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USGS2025

Viral outbreak dynamics and evolution in wildlife at the interface with humans

In this study, we used a multi-faceted approach to understand patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and persistence in a wild white-tailed deer ( Odocoileus virginianus ) population. Serology data indicated transmission of SARS-CoV-2 and persistence during the seven-month sampling period. Traditional disease modelling based on deer-to-deer transmission indicated relatively low prevalence with an R 0 of 1.9 and recovery period of 7 days; however, individual-based modelling informed by GPS tracked-movement data captured a potential transmission event. Phylogenetic analyses revealed a recurring pattern of divergent groups of deer-derived sequences with human-derived sequences falling close to each deer-derived cluster. Further, human-derived sequences were frequently sampled months prior to the deer-derived sequences, indicating repeated human to deer spillover. Using multiple types of data as well as both fine and broad scale analyses, we have characterized a pattern of localized outbreaks of SARS-CoV-2 within white-tailed deer populations that are likely recurring due to frequent spillover events. Our results suggest that while deer-to-deer transmission occurs over small spatiotemporal scales, SARS-CoV-2 persistence over longer periods and across larger regions is likely driven by repeated spillover from human populations.

Pennsylvania↗

USGS2001

Whooping cranes breeding at White Lake, Louisiana, 1939: observations by John J. Lynch, U.S. Bureau of Biological Survey

On 15 May 1939, John J. Lynch of the U.S. Bureau of Biological Survey located 13 whooping cranes (Grus americana), including 2 prefledged young, during an aerial survey near White Lake in southwestern Louisiana. His observation was the last historic record of whooping cranes breeding in the wild in the United States, and it confirmed the presence of a nonmigratory breeding population along the Gulf Coast. While reviewing old U.S. Fish and Wildlife Service files at the National Archives in 1999, we located Lynch's original 1939 field note, 2 letters, 5 photographs, and a draft manuscript describing the discovery; 4 other related letters also were found. Because of their biological and historical interest, we have reproduced the documents in this paper. A thorough assessment of the White Lake marshes as a potential site for returning nonmigratory whooping cranes to southwestern Louisiana should be conducted.

Book chapter↗

USGS1989

Methods for collection and analysis of aquatic biological and microbiological samples

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section. This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples. Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey. This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

Techniques of Water-Resources Investigations↗

USGS2005

Introduced species as evolutionary traps

Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

Ecology Letters↗

USGS2021

Authors’ reply to letter to the editor: Continued improvement to genetic diversity indicator for CBD

We appreciate the encouraging response to our call for indicators for genetic diversity within the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity, CBD (Laikre et al. 2020 ; Hoban et al. 2020 ). In agreement with us, Frankham ( 2021 ) highlights the urgent necessity for the CBD to include an indicator that tracks the maintenance of genetic diversity within populations of all species—wild and domestic. Draft CBD Headline indicators (which all CBD Parties will need to report) do not include genetic diversity within populations of wild species (CBD/SBSTTA/24/3Add.1).

Conservation Genetics↗

USGS2014

Character, distribution, and ecological significance of storm wave-induced scour in Rhode Island Sound, USA

Multibeam bathymetry, collected during NOAA hydrographic surveys in 2008 and 2009, is coupled with USGS data from sampling and photographic stations to map the seabed morphology and composition of Rhode Island Sound along the US Atlantic coast, and to provide information on sediment transport and benthic habitats. Patchworks of scour depressions cover large areas on seaward-facing slopes and bathymetric highs in the sound. These depressions average 0.5-0.8 m deep and occur in water depths reaching as much as 42 m. They have relatively steep well-defined sides and coarser-grained floors, and vary strongly in shape, size, and configuration. Some individual scour depressions have apparently expanded to combine with adjacent depressions, forming larger eroded areas that commonly contain outliers of the original seafloor sediments. Where cobbles and scattered boulders are present on the depression floors, the muddy Holocene sands have been completely removed and the winnowed relict Pleistocene deposits exposed. Low tidal-current velocities and the lack of obstacle marks suggest that bidirectional tidal currents alone are not capable of forming these features. These depressions are formed and maintained under high-energy shelf conditions owing to repetitive cyclic loading imposed by high-amplitude, long-period, storm-driven waves that reduce the effective shear strength of the sediment, cause resuspension, and expose the suspended sediments to erosion by wind-driven and tidal currents. Because epifauna dominate on gravel floors of the depressions and infauna are prevalent in the finer-grained Holocene deposits, it is concluded that the resultant close juxtaposition of silty sand-, sand-, and gravel-dependent communities promotes regional faunal complexity. These findings expand on earlier interpretations, documenting how storm wave-induced scour produces sorted bedforms that control much of the benthic geologic and biologic diversity in Rhode Island Sound.

