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USGS2016

Effects of climate change on tidal marshes along a latitudinal gradient in California

Public Summary The coastal region of California supports a wealth of ecosystem services including habitat provision for wildlife and fisheries. Tidal marshes, mudflats, and shallow bays within coastal estuaries link marine, freshwater and terrestrial habitats, and provide economic and recreational benefits to local communities. Climate change effects such as sea-level rise (SLR) are altering these habitats, but we know little about how these areas will change over the next 50–100 years. Our study examined the projected effects of three recent SLR scenarios produced for the West Coast of North America on tidal marshes in California. We compiled physical and biological data, including coastal topography, tidal inundation, plant composition, and sediment accretion to project how SLR may alter these ecosystems in the future. The goal of our research was to provide results that support coastal management and conservation efforts across California. Under a low SLR scenario, all study sites remained vegetated tidal wetlands, with most sites showing little elevation and vegetation change relative to sea level. At most sites, mid SLR projections led to increases in low marsh habitat at the expense of middle and high marsh habitat. Marshes at Morro Bay and Tijuana River Estuary were the most vulnerable to mid SLR with many areas becoming intertidal mudflat. Under a high SLR scenario, most sites were projected to lose vegetated habitat, eventually converting to intertidal mudflats. Our results suggest that California marshes are vulnerable to major habitat shifts under mid or high rates of SLR, especially in the latter part of the century. Loss of vegetated tidal marshes in California due to SLR is expected to impact ecosystem services that are dependent on coastal wetlands such as wildlife habitat, carbon sequestration, improved water quality, and coastal protection from storms.

California↗

USGS2017

Status and threats analysis for the Florida manatee ( Trichechus manatus latirostris ), 2016

Trichechus manatus (West Indian manatee), especially T. m. latirostris , the Florida subspecies, has been the focus of conservation efforts and extensive research since its listing under the Endangered Species Act of 1973. To determine the status of, and severity of threats to, the Florida manatee, a comprehensive revision and update of the manatee Core Biological Model was completed and used to perform a population viability analysis for the Florida manatee. The probability of the Florida manatee population falling below 500 adults on either the Gulf or East coast within the next 100 years was estimated to be 0.42 percent. This risk of quasi-extinction is low because the estimated adult survival rates are high, the current population size is greater than 2,500 on each coast, and the estimated carrying capacity for manatees is much larger than the current abundance estimates in all four regions of Florida. Three threats contribute in roughly equal measures to the risk of quasi-extinction: watercraft-related mortality, red-tide mortality, and loss of warm-water habitat. Only an increase in watercraft-related mortality has the potential to substantially increase the risk of quasi-extinction at the statewide or coastal level. Expected losses of warm-water habitat are likely to cause a major change in the distribution of the population from the regions where manatees rely heavily on power plant effluents for warmth in winter (Southwest and Atlantic regions) to the regions where manatees primarily use natural springs in winter (Northwest and Upper St. Johns regions). The chances are nearly 50 percent that manatee populations in the Southwest and Atlantic regions will decrease from their 2011 levels by at least 30 percent over the next century. A large number of scenarios were examined to explore the possible effects of potential emerging threats, and in most of them, the risk of quasi-extinction at the coastal scale within 100 years did not rise above 1 percent. The four exceptions are scenarios in which the rate of watercraft-related mortality increases, carrying capacity is only a fraction of the current estimates, a new chronic source of mortality emerges, or multiple threats emerge in concert. Even in these scenarios, however, the risk of falling below 500 adults on either the East coast or the Gulf coast within 100 years from 2011 is less than 10 percent. High adult survival provides the population with strong resilience to a variety of current and future threats. On the basis of these analyses, we conclude that if these threats continue to be managed effectively, manatees are likely to persist on both coasts of Florida and remain an integral part of the coastal Florida ecosystem through the 21st century. If vigilance in management is reduced, however, the scenarios in which manatees could face risk of decline become more likely.

