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USGS2012

A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

Journal of Marine Animals and Their Ecology↗
USGS2012

Biomedical health assessments of the Florida manatee in Crystal River - providing opportunities for training during the capture, handling, and processing of this endangered aquatic mammal

Federal and state researchers have been involved in manatee (Trichechus manatus) biomedical health assessment programs for a couple of decades. These benchmark studies have provided a foundation for the development of consistent capture, handling, and processing techniques and protocols. Biologists have implemented training and encouraged multi-agency participation whenever possible to ensure reliable data acquisition, recording, sample collection, publication integrity, and meeting rigorous archival standards. Under a U.S. Fish and Wildlife Service wildlife research permit granted to the U.S. Geological Survey (USGS) Sirenia Project, federal biologists and collaborators are allowed to conduct research studies on wild and captive manatees detailing various aspects of their biology. Therefore, researchers with the project have been collaborating on numerous studies over the last several years. One extensive study, initiated in 2006 has focused on health and fitness of the winter manatee population located in Crystal River, Florida. During those health assessments, capture, handling, and work-up training has been afforded to many of the participants. That study has successfully captured and handled 123 manatees. The data gathered have provided baseline information on manatee health, reproductive status, and nutritional condition. This research initiative addresses concerns and priorities outlined in the Florida Manatee Recovery Plan. The assessment teams strive to continue this collaborative effort to help advance our understanding of health-related issues confronting manatees throughout their range and interlacing these findings with surrogate species concepts.

Florida↗
USGS2015

Predictive modelling of habitat use by marine predators with respect to the abundance and depth distribution of pelagic prey

Understanding the ecological processes that underpin species distribution patterns is a fundamental goal in spatial ecology. However, developing predictive models of habitat use is challenging for species that forage in marine environments, as both predators and prey are often highly mobile and difficult to monitor. Consequently, few studies have developed resource selection functions for marine predators based directly on the abundance and distribution of their prey. We analysed contemporaneous data on the diving locations of two seabird species, the shallow-diving Peruvian Booby ( Sula variegata ) and deeper diving Guanay Cormorant ( Phalacrocorax bougainvilliorum ), and the abundance and depth distribution of their main prey, Peruvian anchoveta ( Engraulis ringens ). Based on this unique data set, we developed resource selection functions to test the hypothesis that the probability of seabird diving behaviour at a given location is a function of the relative abundance of prey in the upper water column. For both species, we show that the probability of diving behaviour is mostly explained by the distribution of prey at shallow depths. While the probability of diving behaviour increases sharply with prey abundance at relatively low levels of abundance, support for including abundance in addition to the depth distribution of prey is weak, suggesting that prey abundance was not a major factor determining the location of diving behaviour during the study period. The study thus highlights the importance of the depth distribution of prey for two species of seabird with different diving capabilities. The results complement previous research that points towards the importance of oceanographic processes that enhance the accessibility of prey to seabirds. The implications are that locations where prey is predictably found at accessible depths may be more important for surface foragers, such as seabirds, than locations where prey is predictably abundant. Analysis of the relative importance of abundance and accessibility is essential for the design and evaluation of effective management responses to reduced prey availability for seabirds and other top predators in marine systems.

Gulf of Guinea↗
USGS2011

Evaluating the demographic buffering hypothesis with vital rates estimated for Weddell seals from 30years of mark-recapture data

