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USGS2021

Multi-taxa database data dictionary

The conservation of biological resources relies on the successful management of ecological and physiological research data. The Western Ecological Research Center of the U.S. Geological Survey is working with researchers, land managers, and decision makers from non-government organizations and city, county, state, and federal resource agencies to develop data management methods. Access to the most current and applicable research data available in making sound decisions to conserve species diversity is foundational. We sought to accomplish several goals in developing the data management strategy used in the Multi-Taxa database. Data persistence and availability are primary goals of well-developed databases. By documenting and sharing the structure and definitions of Multi-Taxa database, we hope to further the successful management of these crucial data.

Techniques and Methods↗

USGS2017

Using a gradient in food quality to infer drivers of fatty acid content in two filter-feeding aquatic consumers

Inferences about ecological structure and function are often made using elemental or macromolecular tracers of food web structure. For example, inferences about food chain length are often made using stable isotope ratios of top predators and consumer food sources are often inferred from both stable isotopes and fatty acid (FA) content in consumer tissues. The use of FAs as tracers implies some degree of macromolecular conservation across trophic interactions, but many FAs are subject to physiological alteration and animals may produce those FAs from precursors in response to food deficiencies. We measured 41 individual FAs and several aggregate FA metrics in two filter-feeding taxa to (1) assess ecological variation in food availability and (2) identify potential drivers of among-site variation in FA content. These taxa were filter feeding caddisflies (Family Hydropyschidae) and dreissenid mussels (Genus Dreissena ), which both consume seston. Stable isotopic composition (C and N) in these taxa co-varied across 13 sites in the Great Lakes region of North America, indicating they fed on very similar food resources. However, co-variation in FA content was very limited, with only one common FA co-varying across this gradient (α-linolenic acid; ALA), suggesting these taxa accumulate FAs very differently even when exposed to the same foods. Based on these results, among-site variation in ALA content in both consumers does appear to be driven by food resources, along with several other FAs in dreissenid mussels. We conclude that single-taxa measurements of FA content cannot be used to infer FA availability in food resources.

Lake Erie, Lake Huron, Lake Michigan, Lake Ontario↗

USGS2010

Health evaluation of western arctic King Eiders ( Somateria spectabilis )

The western arctic population of King Eiders ( Somateria spectabilis ) has declined by >50% in recent years. A health assessment was conducted for adult King Eiders breeding on the north slope of Alaska, USA, to evaluate body condition ( n =90, 2002–2006) and baseline biochemical and hematologic values ( n =20–30, 2005–2006). Body condition for males and females was excellent. Total protein, calcium, alkaline phosphatase, amylase, and globulin were significantly higher in females than in males, likely because of differences in reproductive physiology. These baseline health data can be used to promote conservation of King Eiders and other closely related species of concern.

Journal of Wildlife Diseases↗

USGS2023

Predicting climate change impacts on poikilotherms using physiologically guided species abundance models

Poikilothermic animals comprise most species on Earth and are especially sensitive to changes in environmental temperatures. Species conservation in a changing climate relies upon predictions of species responses to future conditions, yet predicting species responses to climate change when temperatures exceed the bounds of observed data is fraught with challenges. We present a physiologically guided abundance (PGA) model that combines observations of species abundance and environmental conditions with laboratory-derived data on the physiological response of poikilotherms to temperature to predict species geographical distributions and abundance in response to climate change. The model incorporates uncertainty in laboratory-derived thermal response curves and provides estimates of thermal habitat suitability and extinction probability based on site-specific conditions. We show that temperature-driven changes in distributions, local extinction, and abundance of cold, cool, and warm-adapted species vary substantially when physiological information is incorporated. Notably, cold-adapted species were predicted by the PGA model to be extirpated in 61% of locations that they currently inhabit, while extirpation was never predicted by a correlative niche model. Failure to account for species-specific physiological constraints could lead to unrealistic predictions under a warming climate, including underestimates of local extirpation for cold-adapted species near the edges of their climate niche space and overoptimistic predictions of warm-adapted species.

