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USGS2023

Scale-dependent tradeoffs between habitat and time in explaining Alligator Gar (Atractosteus spatula) movement

Ecological theory predicts that movement by riverine fishes at the population level is characterized by both stationary and mobile individuals together creating a leptokurtic distribution of movement distances. However, studies testing this theory typically ignore spatial heterogeneity in riverscapes, and the theory has not been tested using Alligator Gar ( Atractosteus spatula ), a species of growing interest among anglers and fisheries managers alike. We characterized movements and habitat associations of Alligator Gar in the Brazos River, Texas, at fine (every 2 h for 24 h) and coarse (every month for 16 months) spatiotemporal scales. We tested for the presence of leptokurtosis and relationships between movement distance, habitat dissimilarity, and time-at-large using multivariate and univariate statistical approaches. Dispersal by Alligator Gar revealed leptokurtosis at the coarse scale but not the fine scale. At the fine scale, mixed effects quantile regression revealed there was no relationship between habitat dissimilarity and dispersal distance, but dispersal was positively correlated with time. At the coarse scale, dispersal was positively correlated with increased habitat dissimilarity and time, but only for the most mobile individuals. Our work suggests that short-term movements by riverine Alligator Gar during warm seasons and at base flows increased with time but were unrelated to habitat, and long-term movements over an annual cycle during warm season flow pulses revealed highly mobile members of the population accessed distant and novel floodplain environments.

Environmental Biology of Fishes↗

USGS2005

Multi-stage sampling for large scale natural resources surveys: A case study of rice and waterfowl

Large-scale sample surveys to estimate abundance and distribution of organisms and their habitats are increasingly important in ecological studies. Multi-stage sampling (MSS) is especially suited to large-scale surveys because of the natural clustering of resources. To illustrate an application, we: (1) designed a stratified MSS to estimate late autumn abundance (kg/ha) of rice seeds in harvested fields as food for waterfowl wintering in the Mississippi Alluvial Valley (MAV); (2) investigated options for improving the MSS design; and (3) compared statistical and cost efficiency of MSS to simulated simple random sampling (SRS). During 2000–2002, we sampled 25–35 landowners per year, 1 or 2 fields per landowner per year, and measured seed mass in 10 soil cores collected within each field. Analysis of variance components and costs for each stage of the survey design indicated that collecting 10 soil cores per field was near the optimum of 11–15, whereas sampling >1 field per landowner provided few benefits because data from fields within landowners were highly correlated. Coefficients of variation (CV) of annual estimates of rice abundance ranged from 0.23 to 0.31 and were limited by variation among landowners and the number of landowners sampled. Design effects representing the statistical efficiency of MSS relative to SRS ranged from 3.2 to 9.0, and simulations indicated SRS would cost, on average, 1.4 times more than MSS because clustering of sample units in MSS decreased travel costs. We recommend MSS as a potential sampling strategy for large-scale natural resource surveys and specifically for future surveys of the availability of rice as food for waterfowl in the MAV and similar areas.

Arkansas, Kentucky, Louisiana, Mississippi, Missou↗

USGS2009

Mineral Resource Assessment of Marine Sand Resources in Cape- and Ridge-Associated Marine Sand Deposits in Three Tracts, New York and New Jersey, United States Atlantic Continental Shelf

Demand is growing in the United States and worldwide for information about the geology of offshore continental shelf regions, the character of the seafloor, and sediments comprising the seafloor and subbottom. Interest in locating sand bodies or high quality deposits that have potential as sources for beach nourishment and ecosystem restoration is especially great in some regions of the country. The Atlantic coast, particularly New York and New Jersey, has been the focus of these studies for the past 40 years with widely varying results. This study is the first attempt at applying probability statistics to modeling Holocene-age cape-and ridge-associated sand deposits and thus focuses on distinct sand body morphology. This modeling technique may have application for other continental shelf regions that have similar geologic character and late Quaternary sea-level transgression history. An estimated volume of 3.9 billion m3 of marine sand resources is predicted in the cape-and ridge-associated marine sand deposits in three representative regions or tracts on the continental shelf offshore of New York and New Jersey. These estimates are taken from probabilistic distributions of sand resources and are produced using deposit models and Monte Carlo Simulation (MCS) techniques. The estimated sand resources presented here are for only three tracts as described below and for Holocene age sand resources contained in cape-and ridge-associated marine sand deposit types within this area. Other areas may qualify as tracts for this deposit type and other deposit types and geologic ages (for example, paleo-stream channels, blanket and outwash deposits, ebb-tide shoals, and lower sea level-stand deltas), which are present on the New Jersey and New York continental shelf area but are not delineated and modeled in this initial evaluation. Admittedly, only a portion of these probable sand resources will ultimately be available and suitable for production, dependent largely on geographic, economic, preemptive use, environmental, geologic and political factors. In addition, offshore sand resources should only be considered if the area is seaward of the active zone of significant nearshore sediment transport, about 10 to 12 m in depth, and in sufficiently shallow water so that sand can be extracted within U.S. dredging equipment limits, currently about 40 m in depth. If the material is to be used for beach nourishment, material must be of an appropriate sediment texture and character (grain size, sorting, shape, and color) to match the native beach and have mineralogical properties important to its use. Extraction of sand can disturb or alter the benthic habitat and seafloor ecology, so these factors and other site-specific effects will need to be evaluated for any intended use. These and other factors are not considered in this report but can be expected to reduce the total net volume of sand resources available for production. The purpose of this report is to describe and present results from a probabilistic mineral modeling technique previously applied to onshore mineral resources. This modeling and assessment procedure is being used for the first time to assess and estimate offshore aggregate resources; this study is part of the U.S. Geological Survey (USGS) Marine Aggregates Resources and Processes Project (http://woodshole.er.usgs.gov/project-pages/aggregates/).

