Recombinant inbred line panels inform the genetic architecture and interactions of adaptive traits in Drosophila melanogaster.

The distribution of allelic effects on traits, along with their gene-by-gene and gene-by-environment interactions, contributes to the phenotypes available for selection and the trajectories of adaptive variants. Nonetheless, uncertainty persists regarding the effect sizes underlying adaptations and the importance of genetic interactions. Herein, we aimed to investigate the genetic architecture and the epistatic and environmental interactions involving loci that contribute to multiple adaptive traits using two new panels of Drosophila melanogaster recombinant inbred lines (RILs). To better fit our data, we re-implemented functions from R/qtl (Broman et al. 2003) using additive genetic models. We found 14 quantitative trait loci (QTL) underlying melanism, wing size, song pattern, and ethanol resistance. By combining our mapping results with population genetic statistics, we identified potential new genes related to these traits. None of the detected QTLs showed clear evidence of epistasis, and our power analysis indicated that we should have seen at least one significant interaction if sign epistasis or strong positive epistasis played a pervasive role in trait evolution. In contrast, we did find roles for gene-by-environment interactions involving pigmentation traits. Overall, our data suggest that the genetic architecture of adaptive traits often involves alleles of detectable effect, that strong epistasis does not always play a role in adaptation, and that environmental interactions can modulate the effect size of adaptive alleles.

Closing the gap between science and management of cold-water refuges in rivers and streams.

Human activities and climate change threaten coldwater organisms in freshwater ecosystems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold-water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short-term survival. Globally, cohesive management approaches are needed that consider interlinked physical, biological, and social factors of cold-water refuges. We review current understanding of cold-water refuges, identify gaps between science and management, and evaluate policies aimed at protecting thermally sensitive species. Existing policies include designating cold-water habitats, restricting fishing during warm periods, and implementing threshold temperature standards or guidelines. However, these policies are rare and uncoordinated across spatial scales and often do not consider input from Indigenous peoples. We propose that cold-water refuges be managed as distinct operational landscape units, which provide a social and ecological context that is relevant at the watershed scale. These operational landscape units provide the foundation for an integrated framework that links science and management by (1) mapping and characterizing cold-water refuges to prioritize management and conservation actions, (2) leveraging existing and new policies, (3) improving coordination across jurisdictions, and (4) implementing adaptive management practices across scales. Our findings show that while there are many opportunities for scientific advancement, the current state of the sciences is sufficient to inform policy and management. Our proposed framework provides a path forward for managing and protecting cold-water refuges using existing and new policies to protect coldwater organisms in the face of global change.

Continental-scale analysis of shallow and deep groundwater contributions to streams.

Groundwater discharge generates streamflow and influences stream thermal regimes. However, the water quality and thermal buffering capacity of groundwater depends on the aquifer source-depth. Here, we pair multi-year air and stream temperature signals to categorize 1729 sites across the continental United States as having major dam influence, shallow or deep groundwater signatures, or lack of pronounced groundwater (atmospheric) signatures. Approximately 40% of non-dam stream sites have substantial groundwater contributions as indicated by characteristic paired air and stream temperature signal metrics. Streams with shallow groundwater signatures account for half of all groundwater signature sites and show reduced baseflow and a higher proportion of warming trends compared to sites with deep groundwater signatures. These findings align with theory that shallow groundwater is more vulnerable to temperature increase and depletion. Streams with atmospheric signatures tend to drain watersheds with low slope and greater human disturbance, indicating reduced stream-groundwater connectivity in populated valley settings.

Adapting the Index of Watershed Integrity for Watershed Managers in the Western Balkans Region.

