A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands.

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.

Building a bridge between adaptive capacity and adaptive potential to understand responses to environmental change.

Adaptive capacity is a topic at the forefront of environmental change research with roots in both social, ecological, and evolutionary science. It is closely related to the evolutionary biology concept of adaptive potential. In this systematic literature review, we: (1) summarize the history of these topics and related fields; (2) assess relationship(s) between the concepts among disciplines and the use of the terms in climate change research, and evaluate methodologies, metrics, taxa biases, and the geographic scale of studies; and (3) provide a synthetic conceptual framework to clarify concepts. Bibliometric analyses revealed the terms have been used most frequently in conservation and evolutionary biology journals, respectively. There has been a greater growth in studies of adaptive potential than adaptive capacity since 2001, but a greater geographical extent of adaptive capacity studies. Few studies include both, and use is often superficial. Our synthesis considers adaptive potential as one process contributing to adaptive capacity of complex systems, notes "sociological" adaptive capacity definitions include actions aimed at desired outcome (i.e., policies) as a system driver whereas "biological" definitions exclude such drivers, and suggests models of adaptive capacity require integration of evolutionary and social-ecological system components.

Landscape social-metabolism in food-energy-water systems: Agricultural transformation of the Upper Snake River Basin.

This paper applies a social metabolism framework and energy flow analysis for evaluating agroecosystem and land use transitions in food-energy-water systems using the Upper Snake River Basin (USBR), Idaho, USA as a case-study. The study area is one of the primary agricultural regions of the State of Idaho. Dairy products are the primary agricultural outputs of the region; therefore, we modified a biomass accounting framework to explicitly incorporate the role of manure in the agroecosystem. Despite the increase of cropland between 2002 and 2012 in the basin, a decrease in energy input was observed for crop production. An increase in the industrial energy inputs for dairy production, on the other hand, showed that the basin is a clear example of a metabolic industrialized farm system - an example of land use intensification. We compare the energy return on investments (EROIs) as an indicator of agroecosystem transition for both crop and dairy production during the period 2002 to 2012. Contrary to our expectations, the analysis suggests that livestock production is a relatively energy efficient process in land management in the basin. This is due to the reuse of nutrient by-products from livestock as well as the refuse and residues from crop farming. At the same time, the findings provide insights on the percentage of manure to be reinvested as compost that would improve energy production efficiency. However, the reuse of manure, as it is managed in the basin, may have a negative implication on the nutrient balance of the agroecosystem that needs further investigation. Nonetheless, there is market potential for the reuse and reinvestment of biomass to make energy production in the basin more efficient.

An integrated dataset for stakeholder perceptions of environmental change and instrumented measures of change.

An integrated dataset was developed that combined stakeholder perceptions of environmental change (precipitation, air temperature, water temperature, fish abundance, fish size, residential development) and comparable instrumented measures of environmental changes based on sensor records. All data were transformed to a common 3-point categorical scale to support statistical comparison of social and biophysical change for the same change variables. The integrated dataset is available on Mendeley (http://dx.doi.org/10.17632/cjfxg84bmx.1).

A social-ecological systems approach for environmental management.

Urgent environmental issues are testing the limits of current management approaches and pushing demand for innovative approaches that integrate across traditional disciplinary boundaries. Practitioners, scholars, and policy-makers alike call for increased integration of natural and social sciences to develop new approaches that address the range of ecological and societal impacts of modern environmental issues. From a theoretical perspective, social-ecological systems (SES) science offers a compelling approach for improved environmental management through the application of transdisciplinary and resilience concepts. A framework for translating SES theory into practice, however, is lacking. In this paper, we define the key components of an SES-based environmental management approach. We offer recommendations for integrating an SES approach into existing environmental management practices. Results presented are useful for management professionals that seek to employ an SES environmental management approach and scholars aiming to advance the theoretical foundations of SES science for practical application.

The Science of Firescapes: Achieving Fire-Resilient Communities.

Wildland fire management has reached a crossroads. Current perspectives are not capable of answering interdisciplinary adaptation and mitigation challenges posed by increases in wildfire risk to human populations and the need to reintegrate fire as a vital landscape process. Fire science has been, and continues to be, performed in isolated "silos," including institutions (e.g., agencies versus universities), organizational structures (e.g., federal agency mandates versus local and state procedures for responding to fire), and research foci (e.g., physical science, natural science, and social science). These silos tend to promote research, management, and policy that focus only on targeted aspects of the "wicked" wildfire problem. In this article, we provide guiding principles to bridge diverse fire science efforts to advance an integrated agenda of wildfire research that can help overcome disciplinary silos and provide insight on how to build fire-resilient communities.

Assessing the impacts of local knowledge and technology on climate change vulnerability in remote communities.