1. Life‐history theory predicts that those vital rates that make larger contributions to population growth rate ought to be more strongly buffered against environmental variability than are those that are less important. Despite the importance of the theory for predicting demographic responses to changes in the environment, it is not yet known how pervasive demographic buffering is in animal populations because the validity of most existing studies has been called into question because of methodological deficiencies. 2. We tested for demographic buffering in the southern‐most breeding mammal population in the world using data collected from 5558 known‐age female Weddell seals over 30 years. We first estimated all vital rates simultaneously with mark–recapture analysis and then estimated process variance and covariance in those rates using a hierarchical Bayesian approach. We next calculated the population growth rate’s sensitivity to changes in each of the vital rates and tested for evidence of demographic buffering by comparing properly scaled values of sensitivity and process variance in vital rates. 3. We found evidence of positive process covariance between vital rates, which indicates that all vital rates are affected in the same direction by changes in annual environment. Despite the positive correlations, we found strong evidence that demographic buffering occurred through reductions in variation in the vital rates to which population growth rate was most sensitive. Process variation in vital rates was inversely related to sensitivity measures such that variation was greatest in breeding probabilities, intermediate for survival rates of young animals and lowest for survival rates of older animals. 4. Our work contributes to a small but growing set of studies that have used rigorous methods on long‐term, detailed data to investigate demographic responses to environmental variation. The information from these studies improves our understanding of life‐history evolution in stochastic environments and provides useful information for predicting population responses to future environmental change. Our results for an Antarctic apex predator also provide useful baselines from a marine ecosystem when its top‐ and middle‐trophic levels were not substantially impacted by human activity.

Journal of Animal Ecology↗
USGS2023

Stream hydrology and a pulse subsidy shape patterns of fish foraging

Pulsed subsidy events create ephemeral fluxes of hyper-abundant resources that can shape annual patterns of consumption and growth for recipient consumers. However, environmental conditions strongly affect local resource availability for much of the year, and can heavily impact consumer foraging and growth patterns prior to pulsed subsidy events. Thus, a consumer's capacity to exploit pulse subsidy resources may be influenced by antecedent environmental conditions, but this has rarely been shown in nature and is unknown in aquatic ecosystems. Here, we sought to understand the importance of hydrologic variation and a salmon pulse subsidy on the foraging and growth patterns of two stream salmonids in a coastal southeast Alaska drainage. To do this, we sampled fish stomach contents at a high temporal frequency (daily–weekly measurements) and analyzed fish consumption rates in relation to streamflow and pulse subsidy resource availability. We then explored the influence of interannual hydrologic variation on access to pulse subsidy resources (i.e. whether fish exceeded an egg consumption gape limit) in a bioenergetic simulation. Prior to Pink Salmon spawning, Dolly Varden and Coho Salmon displayed distinct and nonlinear flow-foraging relationships, where forage for both species consisted primarily of macroinvertebrates. During this time period, consumption maxima coincided with baseflow and the highest observed flow conditions, and consumption minima were observed at severe low-water and intermediate flow values. After salmon spawning began, forage was not significantly related to flow and consisted primarily of salmon eggs. Further, consumption rates increased overall, and foraging patterns did not appear to be affected by flow in either species. Bioenergetic simulations revealed that patterns of interannual hydrologic variation may shift Coho Salmon growth trajectories among years. Together, our results suggest that access to marine pulse subsidy resources may depend on whether antecedent hydrologic conditions are suitable for juvenile salmonids to grow large enough to consume salmon eggs by the onset of spawning.

Alaska↗
USGS1988

Food availability controls seasonal cycle of growth in Macoma balthica (L.) in San Francisco Bay, California

A 2-yr field study of growth in the bivalve Macoma balthica (L.) at four locations in San Francisco Bay, California, U.S., showed that the timing and rate of growth (increase in shell length) were related to food supply. This clam feeds on both planktonic and benthic microalgae, depending on availability. Growth was apparently food-limited during some months, during one year more than the other, and at some locations more than others. Tissue-weight changes were also related to food availability. The heaviest animals were found in that year and at those locations with the highest chl a concentrations. Tissue-weight gains usually coincided with increased shell-growth rate or with reproductive development, although some large animals showed weight gain independent of both of these factors during periods with mid-range chl a levels. Weight losses coincided with spawning or periods of low growth rate, except at one station where, during a period when most animals were reproductively ripe, food concentrations were high, and shell growth was rapid, animals lost weight. This study failed to show a relation between salinity and the timing or rate of change of either shell length or tissue weight. The mild temperatures (10-23 ??C water temperature) of the area studied resulted in no growth inhibition due to low temperature, but there was some indication that the high air temperatures found in these intertidal areas limited growth rates. ?? 1988.