Rhode Island↗

USGS1997

Benthic boundary layer processes in the Lower Florida Keys

This special issue of Geo-Marine Letters, "Benthic Boundary Layer Processes in the Lower Florida Keys," includes 12 papers that present preliminary results from the Key West Campaign. The Dry Tortugas and Marquesas Keys test sites were selected by a group of 115 scientists and technicians to study benthic boundary layer processes in a carbonate environment controlled by bioturbation and biogeochemical processes. Major activities included remote sediment classification; high-frequency acoustic scattering experiments; sediment sampling for radiological, geotechnical, biological, biogeochemical, physical, and geoacoustic studies; and hydrodynamic studies using an instrumented tetrapod. All these data are being used to improve our understanding of the effects of environmental processes on sediment structure and behavior.

Florida↗

USGS2007

Suboxic deep seawater in the late Paleoproterozoic: Evidence from hematitic chert and iron formation related to seafloor-hydrothermal sulfide deposits, central Arizona, USA

A current model for the evolution of Proterozoic deep seawater composition involves a change from anoxic sulfide-free to sulfidic conditions 1.8??Ga. In an earlier model the deep ocean became oxic at that time. Both models are based on the secular distribution of banded iron formation (BIF) in shallow marine sequences. We here present a new model based on rare earth elements, especially redox-sensitive Ce, in hydrothermal silica-iron oxide sediments from deeper-water, open-marine settings related to volcanogenic massive sulfide (VMS) deposits. In contrast to Archean, Paleozoic, and modern hydrothermal iron oxide sediments, 1.74 to 1.71??Ga hematitic chert (jasper) and iron formation in central Arizona, USA, show moderate positive to small negative Ce anomalies, suggesting that the redox state of the deep ocean then was at a transitional, suboxic state with low concentrations of dissolved O2 but no H2S. The presence of jasper and/or iron formation related to VMS deposits in other volcanosedimentary sequences ca. 1.79-1.69??Ga, 1.40??Ga, and 1.24??Ga also reflects oxygenated and not sulfidic deep ocean waters during these time periods. Suboxic conditions in the deep ocean are consistent with the lack of shallow-marine BIF ??? 1.8 to 0.8??Ga, and likely limited nutrient concentrations in seawater and, consequently, may have constrained biological evolution. ?? 2006 Elsevier B.V. All rights reserved.

Earth and Planetary Science Letters↗

USGS2021

Impacts of sediment removal from and placement in coastal barrier island systems

Executive Summary On June 24, 2019, Congressman Raul Grijalva of Arizona, Chair of the House Committee on Natural Resources, sent a letter to the directors of the U.S. Fish and Wildlife Service and the U.S. Geological Survey to request their assistance in answering questions regarding coastal sediment resource management within the Coastal Barrier Resources System as defined by the Coastal Barrier Resources Act (Public Law 97–348; 96 Stat. 1653; 16 U.S.C. 3501 et seq.). For the purposes of this response, coastal sediment resource management refers to the removal of sediment from one part of a barrier island system for placement in another part of the coastal system, for either hazard mitigation (for example, erosion or flood control) or coastal restoration (for example, expansion or restoration of beach, dune, and [or] marsh habitats). The specific topics of concern are as follows (paraphrased from Congressman Grijalva’s letter): 1. Disruption of coastal sediment supply resulting from sediment removal and placement, including the replenishment rate of removed sediments and impacts to other components of the barrier island system (discussed in sec. 3). 2. Physical and biological impacts of sediment removal and placement on benthic habitats (discussed in sec. 4). 3. Impacts of sediment removal and placement on fish and other marine species (discussed in sec. 5). 4. Changes in migratory bird nesting and foraging habitats resulting from sediment removal and placement (discussed in sec. 6). 5. Long-term impacts of sediment removal and placement on physical coastal resiliency (discussed in sec. 7).

Open-File Report↗

USGS2010

Limits on the adaptability of coastal marshes to rising sea level

Assumptions of a static landscape inspire predictions that about half of the world's coastal wetlands will submerge during this century in response to sea-level acceleration. In contrast, we use simulations from five numerical models to quantify the conditions under which ecogeomorphic feedbacks allow coastal wetlands to adapt to projected changes in sea level. In contrast to previous sea-level assessments, we find that non-linear feedbacks among inundation, plant growth, organic matter accretion, and sediment deposition, allow marshes to survive conservative projections of sea-level rise where suspended sediment concentrations are greater than ~20 mg/L. Under scenarios of more rapid sea-level rise (e.g., those that include ice sheet melting), marshes will likely submerge near the end of the 21st century. Our results emphasize that in areas of rapid geomorphic change, predicting the response of ecosystems to climate change requires consideration of the ability of biological processes to modify their physical environment.

