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Freshwater mussels (Unionidae): Central and West Texas Final Report

The goal of this study was two-fold: (1) assess the taxonomic identity and phylogenetic placement of Quadrula aurea (Golden Orb) [Federal Candidate], Quadrula houstonensis (Smooth Pimpleback) [Federal Candidate], and Quadrula petrina (Texas Pimpleback) [Federal Candidate] through mitochondrial and nuclear DNA sequencing; and (2) provided additional information on the distribution and abundance for mussel species petitioned for listing under ESA through field surveys in portions of several major rivers in Central and West Texas. The final report is organized by 4 research tasks as per contract (see Appendix A) and submitted proposals. Below is an outline of goal-oriented tasks for this project: Task 1 – Conduct comprehensive surveys of portions of the Brazos, Colorado, and Guadalupe River basins Task 2 – Conduct comprehensive surveys of portions of the Rio Grande Basin Task 3 – Develop conservation status assessment maps for 9 state-threatened mussel species in Texas Task 4 – Delineate species boundaries, test for cryptic species, and assess phylogenetic relationships for threatened Texas mussel species in the genus Quadrula Note the following 2 tasks were either not funded in the current contract or was a modification of the contract and added as a project deliverable: Task 5 – Delineate species boundaries, test for cryptic species, and assess phylogenetic relationships for east Texas mussel species in the genus Fusconaia (Not Funded) Task 6 – Evaluate the conservation status of Texas hornshell and other mussels in the Pecos and Devils Rivers (Contract amendment, results combined with Task 2). Detailed descriptions of the research tasks and findings are found within each chapter of the report. Here, we outline and summarize project deliverables and major findings for each task.

Texas

Introduction to ‘Antarctic climate evolution: View from the margin’

This special issue on “Antarctic Climate Evolution—view from the margin” presents results from modelling studies and reports on geoscience data aimed at improving our understanding of the behaviour of the Antarctic ice sheet and the climate of the region. This research field is of interest because of the sensitivity of the polar regions to global warming, and because of the influence of the Antarctic ice sheet on global sea level and climate through most if not all of the Cenozoic Era. The Antarctic ice sheet both responds to and forces changes on global climate and sea level. We need to be aware of the scale and frequency of these changes if we are to understand past patterns of environmental change elsewhere on earth. It was only three decades ago that we discovered from strata drilled in shelf basins on the Antarctic margin that the Antarctic ice sheet had a history that predated the Quaternary ice ages by over 20 million years ( Hayes et al., 1975 ). Later that year the first interpretation of Antarctic glacial history through the Cenozoic Era from oxygen isotopes, recorded in foraminifera from deep-sea sediment cores, was published ( Shackleton and Kennett, 1975 ). Revisions with a more extensive database have modified the story a little ( Miller et al., 1987 , Zachos et al., 2001 ), and there have been recent attempts to resolve the temperature–ice volume ambiguity ( Lear et al., 2000 ). However, reports on strata drilled on the Antarctic margin have unambiguously shown the character of this huge ice sheet, which was oscillating in the Oligocene ( Barrett et al., 1987 , Barrett, 1999 ) with a period and magnitude comparable with the Northern Hemisphere ice sheets of the Quaternary ( Naish et al., 2001a , Naish et al., 2001b ). In this issue we present further research on the history of the Antarctic ice sheet from Oligocene to recent times, most of them from the Antarctic margin, but with some on the nature of the deep-sea isotope record, and others using recently developed modeling techniques to investigate the influence of atmosphere, ocean and biosphere on past Antarctic climate. This special issue is the third in three years on the theme of Antarctic Climate Evolution. The first followed a workshop in Erice, Sicily, in 2001 to report on results from ANTOSTRAT, a SCAR-sponsored project for gathering and analysing circum-Antarctic seismic data for planning and promoting offshore drilling for climate history. The introduction to that issue (Florindo et al., 2003) provides a review of the recent history of circum-Antarctic drilling by the Ocean Drilling Program (Legs 113, 114, 119, 120, 177, 178, 188 and 189) and the Cape Roberts Project. For a more comprehensive review of earlier drilling in the Ross Sea region (Deep Sea Drilling Project Leg 28, Dry Valley Drilling Project, McMurdo Sound Sediment and Tectonic Studies, Cenozoic Investigations in the western Ross Sea) see Hambrey and Barrett (1993). The first of these issues (Florindo et al., 2003) featured a global plate reconstruction of the Southern Hemisphere through Cenozoic time with emphasis on evolution of Cenozoic seaways (Lawver and Gahagan, 2003) along with a study of the inception and early evolution of the EAIS using a new coupled global climate (GCM)–dynamic ice sheet model (DeConto and Pollard, 2003b), as well as data from recent drilling around the margin covering time period from Cretaceous to the present. A second special issue on the same theme (Florindo et al., 2005) also featured a mix of modelling and data papers with a focus on the Eocene–Oligocene boundary and the initiation of ice sheet growth, including a pioneering attempt to evaluate the relative influence of fluvial versus glacial processes in shaping the landscape of the Prydz Bay sector of Antarctica (Jamieson et al., 2005). The remainder of the issue comprised further papers on seismic stratigraphy and reports from drilling around the margin. The papers to be found in this special issue, like the previous two, maintain the mix of modelling- and data-oriented papers that reflect the range of this research.

