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At least 937 records · Page 52Linked to original sources
USGS2017

Characterization of microsatellite loci for the Gulf Coast waterdog (Necturus beyeri) using paired-end Illumina shotgun sequencing and cross-amplification in other Necturus

Amphibians are one of the most threatened groups of vertebrates (Stuart et al. 2004; Wake and Vredenburg 2008), and the application of molecular techniques to amphibian ecology and genetics has dramatically improved our ability to conserve species and populations (see Shaffer et al. [2015] for review). Microsatellites, tandem repeats of two to six nucleotides in the nuclear genome, are highly variable molecular markers that can be used to describe gene flow and genetic diversity, each of which is positively correlated with population persistence (Allendorf and Luikart 2007; Allentoft and O’Brien 2010; Avise 2004; Selkoe and Toonen 2006). Microsatellite loci have frequently been applied to studies involving terrestrial and pond breeding amphibians (Emel and Storfer 2012), but fewer studies have focused on taxa inhabiting lotic systems (Emel and Storfer 2012). For example, studies characterizing microsatellite loci are completely lacking for a group of permanently aquatic salamanders, the waterdogs and mudpuppies (Family Proteidae, Genus Necturus ) (Rafinesque 1819). The genus Necturus consists of several species of perennibranch salamanders that can be found throughout many freshwater streams, rivers, and lakes in North America (Petranka 1998). Some authorities recognize five species (Crother 2012; Petranka 1998), including the Mudpuppy ( Necturus maculosus ) (Rafinesque 1819), Gulf Coast Waterdog ( N. beyeri ) (Viosca 1937), Black Warrior Waterdog ( N. alabamensis ) (Viosca 1937), Neuse River Waterdog ( N. lewisi ) (Brimley 1924), and Dwarf Waterdog ( N. punctatus ) (Gibbes 1850). This taxonomy also recognizes two subspecies within N. maculosus , including the Common Mudpuppy ( N. m. maculosus ) and the Red River Waterdog ( N. m. louisianensis ) (Crother 2012; Petranka 1998; Schmidt 1953). Other authorities suggest that there are six or seven species within Necturus (Collins 1990; Frost 2016; Powell et al. 2016). These more diverse schemes recognize each of the aforementioned five species while also elevating the Red River Waterdog ( N. louisianensis ) (Collins 1990; Frost 2016; Powell et al. 2016; Viosca 1938) and Löding’s Waterdog ( N. lödingi or N. cf. beyeri ) (Bart et al. 1997; Guyer 2005a; Viosca 1938). Allozyme work by Guttman et al. (1990) suggests that there is at least one cryptic species of Necturus in drainages east of the Mobile Basin and south of the Alabama River, and both Bart et al. (1997) and Guyer (2005a) advise that these populations should be referred to as N. cf. beyeri . However, until range wide studies incorporating genetic and other data are published, we will follow the five species taxonomy outlined by Crother (2012) while acknowledging that certain taxa, such as N. maculosus and N. beyeri , may require systematic revision.

Herpetological Review↗
USGS2010

The transboundary nature of seabird ecology

The term ‘seabird’ is generally applied to avian species that forage in the marine environment over open water. Seabirds typically nest in colonies and are long-lived species with low annual reproductive rates. Seabird breeding sites typically occur on islands or along coasts and as such are often at the boundaries of ecological or political zones. During the breeding season, seabirds cross a very distinct terrestrial/marine ecological boundary on a regular basis to forage. Even relatively ‘local’ species cross multiple jurisdictions within a day (e.g., state lands and waters, and federal waters) while pelagic species may transit through international waters on a daily, weekly, or monthly time-frame. Seabird life-histories expose individuals and populations to environmental conditions affecting both terrestrial and marine habitats. The wide-ranging and transboundary nature of seabird ecology also exposes these species to various environmental and anthropogenic forces such as contamination, commercial fisheries and climate forcing that also are transboundary in nature. Therefore, wherever conservation of seabirds or the management of their populations is the goal, consideration must be given to ecosystem dynamics on land and at sea. Because the jurisdiction of agencies does not cross the land-sea boundary in the same manner as the seabirds they are managing, these efforts are facilitated by multi-agency communication and collaboration. By their very nature and by the nature of the systems that they must function within, seabirds embody the complexity of wildlife ecology and conservation in the twenty-first century.