Bulletin↗

USGS2013

Vascular plant and vertebrate species richness in national parks of the eastern United States

Given the estimates that species diversity is diminishing at 50-100 times the normal rate, it is critical that we be able to evaluate changes in species richness in order to make informed decisions for conserving species diversity. In this study, we examined the potential of vascular plant species richness to be used as a surrogate for vertebrate species richness in the classes of amphibians, reptiles, birds, and mammals. Vascular plants, as primary producers, represent the biotic starting point for ecological community structure and are the logical place to start for understanding vertebrate species associations. We used data collected by the United States (US) National Park Service (NPS) on species presence within parks in the eastern US to estimate simple linear regressions between plant species richness and vertebrate richness. Because environmental factors may also influence species diversity, we performed simple linear regressions of species richness versus natural logarithm of park area, park latitude, mean annual precipitation, mean annual temperature, and human population density surrounding the parks. We then combined plant species richness and environmental variables in multiple regressions to determine the variables that remained as significant predictors of vertebrate species richness. As expected, we detected significant relationships between plant species richness and amphibian, bird, and mammal species richness. In some cases, plant species richness was predicted by park area alone. Species richness of mammals was only related to plant species richness. Reptile species richness, on the other hand, was related to plant species richness, park latitude and annual precipitation, while amphibian species richness was related to park latitude, park area, and plant species richness. Thus, plant species richness predicted species richness of different vertebrate groups to varying degrees and should not be used exclusively as a surrogate for vertebrate species richness. Plant species richness should be included with other variables such as area and climate when considering strategies to manage and conserve species in US National Parks. It is not always appropriate to draw conclusions about analyses of taxonomic surrogates from one area to another. Two patterns evident from the linear regressions were the increase in species richness with the increase of park area and with increase of vascular plant species richness. To test whether there were differences in these patterns among networks, we used analysis of covariance (ANCOVA). Differences among networks were detected only in bird species richness versus plant species richness and for all taxa except mammals for vertebrate species richness versus park area. Some of these results may be due to small sample size among networks, and therefore, low statistical power. Other factors that could have contributed to these results were differences in average park area and habitat heterogeneity among networks, latitudinal gradients, low variation in mean annual precipitation, and different use of vegetation by migratory species. Based on these results we recommend that management of biodiversity be approached from local and site specific criteria rather than applying management directives derived from other regions of the US. It is also recommended that analyses similar to those presented here be conducted for all national parks, once data become available for all networks in the US, to gain a better understanding of how vascular plant species richness, area, and vertebrate species richness are related in the US.

Natural Resource Technical Report NPS/NCR/NCRO/NRT↗

USGS2017

Response of bird community structure to habitat management in piñon-juniper woodland-sagebrush ecotones

Piñon ( Pinus spp.) and juniper ( Juniperus spp.) woodlands have been expanding their range across the intermountain western United States into landscapes dominated by sagebrush ( Artemisia spp.) shrublands. Management actions using prescribed fire and mechanical cutting to reduce woodland cover and control expansion provided opportunities to understand how environmental structure and changes due to these treatments influence bird communities in piñon-juniper systems. We surveyed 43 species of birds and measured vegetation for 1–3 years prior to treatment and 6–7 years post-treatment at 13 locations across Oregon, California, Idaho, Nevada, and Utah. We used structural equation modeling to develop and statistically test our conceptual model that the current bird assembly at a site is structured primarily by the previous bird community with additional drivers from current and surrounding habitat conditions as well as external regional bird dynamics. Treatment reduced woodland cover by >5% at 80 of 378 survey sites. However, habitat change achieved by treatment was highly variable because actual disturbance differed widely in extent and intensity. Biological inertia in the bird community was the strongest single driver; 72% of the variation in the bird assemblage was explained by the community that existed seven years earlier. Greater net reduction in woodlands resulted in slight shifts in the bird community to one having ecotone or shrubland affinities. However, the overall influence of woodland changes from treatment were relatively small and were buffered by other extrinsic factors. Regional bird dynamics did not significantly influence the structure of local bird communities at our sites. Our results suggest that bird communities in piñon-juniper woodlands can be highly stable when management treatments are conducted in areas with more advanced woodland development and at the level of disturbance measured in our study.

Forest Ecology and Management↗

USGS2018

Estimating vegetation biomass and cover across large plots in shrub and grass dominated drylands using terrestrial lidar and machine learning

