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Publications recently added to the Pubs Warehouse

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Estimated total phosphorus loads for selected sites on Great Lakes tributaries, water years 2014–2018

Released March 04, 2021 15:39 EST

2021, Open-File Report 2020-1145

G.F. Koltun

Monthly and annual total phosphorus loads were estimated for water years 2014 through 2018 for 23 streamgaged (gaged) sites on tributaries to the Great Lakes. Processing and regression methods described by Robertson and others (2018) were used with discrete and continuous data collected during water years 2011 and 2018 to update regression models for estimating instantaneous flux with the same form of equations as published by Robertson and others (2018). Monthly and water year average fluxes for all but two of the 23 gage sites were estimated using a weighted combination of results from surrogate models (which have streamflow, turbidity, and seasonal indicators as explanatory variables) and unit-value (UV)-flow models which have only UV streamflow and seasonal indicators as explanatory variables. Two of the gage sites had extensive periods of missing turbidity records, so average flux estimates for those stations were based solely on results from UV-flow models.

For most sites, estimated loads of total phosphorus were computed and summed for water years 2014–2018. The cumulative loads were used to compute yields and flow-weighted mean concentrations for water years 2014–2018. The estimated cumulative total phosphorus loads for water years 2014–2018 ranged from 112 to 11,500 metric tons. The Maumee River site (U.S. Geological Survey gage number 04193500) had the largest estimated cumulative load for water years 2014–2018 and the third largest estimated flow-weighted mean concentration. In fact, the estimated cumulative load at the Maumee River site was more than three times larger than the second largest estimated cumulative load.

Estimated average annual total phosphorus yields and flow-weighted mean concentrations for water years 2014–2018 ranged from 0.016 metric tons per square kilometer to 0.771 metric tons per square kilometer and 0.033 milligram per liter to 0.466 milligram per liter, respectively. The Cattaraugus Creek gage site (U.S. Geological Survey gage number 04213500) had the highest estimated average annual total phosphorus yield and flow-weighted mean concentration. The average annual total phosphorus yield at the Cattaraugus Creek gage site was almost twice as large as the second largest estimated yield.

Cooperative Fish and Wildlife Research Units program—2020 Year in review

Released March 04, 2021 15:20 EST

2021, Circular 1478

John D. Thompson, Donald E. Dennerline, Dawn E. Childs, Patrick G.R. Jodice

Established in 1935, the Cooperative Fish and Wildlife Research Units program (CRU program) is a unique cooperative partnership among State fish and wildlife agencies, universities, the Wildlife Management Institute, the U.S. Geological Survey (USGS), and the U.S. Fish and Wildlife Service. Designed to meet the scientific needs of natural resource management agencies and the necessity for trained professionals in the growing field of wildlife management, the program has grown from the original 9 wildlife-only units to a program that today includes 40 Cooperative Fish and Wildlife Research Units located on university campuses in 38 States. The partnerships that form each unit are some of the USGS’s strongest links to Federal and State land and natural resource agencies as mandated by the Cooperative Research and Training Units Act of 1960 (P.L. 86–686). This report highlights the activities and accomplishments of the program and its cooperators for calendar year 2020.

Practical field survey operations for flood insurance rate maps

Released March 04, 2021 08:00 EST

2021, Open-File Report 2020-1146

Nicholas J. Taylor, Caelan E. Simeone

The U.S. Geological Survey assists the Federal Emergency Management Agency in its mission to identify flood hazards and zones for risk premiums for communities nationwide, by creating flood insurance rate maps through updating hydraulic models that use river geometry data. The data collected consist of elevations of river channels, banks, and structures, such as bridges, dams, and weirs that can affect flow. To account for the model complexity of river structure hydraulics and the fidelity between river channel and structure geometry, two distinct standards for collecting geometry data are presented, both using global navigation satellite system real-time network surveying. This method is adapted from U.S. Geological Survey manuals and is foundational in hydraulic surveying for flood insurance rate maps.

Fungal life-styles and ecosystem dynamics: Biological aspects of plant pathogens, plant endophytes and saprophytes

Released March 04, 2021 00:00 EST

1997, Advances in Botanical Research (24) 169-193

R.J. Rodriguez, R.S. Redman

This chapter discusses various biochemical, genetic, ecological, and evolutionary aspects of fungi that express either symbiotic or saprophytic life-styles. An enormous pool of potential pathogens exists in both agricultural and natural ecosystems, and virtually all plant species are susceptible to one or more fungal pathogens. Fungal pathogens have the potential to impact on the genetic structure of populations of individual plant species, the composition of plant communities and the process of plant succession. Endophytic fungi exist for at least part of their life cycles within the tissues of a plant host. This group of fungi is distinguished from plant pathogens because they do not elicit significant disease symptoms. However, endophytes do maintain the genetic and biochemical mechanisms required for infection and colonization of plant hosts. Fungi that obtain chemical nutrients from dead organic matter are known as saprophytes and are critical to the dynamics and resilience of ecosystems. There are two modes of saprophytic growth: one in which biomolecules that are amenable to transport across cell walls and membranes are directly absorbed, and another in which fungi must actively convert complex biopolymers into subunit forms amenable to transportation into cells. Regardless of life-style, fungi employ similar biochemical mechanisms for the acquisition and conversion of nutrients into complex biomolecules that are necessary for vegetative growth, production and dissemination of progeny, organismal competition, and survival during periods of nutrient deprivation or environmental inclemency.

Groundwater management process simulations using an updated version of the three-dimensional numerical model of groundwater flow in northern Utah Valley, Utah County, Utah

Released March 02, 2021 20:39 EST

2021, Scientific Investigations Report 2021-5010

Bernard J. Stolp, Lynette E. Brooks

Groundwater is a primary source of drinking water in northern Utah County. The groundwater system is recharged mainly from precipitation in the adjacent Wasatch Mountains and infiltration of streamflow. In 2004, groundwater withdrawals were estimated to be roughly 44,500 acre-feet per year. In 2016, groundwater withdrawals were estimated to be greater than 63,400 acre-feet per year. To prepare for anticipated future increases in groundwater withdrawals, local cities identified 16 locations as feasible for managed aquifer recharge. Using an updated version of an existing U.S. Geological Survey groundwater flow model of northern Utah County, the Groundwater-Management Process for MODFLOW-2005 was used to investigate optimal managed aquifer recharge scenarios with the objective of maintaining acceptable reductions in simulated discharge at 12 groundwater discharge areas and flowing wells along Utah Lake.

The Groundwater-Management Process is applied to a 50-year (2017–66) projection of groundwater conditions using average recharge conditions and a linear increase of approximately 750 acre-feet per year of municipal groundwater withdrawals. Two sets of discharge constraints were applied. The first scenario constrains discharge to greater than or equal to 80 percent of the 2016 simulated groundwater discharge along Utah Lake. The constraint was met with a total managed aquifer recharge rate of roughly 7,300 acre-feet per year during 2042–56, and 15,600 acre-feet per year during 2057–66. A second scenario constrains discharge to greater than or equal to 90 percent of the 2016 simulated discharge. This constraint can only be met at 8 of the 12 discharge areas along Utah Lake. This required a managed aquifer recharge rate of roughly 10,000 acre-feet per year during 2042–56 and 15,400 acre-feet per year during 2057–66. For both scenarios, the Groundwater-Management Process indicated that all managed aquifer recharge sites need to be used to meet discharges constraints. The discharge constraints were informally defined on the basis of the water rights hierarchy associated with Utah Lake.

Spatial variation in population dynamics of northern Great Plains piping plovers

Released March 02, 2021 15:55 EST

2021, Open-File Report 2020-1152

Rose J. Swift, Michael J. Anteau, Kristen S. Ellis, Megan M. Ring, Mark H. Sherfy, Dustin L. Toy, David N. Koons

Metapopulation dynamics are determined not only by within-patch birth and death processes but also by between-patch movements of individuals (emigration and immigration). To conserve and manage a species that has a metapopulation structure, defined by local populations that are distributed among patches of suitable habitat, we need to understand each of these vital rates. For the federally listed northern Great Plains Charadrius melodus (Ord, 1824) (piping plover), managers assumed a metapopulation structure consisting of four breeding groups with low, balanced dispersal, which resulted in low extinction risk in a simulation-based viability study. The degree to which the northern Great Plains piping plover breeding population functions as a metapopulation depends on the rate of movement amongst breeding areas. Sources of variation in survival, dispersal probabilities, and dispersal distances were examined for hatch-year and adult piping plovers breeding in the northern Great Plains from 2014 to 2019 focusing on four management units (U.S. Alkali Wetlands, Lake Sakakawea, Garrison Reach of the Missouri River, and Lake Oahe). Additionally, renesting probabilities, renest reproductive success, and reproductive output were investigated from 2014 to 2016 in each of these areas to understand within-patch productivity. This report includes two major sections: (1) a presentation that includes the context, results, and implications of the study, followed by a detailed text methodology, and (2) an appendix that provides synthesized estimates of piping plover vital rates from throughout their range. River and alkali wetland habitats seem to be of higher quality than reservoir habitats, although alkali wetland habitats have lower annual survival, lower reproductive output, and lower fidelity probabilities than riverine habitats. Habitat availability drove dispersal probabilities and dispersal distances for hatch-year and adult piping plovers. Renesting propensity and renest reproductive success were generally low, suggesting that renesting is an uncommon and unproductive strategy to replace most lost reproductive attempts. Estimates indicated high connectivity between the U.S. Alkali Wetlands and the northern river units (Lake Sakakawea, Garrison Reach, Lake Oahe) of the Missouri River, suggesting that the assumed metapopulation structure and population viability may need to be reassessed.

