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At least 19 recordsLinked to original sources

Open-source intelligence for conservation biology

Open-source intelligence (OSINT) evolved in spy agencies but now is rapidly changing many fields of study, from anthropology to zoology. Despite the fact that OSINT occasionally is used in conservation biology, there is little recognition that some tools and frameworks used by conservation professionals are drawn from this well-established field. The history and conceptual foundations of OSINT stem from the intelligence community, although OSINT tools are rapidly being applied in other fields. In conservation biology, OSINT is sometimes used to evaluate wildlife crime, human-wildlife and human-environment interactions, animal behavior, and questions of distribution and abundance. Recognizing the conceptual foundations of the field would allow expansion of conservation biology, not only in the areas noted above, but also, for example, in study of habitat use, habitat change, and animal behavior. This recognition would also provide frameworks for conceptual advancement, especially in terms of data and privacy management. Failure to recognize the underpinnings of OSINT tools in conservation biology harms the field because it limits how research is framed, thought about, and implemented. Likewise, taking an OSINT perspective to conservation problems, rather than simply thinking in terms of big data, can enrich the field, expand science, and increase knowledge and understanding of biology and biodiversity.

Conservation Biology

Clutch may predict growth of hatchling Burmese pythons better than food availability or sex

Identifying which environmental and genetic factors affect growth pattern phenotypes can help biologists predict how organisms distribute finite energy resources in response to varying environmental conditions and physiological states. This information may be useful for monitoring and managing populations of cryptic, endangered, and invasive species. Consequently, we assessed the effects of food availability, clutch, and sex on the growth of invasive Burmese pythons ( Python bivittatus Kuhl) from the Greater Everglades Ecosystem in Florida, USA. Though little is known from the wild, Burmese pythons have been physiological model organisms for decades, with most experimental research sourcing individuals from the pet trade. Here, we used 60 hatchlings collected as eggs from the nests of two wild pythons, assigned them to High or Low feeding treatments, and monitored growth and meal consumption for 12 weeks, a period when pythons are thought to grow very rapidly. None of the 30 hatchlings that were offered food prior to their fourth week post-hatching consumed it, presumably because they were relying on internal yolk stores. Although only two clutches were used in the experiment, we found that nearly all phenotypic variation was explained by clutch rather than feeding treatment or sex. Hatchlings from clutch 1 (C1) grew faster and were longer, heavier, in better body condition, ate more frequently, and were bolder than hatchlings from clutch 2 (C2), regardless of food availability. On average, C1 and C2 hatchling snout-vent length (SVL) and weight grew 0.15 cm d −1 and 0.10 cm d −1 , and 0.20 g d −1 and 0.03 g d −1 , respectively. Additional research may be warranted to determine whether these effects remain with larger clutch sample sizes and to identify the underlying mechanisms and fitness implications of this variation to help inform risk assessments and management.

Biology Open

Effects of exercise and bioprocessed soybean meal diets during rainbow trout rearing

Background: Alternative protein sources to fishmeal in fish feeds are needed. Objectives: Evaluate rearing performance of adult rainbow trout (Oncorhynchus mykiss) (initial weight 139.0 ±1.5 g, length 232.9 ± 0.8 mm, mean ± SE) fed one of the two isonitrogenous and isocaloric diets (46% protein, 16% lipid) and reared at one of the two levels of exercise (water velocities of either 3.6 cm/s or 33.2 cm/s). Methods: Protein in the control diet was based on fishmeal. In the experimental diet, bioprocessed soybean meal replaced approximately 60% of the fishmeal. Fish were fed by hand once-per-day to near satiation, and the food was increased daily. The experiment lasted 90-days. Results: There were no significant differences in gain, percent gain, or specific growth rate between the dietary treatments. However, the amount of food fed and feed conversion ratio was significantly lower in the 60% bioprocessed soybean meal diet. Intestinal morphology, relative fin length, splenosomatic index, hepatosomatic index, and viscerosomatic index were not significantly different in the trout fed either diet. Fish reared at 3.6 cm/s had a significantly lower feed conversion ratio (1.02 ± 0.02) than fish reared at 33.2 cm/s (1.13 ± 0.02). However, there were no significant differences in gain, percent gain, specific growth rate, or percentage mortality in fish reared with or without exercise. No significant interactions were observed between diet and exercise (higher water velocity). Conclusion:Based on these results, at least 60% of the fishmeal in adult rainbow trout diets can be replaced by bioprocessed soybean meal, even if higher water velocities are used to exercise the fish.

