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Invasive exotic plant (IEP) species have been found within the park boundaries of Capitol Reef National Park (CARE) in Utah. Currently, remotely sensed datasets such as the Rangeland Analysis Platform (RAP) from the United States Department of Agriculture (USDA) have been used to investigate IEP species within the park, but validation of the national RAP program is necessary for informing decisions at a local scale. CARE seeks a remote monitoring solution that can precisely target managerial efforts within the park’s challenging terrain and hard-to-reach locations. To fulfill this objective, we harnessed Landsat 8 Operational Land Imager (OLI) imagery and leveraged Random Forest (RF) modeling to generate classification maps characterizing vegetation functional groups for 2013 and 2022 within the park. Subsequently, the Land Change Modeler (LCM) in Idrisi TerrSet facilitated the production of a predicted classification map for 2033. The team also devised an annual grass probability map to accentuate areas impacted by exotic grasses. A comparative assessment between the RF classification map and the RAP map for 2022 revealed an overall agreement of 47.41%, with disparities primarily arising from differences in bare soil and shrub areas. Significantly, the 2022 RF-generated classification map showcased an impressive overall accuracy of 92.17%. In short, the probability map, the land cover change detection spanning 2013 to 2022, and the forecasting of observed trends into the future aids in the evaluation of invasive plant impacts and facilitation of CARE’s preparedness for potential ecological disturbances. Notably, in comparison to the RAP, the RF classification method generates functional group maps that are more representative of the study area.
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Highlights: • Sequence conservation in protein-binding segments in IDRs is analyzed. • Functionally constraint residues in protein-binding segments in IDRs are conserved. • Evolutionary distance should be considered in the comparison of IDRs. • Cryptic binding regions may influence sequence conservation of IDRs. Intrinsically disordered proteins are proteins with intrinsically disordered regions (IDRs) that do not adopt a globular structure in their free state. IDRs have unique regions having protein-binding segments of which play pivotal roles in many biological processes. The binding sites in IDRs are heterogeneous in terms of their sequence conservation: some are conserved and others are not. We have been running a database of intrinsically disordered proteins, IDEAL, and collecting such binding segments, which are called protean segments (ProSs), within it. In this study, we compared the sequence conservation of ProSs, structural domains (SDs), and IDRs other than ProSs (non-ProSs) and found that i) functionally constrained residues in ProSs tend to be conserved, ii) the distribution of conservation scores of ProSs is similar to those of SDs but not non-ProSs, and iii) ProSs found in human proteins are mostly conserved only in vertebrates. These results indicate that the conservation patterns in ProSs principally follow the general rules found in SDs. However, we need to consider evolutionary distance when comparing IDR sequences because ProSs can readily emerge and disappear over the course of protein evolution. Moreover, many ProSs may remain to be identified, which may account for the heterogeneity of the sequence conservation of IDRs.
We consider the issue of strict, fully discrete local energy conservation for a whole class of fully implicit local-charge- and global-energy-conserving particle-in-cell (PIC) algorithms. Earlier studies demonstrated these algorithms feature strict global energy conservation. However, whether a local energy conservation theorem exists (in which the local energy update is governed by a flux balance equation at every mesh cell) for these schemes is unclear. In this study, we show that a local energy conservation theorem indeed exists. We begin our analysis with the 1D electrostatic PIC model without orbit-averaging, and then generalize our conclusions to account for orbit averaging, multiple dimensions, and electromagnetic models (Darwin). In all cases, a temporally, spatially, and particle-discrete local energy conservation theorem is shown to exist, proving that these formulations (as originally proposed in the literature), in addition to being locally charge conserving and globally energy conserving, are strictly locally energy conserving as well. In contrast to earlier proofs of local conservation in the literature, which only considered continuum time, our result is valid for the fully implicit time-discrete version of all models considered, including important features such as orbit averaging. We demonstrate the local-energy-conservation property numerically with a paradigmatic numerical example.