Minnesota↗

USGS2020

Comparison of fecal glucocorticoid metabolite concentrations in hand‐ versus parent‐reared whooping cranes (Grus americana)

Endangered whooping cranes ( Grus americana ) have been produced in captivity for reintroduction programs since the 1980s, using techniques such as artificial insemination, multiple clutching, and captive‐rearing to speed recovery efforts. Chicks are often hand‐reared (HR) by caretakers in crane costumes, socialized into groups and released together, unlike parent‐reared (PR) cranes that are raised individually by a male/female crane pair and released singly. HR cranes historically exhibit greater morbidity rates during development than PR cranes, involving musculoskeletal and respiratory system disease, among others. We hypothesized that HR crane chicks exhibit a higher baseline fecal glucocorticoid metabolite (FGM) concentrations during the development compared with PR chicks. Fecal samples were collected between 15 and 70 days of age from HR ( n = 15) and PR ( n = 8) chicks to test for differences in FGM concentrations using a radioimmunoassay technique following ethanol extraction for steroids. Linear mixed model analysis suggests increasing age of the chick was associated with an increase in FGM ( p < .001). Analysis also supported the interaction between rearing strategy and sex of the crane chick ( p < .01). Female PR chicks had greater FGM concentrations than all other groups (PR male, p < .01; HR female, p < .001; and HR male, p < .001). This result suggests that there may be an effect of rearing strategy on stress physiology of whooping crane chicks, especially among females. Further research is needed to investigate whether the FGM concentrations are reflective of true differences in stress physiology of young cranes and whether this may impact health and conservation success.zo

Zoo Biology↗

USGS2022

Conflict of energies: Spatially modeling mule deer caloric expenditure in response to oil and gas development

Context Wildlife avoid human disturbances, including roads and development. Avoidance and displacement of wildlife into less suitable habitat due to human development can affect their energy expenditures and fitness. The heart rate and oxygen uptake of large mammals varies with both natural aspects of their habitat (terrain, climate, predators, etc.) and anthropogenic influence (noise, light, fragmentation, etc.). Although incorporating physiological analyses of energetics can inform the impacts of both development and conservation, management decisions rarely incorporate individuals’ energetic requirements when deciding on locations for potential development. Objectives We aimed to estimate the change in expected energy expenditure, numerically and spatially, for mule deer to traverse a landscape with varying levels of oil and gas development through time. Methods Using calculations of energy expenditure of mule deer ( Odocoileus hemionus ) by weight, in relation to physical terrain components, plus avoidance factors for anthropogenic disturbance, we developed a spatiotemporal model of the minimum energy required for mule deer to traverse a landscape. We compared expected energy expenditure across 12 study sites with increasing levels of oil and gas development and over time in our study area, on the northern Colorado Plateau of Utah. Results We found that energy expenditure can be increased by development, regardless of terrain, through increased travel distance associated with avoidance behavior. Maximum median energy expenditure to traverse a 1400 ha sample area rose from 1135 to 1935 kilocalories, a 70% increase in energy required of a mule deer. There was a significant relationship between energy expenditure and the size of oil and gas development (p < 0.001), its compactness (p < 0.05), and its ‘thinness’ (p < 0.001), but not terrain ruggedness (p = 0.25). Conclusion As the energy costs of movement correlate across multiple species of large mammals, our analysis of the energetic cost, for mule deer, associated with development can serve as a quantitative representative of the impacts of oil and gas development for multiple mammals—including threatened or endangered species. Our bioenergetic cost-distance model provides a means of delineating impediments to efficient movement and can be used to quantify the expected energetic costs of proposed future developments. As wildlife are exposed to increasing anthropogenic stressors which reduce fitness, it is important to make strategic siting decisions to reduce energetic costs imposed by human activities.