Terrestrial laser scanning (TLS) has been shown to enable an efficient, precise, and non-destructive inventory of vegetation structure at ranges up to hundreds of meters. We developed a method that leverages TLS collections with machine learning techniques to model and map canopy cover and biomass of several classes of short-stature vegetation across large plots. We collected high-definition TLS scans of 26 1-ha plots in desert grasslands and big sagebrush shrublands in southwest Idaho, USA. We used the Random Forests machine learning algorithm to develop decision tree models predicting the biomass and canopy cover of several vegetation classes from statistical descriptors of the aboveground heights of TLS points. Manual measurements of vegetation characteristics collected within each plot served as training and validation data. Models based on five or fewer TLS descriptors of vegetation heights were developed to predict the canopy cover fraction of shrubs (R 2 = 0.77, RMSE = 7%), annual grasses (R 2 = 0.70, RMSE = 21%), perennial grasses (R 2 = 0.36, RMSE = 12%), forbs (R 2 = 0.52, RMSE = 6%), bare earth or litter (R 2 = 0.49, RMSE = 19%), and the biomass of shrubs (R 2 = 0.71, RMSE = 175 g) and herbaceous vegetation (R 2 = 0.61, RMSE = 99 g) (all values reported are out-of-bag). Our models explained much of the variability between predictions and manual measurements, and yet we expect that future applications could produce even better results by reducing some of the methodological sources of error that we encountered. Our work demonstrates how TLS can be used efficiently to extend manual measurement of vegetation characteristics from small to large plots in grasslands and shrublands, with potential application to other similarly structured ecosystems. Our method shows that vegetation structural characteristics can be modeled without classifying and delineating individual plants, a challenging and time-consuming step common in previous methods applying TLS to vegetation inventory. Improving application of TLS to studies of shrub-steppe ecosystems will serve immediate management needs by enhancing vegetation inventories, environmental modeling studies, and the ability to train broader datasets collected from air and space.

Idaho↗

USGS2016

Effects of Climate and land use on diversity, prevalence, and seasonal transmission of avian hematozoa in American Samoa

The indigenous forest birds of American Samoa are increasingly threatened by changing patterns of rainfall and temperature that are associated with climate change as well as environmental stressors associated with agricultural and urban development, invasive species, and new introductions of avian diseases and disease vectors. Long term changes in their distribution, diversity, and population sizes could have significant impacts on the ecological integrity of the islands because of their critical role as pollinators and seed dispersers. We documented diversity of vector borne parasites on Tutuila and Ta‘u Islands over a 10-year period to expand earlier observations of Plasmodium, Trypanosoma , and filarial parasites, to provide better parasite identifications, and to create a better baseline for detecting new parasite introductions. We also identified potential mosquito vectors of avian Plasmodium and Trypanosoma , determined whether land clearing and habitat alterations associated with subsistence farming within the National Park of American Samoa can influence parasite prevalence, and determined whether parasite prevalence is correlated with seasonal changes in rainfall, temperature and wind speed. Three taxonomically distinct lineages of Plasmodium were identified from mosquito vectors and forest birds based on partial sequence data from parasite mitochondrial genes. All three have been described from passerine and galliform birds in Australasia. Two lineages, SCEDEN01 and ORW1, had elongate gametocytes and large schizonts that were consistent with species of Plasmodium in the subgenus Giavannolaia, but were taxonomically distinct from known morphological species of Plasmodium based on a Bayesian phylogenetic analysis of a 478 bp region of the parasite cytochrome b gene. Both are candidates for description as new species. The third lineage (GALLUS02) was detected only in mosquito vectors on Tutuila and was similar in cytochrome b sequence to P. juxtanucleare , a pathogenic species of Plasmodium from chickens and other galliform birds from Australasia, Africa, and South America. Plasmodium relictum , the malarial parasite that has had such a devastating impact on Hawaiian forest birds, was not detected. We observed large, striated trypanosomes in avian hosts from both Tutuila and Ta‘u Islands that fell within the same taxonomic clade as T. corvi and T. culicavium based on 18S ribosomal DNA sequence. We also observed sheathed microfilariae with pointed tails that had some morphological similarities to microfilaria from species of Pelecitus, Struthiofilaria and Eulimdana , but identification will require recovery and examination of adult filarial worms from the connective tissue or body cavities of infected birds. We also observed one or more species of haemococcidians (Isospora, synonym = Atoxoplasma ) within circulating lymphocytes from multiple avian host species. Overall prevalence of Plasmodium was higher on Ta‘u (22%, 75/341) than Tutuila (9.2%, 27/294), with most infections occurring in Polynesian starlings, Samoan starlings, Wattled honeyeaters, and Cardinal honeyeaters. Prevalence was relatively constant from year to year and between seasons at individual study sites, but varied among study sites, with highest rates of infection in areas with agricultural activity at Faleasao (37.4%, 73/195, Ta‘u Island) and Amalau Valley (9.7%, 21/216, Tutuila Island). Prevalence in more remote areas of the National Park of American Samoa was lower, ranging from 1.4% (2/146) at Laufuti and Luatele on Ta‘u to 7.7% (6/78) at Olo Ridge on Tutuila. Similar trends were evident for infections with Trypanosoma and filarial worms. Overall prevalence was not influenced significantly by warmer, wet (summer) or cooler, dry (winter) season. We detected Plasmodium infections in Culex sitiens and C. quinquefasciatus through either salivary gland and midgut dissections or PCR amplification of parasite cytochrome b genes in pooled or individual samples of mosquitoes that were collected on Tutuila. Pooled or individual Aedes oceanicus, A. polynesiensis, A. tutuilae, A. upolensis, A. nocturnus, Aedes (Finlaya) (mixed pools of A. samoanus, A. oceanicus, A. tutuilae), Aedes (Stegomyia) (mixed pools of A. aegypti, A. upolensis, A. polynesiensis ), and C. annulirostris were negative for Plasmodium , but we detected infections with Trypanosoma through midgut and salivary gland dissections in a single C. sitiens from Amalau Valley, Tutuila and three A. oceanicus from Faleasao, Ta‘u. Two of the A. oceanicus from Faleasao amplified successfully with Trypanosoma primers, but sequences were distinctly different from those obtained from avian hosts. We found a strong association between land use and prevalence of mosquito-transmitted parasites on Ta‘u Island with odds of being infected more than 20 times greater in agricultural plots than more remote native forest. This relationship was evident on Tutuila Island but not statistically significant because of the close proximity of study sites and observed movement of birds between native forest and agricultural land. Our data support previous studies that have suggested that Plasmodium and other vector-borne parasites are part of the indigenous parasite fauna in American Samoa. Transmission dynamics appear to be affected by environmental changes associated with land use practices.

