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USGS2018

Integrating physiological stress into the movement ecology of migratory ungulates: A spatial analysis with mule deer

Rapid climate and human land-use change may limit the ability of long-distance migratory herbivores to optimally track or “surf” high-quality forage during spring green-up. Understanding how anthropogenic and environmental stressors influence migratory movements is of critical importance because of their potential to cause a mismatch between the timing of animal movements and the emergence of high-quality forage. We measured stress hormones (fecal glucocorticoid metabolites; FGMs) to test hypotheses about the effects of high-quality forage tracking, human land use, and use of stopover sites on the physiological state of individuals along a migratory route. We collected and analyzed FGM concentrations from 399 mule deer (Odocoileus hemionus) samples obtained along a 241 km migratory route in western Wyoming, USA, during spring 2015 and 2016. In support of a fitness benefit hypothesis, individuals occupying areas closer to peak forage quality had decreased FGM levels. Specifically, for every 10-day interval closer to peak forage quality, we observed a 7% decrease in FGMs. Additionally, we observed support for both an additive anthropogenic stress hypothesis and a hypothesis that stopovers act as physiological refugia, wherein individuals sampled far from stopover sites exhibited 341% higher FGM levels if in areas of low landscape integrity compared to areas of high landscape integrity. Overall, our findings indicate that the physiological state of mule deer during migration is influenced by both anthropogenic disturbances and their ability to track high-quality forage. The availability of stopovers, however, modulates physiological responses to those stressors. Thus, our results support a recent call for the prioritization of stopover locations and connectivity between those locations in conservation planning for migratory large herbivores.

Colorado, Wyoming↗

USGS1984

Optimal timing in biological processes

A general approach for obtaining solutions to a class of biological optimization problems is provided. The general problem is one of determining the appropriate time to take some action, when the action can be taken only once during some finite time frame. The approach can also be extended to cover a number of other problems involving animal choice (e.g., mate selection, habitat selection). Returns (assumed to index fitness) are treated as random variables with time-specific distributions, and can be either observable or unobservable at the time action is taken. In the case of unobservable returns, the organism is assumed to base decisions on some ancillary variable that is associated with returns. Optimal policies are derived for both situations and their properties are discussed. Various extensions are also considered, including objective functions based on functions of returns other than the mean, nonmonotonic relationships between the observable variable and returns; possible death of the organism before action is taken; and discounting of future returns. A general feature of the optimal solutions for many of these problems is that an organism should be very selective (i.e., should act only when returns or expected returns are relatively high) at the beginning of the time frame and should become less and less selective as time progresses. An example of the application of optimal timing to a problem involving the timing of bird migration is discussed, and a number of other examples for which the approach is applicable are described.

American Naturalist↗

USGS2000

Sea otters past and present perspectives

Sea otters have been an important resource for people living along the North Pacific coast for thousands of years. At least two aspects of the sea otters' natural history have linked them with humans: their pelt and their food habits. Sea otter pelts, arguably the finest in the animal kingdom, were fashioned into garments, particularly in northern latitudes, while the presence of sea otters influenced the availability of some marine invertebrates, like snails, clams and abalone, that provided food for coastal people. In addition, sea otters spurred a growing fur trade after Vitus Bering's explorations of the North Pacific in the early 1700s revealed their widespread abundance. This commercial harvest was instrumental in European exploration and settlement of the Pacific Rim and led to the near-extermination of the sea otter, Enhydra lutris, in following centuries. Largely because of their life history and their direct relations with coastal residents, sea otters are a comparatively well-understood marine mammal. During the past few decades, concern for sea otters has broadened to encompass an interest in global resource conservation and restoration, as well as community ecology. This more recent focus on sea otters now extends to humans far removed from marine environments. Early sea otters evolved about 12 million years ago from Eurasian and African ancestors. They reached the North Pacific by way of two proposed migration paths, one along the Bering Land Bridge between northeastern Asia and northwestern North America and a second from the Atlantic Ocean that entered the Pacific through a channel in the central Americas. Modern sea otters occur only in the North Pacific and have occupied their current range for the past 1 million to 3 million years.