Florida↗

USGS2024

Rappahannock tributary summary: A summary of trends in tidal water quality and associated factors, 1985-2022

The Rappahannock Tributary Summary outlines change over time for a suite of monitored tidal water quality parameters and associated potential drivers of those trends for the period of 1985 to 2022, and provides a brief description of the current state of knowledge explaining these observed changes. Water quality parameters described include surface (above pycnocline) total nitrogen (TN), surface total phosphorus (TP), surface water temperature (WTEMP), spring (March-May) and summer (JulySeptember) surface chlorophyll a, summer bottom (below pycnocline) dissolved oxygen (DO) concentrations, and Secchi disk depth (a measure of water clarity). Results for annual bottom TP, bottom TN, surface ortho-phosphate (PO 4 ), surface dissolved inorganic nitrogen (DIN), surface total suspended solids (TSS), and summer surface DO concentrations are provided in Appendix B. Drivers discussed include physiographic watershed characteristics, changes in TN, TP, and sediment loads from the watershed to tidal waters, expected effects of changing land use, and implementation of nutrient management and natural resource conservation practices. Factors internal to estuarine waters that also play a role as drivers are described including biogeochemical processes, physical forces such as winddriven mixing of the water column and increase in rainfall intensity and volume, and biological factors such as phytoplankton biomass and the presence of submerged aquatic vegetation. Continuing to track water quality response and investigating these influencing factors are important steps to understanding water quality patterns and changes in the Rappahannock River. The intended audiences for this report include, but are not limited to, 1) technical managers within jurisdictions who are looking at tidal water quality data and trying to understand why patterns are occurring, 2) local watershed organizations that are trying to understand these analyses and working to connect them to their local area(s), and 3) federal, state, and academic researchers. Figure 1 presents a conceptual model highlighting these intended audiences. Our goal is for the Tributary Summary documents to be sources of readily available background for change over time in tidal water quality observed with monitoring data. The intended purpose of the Tributary Summary documents is to help answer questions related to water quality, show how landscape factors drive water quality change over time, provide support for management decisions that may alter water quality trends and living resources conditions, and highlight where there may be information or knowledge gaps.

Virginia↗

USGS2026

Lower Eastern Shore Tributary summary: A summary of trends in tidal water quality and associated factors, 1985-2023

The Lower Eastern Shore Tributary Summary outlines change over time according to a suite of monitored tidal water quality parameters and associated potential drivers of those trends for the period 1985 – 2023, and provides a brief description of the current state of knowledge explaining these observed changes. Water quality parameters described include surface (above pycnocline) total nitrogen (TN), surface total phosphorus (TP), surface water temperature (WTEMP), spring (March-May) and summer (July-September) surface chlorophyll a, summer bottom (below pycnocline) dissolved oxygen (DO) concentrations, and Secchi disk depth (a measure of water clarity). Results for annual bottom TP, bottom TN, surface ortho-phosphate (PO4), surface dissolved inorganic nitrogen (DIN), surface total suspended solids (TSS), and summer surface DO concentrations are provided in an Appendix B. Drivers discussed include physiographic watershed characteristics, changes in TN, TP, and sediment loads from the watershed to tidal waters, expected effects of changing land use, and implementation of nutrient management and natural resource conservation practices. Factors internal to estuarine waters that also play a role as drivers are described including biogeochemical processes, physical forces such as winddriven mixing of the water column and increase in rainfall intensity and volume, and biological factors such as phytoplankton biomass and the presence of submersed aquatic vegetation. Continuing to track water quality response and investigating these influencing factors are important steps to understanding water quality patterns and changes in the Lower Eastern Shore. The intended audiences for this report include, but are not limited to, 1) technical managers within jurisdictions who use tidal water quality to inform management decisions, 2) local watershed organizations that are trying to understand these analyses and working to connect them to their local area(s), and 3) federal, state, and academic researchers. Figure 1 presents a conceptual model highlighting these intended audiences. The Tributary Summary documents are sources of readily available background for change over time in tidal water quality observed with monitoring data. They help answer questions related to water quality, show how landscape factors drive water-quality changes over time, provide support for management decisions that may alter water quality trends and living resources conditions, and highlight where there may be information or knowledge gaps.

