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Information technology challenges of biodiversity and ecosystems informatics
Computer scientists, biologists, and natural resource managers recently met to examine the prospects for advancing computer science and information technology research by focusing on the complex and often-unique challenges found in the biodiversity and ecosystem domain. The workshop and its final report reveal that the biodiversity and ecosystem sciences are fundamentally information sciences and often address problems having distinctive attributes of scale and socio-technical complexity. The paper provides an overview of the emerging field of biodiversity and ecosystem informatics and demonstrates how the demands of biodiversity and ecosystem research can advance our understanding and use of information technologies.
Selected contributions to ground-water hydrology by C.V. Theis, and a review of his life and work
This publication highlights two previously unpublished papers by C.V. Theis; each is augmented with a discussion that explains why he wrote the paper, attempts to discern why he did not publish the paper, and amplifies the information with reference material not included by Theis. 'A Primer on Anisotropy' was written in the early 1970's to provide practicing hydrogeologists of the day with a method of analyzing ground-water problems involving anisotropic hydraulic-conductivity distribution without using tensor mathematics. The equations were developed for horizontal flow through dipping beds with differing conductivities parallel and perpendicular to the bedding and for flow through dipping beds having three different hydraulic conductivities, one perpendicular to the bedding and two others parallel to the bedding, at an angle to the strike of the beds. Although most colleagues who reviewed the primer in the early 1970's encouraged its publication enthusiastically, at least one suggested the addition of some examples in which the method would be demonstrated. Handwritten notes from Theis' files indicate that he may have worked on some examples and possibly other additions to the paper. The comments by Charles A. Appel include some examples of the primer's use and augment the presentation with references to relevant published papers, both those available to Theis but not cited by him, and subsequent publications. 'Aquifers, Ground-Water Bodies, and Hydrophers' was written in the early 1980's as an attempt to clarify the semantic and conceptual confusion in the use of the term aquifer, applied by some investigators to the saturated part of a permeable formation and by others to the entire permeable formation. The physical distinction between the aquifer and the ground-water body is emphasized, and the term hydropher is proposed to describe the saturated part of a permeable formation. Theis' interest in and familiarity with the French literature on ground water was the basis for a discussion of the French usage, which eschews the term aquifer. The analysis and critique of Theis' palzler explains the 1835 paper from which aquifer was reportedly derived, and provides further justification for the term hydropher. Theis' more important contributions to ground-water hydrology were outgrowths of his solutions to small local water problems based on field investigations. The biographical sketch, drawing extensively from a partial autobiography that Theis had dictated, reveals both the reasons for and the intellectual processes that led to his development of the nonequilibrium concept of ground-water hydraulics. The sketch also describes the background of the man, reviews his career, and portrays the admiration and respect he elicited from his colleagues and associates. The magnitude of Theis' contribution to the science of ground-water hydrology, to the appraisal of the water resources of New Mexico, and to the early research on ground disposal of radioactive wastes is evident from the bibliography of his writings, which includes 168 reports, many of them unpublished. The evolution of his thinking about the role of geologic inhomogeneities in mass transport, conceptualized but not quantified, was the major contribution of the latter part of his career.
Description of Existing Data for Integrated Landscape Monitoring in the Puget Sound Basin, Washington
This report summarizes existing geospatial data and monitoring programs for the Puget Sound Basin in northwestern Washington. This information was assembled as a preliminary data-development task for the U.S. Geological Survey (USGS) Puget Sound Integrated Landscape Monitoring (PSILM) pilot project. The PSILM project seeks to support natural resource decision-making by developing a 'whole system' approach that links ecological processes at the landscape level to the local level (Benjamin and others, 2008). Part of this effort will include building the capacity to provide cumulative information about impacts that cross jurisdictional and regulatory boundaries, such as cumulative effects of land-cover change and shoreline modification, or region-wide responses to climate change. The PSILM project study area is defined as the 23 HUC-8 (hydrologic unit code) catchments that comprise the watersheds that drain into Puget Sound and their near-shore environments. The study area includes 13 counties and more than four million people. One goal of the PSILM geospatial database is to integrate spatial data collected at multiple scales across the Puget Sound Basin marine and terrestrial landscape. The PSILM work plan specifies an iterative process that alternates between tasks associated with data development and tasks associated with research or strategy development. For example, an initial work-plan goal was to delineate the study area boundary. Geospatial data required to address this task included data from ecological regions, watersheds, jurisdictions, and other boundaries. This assemblage of data provided the basis for identifying larger research issues and delineating the study-area boundary based on these research needs. Once the study-area boundary was agreed upon, the next iteration between data development and research activities was guided by questions about data availability, data extent, data abundance, and data types. This report is not intended as an exhaustive compilation of all available geospatial data, rather, it is a collection of information about geospatial data that can be used to help answer the suite of questions posed after the study-area boundary was defined. This information will also be useful to the PSILM team for future project tasks, such as assessing monitoring gaps, exploring monitoring-design strategies, identifying and deriving landscape indicators and metrics, and visual geographic communication. The two main geospatial data types referenced in this report - base-reference layers and monitoring data - originated from numerous and varied sources. In addition to collecting information and metadata about the base-reference layers, the data also were collected for project needs, such as developing maps for visual communication among team members and with outside groups. In contrast, only information about the data was typically required for the monitoring data. The information on base-reference layers and monitoring data included in this report is only as detailed as what was readily available from the sources themselves. Although this report may appear to lack consistency between data records, the varying degree of details contained in this report are merely a reflection of varying source detail. This compilation is just a beginning. All data listed also are being catalogued in spreadsheets and knowledge-management systems. Our efforts are continual as we develop a geospatial catalog for the PSILM pilot project.