State wildlife management agencies in the United States have depended on a “user-pay” funding model for conservation efforts that relies on revenue from hunting license sales and a federal excise tax on firearms, ammunition, and archery equipment. Declines in hunting participation, however, jeopardize sustainability of the current funding model. Ensuring support among stakeholders for wildlife management and conservation may require expanding sources of funding and incorporating the perspectives and values of a diversifying constituency into decision making processes. We used a web-based survey of wildlife-associated recreationists in Michigan, USA to evaluate support for a range of conservation funding policies. Respondents self-identified primarily as hunters (n = 2,558) or wildlife watchers (n = 942). We used binary logistic regression to evaluate support for four conservation funding policy options: state sales tax, lottery proceeds, extractive industry revenue, and a user-based tax on outdoor gear (i.e., “backpack tax”). Determinants of support varied by type of policy and stakeholder characteristics. We found no statistically significant differences between hunters and wildlife watchers in their support for conservation funding policies when accounting for other variables such as wildlife value orientations, engagement in stewardship behaviors, age, and gender. The industry-based policy achieved the greatest level of approval, while the backpack tax had the lowest. Respondents were mixed in their support of the sales tax and lottery proceeds options. Cluster analysis revealed three homogenous groups related to conservation funding policies: “strong support,” “mixed/opposed,” and “anti-backpack tax.” Clusters differed in their support for conservation funding policies and on psychological and demographic variables. The “strong support” and “anti-backpack tax” groups differed in their levels of stewardship engagement, knowledge of conservation funding mechanisms, and support for the backpack tax option. The “mixed-opposed” group tended to be older, less educated, and less likely to be a member of a conservation organization. Results suggest support for conservation funding differs by policy type and social and psychological characteristics of stakeholders. Based on differences in policy support revealed in this study, we suggest a multi-tiered approach to funding conservation and building on support among wildlife stakeholders to mitigate the looming funding crisis for state wildlife agencies.
Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.
Abstract. The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1∘ horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model becomes negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors in early V1 versions decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in V1 results in a very thin model layer at the Earth's surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for V1.
The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations for sea level rise projection. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model is negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in the new model results in a very thin model layer at the Earth’s surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for this model.
In the present study, the multiphase volume distribution problem, where there can be an arbitrary number of phases, is addressed using a consistent and conservative volume distribution algorithm. The proposed algorithm satisfies the summation constraint, the conservation constraint, and the consistency of reduction. The first application of the volume distribution algorithm is to determine the Lagrange multipliers in multiphase Phase-Field models that enforce the mass conservation, and a multiphase conservative Allen-Cahn model that satisfies the consistency of reduction is developed. A corresponding consistent and conservative numerical scheme is developed for the model. The multiphase conservative Allen-Cahn model has a better ability than the multiphase Cahn-Hilliard model to preserve under-resolved structures. The second application is to develop a numerical procedure, called the boundedness mapping, to map the order parameters, obtained numerically from a multiphase model, into their physical interval, and at the same time to preserve the physical properties of the order parameters. Along with the consistent and conservative schemes for the multiphase Phase-Field models, the numerical solutions of the order parameters are reduction consistent, conservative, and bounded, which are theoretically analyzed and numerically validated. Then, the multiphase Phase-Field models are coupled with the momentum equation by satisfying the consistency of mass conservation and the consistency of mass and momentum transport, thanks to the consistent formulation. Finally, it is demonstrated that the proposed model and scheme converge to the sharp-interface solution and are capable of capturing the complicated multiphase dynamics even when there is a large density and/or viscosity ratio.