Palaeogeography, Palaeoclimatology, Palaeoecology

Fish Rhabdoviruses

Many important viral pathogens of fish are members of the family Rhabdoviridae . The viruses in this large group cause significant losses in populations of wild fish as well as among fish reared in aquaculture. Fish rhabdoviruses often have a wide host and geographic range, and infect aquatic animals in both freshwater and seawater. The fish rhabdoviruses comprise a diverse collection of isolates that can be placed in one of two quite different groups: isolates that are members of the established genus Novirhabdovirus , and those that are most similar to members of the genus Vesiculovirus . Because the diseases caused by fish rhabdoviruses are important to aquaculture, diagnostic methods for their detection and identification are well established. In addition to regulations designed to reduce the spread of fish viruses, a significant body of research has addressed methods for the control or prevention of diseases caused by fish rhabdoviruses, including vaccination. The number of reported fish rhabdoviruses continues to grow as a result of the expansion of aquaculture, the increase in global trade, the development of improved diagnostic methods, and heightened surveillance activities. Fish rhabdoviruses serve as useful components of model systems to study vertebrate virus disease, epidemiology, and immunology.

Book chapter

New global high-resolution centerlines dataset of selected river systems

We present the first high resolution (1:20,000) river centerlines shapefiles from 50 large rivers across the world. Rivers were selected based on the criteria of having more than 1000 km length and which have been reported to have a significant contribution to global fishery production. Since large rivers often span multiple countries, the degree of changes (i.e., anthropogenic or climate derived) varies from region to region. These high-resolution layers were developed to enable researchers to delineate accurate river length, from headwaters regions to their delta and assess or visualize the ongoing changes more accurately in these river systems. Further, these polylines could be used in coordination with satellite derived environmental or landscape variables for ecological research (e.g. predicting biodiversity, estimating biomass).

Data in Brief

Vital signs monitoring plan for the Klamath Network: Phase I report

This report chronicles the Phase 1 stage of the vital signs monitoring program for the Klamath Network. It consists of two chapters and eleven appendixes. The purposes of Chapter One are to 1) describe the network administrative structure and approach to planning; 2) introduce the Klamath Network parks, their resources, and environmental settings; 3) explain the need for monitoring changes in resources and supporting environments; 4) identify key information gaps that limit understanding of how to best achieve these monitoring goals. The purpose of Chapter Two is to develop the descriptive information provided in Chapter One into a conceptual basis for vital signs monitoring and to present the Network’s initial suite of conceptual models. The Report Appendices provide in-depth information on a variety of topics researched in preparation of the report, including: detailed natural resource profiles for each park, supporting policies and guidelines, regional fire regimes, vegetation types of the parks, exotic species threats, interagency monitoring programs, air issues, water quality (Phase 1 Report), Network vital signs (Scoping Summary Report), rare species, and rare habitats of the parks.

Report

Integrated science for the study of perfluoroalkyl and polyfluoroalkyl substances (PFAS) in the environment—A strategic science vision for the U.S. Geological Survey

Concerns related to perfluoroalkyl and polyfluoroalkyl substances (PFAS) in sources of drinking water and in natural and engineered environments have captured national attention over the last few decades. This report provides an overview of the science gaps that exist in the fields of study related to PFAS that are relevant to the U.S. Geological Survey mission and identifies opportunities where the U.S. Geological Survey can help address these gaps on the basis of the agency’s capabilities and expertise. The integrated science activities envisioned in this document can be designed to address science needs at local, regional, and national scales and varying timeframes as stakeholders are engaged and their needs evolve. This document is intended as an information resource for U.S. Geological Survey scientists who are prioritizing and planning research related to PFAS and may be useful for developing partnerships and collaborations with other scientists, agencies, and stakeholders.