The Open Biology Journal

Seventy-five years of science—The U.S. Geological Survey’s Western Fisheries Research Center

As of January 2010, 75 years have elapsed since Dr. Frederic Fish initiated the pioneering research program that would evolve into today’s Western Fisheries Research Center (WFRC). Fish began his research working alone in the basement of the recently opened Fisheries Biological Laboratory on Lake Union in Seattle, Washington. WFRC’s research began under the aegis of the U.S. Fish and Wildlife Service and ends its first 75 years as part of the U.S. Geological Survey with a staff of more than 150 biologists and support personnel and a heritage of fundamental research that has made important contributions to our understanding of the biology and ecology of the economically important fish and fish populations of the Nation. Although the current staff may rarely stop to think about it, WFRC’s antecedents extend many years into the past and are intimately involved with the history of fisheries conservation in the Western United States. Thus, WFRC Director Lyman Thorsteinson asked me to write the story of this laboratory “while there are still a few of you around who were here for some of the earlier years” to document the rich history and culture of WFRC by recognizing its many famous scientists and their achievements. This historyalso would help document WFRC’s research ‘footprint’ in the Western United States and its strategic directions. Center Director Thorsteinson concluded that WFRC’s heritage told by an emeritus scientist also would add a texture of legitimacy based on personal knowledge that will all-to-soon be lost to the WFRC and to the USGS. The WFRC story is important for the future as well as for historical reasons. It describes how we got to the place we are today by documenting the origin, original mission, and our evolving role in response to the constantly changing technical information requirements of new environmental legislation and organizational decision-making. The WFRC research program owes its existence to the policy requirements of Federal conservation legislation originating with the construction of Grand Coulee Dam in 1933. The research program was shaped by laws enacted in subsequent years such as the Federal Water Pollution Control Act (1972), National Environmental Policy Act (1973), Endangered Species Act (1974), and Northwest Power Planning Act (1980), to name only a few. The WFRC has not been constrained by direct management or regulatory responsibility for a particular fishery (such as providing sustainable catch limits data to a resource management structure). Thus, WFRC has been able to concentrate on scientific pursuits and information needs required by contemporary environmental legislation. Over the years, we have pioneered in several important areas of fisheries research including the diagnoses and control of diseases in economically important fish, effects of environmental alterations on the physiological quality and survival of Pacific salmon released from federal mitigation hatcheries, applications in biotelemetry, and the bioenergetics of predator-prey interactions in the Columbia River. The WFRC of today is a widely distributed organization in the Western United States. Knowledge of the historical connections and accomplishments of our predecessors is important beyond the sense of pride and unity it instills in the WFRC family of today. For example, a discerning reader will note the evolution of WFRC’s research from a single disciplinary focus (early era—hatchery disease problems), to multiple disciplines (middle to late era—species, populations, habitats; threatened and endangered species), to the present era (multidisciplinary and with increasing process focus). For the benefit of the current WFRC staff, more emphasis has been placed on the early years rather than on the present day because people are quite naturally more familiar with the recent past than with the research done during the first decades of WFRC’s existence. By every rational measure, the WFRC has evolved into a fisheries research organization well positioned to provide the biological information needed to support the continued conservation and management of our Nation’s living aquatic natural resources. The high standard of excellence that connects WFRC’s past to our present research program provides a firm foundation on which to base the work yet to be done. In another 75 years, WFRC will undoubtedly be a very different place than it is today, but its evolution will be forever rooted in the story of the research and of the people related here. More about the diverse fisheries research projects WFRC scientists are conducting today is available at WFRC’s website: http://wfrc.usgs.gov/.