Hood River PIT-tag interrogation system efficiency study. Annual report of U.S. Geological Survey activities: November 2010-October 2011
Introduction During summer 2010, an agreement was made between the US Geological SurveyColumbia River Research Laboratory (USGS-CRRL) and the Confederated Tribes of the Warm Springs (CTWS) to operate an experimental Passive Integrated Transponder (PIT)-tag interrogation system (PTIS) near the mouth of the Hood River for a year and provide fishdetection efficiency estimates (Bonneville Power Administration (BPA) project number 1988- 053-03, contract number 50150). A previous agreement between Oregon Department of Fish and Wildlife (ODFW) and USGS-CRRL had funded materials acquisition, construction, and installation of the PTIS (BPA project number 1988-053-04, contract number 48684). The primary purpose of the project was to test the efficacy of a PTIS in the lower Hood River for providing data on returning adult salmonids to the Hood River as part of the Hood River Production Monitor and Evaluation project (HRPME). Because PIT tags are small, relatively inexpensive, carry no internal battery, and last through the lifespan of most fishes, they are commonly used in long term fish monitoring projects. They have been extensively used in the Columbia River basin to monitor salmonid behavior and survival through life stages and migration routes in the mainstem Columbia River (Skalski et al. 1998; Zabel and Achord 2004). Increasingly, PIT-tag detection equipment has been deployed in streams to investigate salmonid behavior (Zydlewski et al. 2001, 2006; Riley et al. 2003; Bond et al. 2007). Most of the detection systems deployed and evaluated to date have been in much smaller streams than the mainstem of the Hood River (Zydlewski et al. 2001, 2006; Bond et al. 2007; Horton et al. 2007; Connolly et al. 2008), but researchers are attempting to expand detection abilities to larger streams and rivers. Large streams and rivers can prove extremely challenging to monitor. Some systems have showed promise for contributing valuable detection data, others have proved less successful. A detection system in the Klamath River (Beeman et al. 2012), a site similar in size to the Hood River, suffered problems from cables being dislodged and high water that resulted in a detection efficiency estimate for juvenile coho salmon of less than 0.05. An additional USGS-CRRL task, under contract number 50150, was to build three antennas for use with Destron-Fearing 2001F-ISO PIT tag readers. These antennas would be 5 used at the East Fork Hood River Acclimation site. They would be placed in the outflow channel to inform managers about the number of PIT tagged steelhead smolts released to the Hood River after a period of acclimation when some mortality and predation might occur.
Assessment of Hazards Associated with the Bluegill Landslide, South-Central Idaho
The Bluegill landslide, located in south-central Idaho, is part of a larger landslide complex that forms an area the Salmon Falls Creek drainage named Sinking Canyon Recent movement of the Bluegill landslide, apparently beginning sometime in late 1998 or early 1999, has caused a 4.5 ha area of the canyon rim to drop as much as 8 m and move horizontally several meters into the canyon. Upward movement of the toe of the landslide in the bottom of canyon has created a dam that impounds a lake approximately 2 km in length. The landslide is on public administered by the U.S. Bureau of Land Management (BLM). As part of ongoing efforts to address possible public safety concerns, the BLM requested that the U.S. Geological Survey (USGS) conduct a preliminary hazard assessment of the landslide, examine possible mitigation options, and identify alternatives for further study and monitoring of the landslide. This report presents the findings of that assessment based on a field reconnaissance of the landslide on September 24, 2003, a review of data and information provided by BLM and researchers from Idaho State University, and information collected from other sources.