Book chapter↗
USGS2021

Fisheries research and monitoring activities of the Lake Erie Biological Station, 2021

A comprehensive understanding of fish populations and their interactions is the cornerstone of modern fishery management and the basis for Lake Erie’s Fish Community Goals and Objectives (FCOs) developed in 2020 (Francis et al. 2020). The 2021 USGS Lake Erie Biological Station annual report is responsive to these FCOs and the U.S. Geological Survey (USGS) obligations via a Memorandum of Understanding (MOU) in 2004 with the GLFC Council of Lake Committees (CLC) to provide scientific information in support of fishery management. Goals for the USGS Great Lakes Deepwater Fish Assessment and Ecological Studies were to monitor long-term changes in the fish community and population dynamics of key fishes of interest to management agencies (MOU 2004). Specific to Lake Erie, expectations of the MOU were sustained investigations of native percids, forage (prey) fish populations, and Lake Trout. Additionally, this work was conducted under the authority of the Great Lakes Fishery Research Authorization Act of 2019.

Lake Erie↗
USGS2020

Estimation of vital population rates to assess the relative health of mussel assemblages in the Upper Mississippi River

Native freshwater mussels are a guild of benthic, filter feeding invertebrates that perform important ecological functions in rivers. Because of their long lifespans (30–50 years or longer), mussels are slow to respond to human‐induced alterations. Thus, development of sensitive indicators of mussel population responses to river conditions and management would be beneficial. Compared to marine species, estimation of vital rates (e.g. survival, growth) in freshwater mussels has received little attention. We placed passively integrated transponder tags on 578 mussels of four species ( Amblema plicata , Cyclonaias pustulosa , Obliquaria reflexa , and Pleurobema sintoxia ) in a well‐studied mussel assemblage in a side channel of the upper Mississippi River. Growth and survival of tagged mussels were assessed annually for 4 years across core (high density) and peripheral (low density) areas of the assemblage. Overall survival was highly variable, ranging from c . 15 to 90%, and was related to life history, habitat quality, and hydrologic events. Survival, which varied significantly among species and over time, was consistently higher in the dense and species‐rich core of the mussel assemblage, relative to the periphery because substrates were consistently more stable in the core of the mussel bed relative to the periphery. Substrate movement during low flows was an order of magnitude lower in the core relative to the periphery, and survival was inversely related to stability of river substrates. Patterns in habitat‐specific survival indicate source–sink population dynamics such that mussels in the core habitat provide recruitment to the periphery, but mussels in the periphery are subject to unsustainably low survival; additional studies to track the source of recruitment in the periphery are needed to test this hypothesis. Growth rate did not vary significantly between core and peripheral areas but did vary by species. Growth rate (proportional change per year) declined with age, and was similar at mean age for A. plicata (0.016 per year), P. sintoxia (0.015 per year), and C. pustulosa (0.013 per year), but much lower for O. reflexa (0.008 per year). Effective management decisions for mussels requires a better understanding of how vital rates govern populations and how they vary across a suite of physical and biological factors. Information on how population vital rates vary among species and over time gives managers another tool to understand how mussels may respond to management actions such as habitat restoration projects. Given the importance of substrate stability inferred from this study, management actions that maintain or increase substrate stability are likely to result in high quality mussel assemblages and may restore a valuable component of ecosystem function in this region.

Minnesota, Wisconsin↗
USGS2016

Bayesian analysis of Jolly-Seber type models

We propose the use of finite mixtures of continuous distributions in modelling the process by which new individuals, that arrive in groups, become part of a wildlife population. We demonstrate this approach using a data set of migrating semipalmated sandpipers ( Calidris pussila ) for which we extend existing stopover models to allow for individuals to have different behaviour in terms of their stopover duration at the site. We demonstrate the use of reversible jump MCMC methods to derive posterior distributions for the model parameters and the models, simultaneously. The algorithm moves between models with different numbers of arrival groups as well as between models with different numbers of behavioural groups. The approach is shown to provide new ecological insights about the stopover behaviour of semipalmated sandpipers but is generally applicable to any population in which animals arrive in groups and potentially exhibit heterogeneity in terms of one or more other processes.

