Geology topics

Helen R. Sofaer

Publications and source records attributed to Helen R. Sofaer.

35 records · Page 2Linked to original sources

USGS2023

Invasion-mediated mutualism disruption is evident across heterogeneous environmental conditions and varying invasion intensities

The impact of a biological invasion on native communities is expected to be uneven across invaded landscapes due to differences in local abiotic conditions, invader abundance, and traits and composition of the native community. One way to improve predictive ability about the impact of an invasive species given variable conditions is to exploit known mechanisms driving invasive species' success. Invasive plants frequently exhibit allelopathic traits, which can be directly toxic to plants or indirectly impact them via disruption of root symbionts, including mycorrhizal fungi. The indirect mechanism – mutualism disruption – is predicted to impact plants that rely on mycorrhizas but not affect non-mycorrhizal plant species. To assess whether invader-driven mutualism disruption explains observed changes in native plant communities, we analyzed long-term (1998–2018) plant cover data from forest plots across the state of Illinois. We evaluated native plant communities experiencing a range of abundance of invasive allelopathic garlic mustard Alliaria petiolata and varying environmental conditions. Consistent with the mutualism disruption hypothesis, we showed that as garlic mustard abundance increased over time in 0.25 m 2 sampling quadrats, the abundance of mycorrhizal plant species decreased, but non-mycorrhizal plant species did not. Over space and time, garlic mustard abundance predicted plant abundances and diversity at the quadrat level, but this relationship was not present at a larger scale when quadrats were aggregated within sites. Garlic mustard's impact on the plant community was highly localized, yet it was as important as abiotic variables for predicting local plant diversity. We showed that garlic mustard abundance was a key predictor of patterns of plant diversity across invasion intensity and environmental heterogeneity in a way that is consistent with mutualism disruption. Our work indicates that the mutualism disruption hypothesis can provide generalizable predictions of the impacts of allelopathic invasive plants that are evident at a broad spatial scale.

Ecography↗

USGS2023

SPCIS: Standardized Plant Community with Introduced Status database

The movement of plant species across the globe exposes native communities to new species introductions. While introductions are pervasive, two aspects of variability underlie patterns and processes of biological invasions at macroecological scales. First, only a portion of introduced species become invaders capable of substantially impacting ecosystems. Second, species that do become invasive at one location may not be invasive in others; impacts depend on invader abundance and recipient species and conditions. Accounting for these phenomena is essential to accurately understand the patterns of plant invasion and explain the idiosyncratic results reflected in the literature on biological invasions. The lack of community-level richness and the abundance of data spanning broad scales and environmental conditions have until now hindered our understanding of invasions at a macroecological scale. To address this limitation, we leveraged quantitative surveys of plant communities in the USA and integrated and harmonized nine datasets into the Standardized Plant Community with Introduced Status (SPCIS) database. The database contains 14,056 unique taxa identified within 83,391 sampling units, of which 52.6% have at least one introduced species. The SPCIS database includes comparable information on plant species occurrence, abundance, and native status across the 50 U.S. States and Puerto Rico. SPCIS can be used to answer macro-scale questions about native plant communities and interactions with invasive plants. There are no copyright restrictions on the data, and we ask the users of this dataset to cite this paper, the respective paper(s) corresponding to the dataset sampling design (all references are provided in Data S1: Metadata S1: Class II-B-2), and the references described in Data S1: Metadata S1: Class III-B-4 as applicable to the dataset being utilized.

Ecology↗

USGS2023

Invaders at the doorstep: Using species distribution modeling to enhance invasive plant watch lists

Watch lists of invasive species that threaten a particular land management unit are useful tools because they can draw attention to invasive species at the very early stages of invasion when early detection and rapid response efforts are often most successful. However, watch lists typically rely on the subjective selection of invasive species by experts or on the use of spotty occurrence records. Further, incomplete records of invasive plant occurrences bias these watch lists towards the inclusion of invasive plant species that may already be present in a land management unit, because the occurrences have not been formally integrated into publicly accessible biodiversity databases. However, these problems may be overcome by an iterative approach that guides more complete detection and compilation of invasive plant species records within land management units. To address issues from unobserved or unrecorded occurrences, we combined predicted suitable habitat from species distribution models and aggregated invasive plant occurrence records to develop ranked watch lists of 146 priority invasive plant species on >4000 land management units from five different administrative types within the United States. Based on this analysis, we determined that on average 84% of priority invasive plants with suitable habitat within a given land management unit were as yet unobserved, and that 41% of those were ‘doorstep species’ – found within 50 miles of the unit boundary yet not detected within the unit. Two case studies, developed in collaboration with staff at U.S. Fish and Wildlife Service Refuges, showed that by combining both habitat suitability models and invasive plant occurrence records, we could identify additional problematic invasive plants that had been previously overlooked. Model-based watch lists of ‘doorstep species’ are useful tools because they can objectively alert land managers to threats from invasive plants with high likelihood of establishment.