Journal of Experimental Marine Biology and Ecology↗
USGS2014

Standardized phenology monitoring methods to track plant and animal activity for science and resource management applications

Phenology offers critical insights into the responses of species to climate change; shifts in species’ phenologies can result in disruptions to the ecosystem processes and services upon which human livelihood depends. To better detect such shifts, scientists need long-term phenological records covering many taxa and across a broad geographic distribution. To date, phenological observation efforts across the USA have been geographically limited and have used different methods, making comparisons across sites and species difficult. To facilitate coordinated cross-site, cross-species, and geographically extensive phenological monitoring across the nation, the USA National Phenology Network has developed in situ monitoring protocols standardized across taxonomic groups and ecosystem types for terrestrial, freshwater, and marine plant and animal taxa. The protocols include elements that allow enhanced detection and description of phenological responses, including assessment of phenological “status”, or the ability to track presence–absence of a particular phenophase, as well as standards for documenting the degree to which phenological activity is expressed in terms of intensity or abundance. Data collected by this method can be integrated with historical phenology data sets, enabling the development of databases for spatial and temporal assessment of changes in status and trends of disparate organisms. To build a common, spatially, and temporally extensive multi-taxa phenological data set available for a variety of research and science applications, we encourage scientists, resources managers, and others conducting ecological monitoring or research to consider utilization of these standardized protocols for tracking the seasonal activity of plants and animals.

International Journal of Biometeorology↗
USGS2012

Experimentally derived salinity tolerance of hatchling Burmese pythons (Python molurus bivittatus) from the Everglades, Florida (USA)

In a laboratory setting, we tested the ability of 24 non-native, wild-caught hatchling Burmese pythons (Python molurus bivittatus) collected in the Florida Everglades to survive when given water containing salt to drink. After a one-month acclimation period in the laboratory, we grouped snakes into three treatments, giving them access to water that was fresh (salinity of 0, control), brackish (salinity of 10), or full-strength sea water (salinity of 35). Hatchlings survived about one month at the highest marine salinity and about five months at the brackish-water salinity; no control animals perished during the experiment. These results are indicative of a "worst-case scenario", as in the laboratory we denied access to alternate fresh-water sources that may be accessible in the wild (e.g., through rainfall). Therefore, our results may underestimate the potential of hatchling pythons to persist in saline habitats in the wild. Because of the effect of different salinity regimes on survival, predictions of ultimate geographic expansion by non-native Burmese pythons that consider salt water as barriers to dispersal for pythons may warrant re-evaluation, especially under global climate change and associated sea-level-rise scenarios.

Florida↗
USGS1994

Using stable isotopes to determine seabird trophic relationships

1. The stable isotopes of nitrogen (δ 15 N ) and carbon (δ 13 C) were analysed in 22 species of marine birds from coastal waters of the northeast Pacific Ocean. Analyses confirm that stable nitrogen isotopes can predict seabird trophic positions. 2. Based on δ 15 N analyses, seabird trophic-level inferences generally agree with those of conventional dietary studies, but suggest that lower trophic-level organisms are more important to several seabirds than was recognized previously. 3. Stable-carbon isotope analysis may be a good indicator of inshore vs. offshore feeding preference. 4. In general, stable-isotope analysis to determine trophic level offers many advantages over conventional dietary approaches since trophic inferences are based on time-integrated estimates of assimilated and not just ingested foods, and isotopic abundance represents a continuous variable that is amenable to statistical analysis.

Alaska, British Columbia↗
USGS2026

Single receiver target localization in mobile marine acoustic telemetry

Many marine ecological studies track animal movement and migration using acoustic telemetry, in which animals are implanted with acoustic transmitters broadcasting a unique ID code. Receivers detect and decode these transmissions and provide an estimate of the animal’s location. As transmissions can be detected at distances of hundreds of meters to even several kilometers, localization performed using binary detection information is very coarse. Fine-scale localization can be performed using time difference of arrival systems, but such systems are costlier and require a greater number of receivers. We present a Bayesian method for target localization using only binary detection information collected by a single receiver mounted on a mobile platform. The approach reduces error in the location estimate by considering the distance-dependent probability of detection (detection efficiency curve), which must first be characterized. Stationary receivers are used to infer failed detections. This localization method is then used to inform waypoint selection for the mobile platform, using the second nondominated sorting genetic algorithm considering the tradeoff between the travel distance of the platform and localization error. Simulation results examine the effects of detection efficiency curve characteristics, number of transmissions, and travel distance on the localization error. The proposed method is further supported by experimental results from field trials conducted with an autonomous surface vehicle in Lake Huron.