Environmental and Ecological Statistics↗
USGS2012

Spatial ecology of refuge selection by an herbivore under risk of predation

Prey species use structures such as burrows to minimize predation risk. The spatial arrangement of these resources can have important implications for individual and population fitness. For example, there is evidence that clustered resources can benefit individuals by reducing predation risk and increasing foraging opportunity concurrently, which leads to higher population density. However, the scale of clustering that is important in these processes has been ignored during theoretical and empirical development of resource models. Ecological understanding of refuge exploitation by prey can be improved by spatial analysis of refuge use and availability that incorporates the effect of scale. We measured the spatial distribution of pygmy rabbit (Brachylagus idahoensis) refugia (burrows) through censuses in four 6-ha sites. Point pattern analyses were used to evaluate burrow selection by comparing the spatial distribution of used and available burrows. The presence of food resources and additional overstory cover resources was further examined using logistic regression. Burrows were spatially clustered at scales up to approximately 25 m, and then regularly spaced at distances beyond ~40 m. Pygmy rabbit exploitation of burrows did not match availability. Burrows used by pygmy rabbits were likely to be located in areas with high overall burrow density (resource clusters) and high overstory cover, which together minimized predation risk. However, in some cases we observed an interaction between either overstory cover (safety) or understory cover (forage) and burrow density. The interactions show that pygmy rabbits will use burrows in areas with low relative burrow density (high relative predation risk) if understory food resources are high. This points to a potential trade-off whereby rabbits must sacrifice some safety afforded by additional nearby burrows to obtain ample forage resources. Observed patterns of clustered burrows and non-random burrow use improve understanding of the importance of spatial distribution of refugia for burrowing herbivores. The analyses used allowed for the estimation of the spatial scale where subtle trade-offs between predation avoidance and foraging opportunity are likely to occur in a natural system.

Ecosphere↗
USGS2018

Barred owl research needs and prioritization in California

Barred owls (Strix varia) have reached high densities within the range of the northern spotted owl (S. occidentalis caurina) and are rapidly increasing in number within the range of the California spotted owl (S. o. occidentalis). Encroaching populations of barred owls pose a significant competitive threat to the viability of both spotted owl subspecies in California. In response, the Director of the California Department of Fish and Wildlife (CDFW) convened the California Barred Owl Science Team (BOST) to identify and address the threat posed by barred owls to spotted owls in California. BOST is composed of subject matter scientists with a goal to provide objective scientific review and recommendations to CDFW to promote the recovery and conservation of spotted owls in California. In this document, BOST identifies, describes, and prioritizes key research needs for barred owls that have the potential to benefit the conservation of spotted owls in California. Key research needs were identified from multiple in-person and remote meetings of BOST, with considerable input from attending representatives from state and federal natural resource agencies. BOST and liaisons recognize that periodic updates of this document will likely be required as more is learned about the ecology of barred owls in California and research needs and priorities evolve. Research that BOST deemed the most likely to provide a rigorous scientific basis for reducing barred owl populations included experimental removals, along with ecological studies expected to generate information that would provide avenues for the effective management of barred owls. Other high priority research needs include research using biological samples obtained during experimental removals to better understand the ecology of barred owls and the threats they pose to spotted owls and associated wildlife. We conclude the document with a discussion of how projects are related to the State Wildlife Action Plan. In Appendix I, we discuss considerations for maximizing the success of proposed removal experiments and ecological research on barred owls.

Report↗
USGS1958

Distribution and ecology of whistling swans in the Chesapeake Bay region

The Whistling Swan, Olor columbianus , is of particular significance in the Chesapeake Bay region, since major wintering and transient populations occur here regularly, constituting in some years more than half the total population of the species. Some of these concentrations are so large that they attract many bird-watchers, who often travel long distances to see them. Whistling Swans are also of concern to the local shell-fish gatherers, who claim that depredations by these birds cause considerable damage to the supply of commercially valuable long ("soft-shelled") clams. During recent years, there has been an increasing demand from some sources for an open hunting season. It has been suggested that the swan populations may be of sufficient numerical size, to withstand a limited harvest. Because of these considerations, a special effort was made to obtain more information concerning the local distribution, numerical status and ecology of Whistling Swans throughout the Chesapeake Bay region.

