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Propagating observation errors to enable scalable and rigorous enumeration of plant population abundance with aerial imagery

Estimating and monitoring plant population size is fundamental for ecological research, as well as conservation and restoration programs. High-resolution imagery has potential to facilitate such estimation and monitoring. However, remotely sensed estimates typically have higher uncertainty than field measurements, risking biased inference on population status. We present a model that accounts for false negative (missed plants) and false positive (misclassified or double-counted plants) error in counts from high-resolution imagery via integration with ground data. We apply it to estimate the abundance of a foundational shrub species in post-wildfire landscapes in the western United States. In these landscapes, plant recruitment is crucial for ecological recovery but locally patchy, motivating the use of spatially extensive measurements from unoccupied aerial systems (UAS). Integrating >16 ha of UAS imagery with >700 georeferenced field plots, we fit our model to generate insights into the prevalence and drivers of observation errors associated with classification algorithms used to distinguish individual plants, relationships between abundance and landscape context, and to generate spatially explicit maps of shrub abundance. Raw counts of plant abundance in high-resolution imagery resulted in substantial false negative and false positive observation errors. The probability of detecting ( p ) adult plants (≥0.25 m tall) varied between sites within 0.52 < p̂adult < 0.82, whereas the detection of smaller plants (<0.25 m) was lower, 0.03 < p̂small < 0.3. On average, we estimate that 19% of all detected plants were false positive errors, which varied spatially in relation to topographic predictors. Abundance declined toward the interior of previous wildfires and was positively associated with terrain roughness. Our study demonstrates that integrated models accounting for imperfect detection improve estimates of plant population abundance derived from inherently imperfect UAS imagery. We believe such models will further improve inference on plant population dynamics—relevant to restoration, wildlife habitat and related objectives—and echo previous calls for remote sensing applications to better differentiate between ecological and observational processes.

Methods in Ecology and Evolution

Riverscape approaches in practice: Perspectives and applications

Landscape perspectives in riverine ecology have been undertaken increasingly in the last 30 years, leading aquatic ecologists to develop a diverse set of approaches for conceptualizing, mapping and understanding ‘riverscapes’. Spatiotemporally explicit perspectives of rivers and their biota nested within the socio-ecological landscape now provide guiding principles and approaches in inland fisheries and watershed management. During the last two decades, scientific literature on riverscapes has increased rapidly, indicating that the term and associated approaches are serving an important purpose in freshwater science and management. We trace the origins and theoretical foundations of riverscape perspectives and approaches and examine trends in the published literature to assess the state of the science and demonstrate how they are being applied to address recent challenges in the management of riverine ecosystems. We focus on approaches for studying and visualizing rivers and streams with remote sensing, modelling and sampling designs that enable pattern detection as seen from above (e.g. river channel, floodplain, and riparian areas) but also into the water itself (e.g. aquatic organisms and the aqueous environment). Key concepts from landscape ecology that are central to riverscape approaches are heterogeneity, scale (resolution, extent and scope) and connectivity (structural and functional), which underpin spatial and temporal aspects of study design, data collection and analysis. Mapping of physical and biological characteristics of rivers and floodplains with high-resolution, spatially intensive techniques improves understanding of the causes and ecological consequences of spatial patterns at multiple scales. This information is crucial for managing river ecosystems, especially for the successful implementation of conservation, restoration and monitoring programs. Recent advances in remote sensing, field-sampling approaches and geospatial technology are making it increasingly feasible to collect high-resolution data over larger scales in space and time. We highlight challenges and opportunities and discuss future avenues of research with emerging tools that can potentially help to overcome obstacles to collecting, analysing and displaying these data. This synthesis is intended to help researchers and resource managers understand and apply these concepts and approaches to address real-world problems in freshwater management.

Biological Reviews

Springs as hydrologic refugia in a changing climate? A remote sensing approach

Spring‐fed wetlands are ecologically important habitats in arid and semi‐arid regions. Springs have been suggested as possible hydrologic refugia from droughts and climate change; however, springs that depend on recent precipitation or snowmelt for recharge may be vulnerable to warming and drought intensification. Springs that are expected to maintain their ecohydrologic function in a warmer, drier climate may be priorities for conservation and restoration. Identifying such springs is difficult because many springs lack hydrologic records of adequate temporal extent and resolution to assess their resilience to water cycle changes. This study demonstrates proof‐of‐concept for the assessment of certain spring types (i.e., helocrene, hypocrene, and hillslope springs) in terms of hydrologic and ecological resilience to climatic water stress using freely available remote‐sensing and climate data. We used the Normalized Difference Vegetation Index (NDVI) from 1985 through 2011 to delineate surface‐moisture zones (SMZs) associated with 39 clusters of 172 springs in a montane sage‐steppe landscape in southeastern Oregon, USA. We developed and synthesized seven NDVI‐based indicators of SMZ resilience to interannual changes in water availability: (1) mean and (2) standard deviation of July NDVI; (3) mean difference in July NDVI and (4) difference in coefficient of variation for July NDVI between each SMZ and its surrounding watershed; (5) response of SMZ July NDVI to 90‐day antecedent precipitation; (6) response of SMZ July NDVI to the previous winter's snowpack; and (7) range of NDVI values from an exceptionally wet year followed by three dry years. Because all resilience indicators were highly inter‐correlated, we derived an overall metric of SMZ resilience using principal components analysis that accounted for 66% of total variance. This overall resilience score was positively correlated with SMZ elevation, slope, mean annual precipitation, and with the number of associated springs. Resilience was greater for SMZs on topographically shaded, north‐facing slopes. Several high‐resilience SMZs were located immediately below persistent snowbanks, suggesting a possible source of steady recharge throughout the growing season. The approach presented here—if combined with field assessments of spring hydrogeology, discharge, and groundwater age—could help identify spring‐fed wetlands that are most likely to serve as hydrologic refugia from climate change.