contiguous United States↗

USGS2022

Regional models do not outperform continental models for invasive species

Aim : Species distribution models can guide invasive species prevention and management by characterizing invasion risk across space. However, extrapolation and transferability issues pose challenges for developing useful models for invasive species. Previous work has emphasized the importance of including all available occurrences in model estimation, but managers attuned to local processes may be skeptical of models based on a broad spatial extent if they suspect the captured responses reflect those of other regions where data are more numerous. We asked whether species distribution models for invasive plants performed better when developed at national versus regional extents. Location : Continental United States. Methods : We developed ensembles of species distribution models trained nationally, on sagebrush habitat, or on sagebrush habitat within three ecoregions (Great Basin, eastern sagebrush, and Great Plains) for nine invasive plants of interest for early detection and rapid response at local or regional scales. We compared the performance of national versus regional models using spatially independent withheld test data from each of the three ecoregions. Results : We found that models trained using a national spatial extent tended to perform better than regionally trained models. Regional models did not outperform national ones even when considerable occurrence data were available for model estimation within the focal region. Information was often unavailable to fit informative regional models precisely in those areas of greatest interest for early detection and rapid response. Main conclusions : Habitat suitability models for invasive plant species trained at a continental extent can reduce extrapolation while maximizing information on species’ responses to environmental variation. Standard modeling methods can capture spatially varying limiting factors, while regional or hierarchical models may only be advantageous when populations differ in their responses to environmental conditions, a condition expected to be relatively rare at the expanding boundaries of invasive species’ distributions.

NeoBiota↗

USGS2022

Potential cheatgrass abundance within lightly invaded areas of the Great Basin

Context Anticipating where an invasive species could become abundant can help guide prevention and control efforts aimed at reducing invasion impacts. Information on potential abundance can be combined with information on the current status of an invasion to guide management towards currently uninvaded locations where the threat of invasion is high. Objectives We aimed to support management by developing predictive maps of potential cover for cheatgrass ( Bromus tectorum ), a problematic invader that can transform plant communities. We integrated our predictions of potential abundance with mapped estimates of current cover to quantify invasion potential within lightly invaded areas. Methods We used quantile regression to model cheatgrass abundance as a function of climate, weather, and disturbance, treating outputs as low to high invasion scenarios. We developed a species-specific set of covariates and validated model performance using spatially and temporally independent data. Results Potential cheatgrass abundance was higher in areas that had burned, at low elevations, and when fall germination conditions were more favorable. Our results highlight the extensive areas across the Great Basin where cheatgrass abundance could increase to levels that can alter fire behavior and cause other ecological impacts. Conclusions We predict potential cheatgrass abundance to quantify relative invasion risk. Our model results provide high and low scenarios of cheatgrass abundance to guide resource allocation and planning efforts across shrubland ecosystems of the Great Basin that remain relatively uninvaded. Combining information on an invasive species’ current and potential abundance can yield spatial predictions to guide resource allocation and management action.

California, Idaho, Nevada, Oregon, Utah↗

USGS2022

INHABIT: A web-based decision support tool for invasive plant species habitat visualization and assessment across the contiguous United States

Narrowing the communication and knowledge gap between producers and users of scientific data is a longstanding problem in ecological conservation and land management. Decision support tools (DSTs), including websites or interactive web applications, provide platforms that can help bridge this gap. DSTs can most effectively disseminate and translate research results when producers and users collaboratively and iteratively design content and features. One data resource seldom incorporated into DSTs are species distribution models (SDMs), which can produce spatial predictions of habitat suitability. Outputs from SDMs can inform management decisions, but their complexity and inaccessibility can limit their use by resource managers or policy makers. To overcome these limitations, we present the Invasive Species Habitat Tool (INHABIT), a novel, web-based DST built with R Shiny to display spatial predictions and tabular summaries of habitat suitability from SDMs for invasive plants across the contiguous United States. INHABIT provides actionable science to support the prevention and management of invasive species. Two case studies demonstrate the important role of end user feedback in confirming INHABIT’s credibility, utility, and relevance.