Washington

Chemical weathering of the Panola Granite: Solute and regolith elemental fluxes and the weathering rate of biotite

Present-day elemental and mineral weathering rates based on solute fluxes are compared quantitatively to past long-term rates determined from solid-state elemental fractionation in a saprolitic granite regolith at Panola, Georgia, USA. Saturated fluid flow across a low-permeability kaolin duripan controls the rate of steady-state unsaturated flow in the underlying saprolite. Water and Cl mass balances and experimental conductivities produce a minimum fluid flux density of 8x10 -2 m yr -1 and a fluid residence time of 12 years. Solute Si flux, based on pore water concentrations and infiltration rates, is 27 mmoles yr -1 , compared to a long-term flux rate of 17 mmoles yr -1 , based on regolith Si loss and reported 36 Cl dating of the regolith surface. Similarities in short- and long-term fluxes imply that parameters influencing silicate weathering, including precipitation, temperature, and vegetative cover, while not necessarily constant, have not significantly impacted Si leaching rates during the last several hundred thousand years. Linear decreases in solid-state Mg with decreasing regolith depth permit the calculation of the long-term biotite weathering rate under isovolumetric steady-state weathering conditions. A rate constant of 3x10 -17 moles m -2 s -1 is up to 5 orders of magnitude slower than that reported for experimental dissolution of biotite, implying very different reaction kinetics during natural weathering. Short-term biotite weathering fails to produce expected increases in solute Mg and K concentrations with increasing depth and fluid residence times in the regolith. This discrepancy indicates that ion exchange disequilibrium and open-system biologic uptake in an aggrading forest ecosystem are of sufficient magnitudes to overwhelm solute fluxes resulting from biotite weathering.

Georgia

Variability of hydrologic regimes and morphology in constructed open-ditch channels

Open-ditch ecosystems are potential transporters of considerable loads of nutrients, sediment, pathogens and pesticides from direct inflow from agricultural land to small streams and larger rivers. Our objective was to compare hydrology and channel morphology between two experimental open-ditch channels. An open-ditch research facility incorporating a paired design was constructed during 2002 near Lamberton, MN. A200-m reach of existing drainage channel was converted into a system of four parallel channels. The facility was equipped with water level control devices and instrumentation for flow monitoring and water sample collection on upstream and downstream ends of the system. Hydrographs from simulated flow during year one indicated that paired open-ditch channels responded similarly to changes in inflow. Variability in hydrologic response between open-ditches was attributed to differences in open-ditch channel bottom elevation and vegetation density. No chemical, biological, or atmospheric measurements were made during 2003. Potential future benefits of this research include improved biological diversity and integrity of open-ditch ecosystems, reduce flood peaks and increased flow during critical low-flow periods, improved and more efficient nitrogen retention within the open-ditch ecosystem, and decreased maintenance cost associated with reduced frequency of open-ditch maintenance.

Conference Paper

Changes in Selected Metals Concentrations from the Mid-1980s to the Mid-2000s in a Stream Draining the Picher Mining District of Oklahoma

After abandonment in the late 1960s, the Picher mining district of Oklahoma, once the largest source of lead and zinc in the world, continued to be affected by severe environmental degradation, with scattered subsidence and abundant toxic metals such as cadmium and lead seeping from flooded underground mine workings and seeping and running off from as much as 60 million tons of mine tailings remaining at the land surface. Water-quality data collected during the mid-1980s and the mid-2000s at the Tar Creek at 22nd Street Bridge in Miami, Oklahoma streamflow-gaging station (USGS number 07185095), located downstream from much of the district, indicate that total concentrations of iron, manganese, and zinc significantly decreased between the two sampling periods. Those water-quality improvements probably are due to a combination of reclamation activities and natural attenuation processes such as stabilization of exposed minerals in flooded underground mine workings, progressive wind and water erosion of the most readily erodible metalliferous particles from tailings, and colonization of volunteer plants that reduce physical erosion of soils and tailings.

