Geology ReportsSearch

SEARCH · Geology Reports

Results for “Biologist”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

Science, conservation, and camera traps

Biologists commonly perceive camera traps as a new tool that enables them to enter the hitherto secret world of wild animals. Camera traps are being used in a wide range of studies dealing with animal ecology, behavior, and conservation. Our intention in this volume is not to simply present the various uses of camera traps, but to focus on their use in the conduct of science and conservation. In this chapter, we provide an overview of these two broad classes of endeavor and sketch the manner in which camera traps are likely to be able to contribute to them. Our main point here is that neither photographs of individual animals, nor detection history data, nor parameter estimates generated from detection histories are the ultimate objective of a camera trap study directed at either science or management. Instead, the ultimate objectives are best viewed as either gaining an understanding of how ecological systems work (science) or trying to make wise decisions that move systems from less desirable to more desirable states (conservation, management). Therefore, we briefly describe here basic approaches to science and management, emphasizing the role of field data and associated analyses in these processes. We provide examples of ways in which camera trap data can inform science and management.

Book chapter

Estimation of demographic parameters in a tiger population from long-term camera trap data

Chapter 7 (Karanth et al.) illustrated the use of camera trapping in combination with closed population capture–recapture (CR) models to estimate densities of tigers Panthera tigris. Such estimates can be very useful for investigating variation across space for a particular species (e.g., Karanth et al. 2004) or variation among species at a specific location. In addition, estimates of density continued at the same site(s) over multiple years are very useful for understanding and managing populations of large carnivores. Such multi-year studies can yield estimates of rates of change in abundance. Additionally, because the fates of marked individuals are tracked through time, biologists can delve deeper into factors driving changes in abundance such as rates of survival, recruitment and movement (Williams et al. 2002). Fortunately, modern CR approaches permit the modeling of populations that change between sampling occasions as a result of births, deaths, immigration and emigration (Pollock et al. 1990; Nichols 1992). Some of these early “open population” models focused on estimation of survival rates and, to a lesser extent, abundance, but more recent models permit estimation of recruitment and movement rates as well.

Book chapter

Identification of tire leachate toxicants and a risk assessment of water quality effects using tire reefs in canals

Cover is an important component of aquatic habitat and fisheries management. Fisheries biologists often try to improve habitats through the addition of natural and artificial material to improve cover diversity and complexity. Habitat-improvement programs range from submerging used Christmas trees to more complex programs using sophisticated artificial habitat modules. Used automobile tires have been employed in the large scale construction of reefs and fish attractors in marine environments (D'Itri 1985) and to a lesser extent in freshwater (Johnson and Stein 1979) and have been recognized as a durable, inexpensive and long-lasting material which benefits fishery communities. Recent studies by the U.S. Bureau of Reclamation (Mueller and Liston 1991) have quantified the importance of tire reeds to enhancing freshwater canal fisheries in the southwestern United States. These studies have demonstrated that fisheries and aquatic macroinvertebrates are attracted to these structures, increasing species diversity, densities and biomass where reefs are places in canals. Potential benefits to fishermen are great in the form of recreational fishing. However, the use of tire reefs in aquatic environments which have relatively small volumes compared to marine or reservoir environments has raised water quality concerns. Effects of tires on water quality have not typically been studied in the part because of the obvious presence of fishes and other aquatic organisms that make use of tire reefs; the implication being that tires are intert and non-toxic. Little information on effects of tires on water quality is contained in the literature. Stone et al. (1975) demonstrated that tire exposure had no detrimental effects on two species of marine fish while results of Kellough's (1991) freshwater tests were inconclusive, but suggested that some factor in tire leachate was toxic to rainbow trout ( Oncorhynchus mykiss ). Nozaka et al. (1973) found no harmful substances leached from tire material soaked in fresh water. Because there are few data on toxicity associated with tires, this became the focus of our study. Toxicity Identification Evaluation (TUE) procedures developed by the EPA (1991) were used to evaluate water quality impacted by tires.