Alaska Geographic↗

USGS2015

When Siberia came to the Netherlands: The response of continental black-tailed godwits to a rare spring weather event

Summary Extreme weather events have the potential to alter both short- and long-term population dynamics as well as community- and ecosystem-level function. Such events are rare and stochastic, making it difficult to fully document how organisms respond to them and predict the repercussions of similar events in the future. To improve our understanding of the mechanisms by which short-term events can incur long-term consequences, we documented the behavioural responses and fitness consequences for a long-distance migratory bird, the continental black-tailed godwit Limosa limosa limosa , resulting from a spring snowstorm and three-week period of record low temperatures. The event caused measurable responses at three spatial scales – continental, regional and local – including migratory delays (+19 days), reverse migrations (>90 km), elevated metabolic costs (+8·8% maintenance metabolic rate) and increased foraging rates (+37%). There were few long-term fitness consequences, however, and subsequent breeding seasons instead witnessed high levels of reproductive success and little evidence of carry-over effects. This suggests that populations with continued access to food, behavioural flexibility and time to dissipate the costs of the event can likely withstand the consequences of an extreme weather event. For populations constrained in one of these respects, though, extreme events may entail extreme ecological consequences.

Journal of Animal Ecology↗

USGS2025

Chapter 6: Climate change, wildlife, and wildlife habitats in the Oregon Coast Range

Climate change is likely to have profound effects on wildlife species within the Oregon Coast Adaptation Partnership (OCAP) assessment area, although the direction and magnitude of effects are likely to vary across species. Increased mean and extreme temperatures, especially during summer, may cause shifts in plant and animal species ranges, reduce habitat for some temperature-sensitive wildlife, alter plant phenology and the timing of available food resources, and affect species interactions (e.g., predation, competition). Altered timing of precipitation, summer drought, loss of fog, increased flooding events, earlier snowmelt, and rising sea level may reduce plant productivity, increase tree mortality, shift plant species composition, and lead to reduced wildlife habitat and habitat quality for some forests, riparian areas, wetlands, meadows, estuaries, and beaches. In addition, increasing frequency and extent of wildfire and insect outbreaks may reduce the extent of late-successional forest, reduce habitat connectivity, and increase the spread of invasive species. The biggest change expected for the assessment area is an increase in area where climatic conditions favor coastal mixed forest and a large reduction in area favoring montane conifer forest. Although actual changes in forest types may not necessarily occur by the end of the 21st century, climate change may add physiological and behavioral stress to wildlife. Some wildlife species will be able to persist in place and adapt to new conditions; some may be able to migrate to find suitable habitat; and some may be greatly reduced or extirpated from the assessment area or even go extinct. Shifts in major tree and shrub species will play a major role in food, den, and cover availability for wildlife. Rising sea level will reduce low-elevation habitats along the coast. An increase in the frequency of high-severity weather events will increase frequency and magnitude of flooding, including debris flow events. Coupled with increased temperatures during summer, this may reduce or fragment important ecosystems for aquatic and semi-aquatic species. Evaluation of the vulnerabilities of nine wildlife species based on literature reviews suggests that each species has life-history attributes that can lead to resilience or vulnerability to climate change effects. Depending on long-term objectives, several broad adaptation strategies focus on protecting refugia, establishing redundant wildlife strongholds with large-scale connectivity, and promoting structural and biological complexity.

Oregon↗

USGS2009

Recolonization of gravel habitats on Georges Bank (northwest Atlantic)