The Auk↗
USGS2011

Development of a bioenergetics model for age-0 American shad

Bioenergetics modeling can be used as a tool to investigate the impact of non-native age-0 American shad ( Alosa sapidissima ) on reservoir and estuary food webs. The model can increase our understanding of how these fish influence lower trophic levels as well as predatory fish populations that feed on juvenile salmonids. Bioenergetics modeling can be used to investigate ecological processes, evaluate alternative research hypotheses, provide decision support, and quantitative prediction. Bioenergetics modeling has proven to be extremely useful in fisheries research (Ney et al. 1993,Chips and Wahl 2008, Petersen et al. 2008). If growth and diet parameters are known, the bioenergetics model can be used to quantify the relative amount of zooplankton or insects consumed by age-0 American shad. When linked with spatial and temporal information on fish abundance, model output can guide inferential hypothesis development to demonstrate where the greatest impacts of age-0 American shad might occur. Bioenergetics modeling is particularly useful when research questions involve multiple species and trophic levels (e.g. plankton communities). Bioenergetics models are mass-balance equations where the energy acquired from food is partitioned between maintenance costs, waste products, and growth (Winberg 1956). Specifically, the Wisconsin bioenergetics model (Hanson et al. 1997) is widely used in fisheries science. Researchers have extensively tested, reviewed, and improved on this modeling approach for over 30 years (Petersen et al. 2008). Development of a bioenergetics model for any species requires three key components: 1) determine physiological parameters for the model through laboratory experiments or incorporate data from a closely related species, 2) corroboration of the model with growth and consumption estimates from independent research, and 3) error analysis of model parameters. Wisconsin bioenergetics models have been parameterized for many of the salmonids and predatory fishes encountered in the lower Columbia River (Petersen and Ward 1999). The Wisconsin bioenergetics model has not been developed for American shad, however Limburg (1996) parameterized a simplified bioenergetics growth model for this species. A common application for the Wisconsin bioenergetics model is to estimate the consumption or growth of a fish population under different temperature and feeding scenarios (Ney 1993). One advantage of the bioenergetics approach is that consumption can be estimated without direct field measurements of predation rate (prey·predator -1 · day -1 ; Petersen and Ward 1999). Field estimates of fish consumption are time consuming and costly to determine, and estimates may show wide variance due to environmental and sampling variability. However, the consumption parameters used in a newly developed bioenergetics model must be verified with field and laboratory estimates of consumption (Ney 1993). The objective of this research was to parameterize a Wisconsin bioenergetics model for age-0 American shad using published physiological data on American shad and closely related alosine species. The American shad bioenergetics model will be used as a tool to explore various hypotheses about how age-0 American shad directly and indirectly affect Columbia River salmon through ecological interactions in lower Columbia River food webs. One over-arching focus of the larger research project was to identify potential interactions between age-0 American shad and juvenile salmonids, addressing potential outcomes through bioenergetics modeling scenarios. This report contains two bioenergetics modeling applications to demonstrate how these models can be used to address management questions and direct research effort. The first modeling application uses the American shad bioenergetics model described in this report to explore prey consumption by age-0 American shad (Chapter 1, this report). Dietary data on age-0 American shad and previously published reports on the diet of juvenile fall Chinook salmon (Rondorf et al. 1990, USGS unpublished data) suggested there might be considerable dietary overlap between these species in the lower Columbia River. The U.S. Geological Survey (USGS) was interested in using the American shad bioenergetics model to explore hypotheses concerning dietary overlap between age-0 American shad and emigrating fall Chinook salmon. The second modeling application uses the fall Chinook salmon bioenergetics model (Koehler et al. 2006) to explore the growth potential of juvenile fall Chinook salmon predating on age-0 American shad in the lower Columbia River. This modeling was based dietary information on a small number of age-0 fall Chinook salmon (n = 13) collected in John Day Reservoir in 1994 - 1996 (unpublished USGS data). Analysis of this dietary data found that these salmonids were feeding primarily on age-0 American shad (> 75% by weight).

Oregon↗
USGS2016

Ecology of nonnative Siberian prawn ( Palaemon modestus ) in the lower Snake River, Washington, USA

We assessed the abundance, distribution, and ecology of the nonnative Siberian prawn Palaemon modestus in the lower Snake River, Washington, USA. Analysis of prawn passage abundance at three Snake River dams showed that populations are growing at exponential rates, especially at Little Goose Dam where over 464,000 prawns were collected in 2015. Monthly beam trawling during 2011–2013 provided information on prawn abundance and distribution in Lower Granite and Little Goose Reservoirs. Zero-inflated regression predicted that the probability of prawn presence increased with decreasing water velocity and increasing depth. Negative binomial models predicted higher catch rates of prawns in deeper water and in closer proximity to dams. Temporally, prawn densities decreased slightly in the summer, likely due to the mortality of older individuals, and then increased in autumn and winter with the emergence and recruitment of young of the year. Seasonal length frequencies showed that distinct juvenile and adult size classes exist throughout the year, suggesting prawns live from 1 to 2 years and may be able to reproduce multiple times during their life. Most juvenile prawns become reproductive adults in 1 year, and peak reproduction occurs from late July through October. Mean fecundity (189 eggs) and reproductive output (11.9 %) are similar to that in their native range. The current use of deep habitats by prawns likely makes them unavailable to most predators in the reservoirs. The distribution and role of Siberian prawns in the lower Snake River food web will probably continue to change as the population grows and warrants continued monitoring and investigation.