Kansas, Missouri, Oklahoma

Open water dreissenid mussel control projects: Lessons learned from a retrospective analysis

Dreissenid mussels are one of the most problematic aquatic invasive species (AIS) in North America, causing substantial ecological and economic effects. To date, dreissenid mussel control efforts in open water have included physical, biological, and chemical methods. The feasibility of successful dreissenid mussel management or eradication in lakes is relatively undocumented in the freshwater management literature. This review presents information on 33 open water dreissenid mussel control projects in 23 North America lakes. We reviewed data from past dreissenid mussel control projects and identified patterns and knowledge gaps to help inform adaptive management strategies. The three key lessons learned include (1) pre- and post-treatment survey methods that are designed to meet management objectives are beneficial, e.g., by sampling for all life stages and taking into account that no survey method is completely comprehensive; (2) defining the treatment area—particularly ensuring it is sufficiently large to capture all life stages present—is critical to meeting management objectives; and (3) control projects provide an opportunity to collect water chemistry, effects on non-target organisms, and other efficacy-related data that can inform safe and effective adaptive management.

Scientific Reports

Spatial patterns in assemblage structures of pelagic forage fish and zooplankton in western Lake Superior

We assessed abundance, size, and species composition of forage fish and zooplankton communities of western Lake Superior during August 1996 and July 1997. Data were analyzed for three ecoregions (Duluth-Superior, Apostle Islands, and the open lake) differing in bathymetry and limnological and biological patterns. Zooplankton abundance was three times higher in the Duluth-Superior and Apostle Islands regions than in the open lake due to the large numbers of rotifers. Copepods were far more abundant than Cladocera in all ecoregions. Mean zooplankton size was larger in the open lake due to dominance by large calanoid copepods although size of individual taxa was similar among ecoregions. Forage fish abundance and biomass was highest in the Apostle Islands region and lowest in the open lake ecoregion. Lake herring ( Coregonus artedi ), rainbow smelt ( Osmerus mordax ) and deepwater ciscoes ( Coregonus spp.) comprised over 90% of the abundance and biomass of fishes caught in midwater trawls and recorded with hydroacoustics. Growth and condition of fish was good, suggesting they were not resource limited. Fish and zooplankton assemblages differed among the three ecoregions of western Lake Superior, due to a combination of physical and limnological factors related to bathymetry and landscape position.

Michigan, Minnesota, Wisconsin

Status of exotic grasses and grass-like vegetation and potential impacts on wildlife in New England

The Northeastern section of the United States, known as New England, has seen vast changes in land cover and human population over the past 3 centuries. Much of the region is forested; grasslands and other open-land cover types are less common, but provide habitat for many species that are currently declining in abundance and distribution. New England also consists of some of the most densely populated and developed states in the country. The origin, distribution, and spread of exotic species are highly correlated with human development. As such, exotics are common throughout much of New England, including several species of graminoids (grasses and grass-like plants such as sedges and rushes). Several of the more invasive grass species can form expansive dense mats that exclude native plants, alter ecosystem structure and functions, and are perceived to provide little-to-no value as wildlife food or cover. Although little research has been conducted on direct impacts of exotic graminoids on wildlife populations in New England, several studies on the common reed ( Phragmites australis ) in salt marshes have shown this species to have variable effects as cover for birds and other wildlife, depending on the distribution of the plant (e.g., patches and borders of reeds are used more by wildlife than expansive densely growing stands). Direct impacts of other grasses on wildlife populations are largely unknown. However, many of the invasive graminoid species that are present in New England have the capability of outcompeting native plants and thereby potentially affecting associated fauna. Preservation, protection, and restoration of grassland and open-land cover types are complex but necessary challenges in the region to maintain biological and genetic diversity of grassland, wetland, and other open-land obligate species.