Geophysical Research Letters↗

USGS1996

Water-quality, streamflow, and meteorological data for the Tualatin River Basin, Oregon, 1991-93

Surface-water-quality data, ground-water-quality data, streamflow data, field measurements, aquatic-biology data, meteorological data, and quality-assurance data were collected in the Tualatin River Basin from 1991 to 1993 by the U.S. Geological Survey (USGS) and the Unified Sewerage Agency of Washington County, Oregon (USA). The data from that study, which are part of this report, are presented in American Standard Code for Information Interchange (ASCII) format in subject-specific data files on a Compact Disk-Read Only Memory (CD-ROM). The text of this report describes the objectives of the study, the location of sampling sites, sample-collection and processing techniques, equipment used, laboratory analytical methods, and quality-assurance procedures. The data files on CD-ROM contain the analytical results of water samples collected in the Tualatin River Basin, streamflow measurements of the main-stem Tualatin River and its major tributaries, flow data from the USA wastewater-treatment plants, flow data from stations that divert water from the main-stem Tualatin River, aquatic-biology data, and meteorological data from the Tualatin Valley Irrigation District (TVID) Agrimet Weather Station located in Verboort, Oregon. Specific information regarding the contents of each data file is given in the text. The data files use a series of letter codes that distinguish each line of data. These codes are defined in data tables accompanying the text. Presenting data on CD-ROM offers several advantages: (1) the data can be accessed easily and manipulated by computers, (2) the data can be distributed readily over computer networks, and (3) the data may be more easily transported and stored than a large printed report. These data have been used by the USGS to (1) identify the sources, transport, and fate of nutrients in the Tualatin River Basin, (2) quantify relations among nutrient loads, algal growth, low dissolved-oxygen concentrations, and high pH, and (3) develop and calibrate a water- quality model that allows managers to test options for alleviating water-quality problems.

Oregon↗

USGS1997

Investigation into avian mortality in the Playa Lakes region of southeastern New Mexico: Final Report - June 1997

This Final Report is a review of work on a cooperative study undertaken by the USGS Biological Resources Division's National Wildlife Health Center (NWHC) and National Wetlands Research Center (NWRC; formerly the Southern Science Center) from 1994 through 1997. The study was initiated at the request of the Bureau of Land Management (BLM), through a request to the former National Biological Service. The Southeastern New Mexico Playa Lakes Coordinating Committee (SENMPLCC) played an important role in outlining the research needs. The initial Study Plan document, which outlines the background, objectives and methods for the first two years is available as Appendix 1. A letter indicating modifications to the Study Plan was sent to the SENMPLCC chair on April 25,1995, and is Appendix 2. An Interim Report, covering this work was completed and submitted in September 1995. The Literature Review section of the study was completed and presented to SENMPLCC in August, 1995. Following SENMPLCC review, NWHC was asked to develop a series of questions that could be posed from information gained in the initial phase (Appendix 3). The NWHC and NWRC were then directed to begin work to answer the top three questions, within the available fiscal resources. NWRC could continue with work outlined under the original Study Plan (Appendix 1), however an additional Study Plan for experiments performed by NWHC and collaborators and is available as Appendix 4.

New Mexico↗

USGS2009

Thallium isotope evidence for a permanent increase in marine organic carbon export in the early Eocene