Washington↗
USGS2024

Genomic data characterize reproductive ecology patterns in Michigan invasive Red Swamp Crayfish (Procambarus clarkii)

The establishment and spread of invasive species are directly related to intersexual interactions as dispersal and reproductive success are related to distribution, effective population size, and population growth. Accordingly, populations established by r-selected species are particularly difficult to suppress or eradicate. One such species, the red swamp crayfish ( Procambarus clarkii ) is established globally at considerable ecological and financial costs to natural and human communities. Here, we develop a single nucleotide polymorphism (SNP) loci panel for P. clarkii using restriction-associated DNA-sequencing data. We use the SNP panel to successfully genotype 1800 individuals at 930 SNPs in southeastern Michigan, USA. Genotypic data were used to reconstruct pedigrees, which enabled the characterization of P. clarkii's mating system and statistical tests for associations among environmental, demographic, and phenotypic predictors and adult reproductive success estimates. We identified juvenile cohorts using genotype-based pedigrees, body size, and sampling timing, which elucidated the breeding phenology of multiple introduced populations. We report a high prevalence of multiple paternity in each surveyed waterbody, indicating polyandry in this species. We highlight the use of newly developed rapid genomic assessment tools for monitoring population reproductive responses, effective population sizes, and dispersal during ongoing control efforts.

Evolutionary Applications↗
USGS2015

Camera traps and mark-resight models: The value of ancillary data for evaluating assumptions

Unbiased estimators of abundance and density are fundamental to the study of animal ecology and critical for making sound management decisions. Capture–recapture models are generally considered the most robust approach for estimating these parameters but rely on a number of assumptions that are often violated but rarely validated. Mark-resight models, a form of capture–recapture, are well suited for use with noninvasive sampling methods and allow for a number of assumptions to be relaxed. We used ancillary data from continuous video and radio telemetry to evaluate the assumptions of mark-resight models for abundance estimation on a barrier island raccoon (Procyon lotor) population using camera traps. Our island study site was geographically closed, allowing us to estimate real survival and in situ recruitment in addition to population size. We found several sources of bias due to heterogeneity of capture probabilities in our study, including camera placement, animal movement, island physiography, and animal behavior. Almost all sources of heterogeneity could be accounted for using the sophisticated mark-resight models developed by McClintock et al. (2009b) and this model generated estimates similar to a spatially explicit mark-resight model previously developed for this population during our study. Spatially explicit capture–recapture models have become an important tool in ecology and confer a number of advantages; however, non-spatial models that account for inherent individual heterogeneity may perform nearly as well, especially where immigration and emigration are limited. Non-spatial models are computationally less demanding, do not make implicit assumptions related to the isotropy of home ranges, and can provide insights with respect to the biological traits of the local population.

North Carolina↗
USGS2023

Dynamic population models with temporal preferential sampling to infer phenology

To study population dynamics, ecologists and wildlife biologists typically use relative abundance data, which may be subject to temporal preferential sampling. Temporal preferential sampling occurs when the times at which observations are made and the latent process of interest are conditionally dependent. To account for preferential sampling, we specify a Bayesian hierarchical abundance model that considers the dependence between observation times and the ecological process of interest. The proposed model improves relative abundance estimates during periods of infrequent observation and accounts for temporal preferential sampling in discrete time. Additionally, our model facilitates posterior inference for population growth rates and mechanistic phenometrics. We apply our model to analyze both simulated data and mosquito count data collected by the National Ecological Observatory Network. In the second case study, we characterize the population growth rate and relative abundance of several mosquito species in the Aedes genus. Supplementary materials accompanying this paper appear on-line.