HI↗

USGS2019

Statistical power of dynamic occupancy models to identify temporal change: Informing the North American Bat Monitoring Program

Dynamic occupancy models provide a flexible framework for estimating and mapping species occupancy patterns over space and time for large-scale monitoring programs (e.g., the North American Bat Monitoring Program (NABat), the Amphibian Research and Monitoring Initiative). Challenges for designing surveys using the dynamic occupancy modeling framework include defining appropriate derived trend parameters, and providing usable tools for researchers to conduct project-specific sample size investigations. We present a simulation-based power analysis framework for dynamic occupancy models that allows for the incorporation of the underlying environmental space (i.e., as covariates) within a specific study region to inform sample size estimation. We investigate two definitions of temporal trend: (1) a gradual, sustained (linear or nonlinear) change over a period of many years, and (2) an abrupt increase or decrease between two time periods. We draw upon pilot data collected following NABat protocols to inform assumed data generating values in a demonstration of our approach. Due to the complicated parameter structure of dynamic occupancy models, we emphasize the importance of visualizing simulated changes over time based on different parameter settings prior to conducting a power analysis. Our simulations revealed that the linearity of short-term trends (five years in our investigation) conferred higher power with lower sample size than longer trends where occupancy probabilities approached zero (ten years in our investigation). We provide an example of how to use our tools to conduct customized investigations using questions posed by NABat, and in doing so, we shed light on general guidelines that can be applied to programs monitoring species occupancy for other taxa. Importantly, we created an R package to execute our approach for informing program-, species-, and study-specific investigations aimed at identifying changes in species occupancy.

Ecological Indicators↗

USGS2014

Evaluation of a regional monitoring program's statistical power to detect temporal trends in forest health indicators

Forests are socioeconomically and ecologically important ecosystems that are exposed to a variety of natural and anthropogenic stressors. As such, monitoring forest condition and detecting temporal changes therein remain critical to sound public and private forestland management. The National Parks Service’s Vital Signs monitoring program collects information on many forest health indicators, including species richness, cover by exotics, browse pressure, and forest regeneration. We applied a mixed-model approach to partition variability in data for 30 forest health indicators collected from several national parks in the eastern United States. We then used the estimated variance components in a simulation model to evaluate trend detection capabilities for each indicator. We investigated the extent to which the following factors affected ability to detect trends: (a) sample design: using simple panel versus connected panel design, (b) effect size: increasing trend magnitude, (c) sample size: varying the number of plots sampled each year, and (d) stratified sampling: post-stratifying plots into vegetation domains. Statistical power varied among indicators; however, indicators that measured the proportion of a total yielded higher power when compared to indicators that measured absolute or average values. In addition, the total variability for an indicator appeared to influence power to detect temporal trends more than how total variance was partitioned among spatial and temporal sources. Based on these analyses and the monitoring objectives of the Vital Signs program, the current sampling design is likely overly intensive for detecting a 5 % trend·year −1 for all indicators and is appropriate for detecting a 1 % trend·year −1 in most indicators.

New Jersey, Pennsylvania, Virginia, West Virginia↗

USGS2026

Hierarchical mixture models and high-resolution monitoring data can inform siting and operational strategies to mitigate bat fatalities at wind turbines

Bats provide critical ecosystem services, but bat fatalities due to wind energy development may imperil some bat populations. Statistical models are used to estimate the total fatalities that occur based on carcasses observed during monitoring surveys. Current models often estimate fatalities aggregated across species, time, and/or turbines, but fall short of reliably informing siting and operational collision mitigation strategies that account for species-specific fatality patterns on a fine spatiotemporal scale. We developed a hierarchical mixture model for estimating species-specific covariate effects and total fatalities per species at each turbine on weekly intervals. We applied the model to a high-resolution dataset of bat carcasses found during turbine searches across nineteen wind facilities in Iowa over two years. Our model explains species-specific variation in bat fatalities at individual wind turbines according to turbine proximity to bat habitat, turbine design specifications, seasonal trends, and weather conditions such as nightly air temperature, air pressure, and wind speed. Turbines located on the edge of wind facilities had higher fatalities, and proximity to roosting and foraging habitat accounted for variation in species-specific fatality estimates. These insights into turbine placement effects can inform siting strategies. We also discovered species-specific relationships with average nightly wind speed and air temperature, among other weather conditions, that could inform operational mitigation strategies such as smart curtailment. Our model can transform observations of carcasses found during turbine searches across multiple facilities, years, and variable search efforts into estimates of total fatalities per species associated with species-specific spatial, temporal, and environmental covariate effects.

Ecological Informatics↗

USGS2019

Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets

Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides ) species complex, and elevated Nitzschia , Diploneis , and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora , Mayamaea , and Psammodictyon , indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables.