Chapter A6.4. Measurement of pH

Released March 02, 2021 11:55 EST

2021, Techniques and Methods 9-A6.4

U. S. Geological Survey

The “National Field Manual for the Collection of Water-Quality Data” (NFM) provides guidelines and procedures for U.S. Geological Survey (USGS) personnel who collect data used to assess the quality of the Nation’s surface-water and groundwater resources. This chapter, NFM A6.4, provides guidance and protocols for the measurement of pH of a water sample, which include the scientific basis of the measurement, selection and maintenance of equipment, calibration, procedures for measurement and reporting, and troubleshooting. It updates and supersedes USGS Techniques of Water-Resources Investigations, book 9, chapter A6.4, version 2.0, by G.F. Ritz and J.A. Collins. The pH of natural waters is routinely measured when water samples are collected, is often measured continually at USGS streamgages, and is a parameter regularly measured during laboratory and field experiments. The field methods for measuring pH described in this chapter are applicable to most natural waters.

Before 2017, the NFM chapters were released in the USGS Techniques of Water-Resources Investigations series. Effective in 2018, new and revised NFM chapters are being released in the USGS Techniques and Methods series; this series change does not affect the content and format of the NFM. More information is in the general introduction to the NFM (USGS Techniques and Methods, book 9, chapter A0) at The authoritative current versions of NFM chapters are available in the USGS Publications Warehouse at Comments, questions, and suggestions related to the NFM can be addressed to

Procedures for field data collection, processing, quality assurance and quality control, and archiving of relative- and absolute-gravity surveys

Released March 02, 2021 08:20 EST

2021, Techniques and Methods 2-D4

Jeffrey R. Kennedy, Donald R. Pool, Robert L. Carruth

Repeat microgravity surveys carried out using relative- and absolute-gravity meters are useful for identifying changes in subsurface mass, such as the volume of water stored in an aquifer. These surveys require careful field procedures to achieve the part-per-billion accuracy required to measure the small changes in gravity relevant for hydrologic studies. This chapter describes techniques and methods for carrying out gravity surveys, requirements for assuring high-quality survey results, and data processing and archival procedures. The focus is on acquiring and documenting repeat gravity surveys for monitoring changes in groundwater storage. Similar gravity surveys may be completed to evaluate other causes of mass change, such as those caused by magma movement below volcanoes. The methods are also useful for one-time surveys that map spatial gravity variations associated with geologic structures such as faults or sedimentary basins.

Repeat microgravity surveys can be carried out using relative-gravity meters, absolute-gravity meters, or both. Specific locations, known as gravity stations, are visited during each survey. Most commonly, absolute- and relative-gravity are combined using the least-squares method of network adjustment, much like benchmark elevations and relative-height differences in a leveling network. This chapter primarily describes the use of the A-10 absolute-gravity meter manufactured by Micro-g LaCoste, Inc., and relative-gravity meters made by LaCoste & Romberg (no longer in production) and ZLS Corporation, Inc. Field and office procedures are similar for other instruments such as the FG-5 absolute-gravity meter and Scintrex relative-gravity meters, but some adaptation may be required. Quality control for absolute-gravity data focuses primarily on proper field procedures and maintaining the time and distance calibration of the instrument. Quality control for relative-gravity surveys requires careful field procedures, an understanding of how the meter is behaving while in the field, and appropriate postprocessing.

The techniques and methods described in this chapter were developed over 30 years at the USGS Arizona Water Science Center and the Southwest Gravity Program and are the basis for many studies on groundwater-storage change and geologic structure. A description of the Program and complete bibliography is available at

Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis)

Released March 02, 2021 07:05 EST

2021, Ecology and Evolution

Alynn Marie Martin, E. Frances Cassirer, Lisette P. Waits, Raina K. Plowright, Paul C. Cross, Kimberly R. Andrews

Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population‐level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well‐studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family‐based genome‐wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome‐wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP‐based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.

Review of the invasive Asian clam Corbicula spp. (Bivalvia: Cyrenidae) distribution in North America, 1924–2019

Released March 01, 2021 17:11 EST

2021, Scientific Investigations Report 2021-5001

Amy J. Benson, James D. Williams

The bivalve Corbicula is one of the most successful aquatic mollusk invaders in the world. Since being intro­duced to North America from its native range in Asia, it has dispersed widely over a large portion of the continent from southern Canada to Panama. The first evidence of its introduc­tion in the Western Hemisphere was discovered in 1924 in British Columbia, Canada. A review of distribution records from natural history museums, scientific literature, Federal and State agencies, universities, and oral and written commu­nications with scientists has shown the continued dispersal of Corbicula in North America. Since the most recent compre­hensive review of its distribution information through the mid-1980s, Corbicula has been found in an additional 2 Canadian Provinces, 10 U.S. States and Puerto Rico, 9 Mexican States, Cuba, and Panama. The known distribution in North America now includes 47 U.S. States, District of Columbia, Puerto Rico, 3 Canadian Provinces, 16 Mexican States, Cuba, and Panama. Corbicula has been found in three of the Laurentian Great Lakes (Erie, Michigan, Superior) primarily associated with industrial warmwater effluent refugia. Problems associ­ated with Corbicula populations were widely realized not long after its arrival and included negative impacts to power generation, industrial water supply operations, and agricultural water conveyance. In natural settings, impacts on native mus­sels such as altering nutrient cycling, food webs, and sediment distribution dynamics have occurred. In past decades, control of established open water populations had not been a manage­ment priority. With a relatively recent interest in eradication of small, newly established populations, several attempts were made in the United States but were unsuccessful. Recent molecular genetic analyses provide evidence of multiple species and (or) genetically and morphologically distinguish­able “forms” in North America. However, the number and identification of Corbicula species in North America remain unresolved. It appears likely that more than one species of Corbicula has been introduced into U.S. waters.

Compilation of information on occurrence and conservation status for the freshwater mussel fauna of Nebraska, Kansas, and Oklahoma

Released March 01, 2021 13:00 EST

2021, Data Series 1133

Natasha B. Carr, Tammy S. Fancher

The purpose of this data series is to compile information on the occurrence and conservation status of the freshwater mussel fauna of Nebraska, Kansas, and Oklahoma and to map the distribution of a freshwater mussel assemblage for the U.S. Department of the Interior, Bureau of Land Management Rapid Ecoregional Assessment (REA) program. The six focal species in the freshwater mussel assemblage are Amblema plicata (threeridge), Fusconaia flava (Wabash pigtoe), Lampsilis cardium (plain pocketbook), Lampsilis teres (yellow sandshell), Pyganodon grandis (giant floater), and Uniomerus tetralasmus (pondhorn). The focal species were selected using the following criteria: (1) the species are regionally significant, (2) occurrence records are sufficient to map the distribution of the species by hydrologic subbasins, (3) the assemblage includes species representing a range of State-level conservation priorities, and (4) the species are not listed as federally endangered or threatened. In addition, the species represent a broad array of life history strategies and habitat associations.

A total of 61 native species of freshwater mussels have documented occurrences within at least 1 of the 3 States, including 6 species that appear to have been extirpated from all the States and 6 species that may have been extirpated from at least 1 State. Of the 61 species, 8 species (including 3 potentially extirpated species) are listed as federally threatened or endangered and an additional 5 species are ranked as imperiled or vulnerable across their range. Approximately 80 percent of the native species known to have occurred within the three-State area have a secure conservation status, in comparison to only 40 percent of all freshwater mussel species or subspecies occurring within the United States. The compiled records for the contemporary period (1970–2017) documented the occurrence of 24 extant species in Nebraska, 42 in Kansas, and 48 in Oklahoma.