The U.S. Geological Survey Bird Banding Laboratory: an integrated scientific program supporting research and conservation of North American birds
The U.S. Geological Survey (USGS) Bird Banding Laboratory (BBL) was established in 1920 after ratification of the Migratory Bird Treaty Act with the United Kingdom in 1918. During World War II, the BBL was moved from Washington, D.C., to what is now the USGS Patuxent Wildlife Research Center (PWRC). The BBL issues permits and bands to permittees to band birds, records bird band recoveries or encounters primarily through telephone and Internet reporting, and manages more than 72 million banding records and more than 4.5 million records of encounters using state-of-the-art technologies. Moreover, the BBL also issues bands and manages banding and encounter data for the Canadian Bird Banding Office (BBO). Each year approximately 1 million bands are shipped from the BBL to banders in the United States and Canada, and nearly 100,000 encounter reports are entered into the BBL systems. Banding data are essential for regulatory programs, especially migratory waterfowl harvest regulations. The USGS BBL works closely with the U.S. Fish and Wildlife Service (USFWS) to develop regulations for the capture, handling, banding, and marking of birds. These regulations are published in the Code of Federal Regulations (CFR). In 2006, the BBL and the USFWS Division of Migratory Bird Management (DMBM) began a comprehensive revision of the banding regulations. The bird banding community has three major constituencies: Federal and State agency personnel involved in the management and conservation of bird populations that include the Flyway Councils, ornithological research scientists, and avocational banders. With increased demand for banding activities and relatively constant funding, a Federal Advisory Committee (Committee) was chartered and reviewed the BBL program in 2005. The final report of the Committee included six major goals and 58 specific recommendations, 47 of which have been addressed by the BBL. Specifically, the Committee recommended the BBL continue to support science, conservation, and management of birds through the use of banding and banding data and that the BBL be managed by the USGS and located at the USGS Patuxent Wildlife Research Center (PWRC) in Laurel, Maryland. Recommendations that have not been implemented include those already addressed by other organizations, as well as lower priority, such as developing a BBL business plan. The comprehensive review and recommendations of the Committee, the response of the BBL to address the Committee’s recommendations, and other improvements to its operations have positioned the BBL to provide a high level of service to the banding community. As new technologies are developed and incorporated into BBL operations, further efficiencies are expected to enable the BBL to continue to meet emerging scientific needs.
A characterization of the deep-sea coral and sponge community along the Oregon Coast using a remotely operated vehicle on the EXPRESS 2022 expedition
Deep-sea coral and sponge (DSCS) communities serve as essential fish habitat (EFH) by providing shelter and nursery habitat, increasing diversity, and increasing prey availability (Freese and Wing, 2003; Bright, 2007; Baillon et al., 2012; Henderson et al., 2020). Off the U.S. West Coast, threats to these long-lived, fragile organisms from bottom contact fishing gear, potential offshore renewable energy development, and ocean warming and acidification have been the subject of recent research (Gomez et al., 2018; Salgado et al., 2018; Yoklavich, et al., 2018; Gugliotti et al., 2019). Other DSCS studies have reported new species (Yoklavich and Love, 2005), analyzed species distribution and abundance (Tissot et al., 2006, Watters et al., 2022), developed predictive distribution models (Huff et al., 2013; Rooper et al., 2017; Kreidler, 2020), and discovered medicinal uses for corals and sponges (Essack et al., 2011; Shrestha et al., 2018). Due to the vast area of unexplored seafloor within the territorial waters and the U.S. exclusive economic zone (EEZ; 12-200 nautical miles off the coast) and the technological requirements and expense of deep-sea research, there is still much to learn about the distributions and biology of DSCS. This information is critical to resource managers for effective conservation and management of DSCS habitats. In order to minimize the adverse impacts of fishing on EFH, the Pacific Fishery Management Council (PFMC) and National Marine Fisheries Service (NMFS) designated several seafloor habitat areas as EFH conservation areas (EFHCA), first in 2006 (as part of Amendment 19 to the Pacific coast groundfish fishery management plan) and then again in 2020 (as part of Amendment 28). These areas are closed to bottom trawl fishing at a minimum, and in some cases to all bottom contact fishing gears. In addition to protections afforded by EFH-related regulations, the National Marine Sanctuary Program prohibits certain non-fishing activities within areas designated as national marine sanctuaries, such as oil and gas exploration or extraction, cable laying, and other forms of seabed alteration or construction that disturb benthic communities. NOAA’s Deep-Sea Coral