Ecological Indicators↗

USGS2022

Power analysis for detecting the effects of best management practices on reducing nitrogen and phosphorus fluxes to the Chesapeake Bay watershed, USA

In 2010 the U.S. Environmental Protection Agency established the Total Maximum Daily Load (TMDL) which is a “pollution diet” that aims to reduce the amount of nitrogen and phosphorus entering the Chesapeake Bay, the largest estuary in the United States, by 25 and 24% percent, respectively. To achieve this goal the TMDL requires the implementation of Best Management Practices (BMPs), which are accepted land management practices for reducing pollutant runoff to nearby bodies of water. While the TMDL requires that the necessary management actions be in place by 2025 to eventually reach targeted nutrient loads, the ability to detect an effect of BMPs while assuming that one has occurred (i.e. statistical power) is still not well understood. The goal of this study was to investigate the power and required timelines to detect nutrient reductions in streams and rivers as the result of BMP implementation at the Chesapeake Watershed scale. Power estimates were produced using SPAtially Referenced Regression On Watershed attributes (SPARROW) models, which offer a flexible statistical framework and were recently extended to allow for modeling multiple time steps. Nitrogen and phosphorus focused models were calibrated to estimate the power to detect reductions in flux from numerous constituent sources. To confidently detect a decrease in constituent flux reaching the Chesapeake Bay’s tidal waters from a specific constituent source, reductions ranging from 30–60% were required for the nitrogen model. In contrast, reductions of up to 80% were not detectable under the phosphorus model. The timelines necessary to detect reductions in nitrogen flux ranged from 11 to several hundred years under different rates-of-change and management scenarios. The approach proposed here can help better understand the ability to detect the effects of BMPs on a regional scale and help guide future management actions and monitoring programs.

Delaware, Maryland, New York, Pennsylvania, Virgin↗

USGS2017

Evapotranspiration by remote sensing: An analysis of the Colorado River Delta before and after the Minute 319 pulse flow to Mexico

The unique hydrologic conditions characterizing riparian ecosystems in dryland (arid and semi-arid) areas help maintain high biodiversity and support high levels of primary productivity compared to associated uplands. In western North America, many riparian ecosystems have been damaged by altered flow regimes (e.g., impoundments and diversions) and over utilization of water resources (e.g., groundwater pumping for agriculture and human consumption). This has led some state and national governments to provide occasional environmental flows to address the declining condition of such riparian systems. In a historic agreement between the United States and Mexico, 130 million cubic meters (mcm) of water was released to the lower Colorado River Delta in Mexico, with the intent to evaluate the hydrological and biological response of the ecosystem. We used the Moderate Resolution Imaging Spectroradiometer (MODIS) Enhanced Vegetation Index (EVI) to estimate long term (2000–2014) and short term (pre- and post-pulse; 2013 and 2014) evapotranspiration (ET; used herein as an indicator of plant health) of the delta’s riparian corridor. We found the pulse flow helped reverse a decline in ET from 2011 to 2013, with a small, but statistically significant increase in 2014 (P < 0.05). ET was greater than 100 mcm in all years analyzed (even in years without surface flows) and exceeded surface flows in all years except 2000 (result of excess flows following an El Niño cycle in 1997) and 2014 (year of the pulse flow). Based on groundwater salinities and MODIS ET estimates, we estimated groundwater flow into the delta to be ∼103 mcm. Shallow groundwater salinities in the riparian zone increased from 1.30 g L −1 in the most upstream reach to 2.77 g L −1 in the most downstream reach we measured, partly due to uptake of water by riparian vegetation and partly to intrusion of saline agricultural return flows. The disparity between surface flows and ET can likely be explained by the predominantly phreatophytic plants characterizing the area, which draw water from the aquifer. These results also suggest that the deteriorated condition of vegetation within the riparian zone might not be reversed by a single pulse event and could instead require subsequent pulse flows as a long term strategy to restore vegetation in this riparian ecosystem.

Ecological Engineering↗

USGS2013

Approaches to setting organism-based ballast water discharge standards

As a vector by which foreign species invade coastal and freshwater waterbodies, ballast water discharge from ships is recognized as a major environmental threat. The International Maritime Organization (IMO) drafted an international treaty establishing ballast water discharge standards based on the number of viable organisms per volume of ballast discharge for different organism size classes. Concerns that the IMO standards are not sufficiently protective have initiated several state and national efforts in the United States to develop more stringent standards. We evaluated seven approaches to establishing discharge standards for the >50-μm size class: (1) expert opinion/management consensus, (2) zero detectable living organisms, (3) natural invasion rates, (4) reaction–diffusion models, (5) population viability analysis (PVA) models, (6) per capita invasion probabilities (PCIP), and (7) experimental studies. Because of the difficulty in synthesizing scientific knowledge in an unbiased and transparent fashion, we recommend the use of quantitative models instead of expert opinion. The actual organism concentration associated with a “zero detectable organisms” standard is defined by the statistical rigor of its monitoring program; thus it is not clear whether such a standard is as stringent as other standards. For several reasons, the natural invasion rate, reaction–diffusion, and experimental approaches are not considered suitable for generating discharge standards. PVA models can be used to predict the likelihood of establishment of introduced species but are limited by a lack of population vital rates for species characteristic of ballast water discharges. Until such rates become available, PVA models are better suited to evaluate relative efficiency of proposed standards rather than predicting probabilities of invasion. The PCIP approach, which is based on historical invasion rates at a regional scale, appears to circumvent many of the indicated problems, although it may underestimate invasions by asexual and parthenogenic species. Further research is needed to better define propagule dose–responses, densities at which Allee effects occur, approaches to predicting the likelihood of invasion from multi-species introductions, and generation of formal comparisons of approaches using standardized scenarios.