Oregon

Post-wildfire sediment fluxes and turbidity plumes in a coastal-draining watershed

Coastal watersheds impacted by wildfires experience higher erosion resulting in increased sediment delivery to the ocean that alters limiting factors (i.e., light) for marine organisms. With increasing wildfire magnitude and severity, it is critical to explore changes in riverine discharges to the ocean to assess cascading hazards associated with wildfires. In situ data, remotely sensed turbidity data, and hydrological model (Soil and Water Assessment Tool “SWAT”) simulations have been adapted to capture and investigate fire-related land use change impacts on Malibu Creek, California, USA. Modifying SWAT land cover inputs using burn severity data had minimal impact on simulations, requiring additional parameterization for acceptable model performance. Remotely sensed turbidity, in situ discharge, rating curve sediment loads, and SWAT simulated discharge and sediment loads increased following the Woolsey Fire. When compared to in situ and rating curve data in similar non-fire water years, the 2019 Woolsey Fire water year in situ discharge was 1.8 times higher, SWAT simulated discharges were 1.4–1.7 times higher, and rating curve sediment load was 1.3 times higher. However, the SWAT simulated sediment loads were slightly lower (0.8–0.9 times) than rating curve sediment loads in similar non-fire water years. Mean coastal turbidity increased to 18.2 Formazin Nephelometric Unit (FNU) during the first storm post-fire (mean background value of 4.3 FNU). Synergies between methods demonstrated rapid coastal sediment exports (remote sensing) and ongoing erosion post-fire (SWAT). These data are essential to understanding fire-related marine ecological changes and implementing effective management and conservation initiatives.

California

2023-2024 Coastal sage scrub and chaparral community monitoring for western San Diego County