The contemporary distributions of the six focal species were mapped by subbasins and the larger hydrologic subregions. Historical records (prior to 1962) were also mapped but were limited. Amblema plicata, Fusconaia flava, and Lampsilis cardium were present in approximately one-third of all subbasins and slightly more than half of the subregions, primarily along the eastern portion of the three-State area. Lampsilis teres and Uniomerus tetralasmus were more widespread, occurring in close to half of the subbasins and about three-quarters of the subregions. Pyganodon grandis was the most widespread, occurring in about three-quarters of the subbasins and almost all subregions. There were very few subbasins with historical occurrences that lacked contemporary occurrences. The broad-scale distribution maps for the freshwater mussel assemblage presented with this report are intended to contribute baseline information for regional assessments, such as the Southern Great Plains Rapid Ecoregional Assessment. Despite the limitations of the available data, such baseline information can be useful for identifying data gaps, monitoring future trends, identifying conservation priorities, and providing the larger context for more detailed watershed- or catchment-level studies. ScienceBase data release files associated with this data series are available at 10.5066/ P9SBFZJU (Fancher and Carr, 2021)

Geomagnetic monitoring in the mid-Atlantic United States

Released March 01, 2021 12:00 EST

2021, Fact Sheet 2021-3001

Jeffrey J. Love, Kristen A. Lewis

Near historic battlegrounds of the American Civil War, southeast of Fredericksburg, Virginia, on a secluded grassy glade surrounded by forest, a specially designed observatory records the Earth’s changing magnetic field. This facility, the Fredericksburg Magnetic Observatory, is 1 of 14 observatories the U.S. Geological Survey Geomagnetism Program operates at various locations across the United States and its Territories as a service to the Nation and in support of a diversity of governmental, academic, and commercial scientific projects.

Comparing tree-ring based reconstructions of snowpack variability at different scales for the Navajo Nation

Released March 01, 2021 07:53 EST

2021, Climate Services (22)

Rebecca Lynn Brice, Christopher H. Guiterman, Connie A. Woodhouse, Carlee McClellan, Paul Sheppard

Snowpack in the western U.S. is on the decline, largely attributed to increasing temperatures in the region. This is a critical issue for many Native American communities who disproportionately rely on local snow-fed water supplies. In light of a combined ongoing drought and limited climate information for the Navajo Nation, Navajo water managers face decision-making challenges complicated by past and future climate uncertainty. Developed in partnership with the Navajo Nation Water Management Branch, this study documents two snowpack reconstruction options to address Navajo concerns about the amount and variability of snowpack in the Chuska Mountains. We used two separate snowpack datasets with tree rings collected in northern Arizona to develop and evaluate reconstructions of Chuska snowpack and their potential relevance and usefulness to Navajo water managers’ decision-making. We found that both reconstructions skillfully estimated snowpack, though there were differences that may have meaningful implications for water managers. Major snow droughts occurred roughly once per century over the last 300 years, with droughts in 1728–1744, 1818–1834, 1950–1977, and 1999–2006. Extremely dry individual years in each reconstruction punctuate multi-year drought periods in a way that has not been recognized from instrumental data alone and that can have a large influence on the overall intensity of a given drought. The reconstruction that is most representative of Chuska snowpack has less explanatory power than the regionally representative reconstruction, but the Chuska reconstruction effectively captures snowpack extremes and snow drought timing unique to the Chuska Mountains, and may hold greater relevance to Navajo water management.

Rock gnome lichen (Gymnoderma lineare) monitoring assessment, southern Appalachian Mountains, 1983–2008

Released March 01, 2021 07:22 EST

2021, Open-File Report 2021-1011

Andrea Woodward

Rock gnome lichen (Gymnoderma lineare [Evans] Yoshimura and Sharp) was listed as a federally endangered species in 1995. It is endemic to the southern Appalachian Mountains, with most known populations occurring in North Carolina, where it grows on vertical rock faces in the fog zone above an elevation of 1,525 meters or in humid, deep river gorges. Threats to the species include recreational use of habitat by hikers, climbers and sightseers; collectors; changes in microclimate due to loss of Fraser fir (Abies fraseri) to the exotic pest balsam woolly adelgid (Adelges piceae); air pollution; and climate change. Quantified estimates of population size are limited in number and only are available from 1983 to 2008. They show that known rock gnome populations increased in number during this period and increased in size from 1996 to 2008. The period of increase coincided with negative trends in nitrogen and sulfur deposition, stable precipitation and streamflow, and a positive trend in air temperature. Populations may have been afforded greater protection from recreational activities and collectors during this time. Specific incidents of population decline were associated with a high streamflow event and loss of shade owing to a fallen Fraser fir. Although the outlook for rock gnome lichen seems to have improved through 2008, threats from climate change and increasing human activity likely are increasing.

Seal body condition and atmospheric circulation patterns influence polar bear body condition, recruitment, and feeding ecology in the Chukchi Sea

Released February 28, 2021 07:14 EST

2021, Global Change Biology

Karyn D. Rode, Eric V. Regehr, Jeffrey F. Bromaghin, Ryan R. Wilson, Michelle St. Martin, Justin A. Crawford, Lori T. Quakenbush

Polar bears (Ursus maritimus) are experiencing loss of sea ice habitats used to access their marine mammal prey. Simultaneously, ocean warming is changing ecosystems that support marine mammal populations. The interactive effects of sea ice and prey are not well understood yet may explain spatial‐temporal variation in the response of polar bears to sea ice loss. Here, we examined the potential combined effects of sea ice, seal body condition and atmospheric circulation patterns on the body condition, recruitment, diet, and feeding probability of 469 polar bears captured in the Chukchi Sea, 2008‐2017. The body condition of ringed seals (Pusa hispida), the primary prey of females and subadults, was related to dietary proportions of ringed seal, feeding probability, and the body condition of females and cubs. In contrast, adult males consumed more bearded seals (Erignathus barbatus) and exhibited better condition when bearded seal body condition was higher. The litter size, number of yearlings per adult female, and the condition of dependent young were higher following winters characterized by low Arctic Oscillation (AO) conditions, consistent with a growing number of studies. Body condition, recruitment, and feeding probability were either not associated or negatively associated with sea ice conditions, suggesting that, unlike some subpopulations, Chukchi Sea bears are not currently limited by sea ice availability. However, spring sea ice cover declined 2% per year during our study reaching levels not previously observed in the satellite record and resulting in the loss of polar bear hunting and seal pupping habitat. Our study suggests that the status of ice seal populations is likely an important factor that can either compound or mitigate the response of polar bears to sea ice loss over the short‐term. In the long‐term, neither polar bears nor their prey are likely robust to limitless loss of their sea ice habitat.

Composition and distribution of fish environmental DNA in an Adirondack watershed

Released February 26, 2021 10:24 EST

2021, PeerJ (9)

Robert S. Cornman, James E. McKenna Jr., Jennifer A. Fike


Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration.


We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments.


We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.

The contribution of water radiolysis to marine sedimentary life

Released February 26, 2021 08:22 EST

2021, Nature Communications (12)

Justine F. Sauvage, Ashton Flinders, Arthur J. Spivack, Robert Pockalny, Ann G. Dunlea, Chloe H. Anderson, David Smith, Richard W. Murray, Steven D’Hondt

Water radiolysis continuously produces H2 and oxidized chemicals in wet sediment and rock. Radiolytic H2 has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth’s surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H2 production, amplifying yields by up to 27X relative to pure water. In electron equivalents, the global rate of radiolytic H2 production in marine sediment appears to be 1-2% of the global organic flux to the seafloor. However, most organic matter is consumed at or near the seafloor, whereas radiolytic H2 is produced at all sediment depths. Comparison of radiolytic H2 consumption rates to organic oxidation rates suggests that water radiolysis is the principal source of biologically accessible energy for microbial communities in marine sediment older than a few million years. Where water permeates similarly catalytic material on other worlds, life may also be sustained by water radiolysis.

Nitrogen and phosphorus sources and delivery from the Mississippi/Atchafalaya River Basin: An update using 2012 SPARROW models

Released February 26, 2021 07:37 EST

2021, Journal of the American Water Resources Association

Dale M. Robertson, David A. Saad

Nitrogen (N) and phosphorus (P) inputs throughout the Mississippi/Atchafalaya River Basin (MARB) have been linked to the Gulf of Mexico hypoxia and water‐quality problems throughout the MARB. To describe N and P loading throughout the MARB, SPAtially Referenced Regression On Watershed attributes (SPARROW) models were previously developed based on nutrient inputs and management similar to 1992 and 2002. In this study, refined SPARROW models were developed with higher resolution basin delineation, updated (2012) source inputs, improved calibration (load) targets, and additional statistical techniques than used in the previous SPARROW models. Based on the refined models, consistent with past models, N and P loads/yields were the highest from the central part of the MARB (Corn Belt) and along the Mississippi River. Agricultural activities remained the most important N and P source, but more so for N because its input, which could now be distinguished from atmospheric deposition, could be estimated. Natural loss of P from geologic material throughout the MARB was an important source, contributing about 23% of the total P from the MARB, and resulted in specific areas, such as Kentucky and Tennessee, being larger sources of P than previously estimated. This information can help managers decide where efforts will have the largest effects (highest ranked areas) on reducing nutrient loading to the Gulf hypoxia and what are the most important sources of N and P in these areas.