Ecological Applications↗

USGS2021

Development and validation of a spatially-explicit agent-based model for space utilization by African savanna elephants (Loxodonta africana) based on determinants of movement

African elephants (Loxodonta africana) are well-studied and inhabit diverse landscapes that are being transformed by both humans and natural forces. Most tools currently in use are limited in their ability to predict how elephants will respond to novel changes in the environment. Individual-, or agent-based modeling (ABM), may extend current methods in addressing and predicting spatial responses to environmental conditions over time. We developed a spatially explicit agent-based model to simulate elephant space use and validated the model with movement data from elephants in Kruger National Park (KNP) and Chobe National Park (CNP). We simulated movement at an hourly scale, as this scale can reflect switches in elephant behavior due to changes in internal states and short-term responses to the local availability and distribution of critical resources, including forage, water, and shade. Known internal drivers of elephant movement, including perceived temperature and the time since an individual last visited a water source, were linked to the external environment through behavior-based movement rules. Simulations were run on model landscapes representing the wet season and the hot, dry season for both parks. The model outputs, including home range size, daily displacement distance, net displacement distance, and maximum distance traveled from a permanent water source, were evaluated through qualitative and quantitative comparisons to actual elephant movement data from both KNP and CNP. The ABM was successful in reproducing the differences in daily displacements between seasons in each park, and in distances traveled from a permanent water source between parks and seasons. Other movement characteristics, including differences in home range sizes and net daily displacements, were partially reproduced. Out of the all the statistical comparisons made between the empirical and simulated movement patterns, the majority were classified as discrepancies of medium or small effect size. We have shown that a resource-driven model with relatively simple decision rules generates trajectories with movement characteristics that are mostly comparable to those calculated from empirical data. Simulating hourly movement (as our model does) may be useful in predicting how finer-scale patterns of space use, such as those created by foraging movements, are influenced by finer spatio-temporal changes in the environment.

Chobe National Park, Kruger National Park↗

USGS2006

The Amphibian Research and Monitoring Initiative (ARMI): 5-year report

The Amphibian Research and Monitoring Initiative (ARMI) is an innovative, multidisciplinary program that began in 2000 in response to a congressional directive for the Department of the Interior to address the issue of amphibian declines in the United States. ARMI’s formulation was cross-disciplinary, integrating U.S. Geological Survey scientists from Biology, Water, and Geography to develop a course of action (Corn and others, 2005a). The result has been an effective program with diverse, yet complementary, expertise. ARMI’s approach to research and monitoring is multiscale. Detailed investigations focus on a few species at selected local sites throughout the country; monitoring addresses a larger number of species over broader areas (typically, National Parks and National Wildlife Refuges); and inventories to document species occurrence are conducted more extensively across the landscape. Where monitoring is conducted, the emphasis is on an ability to draw statistically defensible conclusions about the status of amphibians. To achieve this objective, ARMI has instituted a monitoring response variable that has nationwide applicability. At research sites, ARMI focuses on studying species/environment interactions, determining causes of observed declines, and developing new techniques to sample populations and analyze data. Results from activities at all scales are provided to scientists, land managers, and policymakers, as appropriate. The ARMI program and the scientists involved contribute significantly to understanding amphibian declines at local, regional, national, and international levels. Within National Parks and National Wildlife Refuges, findings help land managers make decisions applicable to amphibian conservation. For example, the National Park Service (NPS) selected amphibians as a vital sign for several of their monitoring networks, and ARMI scientists provide information and assistance in developing monitoring methods for this NPS effort. At the national level, ARMI has had major exposure at a variety of meetings, including a dedicated symposium at the 2004 joint meetings of the Herpetologists’ League, the American Society of Ichthyologists and Herpetologists, and the Society for the Study of Amphibians and Reptiles. Several principal investigators have brought international exposure to ARMI through venues such as the World Congress of Herpetology in South Africa in 2005 (invited presentation by Dr. Gary Fellers), the Global Amphibian Summit, sponsored by the International Union for Conservation of Nature (IUCN) and Wildlife Conservation International, in Washington, D.C., 2005 (invited participation by Dr. P.S. Corn), and a special issue of the international herpetological journal Alytes focused on ARMI in 2004 (edited by Dr. C.K. Dodd, Jr.). ARMI research and monitoring efforts have addressed at least 7 of the 21 Threatened and Endangered Species listed by the U.S. Fish and Wildlife Service (California red-legged frog [Rana draytonii], Chiricahua leopard frog [R. chiricahuensis], arroyo toad [Bufo californicus], dusky gopher frog [Rana sevosa], mountain yellow-legged frog [R. muscosa], flatwoods salamander [Ambystoma cingulatum], and the golden coqui [Eleutherodactylus jasperi]), and 9 additional species of concern recognized by the IUCN. ARMI investigations have addressed time-sensitive research, such as emerging infectious diseases and effects on amphibians related to natural disasters like wildfire, hurricanes, and debris flows, and the effects of more constant, environmental change, like urban expansion, road development, and the use of pesticides. Over the last 5 years, ARMI has partnered with an extensive list of government, academic, and private entities. These partnerships have been fruitful and have assisted ARMI in developing new field protocols and analytic tools, in using and refining emerging technologies to improve accuracy and efficiency of data handling, in conducting amphibian disease, malformation, and environmental effects research, and in implementing a network of monitoring and research sites. Accomplishments from these endeavors include more than 40 publications on amphibian status and trends, nearly 100 publications on amphibian ecology and causes of declines, and over 30 methodological publications. Several databases have emerged as a result of ARMI and its partnerships; one, a digital atlas of ranges for all U.S. amphibian species, was used by the IUCN to display amphibian distribution maps in the Global Amphibian Assessment Project. Given the scope of ARMI and the panoply of projects, findings have had implications for policy. Investigations that demonstrate amphibian declines or illuminate causes of declines provide valuable information about habitat management, environmental effects, mechanisms for the spread of disease, and human/amphibian interfaces. This information has been made available to land managers, scientists, educators, Congress and other policymakers, and the public. The support afforded ARMI by Congress has been influential in the program’s development and success. The value of ARMI’s efforts will continue to increase as we are able to extend our studies spatially and temporally to answer critical questions with more confidence. We are using ARMI’s resources efficiently and continuing to develop innovative mechanisms for leveraging resources for maximum effectiveness during challenging financial times. This report is a 5-year retrospective of the structure, methodology, progress, and contributions to the broader scientific community that have resulted from this national USGS program. We evaluate ARMI’s success to date, with regard to the challenges faced by the program and the strengths that have emerged. We chart objectives for the next 5 years that build on current accomplishments, highlight areas meriting further research, and direct efforts to overcome existing weaknesses.