PLoSOne↗

USGS2022

Climate matching with the climatchR R package

Climate matching allows comparisons of climatic conditions between different locations to understand location and species range climatic suitability. The approach may be used as part of horizon scanning exercises such as those conducted for invasive species. We implemented the CLIMATCH algorithm into an R package, climatchR . The package allows automated and scripted climate matching exercises across all steps from downloading data to summarizing species climate matches. We also show how climatchR may be used with high-throughput computing to process many species. For example, we were able to calculate climate scores for over 8,000 species in less than 3 days using this package. This automation allows high-throughput processing of species data, a new development for improving the efficiency and speed of climate matching and horizon scanning.

Environmental Software & Modeling↗

USGS2021

Management foundations for navigating ecological transformation by resisting, accepting, or directing social-ecological change

Despite striking global change, management to ensure healthy landscapes and sustained natural resources has tended to set objectives on the basis of the historical range of variability in stationary ecosystems. Many social–ecological systems are moving into novel conditions that can result in ecological transformation. We present four foundations to enable a transition to future-oriented conservation and management that increases capacity to manage change. The foundations are to identify plausible social–ecological trajectories, to apply upstream and deliberate engagement and decision-making with stakeholders, to formulate management pathways to desired futures, and to consider a portfolio approach to manage risk and account for multiple preferences across space and time. We use the Kenai National Wildlife Refuge in Alaska as a case study to illustrate how the four foundations address common land management challenges for navigating transformation and deciding when, where, and how to resist, accept, or direct social–ecological change.

Alaska↗

USGS2021

A science agenda to inform natural resource management decisions in an era of ecological transformation

Earth is experiencing widespread ecological transformation in terrestrial, freshwater, and marine ecosystems that is attributable to directional environmental changes, especially intensifying climate change. To better steward ecosystems facing unprecedented and lasting change, a new management paradigm is forming, supported by a decision-oriented framework that presents three distinct management choices: resist, accept, or direct the ecological trajectory. To make these choices strategically, managers seek to understand the nature of the transformation that could occur if change is accepted while identifying opportunities to intervene to resist or direct change. In this article, we seek to inspire a research agenda for transformation science that is focused on ecological and social science and based on five central questions that align with the resist–accept–direct (RAD) framework. Development of transformation science is needed to apply the RAD framework and support natural resource management and conservation on our rapidly changing planet.

BioScience↗

USGS2021

Modelling presence versus abundance for invasive species risk assessment

Aim Invasive species prevention and management can be guided by comparisons of invasion risk across space and among species. Species distribution models are widely used to assess invasion risk and typically estimate suitability for species presence. However, suitability for presence may not capture patterns of abundance and impact. We asked how models estimating suitability for presence versus suitability for abundance aligned in their implications for risk assessment. Location Western United States. Methods We developed ensembles of species distribution models for presence and for abundance for four invasive plants. We visualized the distribution of presence and abundance in environmental and geographic space and compared model outputs using criteria relevant for decision-making: a comparison of risk across management units for each species, and a ranking of risk among species for each management unit. Results We found good overall agreement between models of presence versus abundance in the relative risk across management units and among species. However, the area predicted to be suitable for invasive species presence was often substantially higher than the area predicted to be suitable for abundance, especially within uninvaded management units. Main conclusions Models of suitability for invasive species presence and abundance yielded similar assessments of relative risk in comparisons across space and species. In addition, we found patterns of presence and abundance in environmental space can guide modelling decisions and model interpretation. Suitability for abundance can improve relative risk assessment when abundance locations occupy a well-defined subset of the environmental space corresponding to presence. Where abundance locations occur throughout this environmental space, as was particularly striking for Taeniatherum caput-medusae, suitability for presence may better reflect risk of ongoing population increases and spread. This species is at risk of becoming abundant across a substantial portion of the western United States.