IEEE Journal of Oceanic Engineering↗
USGS2002

Carboniferous Psammichnites: Systematic re-evaluation, taphonomy and autecology

The ichnogenus Psammichnites Torell 1870 includes a wide variety of predominantly horizontal, sinuous to looped, backfilled traces, characterized by a distinctive median dorsal structure. Though commonly preserved in full relief on upper bedding surfaces, some ichnospecies of Psammichnites may be preserved in negative hyporelief. Psammichnites records the feeding activities of a subsurface animal using a siphon-like device. Several ichnogenera reflect this general behavioral pattern, including Plagiogmus Roedel 1929 and the Carboniferous ichnogenera Olivellites Fenton and Fenton 1937a and Aulichnites Fenton and Fenton 1937b. Based on analysis of specimens from the United States, Spain, and the United Kingdom, three Carboniferous ichnospecies of Psammichnites are reviewed in this paper: P. plummeri (Fenton and Fenton, 1937a), P. grumula (Romano and Meléndez 1979), and P. implexus (Rindsberg 1994). Psammichnites plummeri is the most common Carboniferous ichnospecies and is characterized by a relatively straight, continuous dorsal ridge/groove, fine transverse ridges, larger size range, and non-looping geometric pattern. It represents a grazing trace of deposit feeders. Psammichnites grumula differs from the other ichnospecies of Psammichnites by having median dorsal holes or protruding mounds. The presence of mounds or holes in P. grumula suggests a siphon that was regularly connected to the sediment-water interface. This ichnospecies is interpreted as produced by a deposit feeder using the siphon for respiration or as a device for a chemosymbiotic strategy. Psammichnites implexus is characterized by its consistently smaller size range, subtle backfill structure, and tendency to scribble. Although displaying similarities with Dictyodora scotica , P. implexus is a very shallow-tier, grazing trace. Changes in behavioral pattern, preservational style, and bedform morphology suggest a complex interplay of ecological and taphonomic controls in Carboniferous tidal-flat Psammichnites . A first distributional pattern consists of guided meandering specimens preserved in ripple troughs, probably reflecting food-searching of buried organic matter concentrated in troughs. A second is recorded by concentration of Psammichnites on ripple crests and slopes. In some cases, the course is almost straight to slightly sinuous and closely follows topographic highs, suggesting a direct control of bedform morphology on trace pattern. Occurrences of Carboniferous Psammichnites most likely represent an opportunistic strategy in marginal-marine settings. Analysis of Carboniferous Psammichnites indicates the presence of a siphon-like device in the producer and reestablishes the possibility of a molluscan tracemaker.

Ichnos: An International Journal for Plant and Ani↗
USGS2008

Decreased mortality of lake michigan chinook salmon after bacterial kidney disease challenge: Evidence for pathogen-driven selection?

In the late 1960s, Chinook salmon Oncorhynchus tshawytscha from the Green River, Washington, were successfully introduced into Lake Michigan. During spring from1988 to 1992, large fish die-offs affecting Chinook salmon occurred in the lake. Multiple ecological factors probably contributed to the severity of the fish kills, but the only disease agent found regularly was Renibacterium salmoninarum, the causative agent of bacterial kidney disease. in this study, survival after challenge by R. salmoninarum was compared between two Chinook salmon stocks: a Lake Michigan stock from Wisconsin (WI) and the progenitor stock from the Green River. We found that the WI stock had significantly greater survival than the Green River stock. Next, the WI and Green River stocks were exposed to the marine pathogen Listonella anguillarum (formerly Vibrio anguillarum), one of the causative agents of vibriosis; survival after this challenge was significantly poorer for the WI stock than for the Green River stock. A close genetic relationship between the Green River and WI stocks was confirmed by analyzing 13 microsatellite loci. These results collectively suggest that disease susceptibility of Lake Michigan Chinook salmon has diverged from that of the source population, possibly in response to pathogen-driven selection. ?? Copyright by the American Fisheries Society 2008.