Scientific Investigations Report↗

USGS2013

Identification of metrics to monitor salt marsh integrity on National Wildlife Refuges in relation to conservation and management objectives

Executive Summary Most salt marshes in the US have been degraded by human activities, and threats from physical alterations, surrounding land-use, species invasions, and global climate change persist. Salt marshes are unique and highly productive ecosystems with high intrinsic value to wildlife, and many National Wildlife Refuges (NWRs) have been established in coastal areas to protect large tracts of salt marsh and wetland-dependent species. Various management practices are employed routinely on coastal NWRs to restore and enhance marsh integrity and ensure ecosystem sustainability. Prioritizing NWR salt marshes for application of management actions and choosing among multiple management options requires scientifically-based methods for assessing marsh condition. Monitoring is integral to structured decision-making (SDM), a formal process for decomposing a decision into its essential elements. Within a natural resource context, SDM involves identifying management objectives, alternative management actions, and expected management outcomes. The core of SDM is a set of criteria for measuring system performance and evaluating management responses. Therefore, use of SDM to frame natural resource decisions leads to logical selection of monitoring attributes that are linked explicitly to management needs. We used SDM to guide selection of variables for monitoring the ecological integrity of salt marshes within the National Wildlife Refuge System (NWRS). Our objectives were to identify indicators of salt marsh integrity that are effective across large geographic regions, responsive to a wide range of threats, and feasible to implement within funding and staffing constraints of the NWRS. In April, 2008, we engaged interdisciplinary experts in a week-long rapid prototyping SDM workshop to define the essential elements of salt marsh management decisions on refuges throughout the northeastern, southwestern, and northwestern US, corresponding to respective Regions 5, 2, and 1 of the US Fish and Wildlife Service (FWS). Through this process we identified measurable attributes for monitoring salt marsh ecosystems that are integrated into conservation practice and target management objectives. The following salt marsh attributes were identified through the SDM process either for describing state condition to determine management needs or for evaluating the achievement of management objectives: historical condition and geomorphic setting; ditch density; surrounding land use; ratio of open water area to vegetation area; rate of pesticide application; environmental contaminant concentration; change in marsh surface elevation relative to sea level rise; tidal range and groundwater level; surface topography; salinity; and species composition and abundance of vegetation, invasive species, invertebrates, nekton, and breeding and wintering birds. The identified attributes were too broadly defined to serve as operational monitoring variables. Therefore, we tested specific metrics for quantifying most of these attributes in summers of 2008 and 2009. The first four attributes in the above list can be characterized by office-based analysis of existing GIS data layers. The remaining attributes require field-based methods for assessment. We were forced to exclude a small number of attributes from field tests due to inconsistent data (pesticide application rate, environmental contaminant concentrations) or requirements that exceeded the scope of this project (change in marsh surface elevation; surface topography; benthic invertebrates; wintering birds). We evaluated potential metrics for evaluating all remaining field attributes. In partnership with NWRS biologists, we tested rapid versus intensive metrics for monitoring field attributes (tidal range and groundwater level; marsh surface elevation; salinity; and species composition and abundance of vegetation, invasive species, nekton, and breeding birds) at coastal refuges throughout FWS Region 5. Seven refuges participated in metric testing in 2008: Rachel Carson (ME), Parker River (MA), Wertheim (NY), E. B. Forsythe (NJ), Bombay Hook (DE), Prime Hook (DE), and Eastern Shore of Virginia Complex (VA). These seven and two additional refuges participated in metric testing in 2009: Rhode Island Complex (RI) and Stewart B. McKinney (CT). We based all field metrics on existing protocols for salt marsh assessment. Sampling locations were determined randomly within delineated marsh study units (MSUs) at each refuge. Detailed field methods are provided in appendices to this report. Measurements for individual metrics were averaged across samples within MSUs during each year of sampling. Each year, correlation or regression analysis was conducted on average measurements across MSUs within each attribute set to identify redundant metrics. Statistical redundancy between a pair of metrics within an attribute set (i.e., correlation or regression slopes with p-values < 0.05) was considered justification for eliminating one of the pair from the regional set of monitoring metrics. Decisions regarding metric elimination versus retention were based on feasibility of monitoring, considering such factors as sampling time, resources required, and potential for regional standardization in implementation. The result of these tests is a reduced suite of monitoring metrics that targets NWRS management decisions and is practicable for implementing on a regional scale. Based on these tests, we recommend the following list of metrics for monitoring integrity of NWRS salt marshes (marsh attribute category is in parentheses): (historical condition and geomorphic setting) position of marsh in the landscape, marsh shape, degree of fill and/or fragmentation, degree of tidal flushing, amount of aquatic edge; (ditch density) ranking of ditch density from none to severe; (surrounding land use) relative proportion of agricultural land in a 150-m buffer around the marsh, relative proportion of natural land in a 150-m buffer around the marsh, relative proportion of natural land in a 1-km buffer around the marsh; (ratio of open water area to vegetation area) ratio of open water to emergent herbaceous wetlands within the marsh; (marsh surface elevation) elevation referenced to NAVD88 in a representative area of the marsh; (tidal range and groundwater level) percent of time the marsh surface is flooded during deployment of a continuous water-level monitor at a representative marsh location, mean depth of surface flooding as measured by a continuous water-level monitor at a representative location; (salinity) salinity measured in surface water; (vegetation community) vegetation species richness using the point-intercept method in 100-m diameter survey plots, percent cover of various marsh community types within 100-m diameter survey plots; (invasive species abundance) percent cover of invasive plant species measured using the point-intercept method in 100-m diameter survey plots; (nekton community) nekton density, nekton species richness, length of Fundulus heteroclitus ; (breeding bird community) abundance of Willets counted per point during standard call-broadcast surveys, summed abundance of tidal marsh obligate species (Clapper Rail, Willet, Saltmarsh Sparrow, Seaside Sparrow) counted per point during standard call-broadcast surveys. Metrics describing the historical condition, geomorphic setting, and broad landscape features can be assessed using existing GIS databases. Our results support use of rapid methods to assess the majority of field metrics; only those used to describe the nekton community must be measured using intensive methods (throw traps or ditch nets, dependant on habitat configuration). Implementation of these metrics for quantitative assessment of NWRS salt marsh integrity in FWS Region 5 requires developing sampling designs for each refuge. Additionally, it is important to determine how the monitoring information will be used within a management context. SDM should be used to complete the analysis of salt marsh management decisions. The next steps would involve 1) prioritizing and weighting the management objectives; 2) predicting responses to individual management actions in terms of objectives and metrics; 3) using multiattribute utility theory to convert all measurable attributes to a common utility scale; 4) determining the total management benefit of each action by summing utilities across objectives; and 5) maximizing the total management benefits within cost constraints for each refuge. This process would allow the optimum management decisions for NWRS salt marshes to be selected and implemented based directly on monitoring data and current understanding of marsh responses to management actions. Monitoring the outcome of management actions would then allow new monitoring data to be incorporated into subsequent decisions.