Maryland, Virginia↗

USGS2013

Conditions favouring Bromus tectorum dominance of endangered sagebrush steppe ecosystems

1. Ecosystem invasibility is determined by combinations of environmental variables, invader attributes, disturbance regimes, competitive abilities of resident species and evolutionary history between residents and disturbance regimes. Understanding the relative importance of each factor is critical to limiting future invasions and restoring ecosystems. 2. We investigated factors potentially controlling Bromus tectorum invasions into Artemisia tridentata ssp. wyomingensis communities across 75 sites in the Great Basin. We measured soil texture, cattle grazing intensity, gaps among perennial plants and plant cover including B. tectorum, biological soil crusts (BSCs) and bare soil. Using a priori knowledge, we developed a multivariate hypothesis of the susceptibility of Artemisia ecosystems to B. tectorum invasion and used the model to assess the relative importance of the factors driving the magnitude of such invasions. 3. Model results imply that bunchgrass community structure, abundance and composition, along with BSC cover, play important roles in controlling B. tectorum dominance. Evidence suggests abundant bunchgrasses limit invasions by limiting the size and connectivity of gaps between vegetation, and BSCs appear to limit invasions within gaps. Results also suggest that cattle grazing reduces invasion resistance by decreasing bunchgrass abundance, shifting bunchgrass composition, and thereby increasing connectivity of gaps between perennial plants while trampling further reduces resistance by reducing BSC. 4. Synthesis and applications. Grazing exacerbates Bromus tectorum dominance in one of North America's most endangered ecosystems by adversely impacting key mechanisms mediating resistance to invasion. If the goal is to conserve and restore resistance of these systems, managers should consider maintaining or restoring: (i) high bunchgrass cover and structure characterized by spatially dispersed bunchgrasses and small gaps between them; (ii) a diverse assemblage of bunchgrass species to maximize competitive interactions with B. tectorum in time and space; and (iii) biological soil crusts to limit B. tectorum establishment. Passive restoration by reducing cumulative cattle grazing may be one of the most effective means of achieving these three goals.

Journal of Applied Ecology↗

USGS2013

Fluvial rainbow trout contribute to the colonization of steelhead ( Oncorhynchus mykiss ) in a small stream

Life history polymorphisms provide ecological and genetic diversity important to the long term persistence of species responding to stochastic environments. Oncorhynchus mykiss have complex and overlapping life history strategies that are also sympatric with hatchery populations. Passive integrated transponder (PIT) tags and parentage analysis were used to identify the life history, origin (hatchery or wild) and reproductive success of migratory rainbow/steelhead for two brood years after barriers were removed from a small stream. The fluvial rainbow trout provided a source of wild genotypes to the colonizing population boosting the number of successful spawners. Significantly more parr offspring were produced by anadromous parents than expected in brood year 2005, whereas significantly more parr offspring were produced by fluvial parents than expected in brood year 2006. Although hatchery steelhead were prevalent in the Methow Basin, they produced only 2 parr and no returning adults in Beaver Creek. On average, individual wild steelhead produced more parr offspring than the fluvial or hatchery groups. Yet, the offspring that returned as adult steelhead were from parents that produced few parr offspring, indicating that high production of parr offspring may not be related to greater returns of adult offspring. These data in combination with other studies of sympatric life histories of O. mykiss indicate that fluvial rainbow trout are important to the conservation and recovery of steelhead and should be included in the management and recovery efforts.

Washington↗

USGS2010

An introduction to the practical and ethical perspectives on the need to advance and standardize the intracoelomic surgical implantation of electronic tags in fish

The intracoelomic surgical implantation of electronic tags (including radio and acoustic telemetry transmitters, passive integrated transponders and archival biologgers) is frequently used for conducting studies on fish. Electronic tagging studies provide information on the spatial ecology, behavior and survival of fish in marine and freshwater systems. However, any surgical procedure, particularly one where a laparotomy is performed and the coelomic cavity is opened, has the potential to alter the survival, behavior or condition of the animal which can impair welfare and introduce bias. Given that management, regulatory and conservation decisions are based on the assumption that fish implanted with electronic tags have similar fates and behavior relative to untagged conspecifics, it is critical to ensure that best surgical practices are being used. Also, the current lack of standardized surgical procedures and reporting of specific methodological details precludes cross-study and cross-year analyses which would further progress the field of fisheries science. This compilation of papers seeks to identify the best practices for the entire intracoelomic tagging procedure including pre- and post-operative care, anesthesia, wound closure, and use of antibiotics. Although there is a particular focus on salmonid smolts given the large body of literature available on that group, other life-stages and species of fish are discussed where there is sufficient knowledge. Additional papers explore the role of the veterinarian in fish surgeries, the need for minimal standards in the training of fish surgeons, providing a call for more complete and transparent procedures, and identifying trends in procedures and research needs. Collectively, this body of knowledge should help to improve data quality (including comparability and repeatability), enhance management and conservation strategies, and maintain the welfare status of tagged fish.