The introduction of new technologies into small remote communities can alter how individuals acquire knowledge about their surrounding environment. This is especially true when technologies that satisfy basic needs, such as freshwater use, create a distance (i.e., diminishing exposure) between individuals and their environment. However, such distancing can potentially be countered by the transfer of local knowledge between community members and from one generation to the next. The objective of this study is to simulate by way of agent-based modeling the tensions between technology-induced distancing and local knowledge that are exerted on community vulnerability to climate change. A model is developed that simulates how a collection of individual perceptions about changes to climatic-related variables manifest into community perceptions, how perceptions are influenced by the movement away from traditional resource use, and how the transmission of knowledge mitigates the potentially adverse effects of technology-induced distancing. The model is implemented utilizing climate and social data for two remote communities located on the Seward Peninsula in western Alaska. The agent-based model simulates a set of scenarios that depict different ways in which these communities may potentially engage with their natural resources, utilize knowledge transfer, and develop perceptions of how the local climate is different from previous years. A loosely-coupled pan-arctic climate model simulates changes monthly changes to climatic variables. The discrepancy between the perceptions derived from the agent-based model and the projections simulated by the climate model represent community vulnerability. The results demonstrate how demographics, the communication of knowledge and the types of 'knowledge-providers' influence community perception about changes to their local climate.

The arctic water resource vulnerability index: an integrated assessment tool for community resilience and vulnerability with respect to freshwater.

People in the Arctic face uncertainty in their daily lives as they contend with environmental changes at a range of scales from local to global. Freshwater is a critical resource to people, and although water resource indicators have been developed that operate from regional to global scales and for midlatitude to equatorial environments, no appropriate index exists for assessing the vulnerability of Arctic communities to changing water resources at the local scale. The Arctic Water Resource Vulnerability Index (AWRVI) is proposed as a tool that Arctic communities can use to assess their relative vulnerability-resilience to changes in their water resources from a variety of biophysical and socioeconomic processes. The AWRVI is based on a social-ecological systems perspective that includes physical and social indicators of change and is demonstrated in three case study communities/watersheds in Alaska. These results highlight the value of communities engaging in the process of using the AWRVI and the diagnostic capability of examining the suite of constituent physical and social scores rather than the total AWRVI score alone.

Spatial modeling and habitat quantification for two diadromous fish in New Zealand streams: a GIS-based approach with application for conservation management.

We developed logistic regression models from data on biotic and abiotic variables for 172 sites on Banks Peninsula, New Zealand, to predict the probability of occurrence of two diadromous fish, banded kokopu (Galaxias fasciatus) and koaro (G. brevipinnis). Banded kokopu occurrence was positively associated with small streams and low-intensity land uses (e.g., sheep grazing or forested), whereas intensive land uses (e.g., mixed sheep and cattle farming) and lack of riparian forest cover impacted negatively on occurrence at sampled sites. Also, if forests were positioned predominantly in lowland areas, banded kokopu occurrence declined with increasing distance to stream mouth. Koaro occurrence was positively influenced by catchment forest cover, high stream altitudes, and areas of no farming activity or mixed land uses. Intensive land uses, distance to stream mouth, and presence of banded kokopu negatively influenced koaro occupancy of stream reaches. Banded kokopu and koaro presence was predicted in 86.0% and 83.7% agreement, respectively, with field observations. We used the models to quantify the amount of stream reaches that would be of good, moderate, and poor quality, based on the probability of occurrences of the fish being greater than 0.75, between 0.75 and 0.5, or less than 0.5, respectively. Hindcasting using historical data on vegetation cover undertaken for one catchment, Pigeon Bay, showed they would have occupied most of the waterway before anthropogenic modification. We also modeled potential future scenarios to project potential fish distribution.

Effects of knowledge, personal attribution and perception of ecosystem health on depreciative behaviors in the intertidal zone of Pacific Rim National Park and Reserve.

Human activities levy a biological cost on ecosystems as resources are accessed and utilized at rates which are often incompatible with inherent ecosystem processes and structures. The recreational impact of humans upon intertidal zones and particularly fucoid algal assemblages is one major threat facing coastal ecosystems. The effect of human values, knowledge and perception in effecting biologically costly behaviors has rarely been examined. We hypothesize that with respect to intertidal zones: (1) Personal attribution and perception of ecosystem resiliency are more important than knowledge in determining the extent of depreciative behaviors individuals engage in, and; (2) Individuals who are uncertain about ecosystem resiliency will behave in a manner consistent with the 'precautionary principle'. We measured the depreciative behavior, and the attitudes and perceptions to ecosystem resilience, of visitors to Wick Headland in Pacific Rim National Park, British Columbia. Attitudes, knowledge, perceptions, and personal attribution were measured using questionnaire survey and structured interviews undertaken in situ. Depreciative behaviors of visitors were discreetly observed and correlated to the questionnaire survey and interview responses. We show that visitors who recorded greater knowledge of intertidal ecology engaged in more depreciative behaviors than visitors recording less knowledge. Visitors who perceived high ecosystem resilience in the intertidal zone engaged in significantly more behaviors eliciting biological cost than those who perceived low ecosystem resilience. Visitors who recorded uncertainty regarding ecosystem resilience engaged in significantly more depreciative behaviors than those who perceived low ecosystem resilience but slightly fewer depreciative behaviors than those who perceived high ecosystem resilience. Personal attribution was inversely correlated to the mean number of depreciative behaviors. We discuss the relevance of these results to the management of intertidal zones and marine protected areas, to multiple use management, the management of visitor impact, and natural resource use.