Bulletin of Environmental Contamination and Toxico

Latitude and daily-weather effects on gobbling activity of wild turkeys in Mississippi

Weather has been recognized as a density independent factor influencing the abundance, distribution, and behavior of vertebrates. Male wild turkeys’ ( Meleagris gallopavo ) breeding behavior includes vocalizations and courtship displays to attract females, the phenology of which can vary with latitude. State biologists design spring turkey-hunting season frameworks centered on annual vocalization patterns to maximize hunter engagement. The Mississippi Department of Wildlife, Fisheries, and Parks has traditionally instituted a statewide, 7-week, spring harvest season. However, hunters routinely argue that different peaks in gobbling activity across the state exist. The objective of this study was to determine whether differences in peak gobbling activity existed across a latitudinal gradient of Mississippi and assess the effect of weather on gobbling. During 2008 and 2009, we conducted a statewide gobbling survey. We used generalized additive mixed models to describe the probability and frequency of gobbling activity within northern and southern regions of the state. We also investigated the effect of daily weather conditions on gobbling activity. Our results revealed an approximate 10–14-day difference in peak gobbling activity between southern and northern Mississippi. The majority of all gobbling activity occurred within the current spring harvest framework. Perhaps more importantly, gobbling activity was more prevalent on days of regionally dry conditions (i.e., less humid) according to the Spatial Synoptic Classification. Our results provide information on gobbling activity phenology relative to hunting-season dates and weather-response information. Our approach may be particularly applicable in states with relatively shorter seasons or highly variable daily weather conditions that moderate gobbling frequency.

Mississippi

Colonization of southern flying squirrels (Glaucomys volans) to urban Nebraska: Range expansion or human assisted translocation?

Southern flying squirrels ( Glaucomys volans; Linnaeus 1758) were first observed in Lincoln, Nebraska, in 2018, 80 km north of their described range. Given that southern flying squirrels are a species of concern within Nebraska, determining the origin of this new population (natural expansion or pet-trade) garnered interest from state biologists. Further, the recent colonization of Lincoln by southern flying squirrels presents a unique opportunity to investigate the genetic implications of a founding event on a small arboreal mammal. The Lincoln population had genetic characteristics suggestive of a single-event colonization with fewer rare alleles and lower genetic diversity than potential source populations and a high genetic variation between populations. Sample size and absence of other geographically close populations in our data set make it difficult to ascertain the origin of the Lincoln population. Based on shared co-ancestry and membership assignment clustering algorithms, the Lincoln population had greater genetic associations with an individual sampled from the native south-eastern Nebraska population relative to other studied locations, suggesting that Lincoln was colonized by a native population.

Nebraska

Effects of biotic and abiotic factors on the distribution of trout and salmon along a longitudinal stream gradient

We examined the influence of biotic and abiotic factors on the distribution, abundance, and condition of salmonid fishes along a stream gradient. We observed a longitudinal change in fish distribution with native cutthroat trout, Oncorhynchus clarki utah, and introduced brown trout, Salmo trutta, demonstrating a distinct pattern of allopatry. Cutthroat trout dominated high elevation reaches, while reaches at lower elevations were dominated by brown trout. A transition zone between these populations was associated with lower total trout abundance, consistent changes in temperature and discharge, and differences in dietary preference. Variation in cutthroat trout abundance was best explained by a model including the abundance of brown trout and diel temperature, whereas variation in brown trout abundance was best explained by a model including the abundance of cutthroat trout and discharge. These results suggest the potential for condition-mediated competition between the two species. The results from our study can aid biologists in prioritizing conservation activities and in developing robust management strategies for cutthroat trout. ?? Springer 2005.

Environmental Biology of Fishes

Inference for finite-sample trajectories in dynamic multi-state site-occupancy models using hidden Markov model smoothing

Ecologists and wildlife biologists increasingly use latent variable models to study patterns of species occurrence when detection is imperfect. These models have recently been generalized to accommodate both a more expansive description of state than simple presence or absence, and Markovian dynamics in the latent state over successive sampling seasons. In this paper, we write these multi-season, multi-state models as hidden Markov models to find both maximum likelihood estimates of model parameters and finite-sample estimators of the trajectory of the latent state over time. These estimators are especially useful for characterizing population trends in species of conservation concern. We also develop parametric bootstrap procedures that allow formal inference about latent trend. We examine model behavior through simulation, and we apply the model to data from the North American Amphibian Monitoring Program.