Journal of Agricultural, Biological, and Environme↗
USGS2016

Ecological requirements for pallid sturgeon reproduction and recruitment in the Missouri River—A synthesis of science, 2005 to 2012

This report is intended to synthesize the state of the scientific understanding of pallid sturgeon ecological requirements to provide recommendations for future science directions and context for Missouri River restoration and management decisions. Recruitment of pallid sturgeon has been low to non-existent throughout its range. Emerging understanding of the genetic structure of pallid sturgeon populations sets a broad framework for species and river management decisions, including decisions about managing the future genetic diversity of the species, but also decisions about where and what type of river restoration actions will be effective for subpopulations of this highly migratory species. Adult pallid sturgeon may migrate hundreds of kilometers (km) to spawn and their progeny may disperse even greater distances downstream as drifting free embryos. As a result of their complex life history pallid sturgeon naturally exploit a wide range of habitats during their life cycles. The construction of dams and reservoirs has fragmented habitats and may have shifted Missouri River subpopulations downstream. Research has not identified one primary biological or ecological constraint that appears to limit populations of the pallid sturgeon. With the present (2013) state of knowledge many life stages and life-stage transitions cannot be ruled out as contributing to recruitment failure. Biological opinions in 2000 (and amended in 2003) presented the dominant hypotheses for recruitment failure that existed at that time. Emphasis was on the role of the flow regime, specifically spring flow pulses (“spring rises”), to condition spawning substrate and cue reproductive aggregations and migrations, and on low flows and additional slow, shallow-water area to serve as rearing habitat for age-0 to juvenile pallid sturgeon. Studies on spawning habitat dynamics have documented that habitat patches selected for spawning by fish in the Lower Missouri River (Missouri River downstream from Gavins Point Dam to the confluence with the Mississippi River) are dominantly on outside, revetted bends in the deepest, fastest, and most turbulent water. Studies in more natural habitat on the Yellowstone River have documented spawning in convergent flow in the middle of the channel on discrete patches of gravel within a sand-dominated channel, an arrangement that may be more effective in attracting aggregations of reproductive fish compared to the nearly continuous revetment on the Lower Missouri River. Pallid sturgeon spawn in the spring and early summer during periods of increasing day length. Water temperature consistently exerts a threshold effect for spawning at 16–18 °C. In addition, the role of water temperature is indicated by pauses and reversals in upstream migrations that have been associated with cold weather fronts that create a transient decrease in water temperature. From 2005 to 2012 on the Lower Missouri River, no obvious relations between flow pulses and fish movements and spawning behaviors have been apparent. However, pallid sturgeon tracking at the Upper Missouri–Yellowstone confluence indicates that in most years, most telemetered pallid sturgeon migrate out of the Missouri River and into the Yellowstone River in the June–July timeframe in association with the spring pulse. This pattern was disrupted in 2011 when a high flow pulse with warm temperatures and high turbidity emanated from the Milk River, followed by record releases from Fort Peck Dam, and 36–39 percent of the telemetered population migrated up the Upper Missouri. This result supports the hypothesis that sufficiently large flow pulses may trigger migration and aggregation but it is not clear that functional pulses are within reservoir management authorities. Notably, a pallid sturgeon free embryo was captured on the Upper Missouri River in 2011 and another single, genetically confirmed embryo was captured on the Yellowstone River in 2012. Research on free-embryo drift has indicated the potential for hundreds of miles of downstream dispersal. Lack of distance to accommodate the extended downstream dispersal period of free embryos on the Upper Missouri and Yellowstone Rivers is the predominant hypothesis for recruitment failure in the upper basin. Long drift distances in the Lower Missouri River may be responsible for shifting Lower Missouri River sub-populations further into the Middle Mississippi River. Physical understanding of drift processes indicates that mean velocities could be slowed through decreased discharges or increased channel hydraulic radius (width and topographic diversity) to reduce free-embryo dispersal distances. In addition, the probability that free embryos are transported into and retained in channel-margin habitats is theoretically amenable to channel re-engineering that would increase cross-channel secondary currents in bends or channel expansions. Considerable uncertainty persists, however, about whether extended drift of Lower Missouri River larvae is responsible for recruitment failure. If drift distance is limiting, it is important to discern whether it would be advisable to retain larvae within the Missouri River, and where along the river restoration projects should be placed to optimize survival and growth of age-0 and juvenile sturgeon. Longitudinal differences in female pallid sturgeon fecundity lend support to the hypothesis that recruitment failure may be due, in part, to fish having insufficient nutrition to produce the numbers of gametes needed for the population to grow, perhaps because of simultaneous declines in prey-fish populations and their habitats. Establishing a chain of causality from habitat decline, to prey-fish populations, to sturgeon diets, to sturgeon fecundity, and to pallid sturgeon population growth presents a considerable scientific challenge. In addition to the dominant hypotheses relating pallid sturgeon populations to changes in flow regime and channel morphology, other factors have been identified that might be sources of stress and contribute to recruitment failure. Among these are water quality and contaminants. Ambient water-quality monitoring on the Missouri River has demonstrated summer episodes when dissolved oxygen dips below 5 milligrams per liter, a threshold that may be stressful especially to age-0 and juvenile sturgeon. Documented cases of intersex in shovelnose and pallid sturgeon indicate that agricultural and municipal sources of endocrine disrupting chemicals also may have a role in pallid sturgeon recruitment failure. Scientific understanding of the ecological requirements of pallid sturgeon has increased almost exponentially in the last two decades, and efforts are now turning from understanding fundamental biology of the species to quantifying how population dynamics relate to potential management actions. Progress in developing the science needed to inform management actions on the Missouri River may benefit from continuation of monitoring of reproductive cycles, reproductive movements, growth, and survival of telemetry tagged adults, increased emphasis on focused, complementary field and laboratory studies of factors influencing early life history, implementation of studies to resolve the role of food limitations in growth, survival, and reproductive condition, and implementation of studies designed specifically to parameterize models linking management to populations.