Reviews in Fish Biology and Fisheries↗

USGS2017

Patterns and magnitude of flow alteration in California, USA

Quantifying the natural flow regime is essential for management of water resources and conservation of aquatic ecosystems. Understanding the degree to which anthropogenic activities have altered flows is critical for developing effective conservation strategies. Assessing flow alteration requires estimates of flows expected in the absence of human influence and under current land use and water management. There are several techniques to predict flows in streams and rivers; however, none have been applied to make predictions of natural flow conditions over large regions and time periods. We utilised machine learning statistical models to predict natural monthly flows (natural streamflows without the influence of water management or anthropogenic land use) in California from 1950 to 2015, using time-dependent and fixed watershed variables from reference stream gages. These models were then used to make estimates of mean, maximum and minimum monthly flows in all streams in the state. We compared observed flows measured at 540 stream gages across the state with expected natural flows at the same locations, to quantify the type, frequency and magnitude of flow alteration over the past 20 years (1996–2015). A gage was considered altered if an observed flow metric (monthly mean, annual maximum, annual minimum) fell outside the 80% prediction interval of the modelled flow estimate. We found that 95% of the 540 stream gages in California had at least 1 month of altered flows over the past 20 years, and 11% of gages were frequently altered (over two-thirds of the months recorded had evidence of altered flows). The type of alteration varied across the state with flows being either depleted, inflated or a mix of both at different times of the year. Most altered gages (68%) exhibited both depletion and inflation in monthly flows over the time period. Inflation of monthly mean flows was most prevalent during the summer months, while depletion of monthly flows was evident throughout the year. Type, frequency and magnitude of flow alteration varied by region. Flow depletion was present at >80% of gages in the North Coast and Central Coast, flow inflation was measured at >80% of gages in the South Coast and San Francisco Bay and both depletion and inflation were evident at >80% of gages in the Sacramento River and San Joaquin and Tulare regions. Annual maximum flows were consistently depleted and annual minimum flows were commonly inflated in the Sierra Nevada and Central Valley (Sacramento River and San Joaquin and Tulare regions). This is the first study to comprehensively assess flow alteration at stream gages across California. Understanding the patterns and degree of alteration can aid in prioritising streams for environmental flow assessment and developing conservation strategies for native freshwater biota.

California↗

USGS2013

Projecting demographic responses to climate change: adult and juvenile survival respond differently to direct and indirect effects of weather in a passerine population

Few studies have quantitatively projected changes in demography in response to climate change, yet doing so can provide important insights into the processes that may lead to population declines and changes in species distributions. Using a long-term mark-recapture data set, we examined the influence of multiple direct and indirect effects of weather on adult and juvenile survival for a population of Song Sparrows (Melospiza melodia) in California. We found evidence for a positive, direct effect of winter temperature on adult survival, and a positive, indirect effect of prior rainy season precipitation on juvenile survival, which was consistent with an effect of precipitation on food availability during the breeding season. We used these relationships, and climate projections of significantly warmer and slightly drier winter weather by the year 2100, to project a significant increase in mean adult survival (12-17%) and a slight decrease in mean juvenile survival (4-6%) under the B1 and A2 climate change scenarios. Together with results from previous studies on seasonal fecundity and postfledging survival in this population, we integrated these results in a population model and projected increases in the population growth rate under both climate change scenarios. Our results underscore the importance of considering multiple, direct, and indirect effects of weather throughout the annual cycle, as well as differences in the responses of each life stage to climate change. Projecting demographic responses to climate change can identify not only how populations will be affected by climate change but also indicate the demographic process(es) and specific mechanisms that may be responsible. This information can, in turn, inform climate change adaptation plans, help prioritize future research, and identify where limited conservation resources will be most effectively and efficiently spent.

