The coordination of traits from individual organs to whole plants is under strong selection because of environmental constraints on resource acquisition and use. However, the tight coordination of traits may provide underlying mechanisms of how locally adapted plant populations can become maladapted because of climate change. 2.To better understa...
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Understanding the genetic basis underpinning local adaptation is one of the fundamental issues in ecological and evolutionary biology. In this study, we investigated the genomic basis underlying local adaptation of the Chinese wingnut (Pterocarya stenoptera C. DC). Our population genomic analyses revealed nine spatial genetic clusters across the cu...