Utah↗

USGS1994

Surface disturbance of cryptobiotic soil crusts: nitrogenase activity, chlorophyll content, and chlorophyll degradation

Cryptobiotic soil crusts are an important component of semiarid and arid ecosystems. An important role of these crusts is the contribution of fixed nitrogen to cold‐desert ecosystems. This study examines the residual effects of various intensities and combinations of different surface disturbances (raking, scalping, and tracked vehicles) on nitrogenase activity, chlorophyll content, and chlorophyll degradation in these soil crusts. Nine months after disturbance chlorophyll content of disturbed soils was not statistically different from undisturbed controls, except in the scalped treatments, indicating recovery of this characteristic is fairly quick unless surface material is removed. Differences in chlorophyll degradation among treatments were not statistically significant. However, nitrogenase activity in all treatments showed tremendous reductions, ranging from 77–97%, when compared to the control, indicating this characteristic is slow to recover. Consequently, assessment of crustal recovery from disturbance must include not only visual and biomass characteristics but other physiological measurements as well. Areas dominated by these crusts should be managed conservatively until the implications of crustal disturbance is better understood.

Arid Soil Research and Rehabilitation↗

USGS2022

Thermal performance of the electron transport system Complex III in seven Alabama fishes

Management of fish populations for conservation in thermally variable systems requires an understanding of the fish's underlying physiology and responses to thermal stress. Physiological research at the organismal level provides information on the overall effects of stressors such as extreme temperature fluctuations. While experiments with whole organisms provide information as to the overall effects of temperature fluctuations, biochemical assays of thermal stress provide direct results of exposure that are both sensitive and specific. Electron transport system (ETS; Complex III) assays quantify a rate-limiting step of respiratory enzymes. Parameters that can be estimated via this approach include optimum thermal temperature ( T opt ) and optimal breadth of thermal performance ( T breadth ), which can both be related to organismal-level temperature thresholds. We exposed enzymes of seven fish species (native fish chosen to represent a typical community in Alabama streams) to temperatures in the range 11–44°C. The resultant enzymatic thermal performance curves showed that T opt , the lower temperature for enzyme optimal thermal performance ( T low ), the upper temperature for enzyme optimal thermal performance ( T up ), and T breadth differed among species. Relationships between enzymatic activity and temperature for all fish followed a pattern of steadily increasing enzyme activity to T opt before gradually decreasing with increasing temperature. A comparison of our enzyme optimum and upper-temperature limit results versus published critical thermal maxima values supports that ETS Complex III assays may be useful for assessing organismal-level thermal tolerance.

JEZ-A: Ecological and Integrative Physiology↗

USGS2019

Individual based modelling of fish migration in a 2-D river system: Model description and case study

Context: Diadromous fish populations in the Pacific Northwest face challenges along their migratory routes from declining habitat quality, harvest, and barriers to longitudinal connectivity. These stressors complicate the prioritization of proposed management actions intended to improve conditions for migratory fishes including anadromous salmon and trout. Objectives: We describe a multi-scale hybrid mechanistic–probabilistic simulation model linking migration corridor conditions to fish fitness outcomes. We demonstrate the model’s utility using a case study of salmon and steelhead adults in the Columbia River migration corridor exposed to spatially- and temporally-varying stressors. Methods: The migration corridor simulation model is based on a behavioral decision tree that governs individual interactions with the environment, and an energetic submodel that estimates the hourly costs of migration. Emergent properties of the migration corridor simulation model include passage time, energy use, and survival. Results: We observed that the simulated fish’s initial energy density, the migration corridor temperatures they experienced, and their history of behavioral thermoregulation were the primary determinants of their fitness outcomes. Insights gained from use of the model might be exploited to identify management interventions that increase successful migration outcomes. Conclusions: This paper describes new methods that extend the suite of tools available to aquatic biologists and conservation practitioners. We have developed a 2-dimensional spatially-explicit behavioral and physiological model and illustrated how it can be used to simulate fish migration within a river system. Our model can be used to evaluate trade-offs between behavioral thermoregulation and fish fitness at population scales.