California↗

USGS2014

A capture-recapture model of amphidromous fish dispersal

Adult movement scale was quantified for two tropical Caribbean diadromous fishes, bigmouth sleeper Gobiomorus dormitor and mountain mullet Agonostomus monticola, using passive integrated transponders (PITs) and radio-telemetry. Large numbers of fishes were tagged in Rio Mameyes, Puerto Rico, U.S.A., with PITs and monitored at three fixed locations over a 2-5 year period to estimate transition probabilities between upper and lower elevations and survival probabilities with a multistate Cormack-Jolly-Seber model. A sub-set of fishes were tagged with radio-transmitters and tracked at weekly intervals to estimate fine-scale dispersal. Changes in spatial and temporal distributions of tagged fishes indicated that neither G. dormitor nor A. monticola moved into the lowest, estuarine reaches of Rio Mameyes during two consecutive reproductive periods, thus demonstrating that both species follow an amphidromous, rather than catadromous, migratory strategy. Further, both species were relatively sedentary, with restricted linear ranges. While substantial dispersal of these species occurs at the larval stage during recruitment to fresh water, the results indicate minimal dispersal in spawning adults. Successful conservation of diadromous fauna on tropical islands requires management at both broad basin and localized spatial scales.

Journal of Fish Biology↗

USGS2019

Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska

Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbour similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.

Alaska↗

USGS2026

Investigation of fish communities in natural channel sections of the Mohawk River, New York

Little is known about the natural resources in the natural channel sections of the Mohawk River between Rome and Frankfort, New York, where the river channel runs separately from and parallel to the Erie Canal. This river section runs through multiple locations that are listed as active remediation sites under New York’s Inactive Hazardous Waste Disposal Site Program and has negligible public or commercial access. As a result, there is minimal recreational usage of this river section, and efforts to conduct biological sampling have been limited. To better understand the composition of fish communities and contaminant concentrations in the natural channel of the Mohawk River, the U.S. Geological Survey, in cooperation with the New York State Department of Environmental Conservation, sampled resident fish in the 34-kilometer section from the mouth of Oriskany Creek downstream to Frankfort. Fish communities were sampled using boat electrofishing during 2021, 2023, and 2024 across multiple reaches within this section. These data were used to estimate species richness (number of species), relative abundance and biomass (catch rates), population size structure (distribution of lengths), and fish condition (a proxy for health). Some gamefish specimens were also analyzed to determine contaminant concentrations in fish tissue. A total of 1,531 individual fish and 38 fish species were captured across all surveys. Seventeen of the 38 (45 percent) species were classified as native to the Mohawk River watershed, whereas 21 of the 38 (55 percent) species were classified as nonnative. Some popular gamefish species such as largemouth bass ( Micropterus salmoides ) and smallmouth bass ( Micropterus dolomieu ) were abundant in most reaches, whereas others such as walleye ( Sander vitreus ) and northern pike ( Esox lucius ) were found sporadically. Only one round goby ( Neogobius melanostomus ) was captured, indicating that this high-profile invasive species remains uncommon in this habitat. A backwater reach had the greatest relative abundance and condition of many species. This indicates connected lentic habitats such as oxbows and backwaters may be important nursery and refuge areas in the aquatic ecosystem. Polychlorinated biphenyl (PCB) concentrations in fish tissue were highly elevated relative to the New York State Department of Health (NYSDOH) fish consumption “don’t eat” advisory guideline. Some specimens exceeded the guideline by an order of magnitude or more, particularly those from a localized area downstream from the Utica Harbor Dam. Concentrations of perfluorooctanesulfonic acid (PFOS) often approached the NYSDOH “don’t eat” consumption guideline but only one sample exceeded the guideline. Concentrations of other contaminants such as mercury and pesticides were consistently measured at less than the “don’t eat” consumption guidelines. These data indicate PCBs remain the primary contaminant of concern in the natural channel of the Mohawk River and are readily bioaccumulating in aquatic organisms despite prior remediation measures. Taken together, the findings in this report are intended to inform future decisions related to fisheries management, public access, recreational usage, and fish consumption advisories.