Gravel habitats on continental shelves around the world support productive fisheries but are also vulnerable to disturbance from bottom fishing. We conducted a 2-year in situ experiment to measure the rate of colonization of a gravel habitat on northern Georges Bank in an area closed to fishing (Closed Area II) since December 1994. Three large (0.25 m 2 ) sediment trays containing defaunated pebble gravel were deployed at a study site (47 m water depth) in July 1997 and recovered in June 1999. The undersides of the tray lids positioned 56 cm above the trays served as settlement panels over the same time period. We observed rapid colonization of the gravel substrate (56 species) and the settlement panels (35 species), indicating that colonization of gravel in this region is not limited by the supply of colonists. The species composition of the taxa found in the trays was broadly similar to that we collected over a 10-year period (1994-2004) in dredge samples from gravel sediments at the same site. The increase in abundance of animals in the gravel colonization trays was rapid and reached a level in 2 years that took 4.5 years to achieve in the surrounding gravel sediments once fishing had stopped, based on data from dredge sampling at this site. The increase in biomass of animals found in the sediment trays paralleled the trend of biomass increase observed in dredge samples over the same period (1997-1999) but was lower in value. These data suggest that after rapid initial increase in abundance of organisms, succession proceeded by increasing individual body size. A comparison of settlement panel and tray faunas revealed that the mean biomass of structure-forming epifauna (sponges, bryozoans, anemones, hydroids, colonial tube worms) on the panels was 8 times that found on the trays. Structure-forming taxa constituted 29% of the mean biomass of the panel fauna but only 5.5% of the tray fauna. By contrast, the mean biomass of scavengers (crabs, echinoderms, nudibranchs, gastropods) in the trays was 32 times that on the panels. Colonization of the tray gravel was more rapid for free-living species (many of which are prey for fish) than for structure-forming epifauna, though colonists of the latter species were present. The reduced success of structure-forming species in colonizing the tray gravel possibly is related to factors such as intermittent burial of the gravel by migrating sand and low survival of new recruits due to the presence of high numbers of scavengers on the gravel. These two factors might explain, to varying degree, the slow recolonization of gravel habitats by structure-forming species in Closed Area II of the northern part of Georges Bank. ?? 2009 Elsevier Ltd.

Deep-Sea Research Part II: Topical Studies in Ocea↗

USGS2006

2005 annual progress report: Elk and bison grazing ecology in the Great Sand Dunes complex of lands

In 2000 the U.S. Congress authorized the expansion of the former Great Sand Dunes National Monument by establishing a new Great Sand Dunes National Park and Preserve in its place, and establishing the Baca National Wildlife Refuge. The establishment of Great Sand Dunes National Park and Preserve and the new Baca National Wildlife Refuge in the San Luis Valley (SLV), Colorado was one of the most significant land conservation actions in the western U.S. in recent years. The action was a result of cooperation between the National Park Service (NPS), U.S. Fish and Wildlife Service (USFWS), Bureau of Land Management (BLM), U.S. Forest Service (USDA-FS), and The Nature Conservancy (TNC). The new national park, when fully implemented, will consist of 107,265 acres, the new national preserve 41,872 acres, and the new national wildlife refuge (USFWS lands) 92,180 acres (fig. 1). The area encompassed by this designation protects a number of natural wonders and features including a unique ecosystem of natural sand dunes, the entire watershed of surface and groundwaters that are necessary to preserve and recharge the dunes and adjacent wetlands, a unique stunted forest, and other valuable riparian vegetation communities that support a host of associated wildlife and bird species. When the National Park was initially established, there were concerns about overconcentrations and impacts on native plant communities of the unhunted segments of a large and possibly growing elk (Cervus elaphus) population. This led to the designation of the Preserve as a compromise solution, where the elk could be harvested. The Preserve Unit, however, will not address all the ungulate management challenges. In order to reduce the current elk population, harvests of elk may need to be aggressive. But aggressive special hunts of elk to achieve population reductions can result in elk avoidance of certain areas or elk seeking refuge in areas where they cannot be hunted, while removals of whole herd segments and abandonment or alterations of migration routes can occur (Smith and Robbins, 1994; Boyce and others, 1991). Elk may seek refuge from hunting in the newly expanded Park Unit and TNC lands where they might overconcentrate and impact unique vegetation communities. In these sites of refugia, or preferred loafing sites, elk and bison could accelerate a decline in woody riparian shrubs and trees. This decline may also be due to changes in hydrology, climatic, or dunal processes, but ungulate herbivory might exacerbate the effects of those processes. To address the questions and needs of local resource managers, a multi-agency research project was initiated in 2005 to study the ecology, forage relations, and habitat relations of elk and bison in the Great Sand Dunes–Sangre de Cristo–Baca complex of lands. Meetings and discussions of what this research should include were started in 2001 with representatives from NPS, USFWS, TNC, the Colorado Division of Wildlife (CDOW), and USDA-FS/BLM. The final study plan was successfully funded in 2004 with research scheduled to start in 2005. The research was designed to encompass three major study elements: (1) animal movements and population dynamics, (2) vegetation and nutrient effects from ungulate herbivory, and (3) development of ecological models, using empirical data collected from the first two components, that will include estimates of elk carrying capacity and management scenarios for resource managers.