Wildlife Society Bulletin

Assessing the solubilities and reaction kinetics of aluminous minerals in soils

The use of chemical thermodynamics and reaction kinetics is necessary to quantitatively model the transformation of aluminous minerals and their dissolved constituents in soils and other geochemical systems. Soils are thermodynamically open systems subject to atmospheric and biological forces and do not attain overall thermodynamic equilibrium with respect to either mass or time. However, local or partial equilibrium conditions may persist for particular minerals and their dissolved constituents. Igneous and metamorphic primary minerals break down chemically to yield disordered gels or colloids and constituent ions, which can then reorganize or precipitate to form more stable hydrous oxides, silicates, carbonates or other mineral species. Naturally-occurring iron and aluminum hydrous oxides and kaolin clays, abundant in highly weathered soils, are commonly believed to be the ultimate, stable end products of weathering reactions, but usually are thermodynamically metastable with respect to more perfectly ordered, synthetic specimens. Thermodynamic stability is no guaranty of mineral persistence; with sufficient time, even the most perfectly crystallized, stable mineral will yield to the solubilizing assault of undersaturated surface waters. All of the dissolution and precipitation reactions of soil minerals are driven by energy differences in the thermodynamic stabilities of reactants and products, and the velocities (or kinetics) of such reactions are regulated by variables of the hydrogeochemical environment.

Book chapter

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Nature Reviews Genetics

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

Biologists and environmental scientists now routinely solve computational problems that were unimaginable a generation ago. Examples include processing geospatial data, analyzing -omics data, and running large-scale simulations. Conventional desktop computing cannot handle these tasks when they are large, and high-performance computing is not always available nor the most appropriate solution for all computationally intense problems. High-throughput computing (HTC) is one method for handling computationally intense research. In contrast to high-performance computing, which uses a single "supercomputer," HTC can distribute tasks over many computers (e.g., idle desktop computers, dedicated servers, or cloud-based resources). HTC facilities exist at many academic and government institutes and are relatively easy to create from commodity hardware. Additionally, consortia such as Open Science Grid facilitate HTC, and commercial entities sell cloud-based solutions for researchers who lack HTC at their institution. We provide an introduction to HTC for biologists and environmental scientists. Our examples from biology and the environmental sciences use HTCondor, an open source HTC system.

PLOS Computational Biology

Nutritional content of phytoplankton communities under ice

The effects of winter environmental conditions on lake ecology can be highly variable. Ice and overlying snow isolate the water below, impeding exchange of materials among water, atmosphere, and the watershed. Even with these limitations, biological communities under the ice can persist, where cold tolerant taxa can be especially abundant. Because many under-ice taxa tend to have a suite of unsaturated lipids that enable them to maintain metabolic function during cold conditions, under-ice biological communities may contain highly nutritious resources for higher level consumers relative to warmer, open-water conditions. To examine the effects of ice presence on under-ice biological productivity and nutritional quality, we aggregated data on under-ice physical, chemical, and biological variables from several existing databases. These data are among the most comprehensive, publicly available environmental and phytoplankton data that can be used to compare under-ice and open-water conditions at the community level. To understand how phytoplankton compositional shifts under ice can precipitate shifts in total algal nutritional content available to consumers relative to open water conditions, we merged characteristic phytoplankton fatty acid profiles with phytoplankton community composition data. Our results suggest that even though photosynthetically active radiation under ice is dramatically reduced by snow cover and opaque ice conditions, algal communities can be highly productive. Furthermore, these under-ice communities tend to be dominated by coldwater taxa, which are associated with elevated essential polyunsaturated fatty acids and reduced saturated fatty acids. Saturated fatty acids tend to be most associated with phytoplankton communities in the summer when cyanobacteria are prevalent, while winter communities tend to be most associated with high polyunsaturated fatty acids. As ice duration and quality continue to shift with increasing temperatures worldwide, phytoplankton assemblages are likely to exhibit altered nutritional profiles that have direct and indirect effects on food webs.

Ecopshere

Testing for multiple invasion routes and source populations for the invasive brown treesnake ( Boiga irregularis ) on Guam: implications for pest management