Chapter A6. Section 6.4. pH

Released February 25, 2021 13:10 EST

2008, Techniques of Water-Resources Investigations 09-A6.4

George F. Ritz, J. A. Collins

Measurement of pH is critical to the understanding of the viability and vulnerability of environmental waters and is considered a master variable in determining the aqueous geochemistry of an aqueous system. pH is a measure that represents the hydrogen-ion concentration (activity) of a solution. This section of the National Field Manual (NFM) describes U.S. Geological Survey (USGS) guidance and protocols for measurement of pH in ground and surface waters. Each chapter of the National Field Manual is published separately and revised periodically. Newly published and revised chapters will be announced on the USGS Home Page on the World Wide Web under 'New Publications of the U.S. Geological Survey.'

Implications of historical and contemporary processes on genetic differentiation of a declining boreal songbird: The rusty blackbird

Released February 25, 2021 08:01 EST

2021, Diversity (13)

Robert E. Wilson, Steven M. Matsuoka, Luke L. Powell, James A. Johnson, Dean W. Demarest, Diana Stralberg, Sarah A. Sonsthagen

The arrangement of habitat features via historical or contemporary events can strongly influence genomic and demographic connectivity, and in turn affect levels of genetic diversity and resilience of populations to environmental perturbation. The rusty blackbird (Euphagus carolinus) is a forested wetland habitat specialist whose population size has declined sharply (78%) over recent decades. The species breeds across the expansive North American boreal forest region, which contains a mosaic of habitat conditions resulting from active natural disturbance regimes and glacial history. We used landscape genomics to evaluate how past and present landscape features have shaped patterns of genetic diversity and connectivity across the species’ breeding range. Based on reduced-representation genomic and mitochondrial DNA, genetic structure followed four broad patterns influenced by both historical and contemporary forces: (1) an east–west partition consistent with vicariance during the last glacial maximum; (2) a potential secondary contact zone between eastern and western lineages at James Bay, Ontario; (3) insular differentiation of birds on Newfoundland; and (4) restricted regional gene flow among locales within western and eastern North America. The presence of genomic structure and therefore restricted dispersal among populations may limit the species’ capacity to respond to rapid environmental change.

Elk migration influences the risk of disease spillover in the Greater Yellowstone Ecosystem

Released February 25, 2021 07:16 EST

2021, Journal of Animal Ecology

Nathaniel D. Rayl, J. A. Merkle, Kelly M. Proffitt, E S Almberg, Jennifer D. Jones, Justin Gude, Paul Cross

  1. Wildlife migrations provide important ecosystem services, but they are declining. Within the Greater Yellowstone Ecosystem (GYE) some elk (Cervus canadensis) herds are losing migratory tendencies, which may increase spatiotemporal overlap between elk and livestock (domestic bison [Bison bison] and cattle [Bos taurus]), potentially exacerbating pathogen transmission risk.
  2. We combined disease, movement, demographic, and environmental data from eight elk herds in the GYE to examine the differential risk of brucellosis transmission (through aborted fetuses) from migrant and resident elk to livestock.
  3. For both migrants and residents, we found that transmission risk from elk to livestock occurred almost exclusively on private ranchlands as opposed to state or federal grazing allotments. Weather variability affected the estimated distribution of spillover risk from migrant elk to livestock, with a 7‐12% increase in migrant abortions on private ranchlands during years with heavier snowfall. In contrast, weather variability did not affect spillover risk from resident elk.
  4. Migrant elk were responsible for the majority (68%) of disease spillover risk to livestock because they occurred in greater numbers than resident elk. On a per‐capita basis, however, our analyses suggested that resident elk disproportionately contributed to spillover risk. In five of seven herds, we estimated that the per‐capita spillover risk was greater from residents than from migrants. Averaged across herds, an individual resident elk was 23% more likely than an individual migrant elk to abort on private ranchlands.
  5. Our results demonstrate links between migration behavior, spillover risk, and environmental variability, and highlight the utility of integrating models of pathogen transmission and host movement to generate new insights about the role of migration in disease spillover risk. Further, they add to the accumulating body of evidence across taxa that suggests that migrants and residents should be considered separately during investigations of wildlife disease ecology. Finally, our findings have applied implications for elk and brucellosis in the GYE, and suggest that managers should prioritize actions that maintain spatial separation of elk and livestock on private ranchlands during years when snowpack persists into the risk period.

Mineral commodity summaries 2021

Released February 24, 2021 14:35 EST

2021, Report

U.S. Geological Survey


Each mineral commodity chapter of the 2021 edition of the U.S. Geological Survey (USGS) Mineral Commodity Summaries (MCS) includes information on events, trends, and issues for each mineral commodity as well as discussions and tabular presentations on domestic industry structure, Government programs, tariffs, 5-year salient statistics, and world production and resources. The MCS is the earliest comprehensive source of 2020 mineral production data for the world. More than 90 individual minerals and materials are covered by 2-page synopses.

For mineral commodities for which there is a Government stockpile, detailed information concerning the stockpile status is included in the 2-page synopsis.

Abbreviations and units of measure and definitions of selected terms used in the report are in Appendix A and Appendix B, respectively. Reserves and resources information is in Appendix C, which includes “Part A—Resource and Reserve Classification for Minerals” and “Part B—Sources of Reserves Data.” A directory of USGS minerals information country specialists and their responsibilities is in Appendix D.

The USGS continually strives to improve the value of its publications to users. Constructive comments and suggestions by readers of the MCS 2021 are welcomed.

Volcanic Aquifers of Hawai‘i—Construction and calibration of numerical models for assessing groundwater availability on Kaua‘i, O‘ahu, and Maui

Released February 24, 2021 14:18 EST

2021, Scientific Investigations Report 2020-5126

Scot K. Izuka, Kolja Rotzoll, Tracy Nishikawa

Steady-state numerical groundwater-flow models were constructed for the islands of Kaua‘i, O‘ahu, and Maui to enable quantification of the hydrologic consequences of withdrawals and other stresses that can place limits on groundwater availability. The volcanic aquifers of Hawai‘i supply nearly all drinking water for the islands’ residents, freshwater for diverse industries, and natural discharge to springs, streams, and nearshore areas that support ecosystems, cultural practices, aesthetics, and recreation. Increases in groundwater withdrawal and changes in climate can cause water-table depression, saltwater rise, and reduction of natural groundwater discharge—all of which can limit fresh groundwater availability. The numerical models described in this report are designed to quantify these consequences. Separate models were created for each island using MODFLOW-2005 with the Seawater Intrusion package, which allows simulation of freshwater and saltwater in ocean-island aquifers. Calibration resulted in models that generally replicate observed water-level, stream base-flow, and spring-flow data, and simulate groundwater-flow directions and fresh groundwater thicknesses that are consistent with conceptual models. The calibrated models use hydraulic properties that are consistent with the ranges reported in previous studies. The models show that the relative distribution of fresh groundwater discharge to the ocean, streams, and springs and withdrawals for human use differ substantially among the three islands studied here. These differences indicate that consequences that limit the availability of fresh groundwater for human use are likely to differ among the three islands.

Improved Automated Identification and Mapping of Iron Sulfate Minerals, Other Mineral Groups, and Vegetation using Landsat 8 Operational Land Imager Data, San Juan Mountains, Colorado, and Four Corners Region

Released February 24, 2021 13:10 EST

2021, Scientific Investigations Map 3466

Barnaby W. Rockwell, William R. Gnesda, Albert H. Hofstra

Multispectral remote sensing data acquired by the Landsat 8 Operational Land Imager (OLI) sensor were analyzed using a new, automated technique to generate a map of exposed mineral and vegetation groups in the western San Juan Mountains, Colo., and the Four Corners Region of the United States. Band ratio results were combined into displayed mineral and vegetation groups using Boolean algebra. New analysis logic has been implemented to exploit the coastal aerosol band in Landsat 8 OLI data and identify concentrations of iron sulfate minerals. These may indicate the presence of near-surface pyrite, which can be a potential nonpoint source of acid rock drainage. Zoned occurrences of iron sulfate minerals in areas surrounding and down gradient of known sources of pyrite have been mapped using this technique. They show high correlation with occurrences of jarosite-bearing mineral assemblages, as mapped using airborne imaging spectrometer data and supporting field verification surveys. Mapping the occurrence of iron sulfate minerals produced by the weathering and oxidation of pyrite in exposed hydrothermally altered rocks can also provide an important indicator of the genetic environment of alteration and the associated mineral deposit type. The automated analysis methodology is being employed to rapidly and cost-effectively generate maps of large regions of the United States in support of U.S. Geological Survey mineral resource and mineral-environmental assessments. This map, which includes the ERDAS IMAGINE thematic raster format in the data release, has been attributed by pixel value with mineral and vegetation group classification data, which can be queried in most image processing and GIS software packages.