Colorado↗

USGS2020

Crossroads of highly pathogenic H5N1: overlap between wild and domestic birds in the Black Sea-Mediterranean impacts global transmission

Understanding transmission dynamics that link wild and domestic animals is a key element of predicting the emergence of infectious disease, an event that has highest likelihood of occurring wherever human livelihoods depend on agriculture and animal trade. Contact between poultry and wild birds is a key driver of the emergence of highly pathogenic avian influenza (HPAI), a process that allows for host-switching and accelerated reassortment, diversification and spread of virus between otherwise unconnected regions. This study addresses questions relevant to the spillover of HPAI at a transmission hotspot: what is the nature of the wild bird-poultry interface in Egypt and adjacent Black Sea-Mediterranean countries and how has this contributed to outbreaks occurring worldwide? Using a spatio-temporal model of infection risk informed by satellite tracking of waterfowl and viral phylogenetics, this study identified ecological conditions that contribute to spillover in this understudied region. Results indicated that multiple ducks (Northern Shoveler and Northern Pintail) hosted segments that shared ancestry with HPAI H5 from both clade 2.2.1 and clade 2.3.4 supporting the role of Anseriformes in linking viral populations in East Asia and Africa over large-distances. Quantifying the interface between wild ducks and H5N1-infected poultry revealed an increasing interface in late winter peaking in early spring when ducks expanded their range before migration, with key differences in the timing of poultry contact risk between local and long-distance migrants.

Virus Evolution↗

USGS2012

A standard operating procedure for the surgical implantation of transmitters in juvenile salmonids

Biotelemetry is a useful tool to monitor the movements of animals and is widely applied in fisheries research. Radio or acoustic technology can be used, depending on the study design and the environmental conditions in the study area. A broad definition of telemetry also includes the use of Passive Integrated Transponder (PIT) tags, either separately or with a radio or acoustic transmitter. To use telemetry, fish must be equipped with a transmitter. Although there are several attachment procedures available, surgical implantation of transmitters in the abdominal cavity is recognized as the best technique for long-term telemetry studies in general (Stasko and Pincock, 1977; Winter, 1996; Jepsen, 2003), and specifically for juvenile salmonids, Oncorhynchus spp. (Adams and others, 1998a, 1998b; Martinelli and others, 1998; Hall and others, 2009). Studies that use telemetry assume that the processes by which the animals are captured, handled, and tagged, as well as the act of carrying the transmitter, will have minimal effect on their behavior and performance. This assumption, commonly stated as a lack of transmitter effects, must be valid if telemetry studies are to describe accurately the movements and behavior of an entire population of interest, rather than the subset of that population that carries transmitters. This document describes a standard operating procedure (SOP) for surgical implantation of radio or acoustic transmitters in juvenile salmonids. The procedures were developed from a broad base of published information, laboratory experiments, and practical experience in tagging thousands of fish for numerous studies of juvenile salmon movements near Columbia River and Snake River hydroelectric dams. Staff from the Western Fisheries Research Center's Columbia River Research Laboratory (CRRL) frequently have used telemetry studies to evaluate new structures or operations at hydroelectric dams in the Columbia River Basin, and these evaluations typically require large numbers of tagged fish. For example, a study conducted at the dams on the Columbia River and funded by the U.S. Army Corps of Engineers required tagging and monitoring of 40,000 juvenile salmon during a 3-month migration period (Counihan and others, 2006a, 2006b; Perry and others, 2006). To meet the demands of such a large study, the authors and CRRL staff refined the SOP to increase efficiency in the tagging process while maintaining high standards of fish care. The SOP has been used in laboratory and field settings for more than 15 years, and consistently has produced low mortality rates (<1 percent) and transmitter loss rates (<0.01 percent) in the 24-36 hours after tagging. In addition to describing the detailed surgical procedures required for transmitter implantation, this document provides guidance on fish collection, handling and holding, and the release of tagged fish. Although often overlooked, or at least underemphasized, these processes can have a large impact on the outcome of the tagging procedure. Stress associated with the individual steps in handling and tagging can be cumulative and lethal (Maule and others, 1988; Wedemeyer and others, 1990; Portz and others, 2006), so the goal is to provide the best possible fish care at every step in order to manage the overall effect on study fish.