Journal of Aquatic Animal Health↗
USGS2004

Energy density and variability in abundance of pigeon guillemot prey: Support for the quality-variability trade-off hypothesis

1. The quality-variability trade-off hypothesis predicts that (i) energy density (kJ g-1) and spatial-temporal variability in abundance are positively correlated in nearshore marine fishes; and (ii) prey selection by a nearshore piscivore, the pigeon guillemot (Cepphus columba Pallas), is negatively affected by variability in abundance. 2. We tested these predictions with data from a 4-year study that measured fish abundance with beach seines and pigeon guillemot prey utilization with visual identification of chick meals. 3. The first prediction was supported. Pearson's correlation showed that fishes with higher energy density were more variable on seasonal (r = 0.71) and annual (r = 0.66) time scales. Higher energy density fishes were also more abundant overall (r = 0.85) and more patchy at a scale of 10s of km (r = 0.77). 4. Prey utilization by pigeon guillemots was strongly non-random. Relative preference, defined as the difference between log-ratio transformed proportions of individual prey taxa in chick diets and beach seine catches, was significantly different from zero for seven of the eight main prey categories. 5. The second prediction was also supported. We used principal component analysis (PCA) to summarize variability in correlated prey characteristics (energy density, availability and variability in abundance). Two PCA scores explained 32% of observed variability in pigeon guillemot prey utilization. Seasonal variability in abundance was negatively weighted by these PCA scores, providing evidence of risk-averse selection. Prey availability, energy density and km-scale variability in abundance were positively weighted. 6. Trophic interactions are known to create variability in resource distribution in other systems. We propose that links between resource quality and the strength of trophic interactions may produce resource quality-variability trade-offs.