Western San Diego County is dominated by shrublands supporting biologically diverse native plant and animal communities. Widespread urbanization has led to regional habitat loss and fragmentation, and many species in these shrubland communities are rare, threatened, or endangered. Large-scale, multiple-species conservation planning has resulted in a regional preserve system that focuses on these shrubland communities. Several large-scale threats are leading to type conversion from shrub-dominated to non-native invasive annual grass-dominated vegetation. To understand the changes that are occurring to native shrublands, we have developed a vegetation monitoring program with several components at multiple spatial scales, focused on quantifying coastal sage scrub (CSS) and chaparral vegetation community characteristics. Several drivers of change associated with type conversion of native shrubland to non-native annual grassland have been identified by previous research including increasing fire frequency, nitrogen deposition from air pollution, and prolonged and intense drought associated with changing climate. Loss of ecological integrity indices have been proposed as useful measures of the threat of degradation and type conversion of shrublands in San Diego County. For this study, ecological integrity is defined as a system’s ability to maintain species’ relationships and functions comparable to natural habitat in the region. Previous studies have identified the percent cover of invasive non-native annual grasses as a proxy for overall ecological degradation (loss of integrity) that is consistent across native taxonomic groups. Increased cover of non-native grass is associated with lower integrity of the shrubland vegetation community as shrub-associated plant and animal species are replaced by species preferring grassy and disturbed habitats. The objectives of this CSS and chaparral vegetation community monitoring plan are to: 1) Determine the distribution, composition, structure, and integrity of CSS and chaparral vegetation communities on conserved lands in western San Diego County, 2) Identify whether these attributes of the vegetation communities are changing over time, and 3) Evaluate relationships of known drivers of change (threats) and environmental factors in association with changes in vegetation community attributes. The CSS and chaparral vegetation community monitoring program is divided into four components: 1) vegetation mapping, 2) GIS/remote sensing office analysis of landscape-scale data, 3) permanent field plots using Unmanned Aerial Systems (UAS) and field data collections, and 4) animal and target species surveys and rapid assessment protocols. The first component, which is not detailed in this vegetation monitoring plan, aims to map vegetation communities every 10-15 years based on a classification developed for western San Diego County. High resolution aerial imagery will be used to update the 2012 vegetation map and expand it across the entire study area. The second component uses remote sensing models to annually track ecological integrity of shrublands across the study area and will include a map of areas of change and areas of stability over several decades. These landscape-scale integrity classifications will be used to analyze ecological processes, threats, and abiotic factors relative to changes to shrubland ecological integrity over time and space. The third component includes field surveys of 100 permanent plots across areas historically mapped as shrublands. Surveys in the 1930s mapped vegetation types using plot data. By using this historical classification map, we included areas that have already type-converted from shrubland to non-native annual grassland. The plots were split between CSS (55 plots) and chaparral (45 plots) and stratified into four geographical eco-subregions to guarantee coverage over small patches of habitat along the heavily developed coast. Surveys will include the collection of UAS imagery at a very high resolution. Species-level identifications will be made from the imagery based on a plant list compiled of all species detected in the plot during a thorough field survey by botanists, combined with geo-referenced samples of plant species locations. In addition, herbaceous cover will be estimated in the field using nine 1-m diameter circles (one per subplot) to obtain ocular estimates of cover for each plant species within the circle frame. Soil samples will be collected and analyzed for important element compositions. These data will be analyzed to evaluate plot-level ecological integrity based on species composition and cover. Repeated monitoring will allow evaluation of changes in vegetation attributes over time with known drivers or threats and other environmental factors. In addition, analyses will focus on indicator species and various measures of biological diversity for the vegetation communities. Finally, animal species and rare plants will be assessed using either taxa-based rapid assessment protocols or specialized species-specific protocols for rarer species. The purpose of these assessments is to document the status, habitat, and threat covariates of specific species and confirm the species composition and diversity of animal taxonomic groups (e.g., pollinators). Diversity and abundance of animal species at vegetation plots will be used to refine measures and thresholds of ecological integrity. Rapid assessment protocols for animal taxonomic groups can include multiple detection methods such as, camera traps, cover boards, and bird point counts. Pollinators will be monitored at plots using a protocol currently being developed in conjunction with but separately from this plan. Target rare plant species will be monitored using the regional Inspect and Manage (IMG) protocol that measures the status of rare plant occurrences and habitat and threat covariates over time. Species-specific animal survey methods will be refined as these species are prioritized for future monitoring. The goal of this monitoring program is to classify CSS and chaparral vegetation community integrity, identify areas of degradation across western San Diego County, and characterize drivers, and environmental factors associated with loss of ecological integrity. A combination of vegetation mapping, landscape-scale remote sensing, and field plots will be used to address all the aspects of our research questions. Data compiled and collected will be available to conservation partners to help inform future management decisions.

California

Accuracy of gap analysis habitat models in predicting physical features for wildlife-habitat associations in the southwest U.S.

Despite widespread and long-standing efforts to model wildlife-habitat associations using remotely sensed and other spatially explicit data, there are relatively few evaluations of the performance of variables included in predictive models relative to actual features on the landscape. As part of the National Gap Analysis Program, we specifically examined physical site features at randomly selected sample locations in the Southwestern U.S. to assess degree of concordance with predicted features used in modeling vertebrate habitat distribution. Our analysis considered hypotheses about relative accuracy with respect to 30 vertebrate species selected to represent the spectrum of habitat generalist to specialist and categorization of site by relative degree of conservation emphasis accorded to the site. Overall comparison of 19 variables observed at 382 sample sites indicated ???60% concordance for 12 variables. Directly measured or observed variables (slope, soil composition, rock outcrop) generally displayed high concordance, while variables that required judgments regarding descriptive categories (aspect, ecological system, landform) were less concordant. There were no differences detected in concordance among taxa groups, degree of specialization or generalization of selected taxa, or land conservation categorization of sample sites with respect to all sites. We found no support for the hypothesis that accuracy of habitat models is inversely related to degree of taxa specialization when model features for a habitat specialist could be more difficult to represent spatially. Likewise, we did not find support for the hypothesis that physical features will be predicted with higher accuracy on lands with greater dedication to biodiversity conservation than on other lands because of relative differences regarding available information. Accuracy generally was similar (>60%) to that observed for land cover mapping at the ecological system level. These patterns demonstrate resilience of gap analysis deductive model processes to the type of remotely sensed or interpreted data used in habitat feature predictions. ?? 2010 Elsevier B.V.