Missouri River↗
USGS2015

Global trends in emerging viral diseases of wildlife origin

Fifty years ago, infectious diseases were rarely considered threats to wildlife populations, and the study of wildlife diseases was largely a neglected endeavor. Furthermore, public health leaders at that time had declared that “it is time to close the book on infectious diseases and the war against pestilence won,” a quote attributed to Dr. William H. Stewart in 1967. There is some debate whether he actually said these words; however, they reflect the widespread belief at that time (Spellberg, 2008). Leap forward to today, and the book on infectious diseases has been dusted off. There is general consensus that the global environment favors the emergence of infectious diseases, and in particular, diseases of wildlife origin (Taylor et al., 2001). Examples of drivers of these infectious diseases include climate and landscape changes, human demographic and behavior changes, global travel and trade, microbial adaptation, and lack of appropriate infrastructure for wildlife disease control and prevention (Daszak et al., 2001). The consequences of these emerging diseases are global and profound with increased burden on the public health system, negative impacts on the global economy and food security, declines and extinctions of wildlife species, and subsequent loss of ecosystem integrity. For example, 35 million people are currently living with HIV infection globally (http://www.who.int/gho/hiv/en); 400 million poultry have been culled since 2003 as a result of efforts to control highly pathogenic H5N1 avian influenza (http://www.fao.org/avianflu/en/index.html), and there are increasing biological and ecological consequences. Examples of health threats to biodiversity include the “spillover” of human diseases to great ape populations (Köndgen et al., 2008), the near-extirpation of the black-footed ferret from canine distemper and sylvatic plague (for a review see Abbott et al., 2012), and threats to Hawaiian forest birds from introduced pathogens such as avian malaria and avian pox (van Riper et al., 1986, 2002). There are also newly discovered pathogens or diseases that have resulted in population declines, and global extinctions of several species. Examples include Batrachochytrium dendrobatidis, which causes a cutaneous fungal infection of amphibians and is linked to declines of amphibians globally (Kriger and Hero, 2009); and recently discovered Pseudogymnoascus (Geomyces) destructans, the etiologic agent of white-nose syndrome (WNS), which has caused precipitous declines of North American bat species (Blehert et al., 2009). Furthermore, there is increasing evidence of the subsequent impacts on human and ecosystem health; for example, increasing risk of exposure to Lyme disease as a consequence of decreased biodiversity (LoGiudice et al., 2003) as well as the economic cost of the loss of bats due to decreased insect control services (Boyles et al., 2011). Figure A12-1 is a timeline of important diseases investigated by the U.S. Geological Survey since the 1970s, which illustrates three factors: 1. The unprecedented emergence of new pathogens and geographic spread of known pathogens since the 1990s; 2. Diseases are increasingly causing large-scale, negative impacts on wildlife populations and spreading over larger geographic areas rather than remaining localized; and 3. Diseases are increasingly of concern for multiple sectors, including public health, agriculture and wildlife management agencies. Of increasing concern are these novel diseases such as WNS as they are hard to anticipate, particularly devastating to human health or wildlife populations, challenging to manage, spread over large geographic areas in short time periods, and may result in ecological ripple effects that are difficult to predict. The following article provides examples of recently emerged viral diseases of wildlife origin. The examples have been selected to illustrate the drivers of emerging viral diseases, both novel pathogens and previously known diseases, the impacts of these diseases, as well as the role of wildlife both as “villains” or reservoirs as well as “victims” of these viral diseases. The article also discusses potential management strategies for emerging viral diseases in wildlife populations and future science directions in wildlife health to prevent, prepare, respond to, and recover from these disease events. Finally, the concept of One Health and its potential role in developing solutions to these issues of mutual concern is discussed.