Landscape Ecology↗

USGS2022

Spatial models of jaguar energy expenditure in response to border wall construction and remediation

The construction of a wall at the United States-Mexico border is known to impede and deter movement of terrestrial wildlife between the two countries. One such species is the jaguar, in its northernmost range in the borderlands of Arizona and Sonora. We developed an anisotropic cost distance model for jaguar in a binational crossing area of the Madrean Sky Islands at the United States-Mexico border in Southern Arizona as a case study by using previously collected GPS tracking data for jaguars, bioenergetic calculations for pumas, and a digital elevation model. This model describes projected energy expenditure for jaguar to reach key water sources north of the international border. These desert springs and the broader study region provide vital habitat for jaguar conservation and reintroduction efforts in the United States. An emerging impediment to jaguar conservation and reintroduction is border infrastructure including border wall. By comparing walled and un-walled border sections, and three remediation scenarios, we demonstrate that existing border infrastructure significantly increases energy expenditure by jaguars and that some partial remediation scenarios are more beneficial than others. Our results demonstrate opportunities for remediation. Improved understanding of how border infrastructure impacts physiological requirements and resulting impacts to jaguar and other terrestrial wildlife in the United States-Mexico borderlands may inform conservation management.

Arizona↗

USGS2023

Pathology and infectious agents of unionid mussels: A primer for pathologists in disease surveillance and investigation of mortality events

Freshwater mussels are one of the most imperiled groups of organisms in the world, and more than 30 species have gone extinct in the last century. While habitat alteration and destruction have contributed to the declines, the role of disease in mortality events is unclear. In an effort to involve veterinary pathologists in disease surveillance and the investigation of freshwater mussel mortality events, we provide information on the conservation status of unionids, sample collection and processing techniques, and unique and confounding anatomical and physiological differences. We review the published accounts of pathology and infectious agents described in freshwater mussels including neoplasms, viruses, bacteria, fungi, fungal-like agents, ciliated protists, Aspidogastrea, Digenea, Nematoda, Acari, Diptera, and Odonata. Of the identified infectious agents, a single viral disease, Hyriopsis cumingii plague disease, that occurs only in cultured mussels is known to cause high mortality. Parasites including ciliates, trematodes, nematodes, mites, and insects may decrease host fitness, but are not known to cause mortality. Many of the published reports identify infectious agents at the light or ultrastructural microscopy level with no lesion or molecular characterization. Although metagenomic analyses provide sequence information for infectious agents, studies often fail to link the agents to tissue changes at the light or ultrastructural level or confirm their role in disease. Pathologists can bridge this gap between identification of infectious agents and confirmation of disease, participate in disease surveillance to ensure successful propagation programs necessary to restore decimated populations, and investigate mussel mortality events to document pathology and identify causality.

Veterinary Pathology↗

USGS2014

Dissimilatory reduction of selenate and arsenate in nature

This chapter discusses the biogeochemical reduction of selenate (Se(VI)) and arsenate (As(V)) when they enter anoxic environments and are used as electron acceptors for the oxidation of organic matter. These reductions are of a dissimilative nature and support the anaerobic growth of selected bacteria which conserve energy from this process. The chapter summarizes what is known about the bacteria's taxonomy, physiology, and biochemistry. Reduction to the solid, relatively unreactive Se(0) represents a mechanism for the removal of toxic Se(VI) and Se(IV) from natural waters. The environmental ramifications of these issues are also discussed in the chapter. The number of bacterial species known to respire selenate and arsenate continues to increase. The biological reduction of selenate and arsenate occurs for a number of reasons. In general, these are assimilation, regulation of reducing equivalents, detoxification, and dissimilation. Each is discussed in detail in the chapter. The realization that arsenate and selenate are indeed suitable electron acceptors and are readily available in both natural and contaminated environments suggests that even more unrelated species will be discovered. The initial biochemical studies also suggest that there may be different pathways for selenate and arsenate reduction, with specific terminal reductases and cytochromes.