Ecological Modelling

Mapping cropland fallow areas in myanmar to scale up sustainable intensification of pulse crops in the farming system

Cropland fallows are the next best-bet for intensification and extensification, leading to increased food production and adding to the nutritional basket. The agronomical suitability of these lands can decide the extent of usage of these lands. Myanmar’s agricultural land (over 13.8 Mha) has the potential to expand by another 50% into additional fallow areas. These areas may be used to grow short-duration pulses, which are economically important and nutritionally rich, and constitute the diets of millions of people as well as provide an important source of livestock feed throughout Asia. Intensifying rice fallows will not only improve the productivity of the land but also increase the income of the smallholder farmers. The enhanced cultivation of pulses will help improve nutritional security in Myanmar and also help conserve natural resources and reduce environmental degradation. The objectives of this study was to use remote sensing methods to identify croplands in Myanmar and cropland fallow areas in two important agro-ecological regions, delta and coastal region and the dry zone. The study used moderate-resolution imaging spectroradiometer (MODIS) 250-m, 16-day normalized difference vegetation index (NDVI) maximum value composite (MVC), and land surface water index (LSWI) for one 1 year (1 June 2012–31 May 2013) along with seasonal field-plot level information and spectral matching techniques to derive croplands versus cropland fallows for each of the three seasons: the monsoon period between June and October; winter period between November and February; and summer period between March and May. The study showed that Myanmar had total net cropland area (TNCA) of 13.8 Mha. Cropland fallows during the monsoon season account for a meagre 2.4% of TNCA. However, in the winter season, 56.5% of TNCA (or 7.8 Mha) were classified as cropland fallows and during the summer season, 82.7% of TNCA (11.4 Mha) were cropland fallows. The producer’s accuracy of the cropland fallow class varied between 92 and 98% (errors of omission of 2 to 8%) and user’s accuracy varied between 82 and 92% (errors of commission of 8 to 18%) for winter and summer, respectively. Overall, the study estimated 19.2 Mha cropland fallows from the two major seasons (winter and summer). Out of this, 10.08 Mha has sufficient moisture (either from rainfall or stored soil water content) to grow short-season pulse crops. This potential with an estimated income of US\$ 300 per hectare, if exploited sustainably, is estimated to bring an additional net income of about US\$ 1.5 billion to Myanmar per year if at least half (5.04 Mha) of the total cropland fallows (10.08 Mha) is covered with short season pulses.

GIScience and Remote Sensing

An inventory and typology of permanent floodplain lakes in the Mississippi alluvial valley: A first step to conservation planning

The alluvial valley of the Mississippi River is an extensive area harboring hundreds of lakes created by fluvial dynamics. These floodplain lakes are scattered throughout the valley and carved over thousands of years by shifting river courses and other hydro-fluvial processes associated with contemporary and prehistoric rivers. These lakes have significant ecological importance as they support a large component of North American biodiversity. We used remote sensing to catalog lakes, to characterize morphology, and to construct a typology via cluster analysis. We identified over 1,300 permanent lakes totaling over 100,000 ha. The lakes were classified into 12 types according to lake size, shape, depth, connectivity, inundation frequency, and surrounding landcover. We anticipate that biotic characteristics differ among the 12 types, but large-scale systematic analyses of biotic assemblages of floodplain lakes in the region are mostly absent. Our typology can provide the framework essential for organizing research to define water dynamics, water quality, and ecological conditions such as forests, mussel, fish, and avian communities to construct conservation plans. The typology encourages a large-scale view of the properties of floodplain lakes in the alluvial valley. It is a functional tool that can be used to begin identifying conservation and research needs, adapt monitoring and management programs, customize environmental programs, and use conservation resources more effectively to achieve large-scale management objectives.

Mississippi River

A sagebrush conservation design to proactively restore America’s sagebrush biome

A working group of experts with diverse professional backgrounds and disciplinary expertise was assembled to conceptualize a spatially explicit conservation design to support and inform the Sagebrush Conservation Strategy Part 2. The goal was to leverage recent advancements in remotely sensed landcover products to develop spatially and temporally explicit maps of sagebrush rangeland condition and landscape threats. In addition, the group sought to provide a common basis for understanding the state of sagebrush rangelands through time. First, the study team developed a spatially explicit model to assess geographic patterns in sagebrush ecological integrity and used this model to identify core sagebrush areas (CSAs), growth opportunity areas (GOAs), and other rangeland areas (ORAs) across the biome. Among the identified rangelands, 33.4 million acres were classified as CSAs; 84.3 million acres as GOAs; and 127.2 million acres as ORAs as of 2020. Second, the team sought to demonstrate the ecological relevance of the identified CSAs and GOAs by comparing these data with independent datasets for sagebrush obligate species of conservation concern. Geographical patterns in sagebrush ecological integrity were strongly associated with the occurrence of high-priority species and also displayed clear links to population performance for greater sage-grouse. Third, the team parsed out the type, location, and acres of primary threats within the different categories (CSAs, GOAs, and ORAs) to help focus active management by identifying places where multiagency and organization efforts can protect CSAs and GOAs that have higher levels of integrity with lower cumulative threats. The assessment of the condition of the sagebrush biome (that is, the location, amount, and conservation status) indicated that complex ecosystem function problems are driving ~73 percent of the demonstrated threats within the CSAs and GOAs (rather than point-source problems, such as human development). Fourth, the team developed trend estimates for the identified CSAs and GOAs and three selected primary threats (invasive annual grasses, conifer encroachment, and human modification) to the sagebrush biome from 2001 to 2020. Results showed that an average of 1.3 million acres per year have transitioned to ORAs at an annual rate of −1.34 percent. Fifth, the team developed an approach to integrate climate change effects into the threat-based landscape conservation design and conducted an initial assessment on the magnitude of near-term climate effects in the context of observed historical trends. The team’s analysis suggests that climate change alone is unlikely to be the dominant threat to sagebrush ecological integrity in the next few decades, although interactions of climate with wildfire and invasive annual grasses may be an important threat, especially in the longer term. A spatial overlap analysis was performed and highlighted 45.8 million acres of shared priorities among existing conservation frameworks to help anchor and guide collaborative landscape-scale conservation of areas that still have no to low threats. This information is critical to provide context for decisions about the volume and nature of conservation actions and funding requirements.