and Research Technology Program (DSCRTP) began a 4-yr funding initiative for the U.S. West Coast in 2017. The goals of the West Coast Deep-Sea Coral Initiative (WCDSCI) were to: 1) gather baseline information on areas subject to fishing regulation changes prior to the implementation of Amendment 28; 2) improve our understanding of known DSCS bycatch “hot spots”; and 3) explore and assess DSCS resources within NOAA National Marine Sanctuaries with emphasis on areas of sanctuary resource protection and management concerns. As part of the WCDSCU, an 11-day expedition (3 Sep – 13 Sep 2022) was launched from the NOAA Ship Bell M. Shimada, beginning and ending in Newport, OR. The science team assembled for this cruise were members of the EXpanding Pacific Research and Exploration of Submerged Systems (EXPRESS) campaign, which brings together researchers from federal and nonfederal institutions to collaborate on scientific expeditions targeting the deepwater areas off California, Oregon, and Washington. EXPRESS supports researchers leveraging funding, resources, personnel, and expertise to accomplish more science than would have been possible by a single entity alone. The 2022 expedition included research partners from National Marine Fisheries Service (NMFS) Southwest Fisheries Science Center (SWFSC) and Northwest Fisheries Science Center (NWFSC), Bureau of Ocean Energy Management (BOEM), U.S. Geological Survey (USGS), Pacific Fisheries Management Council Habitat Committee, and Woods Hole Oceanographic Institution.
Distribution and relative abundance of forest birds in relation to burn severity in southeastern Arizona
The frequency of wild and prescribed fires in montane forests of the southwestern United States has increased after a century of fire suppression and subsequent fuels accumulation. To assess the effects of recent fires (median time since fire = 6 yr) on the montane forest bird community, we surveyed birds in 8 Sky Island mountain ranges in southeastern Arizona, USA, and examined how the distribution (i.e., presence-absence) of 65 species and relative abundance of 16 species correlated with evidence of severe and less severe fire at >1,500 survey points. We detected associations between fire and bird presence-absence for 17% of the 65 species analyzed and between fire and bird relative abundance for 25% of the 16 species analyzed. Most species (73%) were positively associated with burned areas and displayed stronger associations (i.e., more extreme odds ratios) with survey points that had evidence of severe as opposed to less severe fire. Positive associations with severe fire were strong (>3 to 1 odds) for western wood-pewee (Contopus sordidulus) and house wren (Troglodytes aedon), and negative associations with severe fire were strong for warbling vireo (Vireo gilvus) and red-breasted nuthatch (Sitta canadensis). Although recent fires appear to have had a positive effect on the distribution and relative abundance of several montane forest bird species in the region, these species are not the open-woodland birds that we would have expected to have benefited from fire based on previous research. Nevertheless, our results confirm associations between fire and bird presence-absence and relative abundance reported previously for 7 species of birds. Our results also provide new information for Grace's warbler (Dendroica graciae) and greater pewee (C. pertinax), 2 species for which fire data were formerly lacking. Managers can use these data to make and test predictions about the effects of future fires, both severe and less severe, on montane forest birds in the southwestern United States.
Management of flood-plain vegetation, 1967 to 1972, San Carlos Indian Reservation, Arizona
During 1967-71, 15,800 acres of flood-plain vegetation were cleared from a 26-mile reach of the Gila River valley and a 9-mile reach of the San Carlos River valley. Both areas are on the San Carlos Apache Indian Reservation, Arizona. The area cleared in the Gila River valley included the Gila River Phreatophyte Project and the clearing was conducted as prescribed by the experimental design of that research program. Establishment of replacement vegetation was attempted on the cleared areas with indifferent success. The report outlines methods used to remove the vegetation and to discourage its subsequent regrowth. Costs of the clearing operation are given by vegetation type, and descriptions of the procedures used for establishing new vegetation are given. Clearing and subsequent maintenance of parts of the flood plain were hampered by channel clogging and subsequent flooding of adjacent areas. Part of the area selected for clearing lies within the San Carlos Reservoir. The wide range of water level in the reservoir further aggravated maintenance of an inflow channel. Both draglines and a dredge were used to open a channel to the reservoir. Because the flow of the Gila River is intermittent, vegetation becomes established in the channel at the head of the reservoir during periods of no flow. The report concludes that the presence of the vegetation promotes silt deposition and further clogging. Inflow channel maintenance is a persistent problem that will require well-planned repetitive clearing of vegetation at the head of the reservoir.