The first high resolution thallium (Tl) isotope records in two ferromanganese crusts (Fe-Mn crusts), CD29 and D11 from the Pacific Ocean are presented. The crusts record pronounced but systematic changes in 205Tl/203Tl that are unlikely to reflect diagenetic overprinting or changes in isotope fractionation between seawater and Fe-Mn crusts. It appears more likely that the Fe-Mn crusts track the Tl isotope composition of seawater over time. The present-day oceanic residence time of Tl is estimated to be about 20,000??yr, such that the isotopic composition should reflect ocean-wide events. New and published Os isotope data are used to construct age models for these crusts that are consistent with each other and significantly different from previous age models. Application of these age models reveals that the Tl isotope composition of seawater changed systematically between ~ 55??Ma and ~ 45??Ma. Using a simple box model it is shown that the present day Tl isotope composition of seawater depends almost exclusively on the ratio between the two principal output fluxes of marine Tl. These fluxes are the rate of removal of Tl from seawater via scavenging by authigenic Fe-Mn oxyhydroxide precipitation and the uptake rate of Tl during low temperature alteration of oceanic crust. It is highly unlikely that the latter has changed greatly. Therefore, assuming that the marine Tl budget has also not changed significantly during the Cenozoic, the low 205Tl/203Tl during the Paleocene is best explained by a more than four-fold higher sequestration of Tl by Fe-Mn oxyhydroxides compared with at the present day. The calculated Cenozoic Tl isotopic seawater curve displays a striking similarity to that of S, providing evidence that both systems may have responded to the same change in the marine environment. A plausible explanation is a marked and permanent increase in organic carbon export from ~ 55??Ma to ~ 45??Ma, which led to higher pyrite burial rates and a significantly reduced flux of Fe-Mn oxide removal as a result of increased biological uptake of Fe and Mn. ?? 2008 Elsevier B.V. All rights reserved.

Earth and Planetary Science Letters↗

USGS1929

A preliminary report on the growth of the rock bass, Ambloplites rupestris (Rafinesque), in two lakes of northern Wisconsin

For several years the Wisconsin Geological and Natural History Survey has been making a limnological study of lakes in the northern part of the State. Because of the fact that so much has been learned of the physical, chemical and biological conditions in these lakes, the region seems particularly favorable for a study of the growth rates of fishes in relation to environmental factors.

Transactions of the Wisconsin Academy of Sciences,↗

USGS1997

A system for monitoring impact of Denali National Park road traffic on wildlife

The Denali National Park and Preserve (DENA) is a 6.03 million acre reserve lying between Anchorage and Fairbanks, Alaska. The park was established in 1917 as a wildlife refuge, and is managed to maintain the wilderness character. With the highest mountain in North America, Mt. McKinley, and the easy availability of wildlife for viewing, the park is Alaska's most favored destination point. From 1972 through 1984, visitation grew from 88, 615 to 394, 426 visitor days per year (GMP, 1986), and then increased by 50,000 per year to 596,000 visitors in 1988. This demand for motorized access to the park, especially along the 92.5 mile-long park road, has resulted in controversy and claims of traffic disturbance to wildlife [(letter from Superintendent, DENA July 13, 1988) (Anchorage Daily News, May 14, 1995; May 26, 1995; February 5, 1996; June 18, 1996) Leo (1987); Lee Rue (1996)].

Biological Science Report↗

USGS2019

Do Indigenous American Peoples’ stories inform the study of dog domestication?

I discuss the article “Relationships Between Indigenous American Peoples and Wolves 1: Wolves as Teachers and Guides” (Fogg et al. 2015) and the book “The First Domestication: How Wolves and Humans Coevolved” (Pierotti and Fogg 2017). The article proposed that published stories about interactions between indigenous American peoples and wolves ( Canis lupus ) provide insight into wolf-human relationships as humans began domesticating wolves. In the book, the authors offer a theory of how wolves and humans coevolved by building on the information in the article and the authors’ long experience with captive and pet wolves, wolf-dog hybrids, and dogs. I (1) present arguments and evidence that question the value of indigenous American stories for drawing conclusions about the relationship between early humans and wolves 14,000 yrs BP; (2) demonstrate how indigenous American stories contradict documented information about wolf biology, behavior, and known interactions with humans; and (3) point out important information not considered by the authors about wolf attacks on humans and the importance of rabies in the wolf-human relationship.