western United States

Landscape capability models as a tool to predict fine-scale forest bird occupancy and abundance

Context Species-specific models of landscape capability (LC) can inform landscape conservation design. Landscape capability is “the ability of the landscape to provide the environment […] and the local resources […] needed for survival and reproduction […] in sufficient quantity, quality and accessibility to meet the life history requirements of individuals and local populations.” Landscape capability incorporates species’ life histories, ecologies, and distributions to model habitat for current and future landscapes and climates as a proactive strategy for conservation planning. Objectives We tested the ability of a set of LC models to explain variation in point occupancy and abundance for seven bird species representative of spruce-fir, mixed conifer-hardwood, and riparian and wooded wetland macrohabitats. Methods We compiled point count data sets used for biological inventory, species monitoring, and field studies across the northeastern United States to create an independent validation data set. Our validation explicitly accounted for underestimation in validation data using joint distance and time removal sampling. Results Blackpoll warbler ( Setophaga striata ), wood thrush ( Hylocichla mustelina ), and Louisiana ( Parkesia motacilla ) and northern waterthrush ( P. noveboracensis ) models were validated as predicting variation in abundance, although this varied from not biologically meaningful (1%) to strongly meaningful (59%). We verified all seven species models [including ovenbird ( Seiurus aurocapilla ), blackburnian ( Setophaga fusca ) and cerulean warbler ( Setophaga cerulea )], as all were positively related to occupancy data. Conclusions LC models represent a useful tool for conservation planning owing to their predictive ability over a regional extent. As improved remote-sensed data become available, LC layers are updated, which will improve predictions.

Landscape Ecology

Quantifying regional ecological dynamics using agency monitoring data, ecological site descriptions, and ecological site groups

Information about what ecological conditions are likely, causes or drivers of degradation, and potential management actions to restore degraded lands may support land conservation and restoration decisions. State-and-transition models (STMs) describe persistent plant and ecological conditions that are possible (the “state”) within a given abiotic setting and drivers or actions that can cause shifts between states (the “transitions”). These primarily conceptual models are widely used to inform resource and conservation decisions. Data-driven STMs have been developed for some lands, but not at regional or national scales. Here, we demonstrate a new repeatable workflow for developing data-driven STMs in the United States (US). The approach leverages predictive maps of Ecological Site Groups (ESGs), extensive field-based Federal monitoring databases, information from Ecological Site Description (ESD) STMs, soil erosion models, remotely sensed productivity, and other available spatial information (fire, land protection, and drought) to provide context and descriptions of the data-driven states, including likely drivers of transitions. Results of this workflow applied to one dryland ESG in the Upper Colorado River Basin in the southwestern US suggest that an Invaded state (16% of 1352 plots) and some occurrences of a Grassland state (30% of plots) are in a degraded or at-risk condition with reduced ecosystem services. The most common drivers of state transitions in the associated ESDs ( n = 26) are related to livestock grazing and fire. The Invaded state in the ESG has evidence of degraded habitat quality and accelerated run-off while the Grassland state occurrences show reduced richness, productivity, and elevated erosion risk by wind. Areas subject to wildfire and with lower protection status had greater probability of Invaded state occurrence, generally supporting drivers in ESDs. The workflow presented here can serve as a template for describing ecological dynamics at regional scales, and support prioritization of land for conservation and climate adaptation activities.