New York↗

USGS2025

Potomac Tributary Summary: A summary of trends in tidal water quality and associated factors, 1985 - 2022

The Potomac Tributary Summary outlines change over time for a suite of monitored tidal water quality parameters and associated potential drivers of those trends for the period of 1985 to 2022, and provides a brief description of the current state of knowledge explaining these observed changes. Water quality parameters described include surface (above pycnocline) total nitrogen (TN), surface total phosphorus (TP), surface water temperature (WTEMP), spring (March-May) and summer (July-September) surface chlorophyll a, summer bottom (below pycnocline) dissolved oxygen (DO) concentrations, and Secchi disk depth (a measure of water clarity). Results for annual bottom TP, bottom TN, surface ortho-phosphate (PO4), surface dissolved inorganic nitrogen (DIN), surface total suspended solids (TSS), and summer surface DO concentrations are provided in Appendix B. Drivers discussed include physiographic watershed characteristics, changes in TN, TP, and sediment loads from the watershed to tidal waters, expected effects of changing land use, and implementation of nutrient management and natural resource conservation practices. Factors internal to estuarine waters that also play a role as drivers are described including biogeochemical processes, physical forces such as wind driven mixing of the water column and increase in rainfall intensity and volume, and biological factors such as phytoplankton biomass and the presence of submerged aquatic vegetation. Continuing to track water quality response and investigating these influencing factors are important steps to understanding water quality patterns and changes in the Potomac River. The intended audiences for this report include, but are not limited to, 1) technical managers within jurisdictions who are looking at tidal water quality data and trying to understand why patterns are occurring, 2) local watershed organizations that are trying to understand these analyses and working to connect them to their local area(s), and 3) federal, state, and academic researchers. Figure 1 presents a conceptual model highlighting these intended audiences. Our goal is for the Tributary Summary documents to be sources of readily available background for change over time in tidal water quality observed with monitoring data. The intended purpose of the Tributary Summary documents is to help answer questions related to water quality, show how landscape factors drive water quality change over time, provide support for management decisions that may alter water quality trends and living resources conditions, and highlight where there may be information or knowledge gaps.

Maryland, Pennsylvania, Virginia, West Virginia↗

USGS2002

Assessing state-wide biodiversity in the Florida Gap analysis project

The Florida Gap (FI-Gap) project provides an assessment of the degree to which native animal species and natural communities are or are not represented in existing conservation lands. Those species and communities not adequately represented in areas being managed for native species constitute 'gaps' in the existing network of conservation lands. The United States Geological Survey Gap Analysis Program is a national effort and so, eventually, all 50 states will have completed it. The objective of FI-Gap was to provide broad geographic information on the status of terrestrial vertebrates, butterflies, skippers and ants and their respective habitats to address the loss of biological diversity. To model the distributions and potential habitat of all terrestrial species of mammals, breeding birds, reptiles, amphibians, butterflies, skippers and ants in Florida, natural land cover was mapped to the level of dominant or co-dominant plant species. Land cover was classified from Landsat Thematic Mapper (TM) satellite imagery and auxiliary data such as the national wetlands inventory (NWI), soils maps, aerial imagery, existing land use/land cover maps, and on-the-ground surveys, Wildlife distribution models were produced by identifying suitable habitat for each species within that species' range, Mammalian models also assessed a minimum critical area required for sustainability of the species' population. Wildlife species richness was summarized against land stewardship ranked by an area's mandates for conservation protection. ?? 2002 Elsevier Science Ltd. All rights reserved.

Journal of Environmental Management↗

USGS2024

Joint spatial modeling bridges the gap between disparate disease surveillance and population monitoring efforts informing conservation of at-risk bat species

White-Nose Syndrome (WNS) is a wildlife disease that has decimated hibernating bats since its introduction in North America in 2006. As the disease spreads westward, assessing the potentially differential impact of the disease on western bat species is an urgent conservation need. The statistical challenge is that the disease surveillance and species response monitoring data are not co-located, available at different spatial resolutions, non-Gaussian, and subject to observation error requiring a novel extension to spatially misaligned regression models for analysis. Previous work motivated by epidemiology applications has proposed two-step approaches that overcome the spatial misalignment while intentionally preventing the human health outcome from informing estimation of exposure. In our application, the impacted animals contribute to spreading the fungus that causes WNS, motivating development of a joint framework that exploits the known biological relationship. We introduce a Bayesian, joint spatial modeling framework that provides inferences about the impact of WNS on measures of relative bat activity and accounts for the uncertainty in estimation of WNS presence at non-surveyed locations. Our simulations demonstrate that the joint model produced more precise estimates of disease occurrence and unbiased estimates of the association between disease presence and the count response relative to competing two-step approaches. Our statistical framework provides a solution that leverages disparate monitoring activities and informs species conservation across large landscapes. Stan code and documentation are provided to facilitate access and adaptation for other wildlife disease applications.