The brown treesnake ( Boiga irregularis ) population on the Pacific island of Guam has reached iconic status as one of the most destructive invasive species of modern times, yet no published works have used genetic data to identify a source population. We used DNA sequence data from multiple genetic markers and coalescent-based phylogenetic methods to place the Guam population within the broader phylogeographic context of B. irregularis across its native range and tested whether patterns of genetic variation on the island are consistent with one or multiple introductions from different source populations. We also modeled a series of demographic scenarios that differed in the effective size and duration of a population bottleneck immediately following the invasion on Guam, and measured the fit of these simulations to the observed data using approximate Bayesian computation. Our results exclude the possibility of serial introductions from different source populations, and instead verify a single origin from the Admiralty Archipelago off the north coast of Papua New Guinea. This finding is consistent with the hypothesis that B. irregularis was accidentally transported to Guam during military relocation efforts at the end of World War II. Demographic model comparisons suggest that multiple snakes were transported to Guam from the source locality, but that fewer than 10 individuals could be responsible for establishing the population. Our results also provide evidence that low genetic diversity stemming from the founder event has not been a hindrance to the ecological success of B. irregularis on Guam, and at the same time offers a unique ‘genetic opening’ to manage snake density using classical biological approaches.

Biological Invasions

Sonoran Desert: Fragile Land of Extremes

'Sonoran Desert: Fragile Land of Extremes' shows how biologists with the U.S. Geological Survey work with other scientists in an effort to better understand native plants and animals such as desert tortoises, saguaro cacti, and Gila monsters. Much of the program was shot in and around Saguaro National Park near Tucson, Arizona. Genetic detective work, using DNA, focuses on understanding the lives of tortoises. Studies of saguaros over many decades clarify how these amazing plants reproduce and thrive in the desert. Threats from fire, diseases in tortoises, and a growing human population motivate the scientists. Their work to identify how these organisms live and survive is a crucial step for the sound management of biological resources on public lands. This 28-minute program, USGS Open-File Report 03-305, was shot entirely in high definition video and produced by the USGS Western Ecological Research Center and Southwest Biological Science Center; produced and directed by Stephen Wessells, Western Region Office of Communications.

Open-File Report

U.S. Geological Survey applied research studies of the Cheyenne River System, South Dakota; description and collation of data, water years 1987-88

The Cheyenne River System in western South Dakota has been impacted by the discharge of about 100 million metric tons of gold-mill tailings to Whitewood Creek near Lead, South Dakota. In April 1985, the U.S. Geological Survey initiated an extensive series of research studies to investigate the magnitude of the impact and to define important processes acting on the contaminated sediments present in the system. The report presents all data collected during the 1987 and 1988 water years for these research studies. Some of the data included have been published previously. Data collected in the 1985 and 1986 water years have been published in a companion report (U.S. Geological Survey Open-File Report 88-484). Hydrologic, geochemical, and biologic data are available for sites on Whitewood Creek, and the Belle Fourche and Cheyenne Rivers. Data complexity varies from routine discharge and water-quality to very complex energy-dispersive x-ray analysis. Methods for sample collection, handling and preservation, and laboratory analysis are also presented. No interpretations or complex statistical summaries are included. (See also W89-08390) (USGS)

Open-File Report

Biome-scale spatial patterns of avian abundance reveal proactive conservation opportunities in North American grasslands

North American grassland birds have experienced steeper population declines than any other avian guild, yet conservation efforts remain largely reactive and fragmented. We used nearly four decades of North American Breeding Bird Survey data to identify biome-scale spatial patterns (clustering) of grassland bird abundance for the Great Plains. Our results reveal an ecological core in the north-central Plains where community-level abundance is either increasing by >100% or remains high and stable, providing a strategic roadmap for a “Defend the Core” conservation approach. This approach flips the script from reactive triage centered on isolated population fragments to a proactive strategy of maintaining large-scale ecosystem integrity. Conversely, we found that population losses are more spatially clustered than wins, reflecting the relentless, one-way movement of woody encroachment and agricultural conversion. This asymmetry supports prioritizing intact landscapes, as current restoration rates are often outpaced by the scale of habitat loss. Notably, we found that community-level spatial clustering is a more robust indicator of biome condition than trends of individual flagship species, suggesting that managing for ecosystem integrity provides a more effective multi-species umbrella. Given our results, there is an opportunity for operationalizing a Great Plains Conservation Design that is ecosystem-centric and rooted in the sustainability of the private-land cattle production that maintains these open spaces. By leveraging avian abundance as a biological sensor, managers and producers can deploy a shared vision that matches the spatial scale of the threats, moving from reactive triage to proactive defense of core working grasslands in North America.

Great Plains biome