Book chapter↗

USGS2015

Evidence for episodic acidification effects on migrating Atlantic salmon Salmo salar smolts

Field studies were conducted to determine levels of gill aluminium as an index of acidification effects on migrating Atlantic salmon Salmo salar smolts in the north-eastern U.S.A. along mainstem river migration corridors in several major river basins. Smolts emigrating from the Connecticut River, where most (but not all) tributaries were well buffered, had low or undetectable levels of gill aluminium and high gill Na + /K + -ATPase (NKA) activity. In contrast, smolts emigrating from the upper Merrimack River basin where most tributaries are characterized by low pH and high inorganic aluminium had consistently elevated gill aluminium and lower gill NKA activity, which may explain the low adult return rates of S. salar stocked into the upper Merrimack catchment. In the Sheepscot, Narraguagus and Penobscot Rivers in Maine, river and year-specific effects on gill aluminium were detected that appeared to be driven by underlying geology and high spring discharge. The results indicate that episodic acidification is affecting S. salar smolts in poorly buffered streams in New England and may help explain variation in S. salar survival and abundance among rivers and among years, with implications for the conservation and recovery of S. salar in the north-eastern U.S.A. These results suggest that the physiological condition of outmigrating smolts may serve as a large-scale sentinel of landscape-level recovery of atmospheric pollution in this and other parts of the North Atlantic region.

Journal of Fish Biology↗

USGS2023

Climate impacts to inland fishes: Shifting research topics over time

Climate change remains a primary threat to inland fishes and fisheries. Using topic modeling to examine trends and relationships across 36 years of scientific literature on documented and projected climate impacts to inland fish, we identify ten representative topics within this body of literature: assemblages, climate scenarios, distribution, climate drivers, population growth, invasive species, populations, phenology, physiology, and reproduction. These topics are largely similar to the output from artificial intelligence application (i.e., ChatGPT) search prompts, but with some key differences. The field of climate impacts on fish has seen dramatic growth since the mid-2000s with increasing popularity of topics related to drivers, assemblages, and phenology. The topics were generally well-dispersed with little overlap of common words, apart from phenology and reproduction which were closely clustered. Pairwise comparisons between topics revealed potential gaps in the literature including between reproduction and distribution and between physiology and phenology. A better understanding of these relationships can help capitalize on existing literature to inform conservation and sustainable management of inland fishes with a changing climate.

PLOS Climate↗

USGS2023

Climate change and coastal wetland salinization: Physiological and ecological consequences for Arctic waterfowl

Coastal wetland salinization related to warming climate has the potential to impact ecological systems globally. In Alaska, the Yukon-Kuskokwim Delta (YKD) supports large concentrations of breeding water birds and is an ecologically important area for conservation of migratory bird biodiversity. On the YKD, the majority of waterfowl nest in low elevation coastal tundra where storm surges drive saline water into terrestrial wetland habitats. Because newly hatched water birds lack functional salt glands to process saline water, salinization may negatively impact their growth and survival. We investigated potential demographic impacts of wetland salinization by conducting controlled physiological experiments to determine consequences of saline water exposure to spectacled Somateria fischeri and Steller's eider Polysticta stelleri ducklings, and analysed habitat suitability based on experimentally defined tolerance thresholds and sampled wetland salinity levels. We found physiological and behavioural pathologies in <1 week old ducklings at exposure levels of 6 parts per thousand (ppt), and found some evidence of reduced growth in ducklings first exposed after 1 week of age. We conclude that the acute toxicity threshold for ducklings <1 week of age is ≤6 ppt. We found that the area of coastal tundra where wetland salinity exceeded 6 ppt varied considerably among years, suggesting that some portion of the breeding range is unsuitable for rearing ducklings in some years. However, we also found that most eiders in most years nested in areas with salinity at or exceeding the tolerance threshold for ducklings, suggesting that nesting eiders do not appear to avoid saline habitats. We suggest that localized fresh water refugia currently may allow resilience to salinization during the critical period. Understanding how species and habitats respond to climate driven changes is essential for predicting future patterns of distribution and abundance, and is necessary for making informed decisions about conservation priorities. Our study provides insights into the extent of wetland salinization in Alaska, mechanism of impact and current ecological consequences on avian communities depending on these habitats. With ongoing climate change, the probability of species crossing physiological tolerance thresholds of wetland salinity may change in the future.