Connecticut, Delaware, Maine, Massachusetts, New J↗

USGS1997

Fish communities of fixed sites in the Western Lake Michigan Drainages, Wisconsin and Michigan, 1993-95

Fish communities were surveyed at 20 wadable stream sites during 1993-95 as part of the U.S. Geological Survey's (USGS) National Water- Quality Assessment (NAWQA) Program's assessment of the Western Lake Michigan Drainages. Part of the NAWQA design is to incorporate ecological data into an overall environmental assessment. Collection of fish-community data was part of this ecological assessment. The Western Lake Michigan Drainages study area is located in eastern Wisconsin and parts of the Upper Peninsula of Michigan. To isolate the effects of individual factors on stream quality, the study area was subdivided into 28 environmental settings, or relatively homogeneous units (RHUs), on the basis of land use/land cover, texture of surficial deposits, and bedrock geology. A fixed monitoring site was established on a wadable stream within 8 of these RHUs to determine the status and trends of water quality in a representative stream. Water-quality characteristics, ecological- community data, and stream-habitat factors were measured at these sites during 1993- 95. Fish communities were sampled at the 8 wadable fixed sites once a year during 1993-95. At three of these sites, multiple-reach samples were collected in 1994 to determine within-site variation. Fish communities also were sampled at an additional 12 sites, 11 in 1993 and one in 1995, within the 6 largest RHUs. The sites, 1-3 per each of the 6 RHUs, were located on streams with drainage basins of similar size as the fixed sites within the same RHUs. A total of 44 fish species from 12 families were collected at the 20 sites. The family with the most species represented were the minnows. The number of species per site ranged from one at a small urban site (Lincoln Creek) in 1995 to 21 at an agricultural site (North Branch Milwaukee River) in 1995. The number of individuals collected in one sampling pass ranged from 21 at a stream in the forested northwest part of the study area (Peshekee River) in 1995 to 498 at an agricultural site (East River) in 1995. White sucker (Catostomus commersoni) were collected at 17 sites, the most of any species. Species that are indicative of a coldwater environment were collected at 12 sites. Detrended correspondence analysis (DCA) of multiple-reach and multiple-year data indicated that species composition at each of these sites were fairly consistent between reaches and years. Thus, for simplicity, most analyses were done using 1993 data only. Index of Biotic Integrity (IBI) scores on 1993 data ranged from very poor at a channelized urban site to excellent at 3 sites; 2 in primarily agricultural areas and 1 in a forested area. Seven sites each scored good or fair, and two sites scored poor. Sites with multiple-year or multiple-reach data did not vary significantly within the error factor of the IBI. DCA of fish-community data from 19 sites indicated that coldwater sites were tightly grouped, whereas warmwater sites showed a larger gradient. This was expected, given the potential for greater diversity among warmwater sites. Fixed sites were shown to be representative of the study area as a whole, while specific fish communities could not be attributed to particular RHUs. Cluster analysis revealed two major groups of sites and two outlier sites. The two groups represented coldwater and warmwater streams, while the outlier sites were the urban site and a species- rich site with high biotic integrity that drains primarily agricultural land. Canonical correspondence analysis (CCA) revealed that soil credibility was a significant predictor of species composition. Though not statistically significant, land use, soil permeability, and bedrock permeability also were indicated as predictors of fish-species composition by CCA.

Michigan, Wisconsin↗