Rangeland Ecology & Management

Satellite time series analysis to quantify changing climax ciénegas using a state and transition model approach

Ciénegas are rare wetlands in arid landscapes of the North American Southwest, historically providing critical ecological and hydrological functions but increasingly threatened by changing climate and land use pressures. This study quantifies changes in ciénega condition and floodplain dynamics using a state-and-transition model (STM) informed by expert knowledge and remote sensing. Key factors include woody plant encroachment, water availability, and soil aggradation. We mapped 31 ciénegas with high-resolution imagery and analyzed Landsat data (1985–2023) to assess vegetation health and moisture using the Normalized Difference Vegetation Index (NDVI) and Normalized Difference Infrared Index (NDII). Results show substantial interannual variability in phenology, water stress, and soil moisture, with regional drying and elevation strongly influencing ciénega resilience. We classified ciénegas into three functional states—healthy, desiccated, and dormant—and mapped their 2023 condition. Trend analyses indicate most ciénegas exhibit greening despite drought, though localized variability underscores the need for site-specific management. None are in a stable climax (reference) state; rather, they transition among states in response to external drivers. Increasing woody plant cover and surface drying, likely linked to declining regional water tables, favor deep-rooted species over wetland grasses—a pattern mirrored in adjacent control plots. Spatially explicit analysis revealed intra-ciénega variability often masked by aggregated data, highlighting the importance of high-resolution monitoring. Seasonal and long-term trends provide context for understanding ciénega dynamics, including degradation and restoration pathways. This study emphasizes the importance of groundwater conservation and demonstrates how remote sensing supports long-term monitoring. The STM framework offers a practical tool for adaptive management to sustain freshwater resources in arid environments.

Arizona, New Mexico

Scenario planning and multispecies occupancy models reveal positive avian responses to restoration of afforested woodlands

Scenario planning is a powerful approach for assessing restoration outcomes under alternative futures. However, developing plausible scenarios remains daunting in complex systems like ecological communities. Here, we used Bayesian multispecies occupancy modeling to develop scenarios to assess woodland restoration outcomes in afforested communities in seven wildlife management areas in Arkansas, U.S.A. Our objectives were (1) to define plausible woodland restoration and afforestation scenarios by quantifying historic ranges of variation in mean tree cover and tree cover heterogeneity from 1986 to 2021 and (2) to predict changes in bird species richness and occupancy patterns for six species of greatest conservation need under two future scenarios: complete afforestation (100% tree cover) and woodland restoration (based on remotely sensed historic tree cover). Using 35 years of remotely sensed tree cover data and 6 years of bird monitoring data, we developed multispecies occupancy models to predict future bird species richness and occupancy under the complete afforestation and woodland restoration scenarios. Between 1986 and 2021, tree cover increased in all study areas—with one increasing 70%. Under the woodland restoration scenario, avian species richness increased up to 20%, and four of six species of greatest conservation need exhibited gains in occupancy probability. The complete afforestation scenario had negligible effects on richness and occupancy. Overall, we found decreasing tree cover to historic levels prior to widespread afforestation would provide community-level benefits and would do little harm even to forest-dependent species of conservation concern. Applying multispecies occupancy modeling within a scenario planning framework allows for comparing multiscale trade-offs between plausible futures.

Restoration Ecology

A framework for guiding management decisions for amphibians in an uncertain future

Managing species in a rapidly changing climate requires knowledge of how species will respond to climate change and other threats while simultaneously developing management actions to reduce threats. Amphibians are one of the most threatened taxa on earth and often serve as the ‘canary in the coalmine’ for the health of ecosystems that countless other species and humans rely on. To understand the status of and guide management for the boreal toad (Anaxyrus boreas boreas), an imperiled amphibian species in the North Central region, we coproduced several products with the Boreal Toad Conservation Team. These products included 1) reconstructed seasonal hydrology patterns for historical boreal toad breeding wetlands and high elevation watersheds in the Southern Rocky Mountain Region (SRMR) from remotely sensed data, 2) current and future predictions of drying rates for historical breeding wetlands, 3) current and future predictions on the status of the boreal toad in the SRMR, and 4) a web tool to guide management actions. While the boreal toad is considered a ‘data rich’ species given data collection efforts that span multiple decades, many amphibian species are considered ‘data poor’, meaning managers lack data on the biology, ecology, or status of the species needed to make sound decisions. To address this knowledge gap, we also quantified drying patterns across watersheds for two ‘data poor’ species in the North Central region at risk from climate change: the Great Basin spadefoot toad ( Spea intermontana ) and the wood frog ( Lithobates sylvaticus ). These new data can guide management decisions for these species by allowing managers to understand habitat changes with respect to water availability, a crucial element for amphibian survival and persistence. Together, these products demonstrate how cutting-edge technology and analytical methods can produce a range of useful information to support amphibian conservation.