Open-File Report↗

USGS2003

Long-term fitness consequences of early conditions in the kittiwake

1. The long - term fitness consequences of conditions during development are receiving growing attention: they are at the interface between ecological and evolutionary processes. We addressed the influence of the length of the rearing period and 'rank' on fitness components in a long -lived seabird species with deferred breeding: the kittiwake (Rissa tridactyla). Rank, which depends on hatching order, was used as a surrogate for dominance status in the brood. Rank could be viewed as a random factor affecting individuals regardless of their possible 'intrinsic quality' at birth. The length of the rearing period was used as a surrogate for parental effort. It reflects the interaction between numerous factors such as environmental conditions , parental quality, reproductive decisions and effort, and also offspring decisions and intrinsic quality at birth. 2. There was evidence of an influence of the length of the rearing period on local survival before recruitment. Individuals with shorter rearing periods had lower local survival during the first winter (e.g. the relationship was positive). They may incur higher mortality. In rank 1 prebreeders, this relationship was negative in older age-classes. Longer rearing periods and better condition at independence may be associated with stronger migrating ability, and prebreeders that have not yet made settlement decisions may emigrate permanently to distant locations. Such a complex pattern may reflect age-related changes in the relative contribution of mortality and permanent emigration to local survival. 3. The length of the rearing period had long - term consequences on reproductive performance. The relationship was positive but the rate of increase decreased slightly at higher values of the covariate. 4. There was an unambiguously negative influence of rank on survival before recruitment and recruitment probability, but not on demographic parameters specific to the reproductive stage. Juniors recruited later than elder siblings. The disadvantage of juniors may be expressed mainly in terms of higher mortality and disappearance from the population before recruitment.

Journal of Animal Ecology↗

USGS2016

Age- and season-specific variation in local and long-distance movement behavior of golden eagles

Animal movements can determine the population dynamics of wildlife. We used telemetry data to provide insight into the causes and consequences of local and long-distance movements of multiple age classes of conservation-reliant golden eagles ( Aquila chrysaetos) in the foothills and mountains near Tehachapi, California. We estimated size and habitat-related correlates of 324 monthly 95 % home ranges and 317 monthly 50 % core areas for 25 birds moving locally over 2.5 years. We also calculated daily, hourly, and total distances traveled for the five of these birds that engaged in long-distance movements. Mean (±SD) monthly home-range size was 253.6 ± 429.4 km 2 and core-area size was 26.4 ± 49.7 km 2 . Consistent with expectations, space used by pre-adults increased with age and was season-dependent but, unexpectedly, was not sex-dependent. For all ages and sexes, home ranges and core areas were dominated by both forest & woodland and shrubland & grassland habitat types. When moving long distances, eagles traveled up to 1588.4 km (1-way) in a season at highly variable speeds (63.7 ± 69.0 km/day and 5.2 ± 10.4 km/h) that were dependent on time of day. Patterns of long-distance movements by eagles were determined by age, yet these movements had characteristics of more than one previously described movement category (migration, dispersal, etc.). Our results provide a context for differentiating among types of movement behaviors and their population-level consequences and, thus, have implications for management and conservation of golden eagle populations. .