Journal of Animal Ecology↗
USGS2019

Natural resource condition assessment: Channel Islands National Park

The Natural Resource Condition Assessment (NRCA) Program aims to provide documentation about the current conditions of important Park natural resources through a spatially explicit, multidisciplinary synthesis of existing scientific data and knowledge. Findings from the NRCA will help Channel Islands National Park (CINP) managers to develop near-term management priorities. The central objectives of this assessment were to evaluate the current conditions and trends of key Park resources, identify important knowledge gaps, and determine key stressors and threats. Because a recent report provided an assessment of marine resources (Engle 2006), which constitute 50% of the park, this NRCA focused on terrestrial resources. For this NRCA, CINP resource managers identified that the greatest Park need was to know whether or not vegetation (primarily woody vegetation) is recovering on the Channel Islands and how this may be influencing recovery of the native terrestrial vertebrates. To address this, the CINP NRCA team evaluated the condition of island vegetation and vertebrate communities using both: 1) already available, summarized information from reports, theses, and journal articles and 2) new analyses of recently available, existing data collected on the islands. Descriptions of specific methods used to analyze available data by the NRCA team are provided within the assessment sections in Chapter 4 of this report. The Team used the Vital Signs indicators as identified by Fancy et al. (2009) for monitoring the condition of Natural Resources in U.S. National Parks. Using this framework, the focal study resource components were the five CINP islands, because these are the bio-geophysical resources of greatest interest to the CINP. Each of the islands has its own unique history of human impacts, ecological conditions, restoration efforts, and natural resource monitoring. The Team evaluated island scrub recovery by assessing changes over time in two metrics: 1) vegetation community structure (species composition, cover, and spatial extent), and 2) vertebrate abundance, relative to the reference condition of each island. The reference conditions for this NRCA were the particular island’s ecological state prior to European settlement or ranching, which represent the ecological state to which the NPS desires the park return. For each metric, the Team determined the Reference Conditions/Values, Current Condition, Trend, and Recovery Potential (based on a review of the literature and from the NRCA team’s analysis of newly available data), Threats and Stressors, Data Gaps, Overall Condition. A qualitative statement of overall current condition was created for each metric, after all data and literature relevant to the measures (i.e., vegetation and vertebrates) of each resource component (i.e., island) were reviewed and evaluated. All information gathered for this NRCA is available and managed by CINP, so that the compilation of resources would be available not only for the assessment team, but will be provided for future Park reference. Chapter 1 of this NRCA provides a descriptive background of NRCAs. Chapter 2 provides Park-wide natural resource background information, while Chapter 3 describes the overall methodological approach used in this assessment. Chapter 4 provides a detailed assessment of each island’s condition, which is then summarized Park-wide and for each island in Chapter 5. Based on both vegetation recovery and vertebrate population abundances, our assessment found Santa Cruz Island (SCI), Santa Rosa Island (SRI), San Miguel Island (SMI), and Anacapa Island (AI) to be, overall, in moderate condition and slowly recovering following the removal of non-native herbivores. The condition of Santa Barbara Island (SBI) is poor and remains in a state that is not likely to improve without assisted recovery by the Park. All islands have exhibited some level of native vegetation recovery, with most of the observed natural recovery occurring on SCI, SRI, SMI, and AI; very little recovery has occurred at present on SBI. Vegetation recovery is uneven across each island and largely limited to mesic areas, such as north-facing slopes. Areas that will likely require some assisted recovery efforts are those that are: at risk of erosion, isolated, lacking native seed banks, and plagued with high competition of non-native grasses and other invasives. Some plant communities, such as exposed upland vegetation on SRI, also have lower natural recovery potential and will likely require assisted recovery. The overall condition of the Park’s terrestrial island vertebrate species generally appears to be good and improving, with high potential for further recovery to reach pre-ranching era reference conditions. This is particularly true for vertebrates on SCI, SRI, and SMI. Although there are limited data for AI, the data that are available suggest that vertebrates on that island are in good condition and improving as well. However, the condition of SBI vertebrates is only moderate, with natural recovery potential being low, with many landbird species’ populations currently declining, extinct, or not improving. An overarching theme across the Park’s terrestrial island vertebrate populations is that many of them are in good condition because the particular animals are habitat generalists, so their population dynamics are not strongly tied to habitat conditions. However, those landbirds associated with riparian vegetation are not showing signs of recovery across the Park islands, and riparian areas appear to be one of the habitats with limited natural recovery potential on the islands. Overwhelmingly, the most critical data gap that emerged from our analysis was the lack of current vegetation maps for most of the islands (AI, SCI, SRI, SMI). The lack of this information made it difficult to assess spatial changes in island vegetation over time, and to relate those changes to observed changes in vertebrate species abundances. Therefore, we were limited in our spatial assessment of vegetation recovery for AI, SCI, SRI, and SMI, and were only able to relate the current vegetation with island landbird analysis for SBI. Another common theme across islands was the lack of information on best techniques for shrub reintroduction and recovery, and the success of invasive species removal and re-vegetation efforts. Abundance, distribution, and habitat affinities of reptiles and amphibians are poorly known for AI, SCI, SRI, and SMI, making it difficult to assess their population condition and trends, and their potential responses to shrub recovery. Mammal and landbird populations are reasonably well-sampled across most of the islands, but data are lacking for most vertebrates from AI, especially West and Middle AI where no vertebrate sampling occurs. The population status, cause of declines, and recovery needs are lacking for several landbird species across multiple islands, including loggerhead shrikes ( Lanius ludovicianus ssp.) on SCI and SRI, and Santa Cruz Island rufous crowned sparrows ( Aimophila ruficeps obscura ) on AI. Additionally, island song sparrows ( Melospiza melodia graminea ) remain extirpated on SBI and data are needed for assessing their recovery potential on the island. The potentially major threats facing the islands’ flora and fauna today are: areas of continued erosion, potential new non-native introductions, and climate change. The Park islands have already experienced warming over the last several decades due to human-induced climate change, and are projected to experience continued warming. These increasing stresses imposed by climate change may slow and inhibit natural recovery potentials for island fauna, and especially flora.

California↗