Animal reservoirs and hosts for emerging alphacoronaviruses and betacoronaviruses

Released February 24, 2021 11:00 EST

2021, Emerging Infectious Diseases

Ria R. Ghai, Ann Carpenter, Amanda Y. Liew, Krystalyn B. Martin, Meghan K. Herring, Susan I. Gerber, Aron J. Hall, Jonathan M. Sleeman, Sophie VonDobschuetz, Casey Barton Behravesh

The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

Geochemical advances in Arctic Alaska oil typing - North Slope oil correlation and charge history

Released February 24, 2021 10:34 EST

2021, Marine and Petroleum Geology (127)

Palma J. Botterell, David W. Houseknecht, Paul G. Lillis, Silvana M. Barbanti, Jeremy E. Dahl, J. Michael Moldowan

The Arctic Alaska petroleum province is geologically and geochemically complex. Mixed hydrocarbon charge from multiple source rocks and/or levels of thermal maturity is common within an individual oil pool. Biomarker and chemometric statistical analyses were used to correlate twenty-nine oils to five oil families derived from: (1) Triassic Shublik Formation (calcareous organofacies), (2) Triassic Shublik Formation (shaly organofacies), (3) Jurassic Kingak Shale, (4) Cretaceous shale (pebble shale unit and Hue Shale), and (5) Paleogene shale (Canning Formation). Age-diagnostic and source-related oil biomarker parameters establish clear genetic relationships between the normal oil-window components and their putative source designations. However, application of diamondoid analyses reveals mixed-oil accumulations with postmature charge contributions (diamondoid-rich and biomarker-poor) in many oils.

Most sampled reservoirs contain a predominant charge derived from a single oil-window source plus a minor contribution from one or more higher maturity source(s). Variations in source organofacies also are recognized in the Shublik, Kingak, and Cretaceous oil families. In some cases, oils from multiple pools within a single field display relatively homogeneous geochemical profiles, suggesting a common source and migration pathway. For example, oil from the significant Pikka discovery is inferred to originate mainly from the calcareous Shublik Formation. In other cases, variability among oils from multiple pools within a single field (e.g., Milne Point, Colville River, and Northstar) likely indicates a more complex source, migration, and charge history. Results may be useful for anticipating the composition of oil charge in stratigraphic traps with low-permeability sandstone reservoirs, where oil gravity and other chemical parameters may influence economic viability.

Fish Rhabdoviruses (Rhabdoviridae)

Released February 24, 2021 08:26 EST

2021, Book chapter, Encyclopedia of Virology 4th Edition

Gael Kurath, David B. Stone

The family Rhabdoviridae currently has 18 genera accepted by the International Committee for Virus Taxonomy (ICTV), and three of those genera contain fish rhabdoviruses. In the genera Novirhabdovirus, Sprivivirus, and Perhabdovirus all viruses infect fish hosts, and there are no fish viruses in any of the other 15 rhabdovirus genera. In the overall phylogeny of the Rhabdoviridae the three fish virus genera are well separated from each other, and the novirhabdovirus genus occupies a position basal to all other genera.

Airborne dust plumes lofted by dislodged ice blocks at Russell crater, Mars

Released February 24, 2021 07:20 EST

2021, Geophysical Research Letters

Cynthia Dinwiddie, Timothy N. Titus

Linear dune gullies on poleward‐facing Martian slopes are enigmatic. Formation by CO2‐ice block or snow cornice falls has been proposed based on optical imagery of bright, high‐albedo features inside gully channels. Because these features often resemble patchy frost residue rather than three‐dimensional blocks, more evidence is needed to support the ice‐block formation mechanism. Satellite imagery captured two simultaneous airborne plumes with in‐channel sources at the Russell crater megadune, thrust up and dispersed outward along the path of linear dune gullies. We use spectral data analyses, climatic analyses of bolometric temperatures and thermal modeling to further develop the mechanistic framework for linear dune gully development. Basal sublimation and CO2 gas venting likely cause CO2‐ice‐block detachment and falls from gully alcoves in southern early spring, accompanied by ice‐block offgassing and saltation of sands and coarse silts that are redeposited around gully channels, and lofting of sublimation lag (coarse dust/silt) into airborne plumes.

Hydrographic and benthic mapping—St. Croix National Scenic Riverway—Osceola landing

Released February 23, 2021 14:19 EST

2021, Open-File Report 2020-1149

Jenny L. Hanson, Jayme M. Strange

High-resolution topographic and bathymetric mapping can assist in the analysis of river habitat. The National Park Service has been planning to relocate a boat ramp along the St. Croix River in Minnesota, across the river from the town of Osceola, Wisconsin, to improve visitor safety, improve operations for commercial use, enhance the overall visitor experience, and eliminate deferred maintenance at the landing. This landing grants access to the St. Croix River, which is a part of the National Park Service St. Croix National Scenic Riverway. Hydrographic and topographic surveys were needed to determine where the new location should be. The objective for these surveys was to provide baseline information in order to assess the direct effects of the landing relocation on physical habitat in areas adjacent to Osceola, Wisconsin. The study area for these surveys was about 18.5 hectares and located directly off the existing landing. Although the existing boat launch is referred to as the Osceola landing, it is located on the Minnesota side of the river and is the busiest National Park Service landing on the St. Croix River (National Park Service St. Croix National Scenic Riverway, 2020). This report documents methods and results of aquatic benthic mapping in a small area of the St. Croix River.

The hydroacoustic and topographic surveys were collected from October 16–17, 2019. The hydrographic surveys consisted of multibeam and sidescan sound navigation and ranging (sonars). The topographic shoreline survey consisted of light detection and ranging (lidar) captured by boat adjacent to riverbanks. Additionally, an acoustic Doppler current profiler was used to measure flow velocities. The water level was higher than normal, and therefore had faster flow during the hydroacoustic surveys. Multibeam, lidar, and sidescan surveys occurred the first day, and the velocity mapping and ground truthing was conducted the second day. Multibeam and lidar provided derivative datasets that included bathymetry and a topobathy with a spatial resolution of 1 foot. From these data, additional data could be measured including slope and terrain ruggedness. Sidescan (acoustic reflectance measures) provided imagery that was used to help with interpretation of the river bottom.

Outcomes from these combined datasets were substrate and bedform maps. Much of the area was covered in sand ripples or small dunes. A small area running adjacent to the deeper valley or cut down the river consisted of harder substrates, such as cobble and gravel. Large woody debris piles were found throughout the study area. Multiple stationary moving-bed tests were completed, and no corrections were recommended for the conditions occurring during survey. Mussel presence was noted in some of the underwater videos. The physical parameters of depth, flow, bedforms, and substrate derived from the datasets provided baseline measures for a benthic habitat map. Further analysis of benthic habitat might be possible with additional biological and chemical data.

Geochemical data for Illinois Basin coal samples, 2015–2018

Released February 23, 2021 13:00 EST

2021, Data Series 1135

Allan Kolker, Clint Scott, Liliana Lefticariu, Maria Mastalerz, Agnieszka Drobniak, Annie Scott

Researchers at the U.S. Geological Survey (USGS) and their collaborators conducted a study of the geochemical properties of coals currently produced for electric power generation in the Illinois Basin in Illinois and Indiana. The study follows from recommendations by an expert panel for the USGS to investigate the distribution and controls of trace constituents such as mercury (Hg) in Illinois Basin coals and the behavior of these constituents in coal preparation. A total of 72 new samples were collected by USGS collaborators between 2015 and 2017. These samples include raw coals, prepared coals, and waste coals from coal preparation. To understand the geochemistry and cleaning behavior of these coals, these samples were subjected to an integrated series of analyses described here, including microanalysis of coal constituents and bulk sample chemical analysis. Of the procedures used, whole-sample Hg analysis quantified overall mercury contents and its reduction by coal preparation. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of pyrite in coal quantified Hg and other potentially harmful elements contained in pyrite, the most likely host of these constituents. Trace elements investigated include those whose emissions are regulated under the U.S. Environmental Protection Agency Mercury and Air Toxics Standards. This report and the corresponding data release, serve as an archive for geochemical data obtained in our study of the geochemistry of Illinois Basin coals. Material included in this report also define approaches used by the USGS over the period of study to characterize coal samples, requiring combined use of results from USGS and non-USGS laboratories.