California, Idaho, Montana, Nevada, Oregon, Utah, ↗

USGS2016

Mortality monitoring design for utility-scale solar power facilities

Introduction Solar power represents an important and rapidly expanding component of the renewable energy portfolio of the United States (Lovich and Ennen, 2011; Hernandez and others, 2014). Understanding the impacts of renewable energy development on wildlife is a priority for the U.S. Fish and Wildlife Service (FWS) in compliance with Department of Interior Order No. 3285 (U.S. Department of the Interior, 2009) to “develop best management practices for renewable energy and transmission projects on the public lands to ensure the most environmentally responsible development and delivery of renewable energy.” Recent studies examining effects of renewable energy development on mortality of migratory birds have primarily focused on wind energy (California Energy Commission and California Department of Fish and Game, 2007), and in 2012 the FWS published guidance for addressing wildlife conservation concerns at all stages of land-based wind energy development (U.S. Fish and Wildlife Service, 2012). As yet, no similar guidelines exist for solar development, and no published studies have directly addressed the methodology needed to accurately estimate mortality of birds and bats at solar facilities. In the absence of such guidelines, ad hoc methodologies applied to solar energy projects may lead to estimates of wildlife mortality rates that are insufficiently accurate and precise to meaningfully inform conversations regarding unintended consequences of this energy source and management decisions to mitigate impacts. Although significant advances in monitoring protocols for wind facilities have been made in recent years, there remains a need to provide consistent guidance and study design to quantify mortality of bats, and resident and migrating birds at solar power facilities (Walston and others, 2015). In this document, we suggest methods for mortality monitoring at solar facilities that are based on current methods used at wind power facilities but adapted for the unique conditions encountered at solar facilities. In particular, unlike at wind-power facilities, the unimpeded access to almost all areas within the facilities, the typically flat terrain, and general absence of thick vegetation allow distance-sampling techniques (Buckland and others, 2001, 2004) to be exploited to advantage at industrial solar sites. These protocols build on the work of Nicolai and others (2011), and as our understanding and techniques for monitoring improve, the methods may be further modified to incorporate improvements in the future. We present case studies based on monitoring methods currently implemented at different utility-scale solar facilities to illustrate how distance-sampling techniques may improve overall detectability without substantially increasing costs. Every facility is unique, and the protocols presented may be adapted based on specific monitoring objectives and conditions at each site. We provide guidance for designing monitoring programs whose objective it is to estimate the total number of bird and bat fatalities occurring at a facility over an extended period of time. We address spatial variation in causes of mortality, as well as potential sources of imperfect detection, for example, animals falling in or moving to unsearched areas, carcasses removed by predators, and carcasses missed by searchers. We suggest methods to estimate and account for each source of imperfect detection. This document focuses on monitoring design only and does not discuss approaches for estimating mortality from collected data. The development of statistically sound estimators relevant to the solar context is a current topic of research, although there are already strong foundations for estimation with distance-sampling methods in similar open, arid environments (Anderson and others, 2001; Freilich and others, 2005). Nonetheless, if protocols described in this document are followed, the resulting data will be adequate and sufficient for estimating mortality using newly formulated estimators.

Open-File Report↗

USGS2015

State-space modeling to support management of brucellosis in the Yellowstone bison population

The bison ( Bison bison ) of the Yellowstone ecosystem, USA, exemplify the difficulty of conserving large mammals that migrate across the boundaries of conservation areas. Bison are infected with brucellosis ( Brucella abortus ) and their seasonal movements can expose livestock to infection. Yellowstone National Park has embarked on a program of adaptive management of bison, which requires a model that assimilates data to support management decisions. We constructed a Bayesian state-space model to reveal the influence of brucellosis on the Yellowstone bison population. A frequency-dependent model of brucellosis transmission was superior to a density-dependent model in predicting out-of-sample observations of horizontal transmission probability. A mixture model including both transmission mechanisms converged on frequency dependence. Conditional on the frequency-dependent model, brucellosis median transmission rate was 1.87 yr −1 . The median of the posterior distribution of the basic reproductive ratio ( R 0 ) was 1.75. Seroprevalence of adult females varied around 60% over two decades, but only 9.6 of 100 adult females were infectious. Brucellosis depressed recruitment; estimated population growth rate λ averaged 1.07 for an infected population and 1.11 for a healthy population. We used five-year forecasting to evaluate the ability of different actions to meet management goals relative to no action. Annually removing 200 seropositive female bison increased by 30-fold the probability of reducing seroprevalence below 40% and increased by a factor of 120 the probability of achieving a 50% reduction in transmission probability relative to no action. Annually vaccinating 200 seronegative animals increased the likelihood of a 50% reduction in transmission probability by fivefold over no action. However, including uncertainty in the ability to implement management by representing stochastic variation in the number of accessible bison dramatically reduced the probability of achieving goals using interventions relative to no action. Because the width of the posterior predictive distributions of future population states expands rapidly with increases in the forecast horizon, managers must accept high levels of uncertainty. These findings emphasize the necessity of iterative, adaptive management with relatively short-term commitment to action and frequent reevaluation in response to new data and model forecasts. We believe our approach has broad applications.