Ethnobiological Letters↗

USGS2023

Deep root activity overprints weathering of petrogenic organic carbon in shale

The oxidation of organic carbon in sedimentary bedrock (petrogenic OC, OC p e t r o "> petro ) is increasingly recognized as a potential source of CO 2 to the atmosphere. Recent studies provide evidence for the mobilization and oxidation of OC p e t r o "> petro in sedimentary bedrock during rock weathering. However, the mechanisms and rates remain uncertain, particularly where overlying soils and vegetation drive contemporaneous oxidation of recently fixed organic carbon. Here, we quantify OC p e t r o "> petro weathering across a 16 m shale depth profile in a steep, rapidly eroding forested hillslope in the Northern California Coast Ranges. We report solid and gas phase radiocarbon and stable isotope analyses of samples extracted from specialized in-situ samplers, and a supporting laboratory incubation experiment of the shale regolith. OC p e t r o "> petro is removed from the weathered bedrock at a rate of approximately 0.12 gC/m 3 yr, which is orders of magnitude lower than the rate of OC p e t r o "> petro oxidation we achieved in the laboratory with crushed samples (557.1 gC/m 3 /yr). This disparity occurs despite high O 2 ( g ) "> 2(g) content across the depth profile, indicating that physical accessibility of OC p e t r o "> petro can regulate oxidative weathering. There is no direct radiocarbon evidence of OC p e t r o "> petro oxidation in CO 2 ( g ) "> 2(g) across the upper 13 m of the weathering profile during both wet and dry seasons. Instead, vadose zone CO 2 ( g ) "> 2(g) production at the site is dominated by respiration of recently fixed carbon associated with deep rooting. OC p e t r o "> petro is clearly mobilized across the vadose zone during weathering in this rapidly eroding, oxygen-rich, biologically dynamic hillslope, but at rates far below what can be measured given the contribution of root-derived CO 2 ( g ) "> 2(g) .

California↗

USGS1993

Volcanic eruption of the mid-ocean ridge along the East Pacific Rise crest at 9°45-52'N: direct submersible observations of seafloor phenomena associated with an eruption event in April, 1991

In April, 1991, we witnessed from the submersible Alvin a suite of previously undocumented seafloor phenomena accompanying an in-progress eruption of the mid-ocean ridge on the East Pacific Rise crest at 9°45′N–52′N. The volume of the eruption could not be precisely determined, although comparison of pre- and post-eruption SeaBeam bathymetry indicate that any changes in ridge crest morphology resulting from the eruption were < 10 m high. Effects of the eruption included: (1) increased abundance and redistribution of hydrothermal vents, disappearance of numerous vent communities, and changes in characteristics of vent fauna and mineral deposits within the eruption area since December, 1989; (2) murkiness of bottom waters up to tens of meters above the seafloor due to high densities of suspended mineral and biogenic particulates; (3) destruction of a vent community by lava flows, mass wasting, and possible hydrovolcanic explosion at a site known as ‘Tubeworm Barbecue’ in the axial summit caldera (ASC) at 9°50.6′N; (4) near-critical temperatures of hydrothermal vent fluids, ranging up to 403°C; (5) temporal variations over a 2 week interval in both temperatures and chemical/isotopic compositions of hydrothermal fluids; (6) unusual compositions of end-member vent fluids, with pH values ranging to a record low of 2.5, salinities ranging as low as 0.3 wt% NaCl (one-twelfth that of seawater), and dissolved gases reaching high concentrations (> 65 mmol/l for both CO 2 and H 2 S); (7) venting at temperatures above 380°C of visually detectable white vapor that transformed to plumes of gray smoke a few centimeters above vent orifices; (8) disorganized venting of both high-temperature fluids (black and gray smoke) and large volumes of cooler, diffuse hydrothermal fluids directly from the basaltic seafloor, rather than from hydrothermal mineral constructions; (9) rapid and extensive growth of flocculent white bacterial mats (species unknown) on and under the seafloor in areas experiencing widespread venting of diffuse hydrothermal fluid; and (10) subseafloor downslope migration of magma normal to the ridge axis in a network of small-scale (1–5 m diameter) lava tubes and channels to distances at least 100–200 m outside the ASC. We suggest that, in April, 1991, intrusion of dikes in the eruption area to < 200 m beneath the ASC floor resulted in phase separation of fluids near the tops of the dikes and a large flux of vapor-rich hydrothermal fluids through the overlying rubbly, cavernous lavas. Low salinities and gas-rich compositions of hydrothermal fluids sampled in the eruption area are appropriate for a vapor phase in a seawater system undergoing subcritical liquid-vapor phase separation (boiling) and phase segregation. Hydrothermal fluids streamed directly from fissures and pits that may have been loci of lava drainback and/or hydrovolcanic explosions. These fissures and pits were lined with white mats of a unique fast-growing bacteria that was the only life associated with the brand-new vents. The prolific bacteria, which covered thousands of square meters on the ridge crest and were also abundant in subseafloor voids, may thrive on high levels of gases in the vapor-rich hydrothermal fluids initially escaping the hydrothermal system. White bacterial particulates swept from the seafloor by hydrothermal vents swirled in an unprecedented biogenic ‘blizzard’ up to 50 m above the bottom. The bacterial proliferation of April, 1991 is likely to be a transient bloom that will be checked quickly either by decline of dissolved gas concentrations in the fluids as rapid heat loss brings about cessation of boiling, and/or by grazing as other organisms are re-established in the biologically devastated area.

Earth and Planetary Science Letters↗