Fragmentation: Is the message clear?
In this paper, we briefly discuss some of the fundamental problems arising from the inherent complexity of larger-scale ecological systems. We examine the tenuous assumption of a direct correspondence between ecological data and theory, we comment on a recent report that evaluated the efficacy of fragmentation experiments, and we briefly assess its implications for ecological research and conservation practice on the landscape scale.
Prevalence of antibodies to type A influenza virus in wild avian species using two serologic assays
Serologic testing to detect antibodies to avian influenza (AI) virus has been an underused tool for the study of these viruses in wild bird populations, which traditionally has relied on virus isolation and reverse transcriptase-polymerase chain reaction (RT-PCR). In a preliminary study, a recently developed commercial blocking enzyme-linked immunosorbent assay (bELISA) had sensitivity and specificity estimates of 82% and 100%, respectively, for detection of antibodies to AI virus in multiple wild bird species after experimental infection. To further evaluate the efficacy of this commercial bELISA and the agar gel immunodiffusion (AGID) test for AI virus antibody detection in wild birds, we tested 2,249 serum samples collected from 62 wild bird species, representing 10 taxonomic orders. Overall, the bELISA detected 25.4% positive samples, whereas the AGID test detected 14.8%. At the species level, the bELISA detected as many or more positive serum samples than the AGID in all 62 avian species. The majority of positive samples, detected by both assays, were from species that use aquatic habitats, with the highest prevalence from species in the orders Anseriformes and Charadriiformes. Conversely, antibodies to AI virus were rarely detected in the terrestrial species. The serologic data yielded by both assays are consistent with the known epidemiology of AI virus in wild birds and published reports of host range based on virus isolation and RT-PCR. The results of this research are also consistent with the aforementioned study, which evaluated the performance of the bELISA and AGID test on experimental samples. Collectively, the data from these two studies indicate that the bELISA is a more sensitive serologic assay than the AGID test for detecting prior exposure to AI virus in wild birds. Based on these results, the bELISA is a reliable species-independent assay with potentially valuable applications for wild bird AI surveillance.
Case histories of organophosphate pesticides killing birds of prey in the United States
Since 1982 when secondary. poisoning of Red-tailed Hawks (Buteo jamaicensis) was documented following the recommended use of famphur on cattle, the Patuxent Wildlife Research Center has tested for organophosphate (OP) poisoning in selected birds of prey found dead. This report documents the circumstances for a number of. cases where birds of prey were killed by OP pesticides in the United States. Many of the cases were brought to our attention by the U S. Fish and Wildlife Service Division of Law Enforcement The cases may be divided into three categories: misuse, approved use, and unknown. Now that we are looking for OP poisoning of birds of prey, we are finding it more frequently than previously suspected.
Effects of temephos (Abate? 4E) on fiddler crabs (Uca pugnax and Uca minax) on a Delaware salt marsh
The non-target effects of temephos (as Abate 4E, 44.6% active ingredient) on fiddler crabs were examined on the salt marsh at Bombay Hook National Wildlife Refuge (NWR), near Dover, DE. Six 170 x 170 m plots were established; 3 were sprayed on 4 occasions at a rate of 1.5 fl oz/acre (0.054 kg active ingredient/ha) and 3 were controls. On each plot, marsh fiddler crab (Uca pugnax) populations were monitored by repeatedly counting the number of burrow holes in 2 counting areas marked out along tidal guts. One half of each counting area was covered with bird netting to evaluate sublethal toxic effects, which, if present, could result in increased susceptibility to bird predation. A statistically significant linear association was established between the number of holes and the number of crabs. No significant differences were found in the numbers of holes (or crabs) in the sprayed vs. control plots and in the covered vs. uncovered sections. However, survival of juvenile crabs in in situ bioassays was significantly reduced (16% lower) by the spraying. Median acetylcholinesterase activity in claw muscle of red-jointed fiddler crabs (U. minax) collected 2 days after an operational spray with Abate 4E was significantly reduced (28% lower) compared to unsprayed crabs. In view of the toxicity to juvenile crabs and the cholinesterase inhibition, we recommend continued monitoring and research for non-target impacts of Abate 4E on fiddler crabs to establish whether the reported level of cholinesterase inhibition results in acute or chronic toxicity.