Conference Paper↗
USGS2019

Environmental DNA sampling reveals high occupancy rates of invasive Burmese pythons at wading bird breeding aggregations in the central Everglades

The Burmese python ( Python bivittatus ) is now established as a breeding population throughout south Florida, USA. However, the extent of the invasion, and the ecological impacts of this novel apex predator on animal communities are incompletely known, in large part because Burmese pythons (hereafter “pythons”) are extremely cryptic and there has been no efficient way to detect them. Pythons are recently confirmed nest predators of long-legged wading bird breeding colonies (orders Ciconiiformes and Pelecaniformes). Pythons can consume large quantities of prey and may not be recognized as predators by wading birds, therefore they could be a particular threat to colonies. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water samples and provides high detection probabilities. We fitted multi-scale Bayesian occupancy models to test the prediction that pythons occupy islands with wading bird colonies at higher rates compared to representative control islands containing no breeding birds. Our results suggest that pythons are widely distributed across the central Everglades in proximity to active wading bird colonies. In support of our prediction that pythons are attracted to colonies, site-level python eDNA occupancy rates were higher at wading bird colonies (ψ = 0.88, 95% credible interval [0.59–1.00]) than at the control islands (ψ = 0.42 [0.16–0.80]) in April through June (n = 15 colony-control pairs). We found our water temperature proxy (time of day) to be informative of detection probability, in accordance with other studies demonstrating an effect of temperature on eDNA degradation in occupied samples. Individual sample concentrations ranged from 0.26 to 38.29 copies/μL and we generally detected higher concentrations of python eDNA in colony sites. Continued monitoring of wading bird colonies is warranted to determine the effect pythons are having on populations and investigate putative management activities.

Florida↗
USGS2014

Evolutionary ecology of resprouting and seeding in fire-prone ecosystems

There are two broad mechanisms by which plant populations persist under recurrent disturbances: resprouting from surviving tissues, and seedling recruitment. Species can have one of these mechanisms or both. However, a coherent framework explaining the differential evolutionary pressures driving these regeneration mechanisms is lacking. We propose a bottom-up approach in addressing this question that considers the relative survivorship of adults and juveniles in an evolutionary context, based on two assumptions. First, resprouting and seeding can be interpreted by analogy with annual versus perennial life histories; that is, if we consider disturbance cycles to be analogous to annual cycles, then resprouting species are analogous to the perennial life history with iteroparous reproduction, and obligate seeding species that survive disturbances solely through seed banks are analogous to the annual life history with semelparous reproduction. Secondly, changes in the selective regimes differentially modify the survival rates of adults and juveniles and thus the relative costs and benefits of resprouting versus seeding. Our approach provides a framework for understanding temporal and spatial variation in resprouting and seeding under crown-fire regimes. It accounts for patterns of coexistence and environmental changes that contribute to the evolution of seeding from resprouting ancestors.

New Phytologist↗
USGS2000

Ecology and demographics of Pacific sand lance, Ammodytes hexapterus Pallas, in Lower Cook Inlet, Alaska

Distinct sand lance populations occur within the relatively small geographic area of Lower Cook Inlet, Alaska. Marked meso-scale differences in abundance, growth, and mortality exist as a consequence of differing oceanographic regimes. Growth rate within populations (between years) was positively correlated with temperature. However, this did not extend to inter-population comparisons where differing growth rates were better correlated to marine productivity. Most sand lance reached maturity in their second year. Field observations and indices of maturity, gonad development, and ova-size distribution all indicated that sand lance spawn once each year. Sand lance spawned intertidally in late September and October on fine gravel/sandy beaches. Embryos developed over 67 days through periods of intertidal exposure and sub-freezing air temperatures. Mean dry-weight energy value of sand lance cycles seasonally, peaking in spring and early summer (20.91 kJg -1 for males, 21.08 kJg -1 for females), and subsequently declining by about 25% during late summer and fall (15.91 kJg -1 for males, 15.74 kJg -1 for females). Sand lance enter the winter with close to their minimum whole body energy content. Dry weight energy densities of juveniles increased from a minimum 16.67 kJg -1 to a maximum of 19.68 kJg -1 and are higher than adults in late summer.

Alaska↗