Circular

Late Pleistocene through Holocene landscape evolution of the White River Badlands, South Dakota

Badlands are common arid and semiarid landscapes long recognized in slope development and erosion rate studies by preeminent geomorphologists including Gilbert, Davis, and Schumm. The trip described here will examine in detail Quaternarystrata and landscape evolution in arguably the most famous badlands, the White River Badlands of South Dakota, which were pivotal during development of vertebrate paleontology in North America. Geologists have collected fossils from the White River Group there nearly every field season since the mid-1800s; however, until recently, little work was reported on the extensively exposed Quaternary strata. The White River Badlands are also a proposed dust source for the widespread PeoriaLoess of the Central Great Plains. The research highlighted on this trip includes (1) luminescence and radiocarbon ages from late Pleistocene through Holocene eolian sand, (2) radiocarbon ages from Holocene eolian cliff-top deposits, (3) luminescenceages from late Pleistocene fluvial silts, (4) radiocarbon ages of late Holocene fluvial silts, and (5) cosmogenic ages on ventifacts from the adjoining upper prairie. These new studies will facilitate discussions, including (1) late Quaternary paleoenvironments,(2) late Quaternary fluvial incision rates and episodes, (3) up-wind sediment supply of late Quaternary nonglaciogenic loess, (4) landscape evolution spanning late Pleistocene tableland through late Holocene sod table development, and (5) modern erosion-pedimentation rates.

South Dakota

A preliminary report of ongoing research of the ecology of Black-capped Petrel (Pterodroma hasitata) in Sierra de Bahoruco, Dominican Republic – I: GPS tracking of breeding adults

The Black-capped Petrel (also known regionally as Diablotin) is a gadfly petrel endemic to the Caribbean. Population estimates based on at-sea observations range from 2,000 to 4,000 individuals, with a fragmented breeding population estimated at 500 to 1,000 pairs. At sea, the expansive marine range of the species exposes it to many conservation threats including fisheries activity, offshore energy development, marine pollution including mercury bio-accumulation, and climate change. Such disturbances at sea have been under-studied although they are likely to impact the survival of the species.

Sierra de Bahoruco

U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative-2009 Annual Report

This is the second report produced by the U.S. Geological Survey (USGS) for the Wyoming Landscape Conservation Initiative (WLCI) to detail annual work activities. The first report described work activities for 2007 and 2008; this report covers work activities conducted in 2009. Important differences between the two reports are that (1) this report does not lump all the Effectiveness Monitoring activities together as last year's report did, which will allow WLCI partners and other readers to fully appreciate the scope and accomplishments of those activities, and (2) this report does not include a comprehensive appendix of the background details for each work activity. In 2009, there were 29 ongoing or completed activities, and there were 5 new work activities conducted under the 5 original major multi-disciplinary science and technical assistance activities: (1) Baseline Synthesis; (2) Targeted Monitoring and Research; (3) Data and Information Management; (4) Integration and Coordination; and (5) Decisionmaking and Evaluation. New work included (1) developing a soil-quality index, (2) developing methods for assessing levels of and relationships between mercury and soil organic matter, and (3) ascertaining element source, mobility, and fate. Additionally, (4) remotely sensed imagery was used to assess vegetation as an indicator of soil condition and geology, and (5) an Integrated Assessment (IA) was initiated to synthesize what has been learned about WLCI systems to date, and to develop associated decision tools, maps, and a comprehensive report.

Open-File Report

Chemical analysis and modes of occurrence of selected trace elements in a Powder River basin coal and its corresponding simulated cleaned coal