Abstract In this paper, we propose a novel Local Macroscopic Conservative (LoMaC) low rank tensor method for simulating the Vlasov-Poisson (VP) system. The LoMaC property refers to the exact local conservation of macroscopic mass, momentum and energy at the discrete level. This is a follow-up work of our previous development of a conservative low rank tensor approach for Vlasov dynamics ( arXiv:2201.10397 ). In that work, we applied a low rank tensor method with a conservative singular value decomposition to the high dimensional VP system to mitigate the curse of dimensionality, while maintaining the local conservation of mass and momentum. However, energy conservation is not guaranteed, which is a critical property to avoid unphysical plasma self-heating or cooling. The new ingredient in the LoMaC low rank tensor algorithm is that we simultaneously evolve the macroscopic conservation laws of mass, momentum and energy using a flux-difference form with kinetic flux vector splitting; then the LoMaC property is realized by projecting the low rank kinetic solution onto a subspace that shares the same macroscopic observables by a conservative orthogonal projection. The algorithm is extended to the high dimensional problems by hierarchical Tuck decomposition of solution tensors and a corresponding conservative projection algorithm. Extensive numerical tests on the VP system are showcased for the algorithm’s efficacy.
In recent years, shade coffee certification programs have attracted increasing attention from forest conservation and development organizations. The certification programs could be expected to promote forest conservation by providing a premium price to shade coffee producers. However, little is known about the significance of the conservation efforts generated by certification programs. In particular, the relationship between the impact of the certification and producer characteristics has yet to be examined. The purpose of this study, which was conducted in Ethiopia, was to examine the impact of a shade coffee certification program on forest conservation and its relationship with the socioeconomic characteristics of the producers. Remote sensing data of 2005 and 2010 was used to gauge the changes in forest area. Employing a probit model, we found that a forest coffee area being certified increased the probability of forest conservation by 19.3 percentage points relative to forest coffee areas lacking certification. We also found that although economically poor producers tended to engage in forest clearing, the forest coffee certification program had a significant impact on these producers. This result suggests that the certification program significantly affects the behaviors of economically poor producers and motivates these producers to conserve the forest. -- Highlights: • We employed the probit mode to evaluate the impact of the shade coffee certification on forest conservation in Ethiopia. • We estimated how the impact of the certification varied among producers with different characteristics. • The certification increased the probability of conserving forest by 19.3 percentage points. • Certification program motivated the economically poor producers to conserve the forest.
Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation-planning process. By doing so, it may be possible to conserve an abiotically diverse "stage" upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time-albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. Lastly, we conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions.
The recognition that agricultural systems provide services beyond food production has motivated federal legislation and associated programs that promote sustainable management and conservation of productive working lands. This study evaluates the ability of the USDA Natural Resources Conservation Service's (NRCS) Conservation Measurement Tool (CMT), which has been used to determine eligibility for enrollment in the Conservation Stewardship Program, to reflect changes in ecosystem services resulting from the use of conservation management practices on croplands. This work evaluates four macroconcerns or outcomes (soil erosion, soil quality, water quality, and air quality) that are quantified within the tool by comparing CMT scores tabulated according to practices reported by farmers involved in grain producing operations in the US Midwest with soil health measures (dynamic soil properties [DSPs]) determined on 72 Illinois farm fields. Three management practice categories-Conventional, Conservation, and Organic-were evaluated. The CMT identified significant differences among management categories, and scores ranked consistently higher for Organic than Conventional or Conservation systems. Direct analysis of DSPs suggested that there were relatively small differences among soil health indicators measured on farms under varied management; this implies that the CMT might be overemphasizing the influence of selected management practices. The evaluation of multivariate relationships between the practices scored in the CMT and DSPs revealed that soil properties like soil pH and particulate organic matter-carbon (POM-C) can be used to improve the accuracy of the tool. They also show how relationships between questions (practices) and outcomes suggested by DSPs vary among farming categories and suggest this type of practice-based tool should be adapted by embedding factors to scale farming systems or, preferably, by adding questions that better describe important factors (e.g., plant productivity and fertilizer timing, rate, and form of application) and their interactions with other factors known to influence specific outcomes. This work shows how field data describing practices, properties, and outcomes can be used to statistically evaluate and refine conservation scoring tools.