Functional Ecology↗

USGS1994

Lipids and proteins in the Rathke's gland secretions of the North American mud turtle ( Kinosternon subrubrum )

Lipids and proteins in the Rathke's gland secretions of the North American mud turtle ( Kinosternon subrubrum , Kinosternidae) were analyzed by gas chromatography-mass spectrometry (GC-MS) and SDS-polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Analysis by GC-MS indicates 2,3-dihydroxypropanal and C 3 –C 24 free or esterified fatty acids. Analysis by SDS-PAGE indicates a major protein component with an approximate molecular mass of 60 kDa and minor components ranging from ca. 23 to 34 kDa. The major component of K. subrubrum glandular secretions exhibits a mobility that matches that of the Kemp's ridley sea turtle ( Lepidochelys kempi , Cheloniidae), suggesting that these proteins are evolutionarily conserved.

Comparative Biochemistry and Physiology, Part B: C↗

USGS2014

Transcriptomic analysis of the mussel Elliptio complanata identifies candidate stress-response genes and an abundance of novel or noncoding transcripts

Mussels are useful indicator species of environmental stress and degradation, and the global decline in freshwater mussel diversity and abundance is of conservation concern. Elliptio complanata is a common freshwater mussel of eastern North America that can serve both as an indicator and as an experimental model for understanding mussel physiology and genetics. To support genetic components of these research goals, we assembled transcriptome contigs from Illumina paired-end reads. Despite efforts to collapse similar contigs, the final assembly was in excess of 136,000 contigs with an N50 of 982 bp. Even so, comparisons to the CEGMA database of conserved eukaryotic genes indicated that ∼20% of genes remain unrepresented. However, numerous candidate stress-response genes were present, and we identified lineage-specific patterns of diversification among molluscs for cytochrome P450 detoxification genes and two saccharide-modifying enzymes: 1,3 beta-galactosyltransferase and fucosyltransferase. Less than a quarter of contigs had protein-level similarity based on modest BLAST and Hmmer3 statistical thresholds. These results add comparative genomic resources for molluscs and suggest a wealth of novel proteins and noncoding transcripts.

PLoS ONE↗

USGS2014

Predicted changes in climatic niche and climate refugia of conservation priority salamander species in the northeastern United States

Global climate change represents one of the most extensive and pervasive threats to wildlife populations. Amphibians, specifically salamanders, are particularly susceptible to the effects of changing climates due to their restrictive physiological requirements and low vagility; however, little is known about which landscapes and species are vulnerable to climate change. Our study objectives included, (1) evaluating species-specific predictions (based on 2050 climate projections) and vulnerabilities to climate change and (2) using collective species responses to identify areas of climate refugia for conservation priority salamanders in the northeastern United States. All evaluated salamander species were projected to lose a portion of their climatic niche. Averaged projected losses ranged from 3%–100% for individual species, with the Cow Knob Salamander ( Plethodon punctatus ), Cheat Mountain Salamander ( Plethodon nettingi ), Shenandoah Mountain Salamander ( Plethodon virginia ), Mabee’s Salamander ( Ambystoma mabeei ), and Streamside Salamander ( Ambystoma barbouri ) predicted to lose at least 97% of their landscape-scale climatic niche. The Western Allegheny Plateau was predicted to lose the greatest salamander climate refugia richness ( i.e. , number of species with a climatically-suitable niche in a landscape patch), whereas the Central Appalachians provided refugia for the greatest number of species during current and projected climate scenarios. Our results can be used to identify species and landscapes that are likely to be further affected by climate change and potentially resilient habitats that will provide consistent climatic conditions in the face of environmental change.

Forests↗