Diversity and Distributions↗

USGS2020

Negative effects of an allelopathic invader on AM fungal plant species drive community‐level responses

The mechanisms causing invasive species impact are rarely empirically tested, limiting our ability to understand and predict subsequent changes in invaded plant communities. Invader disruption of native mutualistic interactions is a mechanism expected to have negative effects on native plant species. Specifically, disruption of native plant‐fungal mutualisms may provide non‐mycorrhizal plant invaders an advantage over mycorrhizal native plants. Invasive Alliaria petiolata (garlic mustard) produces secondary chemicals toxic to soil microorganisms including mycorrhizal fungi, and is known to induce physiological stress and reduce population growth rates of native forest understory plant species. Here, we report on a 11‐yr manipulative field experiment in replicated forest plots testing if the effects of removal of garlic mustard on the plant community support the mutualism disruption hypothesis within the entire understory herbaceous community. We compare community responses for two functional groups: the mycorrhizal vs. the non‐mycorrhizal plant communities. Our results show that garlic mustard weeding alters the community composition, decreases community evenness, and increases the abundance of understory herbs that associate with mycorrhizal fungi. Conversely, garlic mustard has no significant effects on the non‐mycorrhizal plant community. Consistent with the mutualism disruption hypothesis, our results demonstrate that allelochemical producing invaders modify the plant community by disproportionately impacting mycorrhizal plant species. We also demonstrate the importance of incorporating causal mechanisms of biological invasion to elucidate patterns and predict community‐level responses.

Ecology↗

USGS2020

A modeling workflow that balances automation and human intervention to inform invasive plant management decisions at multiple spatial scales

Predictions of habitat suitability for invasive plant species can guide risk assessments at regional and national scales and inform early detection and rapid-response strategies at local scales. We present a general approach to invasive species modeling and mapping that meets objectives at multiple scales. Our methodology is designed to balance trade-offs between developing highly customized models for few species versus fitting non-specific and generic models for numerous species. We developed a national library of environmental variables known to physiologically limit plant distributions and relied on human input based on natural history knowledge to further narrow the variable set for each species before developing habitat suitability models. To ensure efficiency, we used largely automated modeling approaches and human input only at key junctures. We explore and present uncertainty by using two alternative sources of background samples, including five statistical algorithms, and constructing model ensembles. We demonstrate the use and efficiency of the Software for Assisted Habitat Modeling [SAHM 2.1.2], a package in VisTrails, which performs the majority of the modeling analyses. Our workflow includes solicitation of expert feedback on model outputs such as spatial prediction results and variable response curves, and iterative improvement based on new data availability and directed field validation of initial model results. We highlight the utility of the models for decision-making at regional and local scales with case studies of two plant species that invade natural areas: fountain grass ( Pennisetum setaceum ) and goutweed ( Aegopodium podagraria ). By balancing model automation with human intervention, we can efficiently provide land managers with mapped predicted distributions for multiple invasive species to inform decisions across spatial scales.

PLoS ONE↗

USGS2020

Human-associated species dominate passerine communities across the United States

Aim Human development and agriculture can have transformative and homogenizing effects on natural systems, shifting the composition of ecological communities towards non-native and native species that tolerate or thrive under human-dominated conditions. These impacts cannot be fully captured by summarizing species presence, as they include dramatic changes to patterns of species abundance. However, how human land use patterns and species invasions intersect to shape patterns of abundance and dominance within ecological communities is poorly understood even in well-known taxa. Location Conterminous United States. Time period 2010–2012. Major taxa studied Passeriformes. Methods We analyse continental-scale monitoring data to study the proportional abundance of non-native and native synanthropic species within passerine bird communities. Synanthropic species are those that benefit from an association with humans. We estimate how the amount and configuration of human development and agriculture relate to the degree to which human-associated species dominate passerine communities across the continent. Results Human-associated species comprised the majority of detected passerine individuals across two-thirds of bird surveys. Non-native and synanthropic species responded differently to land cover and reached highest relative abundance in different portions of the continent. The proportional abundance of synanthropic birds increased rapidly with development, but was not related to the configuration of land cover. The proportion of non-native individuals was higher when intensively-used land cover was more aggregated. Main conclusions Even low amounts of intensively-used lands were associated with a dramatic reshaping of passerine communities, with consequences for patterns of relative abundance across the continent.