U.S. Geological Survey wildland fire science strategic plan, 2021–26

Released February 23, 2021 10:25 EST

2021, Circular 1471

Paul F. Steblein, Rachel A. Loehman, Mark P. Miller, Joseph R. Holomuzki, Suzanna C. Soileau, Matthew L. Brooks, Mia Drane-Maury, Hannah M. Hamilton, Jason W. Kean, Jon E. Keeley, Robert R. Mason Jr., Alexa J. McKerrow, James R. Meldrum, Edmund B. Molder, Sheila F. Murphy, Birgit Peterson, Geoffrey S. Plumlee, Douglas J. Shinneman, Phillip J. van Mantgem, Alison York

The U.S. Geological Survey (USGS) Wildland Fire Science Strategic Plan defines critical, core fire science capabilities for understanding fire-related and fire-responsive earth system processes and patterns, and informing management decision making. Developed by USGS fire scientists and executive leadership, and informed by conversations with external stakeholders, the Strategic Plan is aligned with the needs of the fire science stakeholder community–fire, land, natural resource, and emergency managers from Federal, State, Tribal, and community organizations, as well as members of the scientific community. The Strategic Plan is composed of four integrated priorities, each with associated goals and specific strategies for accomplishing the goals: Priority 1: Produce state-of-the-art, actionable fire science; Priority 2: Engage stakeholders in science production and science delivery; Priority 3: Effectively communicate USGS fire science capacity, products, and information to a broad audience; and Priority 4: Enhance USGS organizational structure and advance support for fire science. The priorities of this Strategic Plan define the USGS’s commitment to producing and delivering cutting edge fire science, information, and decision-support tools in support of national, regional, and local priorities and stakeholder needs.

Wildland fire science at the U.S. Geological Survey—Supporting wildland fire and land management across the United States postcard

Released February 23, 2021 10:25 EST

2019, General Information Product 190

Paul F. Steblein, Mark P. Miller, Suzanna C. Soileau

The U.S. Geological Survey’s Wildland Fire Science Program produces information to identify the causes of wildfires, understand the impacts and benefits of both wildfires and prescribed fires, and help prevent and manage larger, catastrophic events. USGS fire scientists provide information and develop tools that are widely used by stakeholders to make decisions before, during, and after wildfires in desert, grassland, tundra, wetland, and forest ecosystems across the United States. Active areas of research include—

  • Wildland fire behavior and risk management
  • Fire ecology, fire effects, and post-fire restoration of ecosystems
  • Risk assessments for human health, public safety, and the Nation’s infrastructure
  • Remote sensing and geospatial tools and data.

Wildland Fire Science—Supporting wildland fire and land management

Released February 23, 2021 10:25 EST

2019, Fact Sheet 2019-3025

Paul F. Steblein, Mark P. Miller, Suzanna C. Soileau

The U.S. Geological Survey's Wildland Fire Science Program produces fundamental information to identify the causes of wildfires, understand the impacts and benefits of both wildfires and prescribed fires, and help prevent and manage larger, catastrophic events. Our fire scientists provide information and develop tools that are widely used by stakeholders to make decisions before, during, and after wildfires in desert, grassland, tundra, wetland, and forest ecosystems across the United States.

Characterizing 12 years of wildland fire science at the U.S. Geological Survey: Wildland Fire Science Publications, 2006–17

Released February 23, 2021 10:25 EST

2019, Open-File Report 2019-1002

Paul F. Steblein, Mark P. Miller

Wildland fire characteristics, such as area burned, number of large fires, burn intensity, and fire season duration, have increased steadily over the past 30 years, resulting in substantial increases in the costs of suppressing fires and managing damages from wildland fire events (National Academies of Sciences, Engineering, and Medicine, 2017). Wildland fire management could benefit from sound decision making based on reliable scientific information. Fire scientists produce data, tools, and information to support fire and land management decision making. With ever-changing land use scenarios, environmental conditions, and emerging technological capabilities, new assessments and studies are continually needed. Established by Congress in 1879, the U.S. Geological Survey (USGS) is the primary science branch of the Department of the Interior (DOI), which manages more than 400 million acres of public lands in the United States. The USGS has more than 100 scientists across seven Mission Areas that help address the wildland fire science needs of DOI bureaus and their stakeholders. The diverse expertise of these scientists allows them to address complex interdisciplinary challenges. In this report, we identify and characterize scientific literature produced by USGS scientists during 2006–17 that addresses topics associated with wildland fire science. Our goals were to (1) make the most complete list possible of product citations readily available in an organized format, and (2) use bibliometric analysis approaches to highlight the productivity of USGS scientists and the impact of contributions that the Bureau has provided to the scientific, land management, and fire management communities.

Rangeland fractional components across the western United States from 1985 to 2018

Released February 23, 2021 08:51 EST

2021, Remote Sensing (13)

Matthew B. Rigge, Collin G. Homer, Hua Shi, Debra K. Meyer, Brett Bunde, Brian J. Granneman, Kory Postma, Patrick Danielson, Adam Case, George Z. Xian

Monitoring temporal dynamics of rangelands to detect and understand change in vegetation cover and composition provides a wealth of information to improve management and sustainability. Remote sensing allows the evaluation of both abrupt and gradual rangeland change at unprecedented spatial and temporal extents. Here, we describe the production of the National Land Cover Database (NLCD) Back in Time (BIT) dataset which quantified the percent cover of rangeland components (bare ground, herbaceous, annual herbaceous, litter, shrub, and sagebrush (Artemisia spp. Nutt.) across the western United States using Landsat imagery from 1985 to 2018. We evaluate the relationships of component trends with climate drivers at an ecoregion scale, describe the nature of landscape change, and demonstrate several case studies related to changes in grazing management, prescribed burns, and vegetation treatments. Our results showed the net cover of shrub, sagebrush, and litter significantly (p < 0.01) decreased, bare ground and herbaceous cover had no significant change, and annual herbaceous cover significantly (p < 0.05) increased. Change was ubiquitous, with a mean of 92% of pixels with some change and 38% of pixels with significant change (p < 0.10). However, most change was gradual, well over half of pixels have a range of less than 10%, and most change occurred outside of known disturbances. The BIT data facilitate a comprehensive assessment of rangeland condition, evaluation of past management actions, understanding of system variability, and opportunities for future planning.

Quantifying microplastics in Indiana’s Lake Michigan watershed and submerged aquatic vegetation

Released February 23, 2021 07:49 EST

2020, Newsletter

Julie R. Peller, Meredith B. Nevers, Muruleedhara Byappanahalli, Mary Anne Evans

Environmental breakdown of plastics produces synthetic microfibers, a class of microplastics that are most prevalent in surface waters. A main source of these pollutants is wastewater treatment plants which discharge into surface waters, including those that flow into Lake Michigan. Microplastics can settle into aquatic sediment or exist for lengths of time in the swash zone of the lakes; they can be ingested by organisms or concentrated in algae or other lake plankton, among other possibilities. As part of a larger Great Lakes study of the growth and senescence of submerged aquatic vegetation (SAV), the loads of synthetic microfibers in the SAV have been determined from Lake Michigan samples collected during the summer months of 2018, 2019 and 2020, and from various samples collected in the watershed and along the shoreline in Northwest Indiana. In order to effectively address microplastics pollution, a complete understanding of the distribution and fate of these pollutants is needed; this project is working toward that goal.

Atmospheric nitrogen deposition in the Chesapeake Bay watershed: A history of change

Released February 23, 2021 06:47 EST

2021, Atmospheric Environment (251)

Douglas A. Burns, Gopal Bhatt, Lewis Linker, Jesse Bash, Paul Capel, Gary Wynee Shenk

The Chesapeake Bay watershed has been the focus of pioneering studies of the role of atmospheric nitrogen (N) deposition as a nutrient source and driver of estuarine trophic status. Here, we review the history and evolution of scientific investigations of the role of atmospheric N deposition, examine trends from wet and dry deposition networks, and present century-long (1950–2050) atmospheric N deposition estimates. Early investigations demonstrated the importance of atmospheric deposition as an N source to the Bay, providing 25%–40% among all major N sources. These early studies led to the unprecedented inclusion of targeted decreases in atmospheric N deposition as part of the multi-stakeholder effort to reduce N loads to the Bay. Emissions of nitrogen oxides (NOx) and deposition of wet nitrate, oxidized dry N, and dry ammonium (NH4+) sharply and synchronously declined by 60%–73% during 1995–2019. These decreases largely resulted from implementation of Title IV of the 1990 Clean Air Act Amendments, which began in 1995. Wet NH4+ deposition shows no significant trend during this period. The century-long atmospheric N deposition estimates indicate an increase in total atmospheric N deposition in the Chesapeake watershed from 1950 to a peak of ~15 kg N/ha/yr in 1979, trailed by a slight decline of <10% through the mid-1990s, and followed by a sharp decline of about 40% thereafter through 2019. An additional 21% decline in atmospheric N deposition is projected from 2015 to 2050. A comparison of the Potomac River and James River watersheds indicates higher atmospheric N deposition in the Potomac, likely resulting from greater emissions from higher proportions of agricultural and urban land in this basin. Atmospheric N deposition rose from 30% among all N sources to the Chesapeake Bay watershed in 1950 to a peak of 40% in 1973, and a decline to 28% by 2015. These data highlight the important role of atmospheric N deposition in the Chesapeake Bay watershed and present a potential opportunity for decreases in deposition to contribute to further reducing N loads and improving the trophic status of tidal waters.