Wyoming↗

USGS2020

Detecting commonality in multidimensional fish movement histories using sequence analysis

Background Acoustic telemetry, for tracking fish movement histories, is multidimensional capturing both spatial and temporal domains. Oftentimes, analyses of such data are limited to a single domain, one domain nested within the other, or ad hoc approaches that simultaneously consider both domains. Sequence analysis, on the other hand, offers a repeatable statistical framework that uses a sequence alignment algorithm to calculate pairwise dissimilarities among individual movement histories and then hierarchical agglomerative clustering to identify groups of fish with similar movement histories. The objective of this paper is to explore how acoustic telemetry data can be fit to this statistical framework and used to identify commonalities in the movement histories of acoustic-tagged sea lamprey during upstream migration through the St. Clair-Detroit River System. Results Five significant clusters were identified among individual fish. Clusters represented differences in timing of movements (short vs long duration in the Detroit R. and Lake St. Clair); extent of upstream migration (ceased migration in Lake St. Clair, lower St. Clair R., or upper St. Clair R.), and occurrence of fallback (return to Lake St. Clair after ceasing migration in the St. Clair R.). Inferences about sea lamprey distribution and behavior from these results were similar to those reached in a previous analysis using ad-hoc analysis methods. Conclusions The repeatable statistical framework outlined here can be used to group sea lamprey movement histories based on shared sequence characteristics (i.e., chronological order of “states” occupied). Further, this framework is flexible and allows researchers to define a priori the movement aspect (e.g., order, timing, duration) that is important for identifying both common or previously undetected movement histories. As such, we do not view sequence analysis as a panacea but as a useful complement to other modelling approaches (i.e., exploratory tool for informing hypothesis development) or a stand-alone semi-quantitative method for generating a simplified, temporally and spatially structured view of complex acoustic telemetry data and hypothesis testing when observed patterns warrant further investigation.

Michigan↗

USGS2015

Bahamas connection: residence areas selected by breeding female loggerheads tagged in Dry Tortugas National Park, USA

Background Delineation of home ranges, residence and foraging areas, and migration corridors is important for understanding the habitat needs for a given species. Recently, many population segments of Northwest Atlantic loggerhead sea turtles ( Caretta caretta ) were designated as endangered or threatened; the smallest subpopulation is in the Dry Tortugas. Foraging and residence areas for this subpopulation have not been defined outside the Gulf of Mexico. Here, for Dry Tortugas loggerheads that traveled to the Bahamas, we use a combination of switching state-space modeling (SSM) and home-range estimators to determine migration period, spatially delineate and describe residence areas, and examine inter-annual home-range repeatability. Results In 5,973 tracking days, migration dates for Dry Tortugas loggerheads traveling to the Bahamas occurred during July–September, with turtles tracked twice showing remarkably similar migration paths and timing of departure from nesting sites. Core-use residence areas for 19 loggerheads ranged from 3.7 to 179.5 km 2 (mean ± 1 SD = 56.2 ± 49.5 km 2 ). For three turtles, we found inter-annual home-range repeatability, with centroids of core areas only 0.7–2.9 km apart and significant overlap of inter-annual 50% kernel contours. Conclusions We demonstrate a previously unknown link between Dry Tortugas nesting beaches and Bahamas residence areas; 17/39 (43.6%) of nesting loggerheads tagged in and tracked from the Dry Tortugas take up residence at sites in the Bahamas. Residence area estimates for these turtles were similar in size to previous foraging area estimates for two turtles tracked to the Bahamas in other studies. We show inter-annual residence area repeatability, and that residence areas of different individuals generally did not overlap. We suggest that these loggerheads possibly establish territories.