Global Ecology and Biogeography↗

USGS2020

Co-occurrence and occupancy dynamics of mourning doves and Eurasian collared-doves

Understanding how land cover and potential competition with invasive species shape patterns of occupancy, extirpation, and colonization of native species across a landscape can help target management for declining native populations. Mourning dove ( Zenaida macroura ) populations have declined throughout the United States from 1965–2015. The expansion of the Eurasian collared‐dove ( Streptopelia decaocto ), an introduced species with similar food preferences, may further threaten mourning dove populations. We analyzed data from 2009–2016 from a large‐scale monitoring program in the Western Great Plains of the United States in a 2‐species occupancy model to assess the effects of collared‐doves on mourning dove distributions, while accounting for imperfect detection and variation in land cover across the landscape. Mourning dove occupancy was stable or increasing across our study area, and despite overlap in resource use and co‐occurrence between mourning doves and Eurasian collared‐doves, we found no evidence that collared‐doves are extirpating mourning doves from preferred habitat during the breeding season.

Texas, Oklahoma, Kansas, Nebraska, South Dakota, N↗

USGS2019

The development and delivery of species distribution models to inform decision-making

Information on where species occur is central to conservation and management decisions, but knowledge of distributions can be coarse or incomplete. Species distribution models provide a tool for mapping suitable habitat, and can produce credible, defensible, and repeatable predictive information with which to inform decisions. However, these models are sensitive to data inputs and methodological choices, making it important to assess the reliability and utility of model predictions. We provide a rubric that model developers can use to communicate a model’s attributes and its appropriate uses. We emphasize the importance of tailoring model development and delivery to the species of interest and the intended use, and the advantages of iterative modeling and validation. We highlight how species distribution models have been used to design surveys for new populations, prioritize actions across space, and support regulatory decision-making and compliance, tying these examples back to our rubric.

BioScience↗

USGS2019

Non-native plants have greater impacts because of differing per-capita effects and non-linear abundance-impact curves

Invasive, non-native species can have tremendous impacts on biotic communities, where they reduce the abundance and diversity of local species. However, it remains unclear whether impacts of non-native species arise from their high abundance or whether each non-native individual has a disproportionate impact – i.e., a higher per-capita effect – on co-occurring species compared to impacts by native species. Using a long-term study of wetlands, we asked how temporal variation in dominant native and non-native plants impacted the abundance and richness of other plants in the recipient community. Non-native plants reached higher abundances than natives and had greater per-capita effects. The abundance-impact relationship between plant abundance and richness was nonlinear. Compared with increasing native abundance, increasing non-native abundance was associated with steeper declines in richness because of greater per-capita effects and nonlinearities in the abundance-impact relationship. Our study supports eco-evolutionary novelty of non-natives as a driver of their outsized impacts on communities.

Illinois↗

USGS2019

Clustering and ensembling approaches to support surrogate-based species management

Aim Surrogate species can provide an efficient mechanism for biodiversity conservation if they encompass the needs or indicate the status of a broader set of species. When species that are the focus of ongoing management efforts act as effective surrogates for other species, these incidental surrogacy benefits lead to additional efficiency. Assessing surrogate relationships often relies on grouping species by distributional patterns or by species traits, but there are few approaches for integrating outputs from multiple methods into summaries of surrogate relationships that can inform decision‐making. Location Prairie Pothole Region of the United States. Methods We evaluated how well five upland‐nesting waterfowl species that are a focus of management may act as surrogates for other wetland‐dependent birds. We grouped species by their patterns of relative abundance at multiple scales and by different sets of traits, and evaluated whether empirical validation could effectively select among the resulting species groupings. We used an ensemble approach to integrate the different estimated relationships among species and visualized the ensemble as a network diagram. Results Estimated relationships among species were sensitive to methodological decisions, with qualitatively different relationships arising from different approaches. An ensemble provided an effective tool for integrating across different estimates and highlighted the Sora ( Porzana carolina ), American Avocet ( Recurvirostra Americana ) and Black Tern ( Chlidonias niger ) as the non‐waterfowl species expected to show the strongest incidental surrogacy relationships with the waterfowl that are the focus of ongoing management. Main conclusions An ensemble approach integrated multiple estimates of surrogate relationship strength among species and allowed for intuitive visualizations within a network. By accounting for methodological uncertainty while providing a simple continuous metric of surrogacy, our approach is amenable to both further validation and integration into decision‐making.

Alberta, Iowa, Manitoba, Minnesota, Montana, North↗