Environmental and Ecological Statistics

Range-wide ecology, conservation, and research needs for yellow lampmussel (Lampsilis cariosa)

The freshwater mussel yellow lampmussel ( Lampsilis cariosa ) is declining throughout its range along the Atlantic Slope of the eastern United States and Canada, and the species is a target for proactive conservation to avoid federal listing. This paper synthesizes information about the ecology (physiology and life history, host fishes, and habitat), species distribution, genetics, and threats to L. cariosa . Identified threats include climate change, habitat alteration, and invasive species, dependent on location. We outline 16 emergent research and conservation management needs based on literature review and discussion with stakeholders (state and federal mussel biologists, researchers, and tribal groups). These needs range from research on the basic physiology and behavior of the species, to creating standardized protocols for surveys and DNA sampling, to ultimately developing a range-wide species conservation and restoration plan. Addressing these information gaps and incorporating the findings into future management may facilitate the implementation and success of large-scale restoration and conservation initiatives such as habitat protection and reintroduction of L. cariosa to historical locations.

Hydrobiologia

Hierarchical patch delineation in fragmented landscapes

Purpose We developed a tool, FragPatch (FP), to delineate habitat patches for highly fragmented landscapes from a user-defined suitability map and two landscape perception values for a species of interest. Methods We wrote a Python script in ArcGIS to delineate habitat patch networks using the user inputs and ArcGIS tools such as Euclidean distance, focal maximum, and reclassify. We validated the tool from mapped locations of urban deer and classified imagery for Syracuse, New York, USA. Results FP successfully delineated salient patch networks and functional connectivity for white-tailed deer ( Odocoileus virginianus borealis ) in our fragmented study area, and complements a similar tool, PatchMorph (PM), developed for rural landscape with more uniform land cover. Conclusions A trade-off exists when choosing to use FP or PM and the decision must rely upon a well-defined research question. FP is better suited for isolating patches of habitat when the surrounding matrix is of low quality and suitable areas are highly scattered on the landscape. PM is able to identify patches when the matrix is more uniform, and is better at identifying broader scale connectivity than FP. We expect species biologists and urban landscape planners to use FP to better define patch networks and to understand the implications of fragmentation on a range of species population concerns, including conflicts with human uses.

Landscape Ecology

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

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

Landscape Ecology

The ten steps to responsible Inland fisheries in practice: Reflections from diverse regional case studies around the globe

Inland fisheries make substantial contributions to food security and livelihoods locally, regionally, and globally but their conservation and management have been largely overlooked by policy makers. In an effort to remedy this limited recognition, a cross-sectoral community of scientists, practitioners, and policy makers from around the world convened a high-level meeting in 2015 at the Food and Agriculture Organization of the United Nations headquarters in Rome, Italy to develop recommendations for sustainable inland fisheries management. This meeting resulted in the production of the Rome Declaration, outlining ten key steps needed to achieve responsible inland fisheries. When the Ten Steps were conceived, they were framed in a global context because inland fisheries around the world face similar challenges, and it was hoped that these large-scale and ambitious steps would draw the attention of regional or international bodies for greater investment in their proper management. Most inland fisheries, however, are managed at a local (often community, watershed, or waterbody) scale with the “on-the-ground” practitioners, managers, assessment biologists, and stewardship officers responsible for achieving the promise of the Ten Steps. Here, we reflect on the relevance of the Ten Steps to practitioners using six regional case studies from around the globe (North America, South America, Europe, Asia, Australia, and Africa) to identify the extent to which existing efforts align with the Ten Steps and where there are opportunities to do more. Learning what is effective from local/regional actions should better inform a more global “action plan” and provide tangible guidance for implementation recognizing that global guidance needs to be informed by and acted upon by local practitioners. We conclude by considering the common challenges, synergies, and other emergent properties that arise from these case studies, and use these as a path forward to advancing responsible management of inland fisheries through the Rome Declaration. Of particular importance is the need to balance the high-level aspirational goals of the Ten Steps with the local cultural, socio-economic, and institutional realities that ultimately influence how humans interact with fisheries resources and aquatic ecosystems. This assessment provides valuable information on how to refine and implement the Ten Steps recognizing that success will require coordinated efforts among on-the-ground practitioners, scientists, stakeholders, rightsholders and international decision makers.