Sustainable development supports watershed processes and functions. To aid the sustainable development of the western Balkans' transboundary river and lake basins, the Regional Environmental Center for Central and Eastern Europe and the US Environmental Protection Agency (EPA) adapted the EPA's Index of Watershed Integrity (IWI) following the devasting 2014 floods in Albania, Bosnia and Herzegovina, Kosovo, North Macedonia, Montenegro, and Serbia. The IWI evaluates six watershed functions based on a suite of anthropogenic stressors (e.g., impervious surfaces, reservoirs). A key feature of the IWI is its ability to accumulate the impact of upstream activities of any specific location in a river network. A novel feature of the IWI, compared with other watershed assessment tools, is its capacity to provide actionable information at the local scale. IWI scores-ranging from 0 (low integrity) to 1 (high integrity)-calculated for the 1084 catchments of the study area indicated highest integrity in the Alpine geographic region (mean = 0.55, standard deviation (SD) = 0.11) and intermediate to lowest integrity within the Mediterranean (mean = 0.49, SD = 0.12) and Continental (mean = 0.40, SD = 0.10) geographic regions. The IWI results are presented hierarchically for data analysts (stressor, functional component, Index of Catchment Integrity and IWI), ecologists (stream/catchment, watershed, basin), and managers (local, national, international). We provide real-world examples for managers, and suggestions for improving the assessment.

Revising the index of watershed integrity national maps.

Watersheds provide a range of services valued by society, incorporating biotic and abiotic functions within their boundaries. Recently, an operational definition of watershed integrity was applied and indices of watershed integrity (IWI) and catchment integrity (ICI) were developed and mapped for the conterminous United States. However, these indices were originally derived using equally-weighted first-order approximations of relationships between anthropogenic stressors (obtained from the U.S. EPA's StreamCat dataset) and six watershed functions. In addition, the original calculations of the IWI and ICI did not standardize metrics across these differing scales, resulting in IWI and ICI values that are not directly comparable. We provide an example of how to iteratively update the stressor-watershed function relationships using random forest models and a nationwide response metric representative of one of the six watershed functions. Specifically, we focused on the chemical regulation function (CHEM) of IWI and ICI by relating a composite metric of chemical water quality from 1914 samples to land use metrics explicit to CHEM to refine the nature of these relationships (e.g., non-linear versus linear). The rate of nitrogen fertilizer, agricultural land use, and urban land use were found to be the three most important stressors predicting the national water quality response metric. Revision of CHEM values improved the prediction of several regional- to national-scale water quality indicators. In all cases, exponential decay curves replaced the original negative linear relationship for CHEM. Therefore, the original IWI and ICI values are probably over-estimates of the actual integrity of the Nation's watersheds and catchments. With these revisions, we provide updated national maps of IWI and ICI. The methods outlined here can be implemented iteratively as more and better data become available for all six of the watershed functions to elevate the accuracy and applicability of these indices to various land management issues.

Performance of National Maps of Watershed Integrity at Watershed Scales.

Watershed integrity, the capacity of a watershed to support and maintain ecological processes essential to the sustainability of services provided to society, can be influenced by a range of landscape and in-stream factors. Ecological response data from four intensively monitored case study watersheds exhibiting a range of environmental conditions and landscape characteristics across the United States were used to evaluate the performance of a national level Index of Watershed Integrity (IWI) at regional and local watershed scales. Using Pearson's correlation coefficient (r), and Spearman's rank correlation coefficient (rs ), response variables displayed highly significant relationships and were significantly correlated with IWI and ICI (Index of Catchment Integrity) values at all watersheds. Nitrogen concentration and flux-related watershed response metrics exhibited significantly strong negative correlations across case study watersheds, with absolute correlations (|r|) ranging from 0.48 to 0.97 for IWI values, and 0.31 to 0.96 for ICI values. Nitrogen-stable isotope ratios measured in chironomids and periphyton from streams and benthic organic matter from lake sediments also demonstrated strong negative correlations with IWI values, with |r| ranging from 0.47 to 0.92, and 0.35 to 0.89 for correlations with ICI values. This evaluation of the performance of national watershed and catchment integrity metrics and their strong relationship with site level responses provides weight-of-evidence support for their use in state, local and regionally focused applications.

Inferring watershed hydraulics and cold-water habitat persistence using multi-year air and stream temperature signals.