Florida↗

USGS1996

Incidence of Renibacterium salmoninarum infections in juvenile hatchery spring chinook salmon in the Columbia and Snake Rivers

From 1988 through 1992, we assessed the prevalence (frequency of occurrence) and severity (degree of infection) of Renibacterium salmoninarum (RS) among fish in marked groups of Columbia River basin and Snake River basin hatchery spring chinook salmon Oncorhynchus tshawytscha before release and during their seaward migration. During the study, prevalence of RS infection decreased (from >90% to <65%) in six of the eight hatchery groups. We attributed this decrease to changes in hatchery practices that reduced vertical and horizontal transmission. Fish from Snake River hatcheries had a higher prevalence of infection when sampled at dams (mean >90%) than in the hatchery (mean <70%), but there were no differences in similar comparisons of Columbia River fish. Although prevalence and severity of RS infection were not correlated in the groups studied, it appears that fish from the Snake River were more severely infected than those from the Columbia River. Some groups of Snake River fish had higher severity of infection at dams than in the hatchery, but infection in fish from Columbia River hatcheries did not change. These differences between Snake River and Columbia River fish might have resulted from differences in river conditions and the distances from hatcheries to dams.

Oregon, Washington↗

USGS2020

Mast seeding patterns are asynchronous at a continental scale

Resource pulses are short duration, high magnitude, rare events that drive the dynamics of both plant and animal populations and communities1. Mast seeding is perhaps the most common type of resource pulse occurring in terrestrial ecosystems2, is characterized by the synchronous and highly variable production of seed crops by a population of perennial plants3,4, and is widespread both taxonomically and geographically5. The rare production of abundant seed crops (‘mast events’) that are orders of magnitude higher than in low seed years lead to high reproductive success in seed consumers, and has cascading impacts in ecosystems2,6. While it is suggested that mast seeding is synchronized at continental scales7, studies are largely constrained to local areas covering 10-100’s of kilometers. Furthermore, summer temperature, which acts as a cue in mast seeding8, shows patterns at continental scales manifested as a juxtaposition of positive and negative anomalies that have been linked to irruptive movements of boreal seed eating birds9. Here we show a breakdown in synchrony of mast seeding patterns across space, leading to asynchrony at a continental scale. We found in an analysis of synchrony for a transcontinental North America tree species spanning distances >5,200 km that mast seeding patterns were significantly asynchronous at distances >2,000 km apart. Other studies have shown declines in synchrony across distance, but not asynchrony. Spatio-temporal variation in summer temperatures at the continental scale drives patterns of synchrony in mast seeding, and we anticipate this impacts the spatial dynamics of numerous seed-eating communities, from insects to small mammals to the large-scale migration patterns of boreal seed eating birds.

Nature Plants↗

USGS2005

The effect of thiamine injection on upstream migration, survival, and thiamine status of putative thiamine-deficient coho salmon

A diet containing a high proportion of alewives Alosa pseudoharengus results in a thiamine deficiency that has been associated with high larval salmonid mortality, known as early mortality syndrome (EMS), but relatively little is known about the effects of the deficiency on adults. Using thiamine injection (50 mg thiamine/kg body weight) of ascending adult female coho salmon Oncorhynchus kisutch on the Platte River, Michigan, we investigated the effects of thiamine supplementation on migration, adult survival, and thiamine status. The thiamine concentrations of eggs, muscle (red and white), spleen, kidney (head and trunk), and liver and the transketolase activity of the liver, head kidney, and trunk kidney of fish injected with thiamine dissolved in physiological saline (PST) or physiological saline only (PS) were compared with those of uninjected fish. The injection did not affect the number of fish making the 15-km upstream migration to a collection weir but did affect survival once fish reached the upstream weir, where survival of PST-injected fish was almost twice that of controls. The egg and liver thiamine concentrations in PS fish sampled after their upstream migration were significantly lower than those of uninjected fish collected at the downstream weir, but the white muscle thiamine concentration did not differ between the two groups. At the upper weir, thiamine levels in the liver, spleen, head kidney, and trunk kidney of PS fish were indistinguishable from those of uninjected fish (called "wigglers") suffering from a severe deficiency and exhibiting reduced equilibrium, a stage that precedes total loss of equilibrium and death. For PST fish collected at the upstream weir, total thiamine levels in all tissues were significantly elevated over those of PS fish. Based on the limited number of tissues examined, thiamine status was indicated better by tissue thiamine concentration than by transketolase activity. The adult injection method we used appears to be a more effective means of increasing egg thiamine levels than immersion of eggs in a thiamine solution. ?? Copyright by the American Fisheries Society 2005.

Journal of Aquatic Animal Health↗