Reviews in Fish Biology and Fisheries

Presence of indicator plant species as a predictor of wetland vegetation integrity

We fit regression and classification tree models to vegetation data collected from Ohio (USA) wetlands to determine (1) which species best predict Ohio vegetation index of biotic integrity (OVIBI) score and (2) which species best predict high-quality wetlands (OVIBI score >75). The simplest regression tree model predicted OVIBI score based on the occurrence of three plant species: skunk-cabbage (Symplocarpus foetidus), cinnamon fern (Osmunda cinnamomea), and swamp rose (Rosa palustris). The lowest OVIBI scores were best predicted by the absence of the selected plant species rather than by the presence of other species. The simplest classification tree model predicted high-quality wetlands based on the occurrence of two plant species: skunk-cabbage and marsh-fern (Thelypteris palustris). The overall misclassification rate from this tree was 13 %. Again, low-quality wetlands were better predicted than high-quality wetlands by the absence of selected species rather than the presence of other species using the classification tree model. Our results suggest that a species’ wetland status classification and coefficient of conservatism are of little use in predicting wetland quality. A simple, statistically derived species checklist such as the one created in this study could be used by field biologists to quickly and efficiently identify wetland sites likely to be regulated as high-quality, and requiring more intensive field assessments. Alternatively, it can be used for advanced determinations of low-quality wetlands. Agencies can save considerable money by screening wetlands for the presence/absence of such “indicator” species before issuing permits.

Ohio

Heightened exposure to parasites favors the evolution of immunity in brood parasitic cowbirds

Immunologists and evolutionary biologists are interested in how the immune system evolves to fit an ecological niche. We studied the relationship between exposure to parasites and strength of immunity by investigating the response of two species of New World cowbirds (genus Molothrus , Icteridae), obligate brood parasites with contrasting life history strategies, to experimental arboviral infection. The South American shiny cowbird ( M. bonariensis ) is an extreme host - generalist that lays its eggs in the nests of >225 different avian species. The Central American bronzed cowbird ( M. aeneus ) is a relative host - specialist that lays its eggs preferentially in the nests of approximately 12 orioles in a single sister genus. West Nile virus provided a strong challenge and delineated immune differences between these species. The extreme host-generalist shiny cowbird, like the North American host-generalist, the brown-headed cowbird, showed significantly lower viremia to three arboviruses than related icterid species that were not brood parasites. The bronzed cowbird showed intermediate viremia. These findings support the interpretation that repeated exposure to a high diversity of parasites favors the evolution of enhanced immunity in brood parasitic cowbirds and makes them useful models for future studies of innate immunity.

Evolutionary Biology

Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection

We characterized variation within the mitochondrial genomes of the invasive silver carp ( Hypophthalmichthys molitrix ) and bighead carp ( H. nobilis ) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis . The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.

Conservation Genetics Resources

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

Disappearance of the cascades frog Rana cascadae at the southern end of its range, California, USA

It has recently become evident that amphibian species in many areas of the world have suffered serious declines. Healthy, seemingly well-protected populations have disappeared for no obvious reason. Data from historic accounts and museum records indicate that the Cascades frog, Rana cascadae , was once abundant at the southern end of its range in the vicinity of Lassen Volcanic National Park, California, USA. We conducted intensive searches at all 16 sites where R. cascadae had previously been recorded in the Lassen area, plus 34 additional sites with suitable habitat. Whereas earlier biologists could sometimes find 40 or more frogs at some of these sites, we were only able to locate two frogs at a single locality. This represents a precipitous decline over a period of <15 years. The decline seems to have been caused by a combination of local factors, including (1) the presence of non-native, predatory fish which have restricted habitat and limited dispersal of frogs; (2) loss of breeding habitat due to a five-year drought; and (3) the gradual loss of open meadows and associated aquatic habitats. The loss of frogs suggests that some common management practices in parks and wilderness areas may be endangering some of the species these areas are intended to protect. Similar local factors may account for amphibian declines reported elsewhere and should be carefully evaluated along with possible global effects.