Colorado, New Mexico, Wyoming

Range-wide assessment of livestock grazing across the sagebrush biome

Domestic livestock grazing occurs in virtually all sagebrush habitats and is a prominent disturbance factor. By affecting habitat condition and trend, grazing influences the resources required by, and thus, the distribution and abundance of sagebrush-obligate wildlife species (for example, sage-grouse Centrocercus spp.). Yet, the risks that livestock grazing may pose to these species and their habitats are not always clear. Although livestock grazing intensity and associated habitat condition may be known in many places at the local level, we have not yet been able to answer questions about use, condition, and trend at the landscape scale or at the range-wide scale for wildlife species. A great deal of information about grazing use, management regimes, and ecological condition exists at the local level (for individual livestock management units) under the oversight of organizations such as the Bureau of Land Management (BLM). However, the extent, quality, and types of existing data are unknown, which hinders the compilation, mapping, or analysis of these data. Once compiled, these data may be helpful for drawing conclusions about rangeland status, and we may be able to identify relationships between those data and wildlife habitat at the landscape scale. The overall objective of our study was to perform a range-wide assessment of livestock grazing effects (and the relevant supporting data) in sagebrush ecosystems managed by the BLM. Our assessments and analyses focused primarily on local-level management and data collected at the scale of BLM grazing allotments (that is, individual livestock management units). Specific objectives included the following: 1. Identify and refine existing range-wide datasets to be used for analyses of livestock grazing effects on sagebrush ecosystems. 2. Assess the extent, quality, and types of livestock grazing-related natural resource data collected by BLM range-wide (i.e., across allotments, districts and regions). 3. Compile and synthesize recommendations from federal and university rangeland science experts about how BLM might prioritize collection of different types of livestock grazing-related natural resource data. 4. Investigate whether range-wide datasets (Objective 1) could be used in conjunction with remotely sensed imagery to identify across broad scales (a) allotments potentially not meeting BLM Land Health Standards (LHS) and (b) allotments in which unmet standards might be attributable to livestock grazing. Objective 1: We identified four datasets that potentially could be used for analyses of livestock grazing effects on sagebrush ecosystems. First, we obtained the most current spatial data (typically up to 2007, 2008, or 2009) for all BLM allotments and compiled data into a coarse, topologically enforced dataset that delineated grazing allotment boundaries. Second, we obtained LHS evaluation data (as of 2007) for all allotments across all districts and regions; these data included date of most recent evaluation, BLM determinations of whether region-specific standards were met, and whether BLM deemed livestock to have contributed to any unmet standards. Third, we examined grazing records of three types: Actual Use (permittee-reported), Billed Use (BLM-reported), and Permitted Use (legally authorized). Finally, we explored the possibility of using existing Natural Resources Conservation Service (NRCS) Ecological Site Description (ESD) data to make up-to-date estimates of production and forage availability on BLM allotments. Objective 2: We investigated the availability of BLM livestock grazing-related monitoring data and the status of LHS across 310 randomly selected allotments in 13 BLM field offices. We found that, relative to other data types, the most commonly available monitoring data were Actual Use numbers (permittee-reported livestock numbers and season-of-use), followed by Photo Point, forage Utilization, and finally, Vegetation Trend measurement data. Data availability and frequency of data collection varied across allotments and field offices. Analysis of the BLM's LHS data indicated 67 percent of allotments analyzed were meeting standards. For those not meeting standards, livestock were considered the causal factor in 45 percent of cases (about 15 percent of all allotments). Objective 3: We sought input from 42 university and federal rangeland science experts about how best to prioritize rangeland monitoring activities associated with ascertaining livestock impacts on vegetation resources. When we presented a hypothetical scenario to these scientists and asked them to prioritize monitoring activities, the most common response was to measure ground and vegetation cover, a variable that in many cases (10 of 13 field offices sampled) BLM had already identified as a monitoring priority. Experts identified several other traditional (for example, photo points) and emerging approaches (for example, high-resolution aerial photography) to monitoring. Objective 4: We used spatial allotment data (described in Objective 1) and remotely sensed vegetation data (sagebrush cover, herbaceous vegetation cover, litter and bare soil) to assess differences in allotment LHS status ("Not met" vs. "Met"; if "Not met" - livestock-caused vs. not). We then developed logistic regression models, using vegetation variables to predict LHS status of BLM allotments in sagebrush steppe habitats in Wyoming and portions of Montana and Colorado. In general, we found that more consistent data collection at the local level might improve suitability of data for broad-scale analyses of livestock impacts. As is, data collection methodologies varied across field offices and States, and we did not find any local-level monitoring data (Actual Use, Utilization, Vegetation Trend) that had been collected consistently enough over time or space for range-wide analyses. Moreover, continued and improved emphasis on monitoring also may aid local management decisions, particularly with respect to effects of livestock grazing. Rangeland science experts identified ground cover as a high monitoring priority for assessing range condition and emphasized the importance of tracking livestock numbers and grazing dates. Ultimately, the most effective monitoring program may entail both increased data collection effort and the integration of alternative monitoring approaches (for example, remote sensing or monitoring teams). In the course of our study, we identified three additional datasets that could potentially be used for range-wide analyses: spatial allotment boundary data for all BLM allotments range-wide, LHS evaluations of BLM allotments, and livestock use data (livestock numbers and grazing dates). It may be possible to use these spatial datasets to help prioritize monitoring activities over the extensive land areas managed by BLM. We present an example of how we used spatial allotment boundary data and LHS data to test whether remotely sensed vegetation characteristics could be used to predict which allotments met or did not meet LHS. This approach may be further improved by the results of current efforts by BLM to test whether more intensive (higher resolution) LHS assessments more accurately describe land health status. Standardized data collection in more ecologically meaningful land units may improve our ability to use local-level data for broad-scale analyses.