Evaluating fish rescue as a drought adaptation strategy using a life cycle modeling approach for imperiled coho salmon

Released February 22, 2021 08:30 EST

2021, North American Journal of Fisheries Management (41) 3-18

Brittany A Beebe, Kale T Bentley, Thomas W. Buehrens, Russell Perry, Jonathan B. Armstrong

Projected intensification of drought as a result of climate change may reduce the capacity of streams to rear fish, exacerbating the challenge of recovering salmonid populations listed under the Endangered Species Act. Without management intervention, some stocks will likely go extinct as stream drying and fragmentation reduce juvenile survival to unsustainable levels. To offset drought‐related mortality, fish rescue programs have proliferated, whereby juvenile salmonids are captured and transferred to off‐site rearing facilities. However, the efficacy of this potential conservation tool remains poorly understood. We developed a life cycle model to examine the implications of fish rescue on the abundance of Coho Salmon Oncorhynchus kisutch across serial life stages. The simulation model examines scenarios with varying quantities of rescued fish, time in captivity, drought severity, and reduced smolt‐to‐adult return rates. Our results indicate that fish rescue can increase the abundance of adults and lower extinction risk, particularly for fish held in captivity for a full year. However, fish rescue can also decrease the abundance of adults and increase extinction risk if fish are held only for summer and there is limited winter habitat. We found that when fish rescue did increase returns, it functioned more like a stock enhancement program than a drought mitigation tool and it would likely lead to consecutive generations of captive rearing, which has been shown to have negative effects on fitness. We translated our model into an R Shiny application (https://shiny.wdfw‐ that allows users to explore how fish rescue affects Coho Salmon population dynamics through customized parameterization of the model to represent different systems or different assumptions about the effects of fish rescue.

Extreme Quaternary plate boundary exhumation and strike slip localized along the southern Fairweather fault, Alaska, USA

Released February 22, 2021 07:02 EST

2021, Geology (49)

Richard O. Lease, Peter Haeussler, Robert C. Witter, Daniel F. Stockli, Adrian Bender, Harvey Kelsey, Paul O'Sullivan

The Fairweather fault (southeastern Alaska, USA) is Earth’s fastest-slipping intracontinental strike-slip fault, but its long-term role in localizing Yakutat–(Pacific–)North America plate motion is poorly constrained. This plate boundary fault transitions northward from pure strike slip to transpression where it comes onshore and undergoes a <25°, 30-km-long restraining double bend. To the east, apatite (U-Th)/He (AHe) ages indicate that North America exhumation rates increase stepwise from ~0.7 to 1.7 km/m.y. across the bend. In contrast, to the west, AHe age-depth data indicate that extremely rapid 5–10 km/m.y. Yakutat exhumation rates are localized within the bend. Further northwest, Yakutat AHe and zircon (U-Th)/He (ZHe) ages gradually increase from 0.3 to 2.6 Ma over 150 km and depict an interval of extremely rapid >6–8 km/m.y. exhumation rates that increases in age away from the bend. We interpret this migration of rapid, transient exhumation to reflect prolonged advection of the Cenozoic–Cretaceous sedimentary cover of the eastern Yakutat microplate through a stationary restraining bend along the edge of the North America plate. Yakutat cooling ages imply a long-term strike-slip rate (54 ± 6 km/m.y.) that mimics the millennial (53 ± 5 m/k.y.) and decadal (46 mm/yr) rates. Fairweather fault slip can account for all Pacific–North America relative plate motion throughout Quaternary time and indicates stability of highly localized plate boundary strike slip on a single fault where extreme rock uplift rates are persistently localized within a restraining bend.

Amateur radio operators help fill earthquake donut holes

Released February 22, 2021 06:32 EST

2021, Eos, American Geophysical Union (102)

David J. Wald, Vince Quitoriano, Oliver Dully

If you’ve ever seen tall antennas rising from everyday residences in your community and wondered what they are for, it could be that those homes belong to ham radio enthusiasts who enjoy communicating with each other over the airwaves. In addition to having fun with their radios and finding camaraderie, many ham radio operators are also prepared to help neighbors and authorities communicate during disasters. One such group of radio enthusiasts is poised now to serve yet another important role: They will be contributing to a more robust delivery mechanism for critical seismic intensity reports after major earthquakes through the U.S. Geological Survey’s (USGS) Did You Feel It? (DYFI) system.

Local explosion detection and infrasound localization by reverse time migration using 3-D finite-difference wave propagation

Released February 21, 2021 07:32 EST

2021, Frontiers in Earth Science (9)

David Fee, Liam Toney, Keehoon Kim, Richard Sanderson, Alexandra M. Iezzi, Robin S Matoza, Silvio DeAngelis, Art Jolly, John J. Lyons, Matthew M. Haney

Infrasound data are routinely used to detect and locate volcanic and other explosions, using both arrays and single sensor networks. However, at local distances (<15 km) topography often complicates acoustic propagation, resulting in inaccurate acoustic travel times leading to biased source locations when assuming straight-line propagation. Here we present a new method, termed Reverse Time Migration-Finite-Difference Time Domain (RTM-FDTD), that integrates numerical modeling into the standard RTM back-projection process. Travel time information is computed across the entire potential source grid via FDTD modeling to incorporate the effects of topography. The waveforms are then back-projected and stacked at each grid point, with the stack maximum corresponding to the likely source. We apply our method to three volcanoes with different network configurations, source-receiver distances, and topography. At Yasur Volcano, Vanuatu, RTM-FDTD locates explosions within ∼20 m of the source and differentiates between multiple vents. RTM-FDTD produces a more accurate location for the two Yasur subcraters than standard RTM and doubles the number of detected events. At Sakurajima Volcano, Japan, RTM-FDTD locates the source within 50 m of the active vent despite notable topographic blocking. The RTM-FDTD location is similar to that from the Time Reversal Mirror method, but is more computationally efficient. Lastly, at Shishaldin Volcano, Alaska, RTM and RTM-FDTD both produce realistic source locations (<50 m) for ground-coupled airwaves recorded on a four-station seismic network. We show that RTM is an effective method to detect and locate infrasonic sources across a variety of scenarios, and by integrating numerical modeling, RTM-FDTD produces more accurate source locations and increases the detection capability.

Gulf of Mexico blue hole harbors high levels of novel microbial lineages

Released February 21, 2021 06:58 EST

2021, Interational Society of Microbial Ecology (ISME) Journal

N.V. Patin, Z.A. Dietrich, A. Stancil, M. Quinan, J.S. Beckler, E.R. Hall, J Culter, Christopher Smith, Martial Taillefert, F.J. Stewart

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40–75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80–110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

Azorella compacta's long-term growth rate, longevity, and potential for dating geomorphological and archaeological features in the arid southern Peruvian Andes

Released February 21, 2021 06:46 EST

2021, Journal of Arid Environments (188)

Christopher Harpel, Catherine Kleier, Rigoberto Aguilar

We determine the long-term growth rate and longevity of an Azorella compacta growing on Misti volcano, near Arequipa, Peru to investigate the species' capacity as a geochronological resource. Using 14C dating on stem pieces sequestered within the plant's cushion, which grows larger through time, we obtain ages of 15 ± 15 14C yrs BP and 165 ± 15 14C yrs BP at depths of 15 cm and 29 cm below the cushion's living surface, respectively. Applying a mixed calibration curve with a Bayesian growth model yields calendar age ranges of 1948–1958 CE and 1802–1935 CE for our 14C dates, respectively. Such ages provide sufficiently precise constraints for investigations requiring dating during the last few hundred years when individual 14C dates yield imprecise calendar age ranges. We infer a long-term growth rate of 1.3–3.5 mm yr−1, corroborating published maximum short-term growth rates. Extrapolating our growth model to the A. compacta's core suggests that it began growing as early as 1462–1830 CE. At such age it lived through myriad important geological and historical events, including regional earthquakes, volcanic unrest at Misti, decades to centuries of the Little Ice Age, and a broad transect of Peruvian history possibly beginning during the Inca Empire. A. compacta may provide another important geochronological resource in the arid Central Andes that can be applied to date volcanological, glacial, mass-movement, and archaeological features, especially where dendrochronology and lichenometry are not possible.

Long-term trends in regional wet mercury deposition and lacustrine mercury concentrations in four lakes in Voyageurs National Park

Released February 20, 2021 08:38 EST

2021, Applied Sciences (11)

Mark E. Brigham, David D. VanderMeulen, Collin Eagles-Smith, David P. Krabbenhoft, Ryan P. Maki, John F. DeWild

Although anthropogenic mercury (Hg) releases to the environment have been substantially lowered in the United States and Canada since 1990, concerns remain for contamination in fish from remote lakes and rivers where atmospheric deposition is the predominant source of mercury. How have aquatic ecosystems responded? We report on one of the longest known multimedia data sets for mercury in atmospheric deposition: aqueous total mercury (THgaq), methylmercury (MeHgaq), and sulfate from epilimnetic lake-water samples from four lakes in Voyageurs National Park (VNP) in northern Minnesota; and total mercury (THg) in aquatic biota from the same lakes from 2001–2018. Wet Hg deposition at two regional Mercury Deposition Network sites (Fernberg and Marcell, Minnesota) decreased by an average of 22 percent from 1998–2018; much of the decreases occurred prior to 2009, with relatively flat trends since 2009. In the four VNP lakes, epilimnetic MeHgaq concentrations declined by an average of 44 percent and THgaq by an average of 27 percent. For the three lakes with long-term biomonitoring, temporal patterns in biotic THg concentrations were similar to patterns in MeHgaq concentrations; however, biotic THg concentrations declined significantly in only one lake. Epilimnetic MeHgaq may be responding both to a decline in atmospheric Hg deposition as well as a decline in sulfate deposition, which is an important driver of mercury methylation in the environment. Results from this case study suggest that regional- to continental-scale decreases in both mercury and sulfate emissions have benefitted aquatic resources, even in the face of global increases in mercury emissions.