California

Rivers and streams: Physical setting and adapted biota

Streams and rivers are enormously important, with their ecological, and economic value, greatly outweighing their significance on the landscape. Lotic ecology began in Europe with a focus on the distribution, abundance, and taxonomic composition of aquatic organisms and in North American with a focus on fishery biology. Since 1980, stream/river research has been highly interdisciplinary, involving fishery biologists, aquatic entomologists, algologists, hydrologists, geomorphologists, microbiologists, and terrestrial plant ecologists. Stream and river biota evolved in response to, and in concert with, the physical and chemical setting. Streams/rivers transport water and move sediments to the sea as part of the hydrologic cycle that involves evaporation, plant evapotranspiration, and precipitation. Ephemeral streams flow only in the wettest year, intermittent streams flow predictably every year during capture of surface runoff, and perennial streams flow continuously during wet and dry periods, receiving both stormflow and groundwater baseflow. The lotic biota, for example, algae, macrophytes, benthic invertebrates, and fishes, have evolved adaptations to their running-water setting. Dominant physical features of this setting are current, substrate, and temperature. Key chemical constituents are dissolved gases, dissolved inorganic ions and compounds, particulate inorganic material, particulate organic material, and dissolved organic ions (nitrogen and phosphorus) and compounds.

Book chapter

Waterfowl communities in the northern plains: Chapter 13

Features that determine the composition of avian communities have received extensive and enthusiastic attention, both empirically and theoretically (e.g., Cody 1974; Strong et al. 1984; Wiens, 1989a,b). Interspecific competition for limited resources is one influence widely regarded as critical, but others include species-specific responses to environmental conditions, predation, parasitism, commensal and mutualistic interactions, disturbance and chance, and historical events (Wiens, 1989b). Despite the attention they have received, the relative importance of the different features remains highly controversial. Certainly the community of birds present in an area will be but a subset of the total population of each constituent species; thus, the total population size of each species is a potential influence on local communities. Since many bird communities in the temperate zone are reconstituted annually with migrants, the geographical location of a site within the breeding range is an important feature; clearly, an avian community outside the normal breeding range of a particular species is unlikely to include that species, irrespective of the suitability of vegetation and other habitat features. Further, suitable habitat encountered earlier in spring migration is more likely to be occupied than is habitat encountered later. And the breeding ranges of birds are known to shift from year to year, depending on climatic conditions, a phenomenon that represents a modification of the general breeding range at a finer scale of resolution. The return of migrant birds to areas from which they fledged or where they previously bred modifies the occupancy of a particular habitat (HildTn 1964); likewise, traditional use of breeding sites by birds can induce species to persist in unsuitable habitat (Wiens 1985). Thus site fidelity can weaken the relationship between habitat quality and number of birds on an area (Wiens 1985). Waterfowl have received less attention from community ecologists than have many other groups of birds despite the importance attributed to waterfowl by biologists more generally, as well as by the public. Exceptions include work by Nudds and colleagues in Canada and by P?ysS and colleagues in Finland (see Nudds 1992 and references contained therein). Further, waterfowl are important ecologically; in much of the prairie of the North American midcontinent, waterfowl are numerically among the most common bird species and are certainly dominant in terms of biomass. This chapter addresses some influences on waterfowl communities in mixed-grass prairie pothole habitat. It takes a temporal perspective, based on annual censuses of breeding ducks for 25 years on a specific study area at Woodworth, North Dakota. Any changes in the structural features of the habitat that may have occurred during this period at the census site were at most gradual. I examine how the waterfowl communities varied in response to influences that did change annually, such as climate, conditions of the wetlands on the study area, the regional populations of birds from which the communities were constituted, and the population at Woodworth during the previous year. The results of the analyses are interpreted relative to individual characteristics of 11 waterfowl species: Mallard ( Anas platyrhynchos ), Gadwall ( Anas strepera ), Green-winged Teal ( Anas crecca ), Blue-winged Teal ( Anas discors ), Northern Pintail ( Anas acuta ), Northern Shoveler ( Anas clypeata ), American Wigeon ( Anas americana ), Canvasback ( Aythya valisineria ), Redhead ( Aythya americana ), Lesser Scaup ( Aythya affinis ), and Ruddy Duck ( Oxyura jamaicensis ).

Book chapter