Streams strongly influenced by groundwater discharge may serve as "climate refugia" for sensitive species in regions of increasingly marginal thermal conditions. The main goal of this study is to develop paired air and stream water annual temperature signal analysis techniques to elucidate the relative groundwater contribution to stream water and the effective groundwater flowpath depth. Groundwater discharge to streams attenuates surface water temperature signals, and this attenuation can be diagnostic of groundwater gaining systems. Additionally, discharge from shallow groundwater flowpaths can theoretically transfer lagged annual temperature signals from aquifer to stream water. Here we explore this concept using multi-year temperature records from 120 stream sites located across 18 mountain watersheds of Shenandoah National Park, VA, USA and a coastal watershed in Massachusetts, USA. Both areas constitute important cold-water habitat for native brook trout (Salvelinus fontinalis). Observed annual temperature signals indicate a dominance of shallow groundwater discharge to streams in the National Park, in contrast to the coastal watershed that has strong, apparently deeper, groundwater influence. The average phase lag from air to stream signals in Shenandoah National Park is 11 d; however, extended lags of approximately 1 month were observed in a subset of streams. In contrast, the coastal stream has pronounced attenuation of annual temperature signals without notable phase lag. To better understand these observed differences in signal characteristics, analytical and numerical models are used to quantify mixing of the annual temperature signals of surface and groundwater. Simulations using a total heat budget numerical model indicate groundwater-induced annual temperature signal phase lags are likely to show greater downstream propagation than the related signal amplitude attenuation. The measurement of multi-seasonal paired air and water temperatures offers great promise toward understanding catchment processes and informing current cold-water habitat management at ecologically-relevant scales.

Mapping watershed integrity for the conterminous United States.

Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high (r = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability of the IWI and ICI to predict six continuous site-level indicators with regression analyses - three biological indicators and principal components derived from water quality, habitat, and combined water quality and habitat variables - using data from EPA's National Rivers and Streams Assessment. Relationships were highly significant, but the IWI only accounted for 1-12% of the variation in the four biological and habitat variables. The IWI accounted for over 25% of the variation in the water quality and combined principal components nationally, and 32-39% in the Northern and Southern Appalachians. We also used multinomial logistic regression to compare the IWI with the categorical forms of the three biological indicators. Results were consistent: we found positive associations but modest results. We compared how the IWI and ICI predicted the water quality PC relative to agricultural and urban land use. The IWI or ICI are the best predictors of the water quality PC for the CONUS and six of the nine ecoregions, but they only perform marginally better than agriculture in most instances. However, results suggest that agriculture would not be appropriate in all parts of the country, and the index is meant to be responsive to all stressors. The IWI in its present form (available through the StreamCat website; https://www.epa.gov/national-aquatic-resource-surveys/streamcat) could be useful for management efforts at multiple scales, especially when combined with information on site condition. The IWI could be improved by incorporating empirical or literature-derived relationships between functional components and stressors. However, limitations concerning the absence of data for certain stressors should be considered.

Improving the environment for immobilized dehydrogenase enzymes by modifying Nafion with tetraalkylammonium bromides.

Recent research in our group has shown that mixture-casting Nafion with quaternary ammonium bromides can increase the electrochemical flux of redox couples through the membrane and allow for larger redox species to diffuse to the electrode surface. The research has also suggested that when these salts are cast with Nafion micellar pore size is changing. Therefore, it was proposed that the quaternary ammonium salts could be employed to tailor the structure of the Nafion membrane for immobilizing enzymes in the polymer. For cations with a high affinity for the sulfonic acid groups of Nafion, the modified structure of Nafion can also help to stabilize the enzyme and increase activity by providing a protective outer shell and an ideal chemical environment that resists a decrease in pH within the pore structure. This research examines the ability to immobilize dehydrogenase enzymes in Nafion that has been modified with quaternary ammonium bromides. Fluorescence assays, fluorescence microscopy, and cyclic voltammetric studies were employed to analyze the ability to immobilize an enzyme within the membrane, to determine the activity of the immobilized enzyme and to examine the transport of coenzyme within the membrane. Dehydrogenase enzymes immobilized in tetrabutylammonium bromide/Nafion membranes have shown high catalytic activity and enzyme active lifetimes of greater than 45 days. A variety of dehydrogenase enzymes have been successfully immobilized in the membrane, including: alcohol dehydrogenase, aldehyde dehydrogenase, glucose dehydrogenase, and lactic dehydrogenase.