This report provides semi-quantitative data on modes of occurrence of 19 elements in as-mined Powder River Basin coal and its corresponding simulated cleaned coal. The data are in support of the project "Prediction of Trace Element Removal from Coal" --a Cooperative Research and Development Agreement (CRADA) with CQ Inc. The purpose of this CRADA is to apply modes of occurrence information to coal cleaning procedures. Techniques used in this study include sequential selective leaching procedures, scanning electron microscopy, X-ray diffraction analysis, and electron microprobe analysis. Selective leaching results indicate that greater than 40 percent of the elements Co, U, Be, Ca, Fe, Mn, Ba, Zn, Cd, Pb are associated with HCIsoluble carbonates, iron oxides, or monosulfides, greater than 40 percent of the Al, Cr and Mo are associated with HF-soluble silicates, greater than 40 percent of the Ni, Cu, As and Sb are associated with acid-insoluble phases and/or organic matter, and greater than 50 percent of the Hg is associated with HMDs-soluble pyrite. Thirty percent of the Th was leached by HCI and 30 percent of this element was leached by HF. Scanning electron microscopy indicates that quartz, kaolinite, illite and iron oxide, possibly hematite, are the major minerals present. X-ray diffraction analysis confirmed that quartz, kaolinite and hematite are present, but did not determine illite, indicating that illite in these coals is of low abundance or is poorly crystalline. Electron microprobe data indicate that concentrations of the chalcophile elements As, Se, Cu, Ni, Zn, and Cd in most pyrite grains are at or below the detection limit of about 100-200 ppm in both the as-mined coal and its corresponding simulated cleaned coal product. The results of this project should aid in the development of models for predicting the response of potentially toxic trace elements in commercial coal cleaning procedures.

Open-File Report

Detecting algal toxins and organic contaminants of concern in the environment

The U.S. Geological Survey (USGS) Kansas Water Science Center Organic Geochemistry Research Laboratory (OGRL) was established in 1987. The OGRL is a multidisciplinary program that contributes knowledge about the distribution, fate, transport, and effects of new and understudied organic compounds that may affect human health and (or) ecosystems. The OGRL consists of two units: Algal and Other Environmental Toxins Unit and Environmental Organic Chemistry Unit. The OGRL does independent and collaborative research, develops robust analytical methods, and provides fee-for-service analytical laboratory analyses.

Fact Sheet

Mangrove postcard

Mangrove ecosystems protect vulnerable coastlines from storm effects, recycle nutrients, stabilize shorelines, improve water quality, and provide habitat for commercial and recreational fish species as well as for threatened and endangered wildlife. U.S. Geological Survey scientists conduct research on mangrove ecosystems to provide reliable scientific information about their ecology, productivity, hydrological processes, carbon storage stress response, and restoration success. The Mangrove Science Network is a collaboration of USGS scientists focused on working with natural resource managers to develop and conduct research to inform decisions on mangrove management and restoration. Information about the Mangrove Science Network can be found at: http://www.usgs.gov/ecosystems/environments/mangroves.html .

General Information Product

Cyanobacterial harmful algal blooms and U.S. Geological Survey science capabilities

Cyanobacterial harmful algal blooms (CyanoHABs) are increasingly a global concern because CyanoHABs pose a threat to human and aquatic ecosystem health and cause economic damages. Despite advances in scientific understanding of cyanobacteria and associated compounds, many unanswered questions remain about occurrence, environmental triggers for toxicity, and the ability to predict the timing, duration, and toxicity of CyanoHABs. U.S. Geological Survey (USGS) scientists are leading a diverse range of studies to address CyanoHAB issues in water bodies throughout the United States, using a combination of traditional methods and emerging technologies, and in collaboration with numerous partners. By providing practical applications of cutting edge CyanoHAB research, USGS studies have advanced scientific understanding, enabling the development of approaches to help protect ecological and human health.

Open-File Report

Analytical method codes and descriptions for well and outcrop samples: Eastern Gas Shales Project data system

The United States Geological Survey and Petroleum Information Corporation (PI) of Denver have created a large computerized file of sample data for the Eastern Gas Shales Project (EGSP) as a responsibility to the U.S. Department of Energy (DOE), Morgantown Energy Technology Center (METC), Morgantown, West Virginia. The EGSP was initiated in 1976 by METC to investigate gas resources in Devonian shales found in the Appalachian basin. An objective of the EGSP is to accumulate a data base characterizing these shale units which can be used to assess future development of the gas resource. More than 30 government and industry participants served as contractors and contributed data from their research.

Open-File Report

Integrating authentic scientific research in a conservation course–based undergraduate research experience

Course-based undergraduate research experiences (CUREs) have been developed to overcome barriers including students in research. However, there are few examples of CUREs that take place in a conservation and natural resource context with students engaging in field research. Here, we highlight the development of a conservation-focused CURE integrated to a research program, research benefits, student self-assessment of learning, and perception of the CURE. With the additional data, researchers were able to refine species distribution models and facilitate management decisions. Most students reported gains in their scientific skills, felt they had engaged in meaningful, real-world research. In student reflections on how this experience helped clarify their professional intentions, many reported being more likely to enroll in graduate programs and seek employment related to science. Also interesting was all students reported being more likely to talk with friends, family, or the public about wildlife conservation issues after participating, indicating that courses like this can have effects beyond the classroom, empowering students to be advocates and translators of science. Field-based, conservation-focused CUREs can create meaningful conservation and natural resource experiences with authentic scientific teaching practices.