Journal of Agricultural, Biological and Environmen↗

USGS2018

Managing forest habitat for conservation-reliant species in a changing climate: The case of the endangered Kirtland’s Warbler

Conservation and recovery of species of concern necessitates evaluating forest habitat conditions under changing climate conditions, especially in the early stages of the delisting process. Managers must weigh implications of near-term habitat management activities within the context of changing environmental conditions and a species’ biological traits that may influence their vulnerability to changing conditions. Here we applied established population-habitat relationships based on decades of monitoring and research-management collaborations for the Kirtland’s Warbler ( Setophaga kirtlandii ) to project potential impacts of changing environmental conditions to breeding habitat distribution, quantity, and quality in the near future. Kirtland’s warblers are habitat-specialists that nest exclusively within dense jack pine ( Pinus banksiana ) forests between ca. 5–20 years of age. Using Random Forests to predict changes in distribution and growth rate of jack pine under future scenarios, results indicate the projected distribution of jack pine will contract considerably (ca. 75%) throughout the Lake States region, U.S.A. in response to projected environmental conditions in 2099 under RCP 4.5 and 8.5 climate scenarios regardless of climate model. Reduced suitability for jack pine regeneration across the Lake States may constrain management options, especially for creating high stem-density plantations nesting habitat. However, conditions remain suitable for jack pine regeneration within their historical and current core breeding range in northern Lower Michigan and several satellite breeding areas. Projected changes in jack pine growth rates varied within the core breeding area, but altered growth rates did not greatly alter the duration that habitat remained suitable for nesting by the Kirtland’s Warblers. These findings contribute to Kirtland’s Warbler conservation by informing habitat spatial planning of plantation management to provide a constant supply of nesting habitat based on the spatial variability of potential loss or gain of lands environmentally suitable for regenerating jack pine in the long-term.

Michigan, Wisconsin↗

USGS2019

Whooping Cranes past and present

The Whooping Crane ( Grus americana ), endemic to North America, is the rarest of all crane species. It is believed that in the early 1800s, the Whooping Crane was widespread in North America, though it was never very abundant. Whooping Crane numbers decreased precipitously as westward migration of Euro-American settlers converted prairie to cropland and the birds were hunted. By the early 1940s the total population was as low as 21 individuals; the migratory Aransas-Wood Buffalo Population, from which all extant Whooping Cranes are descended, dwindled to 16 in 1941. The threat of extinction was very real. These dire circumstances excited the interest of ornithologists and conservationists in the United States and Canada, and much has been accomplished since to conserve the species. To describe the historical and ongoing conservation activities for Whooping Cranes, we distinguish two eras of Whooping Crane Conservation: before 1950 and after 1950. The first era was characterized by publicizing the plight of the Whooping Crane and halting hunting and habitat destruction. The second era, continuing to the present, has been characterized by development of information about cranes through scientific study, conservation efforts of governmental and nongovernmental organizations, protection of the species under the Endangered Species Act in the United States and the Species at Risk Act in Canada, habitat protection, and reintroduction of new populations of Whooping Cranes. Publication of the monograph, The Whooping Crane by Robert Porter Allen, in 1952 stimulated much of the work of the second era, and still stands as the definitive work on the biology of Whooping Cranes. The remnant Aransas Wood Buffalo Population, which is crucial to species recovery, has grown to over 430 birds as of winter 2016–17. Four reintroduced populations were started in the second era; two are currently active efforts (the Eastern Migratory population and the Louisiana Nonmigratory Population), although neither population is selfsustaining. This volume gathers together the current scientific information about Whooping Cranes and the experiences of various reintroduction and management operations, to provide a baseline from which a third era of Whooping Crane conservation may be launched.

Book chapter↗

USGS2011

Projected evolution of California's San Francisco Bay-Delta-River System in a century of continuing climate change

Background Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. Methodology/Principal Findings We linked a series of models to investigate responses of California's San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010–2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. Conclusions/Significance Most of these environmental indicators change substantially over the 21 st century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

California↗