Open-File Report

Climate refugia for Pinus spp. in topographic and bioclimatic environments of the Madrean sky islands of México and the United States

Climate refugia, or places where habitats are expected to remain relatively buffered from regional climate extremes, provide an important focus for science and conservation planning. Within high-priority, multi-jurisdictional landscapes like the Madrean sky islands of the United States and México, efforts to identify and manage climate refugia are hindered by the lack of high-quality and consistent transboundary datasets. To fill these data gaps, we assembled a bi-national field dataset ( n = 1416) for five pine species ( Pinus spp.) and used generalized boosted regression to model pine habitats in relation to topographic variability as a basis for identifying potential microrefugia at local scales in the context of current species’ distribution patterns. We developed additional models to quantify climatic refugial attributes using coarse scale bioclimatic variables and finer scale seasonal remote sensing indices. Terrain metrics including ruggedness, slope position, and aspect defined microrefugia for pines within elevation ranges preferred by each species. Response to bioclimatic variables indicated that small shifts in climate were important to some species (e.g., P. chihuahuana, P. strobiformis ), but others exhibited a broader tolerance (e.g., P. arizonica ). Response to seasonal climate was particularly important in modeling microrefugia for species with open canopy structure and where regular fires occur (e.g., P. engelmannii and P. chihuahuana ). Hotspots of microrefugia differed among species and were either limited to northern islands or occurred across central or southern latitudes. Mapping and validation of refugia and their ecological functions are necessary steps in developing regional conservation strategies that cross jurisdictional boundaries. A salient application will be incorporation of climate refugia in management of fire to restore and maintain pine ecology.

Arizona, Chihuahua, New Mexico, Sonora

Data management challenges in species distribution modeling

An important component in the fields of ecology and conservation biology is understanding the environmental conditions and geographic areas that are suitable for a given species to inhabit. A common tool in determining such areas is species distribution modeling which uses computer algorithms to determine the spatial distribution of organisms. Most commonly the correlative relationships between the organism and environmental variables are the primary consideration. The data requirements for this type of modeling consist of known presence and possibly absence locations of the species as well as the values of environmental or climatic covariates thought to define the species habitat suitability at these locations. These covariate data are generally extracted from remotely sensed imagery, interpolated/gridded historical climate data, or downscaled climate model output. Traditionally, ecologists and biologists have constructed species distribution models using workflows and data that reside primarily on their local workstations or networks. This workflow is becoming challenging as scientists increasingly try to use these modeling techniques to inform management decisions under different climate change scenarios. This challenge stems from the fact that remote sensing products, gridded historical climate, and downscaled climate models are not only increasing in spatial and temporal resolution but proliferating as well. Any rigorous assessment of uncertainty requires a computationally intensive sensitivity analysis accounting for various sources of uncertainty. The scientists fitting these models generally do not have the background in computer science required to take advantage of recent advances in web-service based data acquisition, remote high-powered data processing, or scientific workflow systems. Ecologists in the field of modeling are in need of a tractable platform that abstracts the inherent computational complexity required to incorporate the burgeoning field of coupled climate and ecological response modeling. In this paper we describe the computational challenges in species distribution modeling and solutions using scientific workflow systems. We focus on the Software for Assisted Species Modeling (SAHM) a package within VisTrails, an open-source scientific workflow system.

Bulletin of the Technical Committee on Data Engine

Mapping predicted ecological states at landscape scales using remote sensing data and machine learning

Dryland ecosystems, covering 45% of the Earth's land and supporting over one-third of the global population, face significant threats from land degradation and ecological state change. Managing these ecosystems is complex, and science-based frameworks like Ecological Site Descriptions and state-and-transition models are essential tools for guiding decisions to support ecological health while maintaining stakeholder values such as grazing, wildlife, and recreation. However, alignment of these frameworks with smaller scale soil survey maps limits their applicability to broader ecological processes. Here, we extend these frameworks to larger landscapes with a machine learning approach that integrates large-scale, high-resolution vegetation data with identified ecological states from a data-driven state-and-transition model developed for a landscape-scale Ecological Site Group. A “global” model, which used combined inputs from multiple remotely sensed datasets, outperformed individual dataset models based on evaluation with independent data. Ecological state maps generated through this approach broaden the utility of state-and-transition models across Ecological Site Groups, providing a more spatially robust tool for land management at watershed and larger landscape scales. These methods, and the associated ecological state maps, can help meet critical needs for improved land condition assessments that support development of resource management plans and help identify priority areas for restoration and conservation.

Arizona, Colorado, New Mexico, Utah, Wyoming