Natural Sciences Education

Multipurpose Wetlands Phase II/III: final design and ongoing research investigations

The Eastern Municipal Water District (EMWD), the Bureau of Reclamation (USBR), and the National Biological Survey (NBS), in consultation with other governmental agencies, the academic community, and environmental groups, are involved in a cooperative wetlands research and demonstration effort. This report reflects progress through the first 3 years of a 5-year program. The goal of the Multipurpose Wetlands Research and Demonstration Project is to evaluate and expand the use of reclaimed water and contaminated ground water through the incorporation of multipurpose constructed wetlands into EMWD's total water resources management program. The focus of the wetlands is the development of design, construction, and operation criteria that will provide a cost-effective and innovative alternative for managing water resources and provide other public benefits in arid areas. The program also recognizes the fact that naturally-occurring wetlands, both coastal and inland, have been disappearing at an alarming rate.

Report

Test and calibration of the Digital World-Wide Standardized Seismograph

During the past decade there has been steady progress in the modernization of the global seismograph network operated by the U.S. Geological Survey (USGS). The World-Wide Standardized Seismograph Network (WWSSN) has been augmented by new stations with advanced instrumentation, including the Seismic Research Observatories (SRO) and the modified High-Gain Long-Period (ASRO) stations. One goal in the modernization effort has been to improve signal resolution in the long-period band. A second goal has been to generate a global digital data base to support contemporary computer-based analysis and research. In 1976, a Panel on Seismograph Networks was established by the Committee on Seismology of the National Academy of Sciences to review progress in network seismology and recommend actions that would lead to an improved global data base for seismology. One recommendation in the Panel report (Engdahl, 1977) called for upgrading selected WWSSN stations by the installation of digital recorders. This was viewed as an economical way of expanding the digital network, which had proven itself to be a very promising new tool for earthquake and explosion research. Funds for the development and assembly of 15 digital recorders were provided to the USGS by the Defense Advanced Research Projects Agency and an ad Inoc panel of scientists was convened by the Committee on Seismology to advise the USGS on the selection of stations to be upgraded and on data recording requirements, A total of 19 digital World-Wide Standardized Seismograph (DWWSS) systems will be operational when all are installed. The additional systems were made available through purchase by the USGS and other organizations; for example, the University of Bergen purchased and installed a DWWSS-type recorder and agreed to furnish the USGS with the data. A list of operational and planned DWWSS network stations is given in Table 1.1. As one might expect, the digital recorder turned out to be somewhat more sophisticated than the original concept. It was decided to record three components of long-period data continuously, three components of intermediateperiod data in an event mode, and the vertical-component short-period data in and event mode (with the capability of adding short-period horizontal channels in the future). Special amplifiers were developed for use with the WWSS seismometers, and a 16-bit fixed-point analog-to-digital converter was chosen to provide increased resolution (as opposed to a 16-bit gain-ranged encoder). The microprocessor-based digital recording systems were developed and assembled at the USGS Albuquerque Seismological Laboratory (ASL) and ASL-based technicians began installation at WWSSN stations in 1980. The current and proposed locations of the DWWSSN stations, together with other stations in the Global Digital Seismograph Network (GDSN), are shown on the map in Figure 1.1. A system was operated at Albuquerque for about 18 months, serving as a test bed for evaluation studies. Although the network hardware has been available for some time, the installation of the DWWSSN has proceeded slowly. The National Science Foundation supported installation of six stations and the USGS is funding installation of most of the others; however, the network completion date is conjectural because of funding uncertainties. The DWWSSN stations are supported with supplies and technical assistance from ASL (subject to availability of funds). Data recorded on magnetic tapes are mailed to ASL where they are reviewed for quality, then merged with other GDSN station data on the network-day tapes. Hoffman (1980) provides a description of the network-day tape format. Zirbes and Buland (1981) have developed and published user software for reading and interpreting the day tapes. This report will serve several purposes. One is to provide nominal system transfer functions and calibration information that are needed in the analysis of DWWSSN data. A second purpose is to report on an evaluation of operating characteristics (calibration stability, noise levels, and linearity) that may limit the usefulness of the data and to determine if modifications may be needed to improve the data. It is not an exhaustive study in this respect. We continue to depend mostly on data user feedback to point out deficiencies and we solicit comments whenever anomalies are observed in the data.

Open-File Report