Salinity changes the dynamics of pyrethroid toxicity in terms of behavioral effects on newly hatched delta smelt larvae

Released February 20, 2021 06:37 EST

2021, Toxics (9)

Amelie Segarra, Florian Mauduit, Nermeen Amer, Felix KJ Biefel, Michelle Hladik, Richard E Connon, Susanne M. Brander

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.

Petrology and geochronology of 1.48 to 1.45 Ga igneous rocks in the St. Francois Mountains terrane, southeast Missouri

Released February 19, 2021 16:00 EST

2021, Professional Paper 1866

Edward A. du Bray, John N. Aleinikoff, Warren C. Day, Leonid A. Neymark, Seth D. Burgess

The igneous geology of the St. Francois Mountains terrane in southeast Missouri is dominated by the products of 1.48 to 1.45 billion year old volcanic and plutonic magmatism but also includes volumetrically minor, compositionally bimodal contributions added during plutonism between 1.34 and 1.27 billion years ago. The 1.48 to 1.45 billion year old igneous rocks in the St. Francois Mountains terrane are bimodally distributed between volumetrically dominant felsic rocks and volumetrically minor rocks with mafic to intermediate compositions. All of these rocks are ferroan, which like most of their trace element abundances, suggests a genesis associated with farfield intraplate extensional tectonism and decompression-related magmatism. The diversity of compositions among 1.48 to 1.45 billion year old igneous rocks in the St. Francois Mountains terrane probably reflects mixtures of mantle-derived mafic inputs and low-degree partial melting of more evolved crustal protoliths. Newly determined ages define essentially continuous magmatism during the 30-million-year period between 1.48 and 1.45 billion years ago. The products of this magmatism are essentially coeval, whether intrusive or extrusive or having mafic, intermediate, or felsic compositions. In addition, the iron oxide-apatite (for example, Pea Ridge) and likely the iron oxide-copper gold (Boss) deposits in the St. Francois Mountains terrane have ages coincident with this magmatic episode. Spatial and temporal relations between 1.48 to 1.45 billion year old igneous rocks in the St. Francois Mountains terrane and the mineral deposits they host suggest the associated magmatic and mineralization processes are also genetically related.

Geochemical, petrographic, geochronologic, and terrane-wide physical characteristics of the 1.48 to 1.45 billion year old igneous rocks in the St. Francois Mountains terrane are consistent with an origin involving extension well inboard from the margin of the Laurentian craton, associated mantle upwelling, lower crustal melting in response to mantle-derived thermal inputs, and mixing of mantle- and juvenile lower crustal-derived melts. Significant major and trace element compositional dispersion characteristics of these rocks likely reflect midcrustal magma reservoir fractionation of their principal rock-forming minerals. The resultant magmas constitute a series of variably hybridized reservoirs, emplaced at upper levels in the crust, that form a series of plutonic and associated eruptive products.

Mangrove species’ response to sea-level rise across Pohnpei, Federated States of Micronesia

Released February 19, 2021 10:56 EST

2021, Open-File Report 2021-1002

Kevin J. Buffington, Richard A. MacKenzie, Joel A. Carr, Maybeleen Apwong, Ken W. Krauss, Karen M. Thorne

Mangrove forests are likely vulnerable to accelerating sea-level rise; however, we lack the tools necessary to understand their future resilience. On the Pacific island of Pohnpei, Federated States of Micronesia, mangroves are habitat to endangered species and provide critical ecosystem services that support local communities. We developed a generalizable modeling framework for mangroves that accounts for species interactions and the belowground processes that dictate soil elevation. The modeling framework was calibrated with extensive field datasets, including accretion rates derived from thirty 1-meter-deep soil cores dated with lead-210, more than 300 forest inventory plots, water-level monitoring, and differential leveling elevation surveys. We applied the model using a community of five mangrove species and across seven regions around Pohnpei to identify which regions are most vulnerable to sea-level rise. The responses of mean elevation and the mangrove community  composition were analyzed under four global sea-level rise scenarios: an increase of 37, 52, 67, or 117 centimeters by 2100. The model was validated against a 20-year surface elevation table record (1999–2019) and showed good agreement when driven by observed water levels.

The model projected that mangroves around Pohnpei can build their elevations relative to moderate rates of sea-level rise to prevent submergence, with limited changes in mangrove community composition through 2060. By 2100, however, the model projected a decreasing abundance of high-elevation mangrove species and an increasing abundance of lower elevation species adapted to more persistent flooding. Under higher sea-level rise scenarios, forest elevation decreased substantially relative to mean sea level and there were more drastic changes in the tree community composition and loss of suitable mangrove habitat by 2100. Variation in accretion rates, water levels, and initial forest elevation led to differential  vulnerability around the island, such that mangroves on the leeward side of the island generally were the most at-risk to higher rates of sea-level rise. Our findings indicate that the relatively undisturbed state of the mangrove forests and the surrounding landscape is an important factor in their ability to keep pace with sea-level rise.

Determination of vadose zone and saturated zone nitrate lag times using long-term groundwater monitoring data and statistical machine learning

Released February 19, 2021 08:20 EST

2021, Hydrology and Earth System Sciences (25) 811-829

Martin J. Wells, Troy E. Gilmore, Natalie Nelson, Aaron Mittelstet, John K. Böhlke

In this study, we explored the use of statistical machine learning and long-term groundwater nitrate monitoring data to estimate vadose zone and saturated zone lag times in an irrigated alluvial agricultural setting. Unlike most previous statistical machine learning studies that sought to predict groundwater nitrate concentrations within aquifers, the focus of this study was to leverage available groundwater nitrate concentrations and other environmental variables to determine mean regional vertical velocities (transport rates) of water and solutes in the vadose zone and saturated zone (3.50 and 3.75 m yr−1, respectively). The statistical machine learning results are consistent with two primary recharge processes in this western Nebraska aquifer, namely (1) diffuse recharge from irrigation and precipitation across the landscape and (2) focused recharge from leaking irrigation conveyance canals. The vadose zone mean velocity yielded a mean recharge rate (0.46 m yr−1) consistent with previous estimates from groundwater age dating in shallow wells (0.38 m yr−1). The saturated zone mean velocity yielded a recharge rate (1.31 m yr−1) that was more consistent with focused recharge from leaky irrigation canals, as indicated by previous results of groundwater age dating in intermediate-depth wells (1.22 m yr−1). Collectively, the statistical machine learning model results are consistent with previous observations of relatively high water fluxes and short transit times for water and nitrate in the primarily oxic aquifer. Partial dependence plots from the model indicate a sharp threshold in which high groundwater nitrate concentrations are mostly associated with total travel times of 7 years or less, possibly reflecting some combination of recent management practices and a tendency for nitrate concentrations to be higher in diffuse infiltration recharge than in canal leakage water. Limitations to the machine learning approach include the non-uniqueness of different transport rate combinations when comparing model performance and highlight the need to corroborate statistical model results with a robust conceptual model and complementary information such as groundwater age.

Towards an urgent yet deliberate conservation strategy: Sustaining social-ecological systems in rangelands of the Northern Great Plains, Montana

Released February 19, 2021 08:05 EST

2021, Ecology and Society (1)

Katie Epstein, David J. A. Wood, Kelli Roemer, Bryce Currey, Hannah Duff, Justin D Gay, Hannah Goemann, Sasha Loewen, Megan C Milligan, John A F Wendt, E N Jack Brookshire, Bruce D. Maxwell, Lance B. McNew, Dave B McWethy, Paul C. Stoy, Julia Hobson Haggerty

Urgency and deliberateness are often at odds when executing conservation projects, especially as the scale and complexity of objectives increases. The pace of environmental degradation supports immediate and measurable action. However, best practices for adaptive governance and building resilient social-ecological systems call for more deliberate efforts and participatory processes, which can be slow. We explore conflicts between urgency and deliberateness and the potential for their reconciliation through a case study of the challenges of conserving native rangelands in North America’s Northern Great Plains, an ecoregion targeted for global conservation initiatives. This region is undergoing a significant social-ecological transition, which underscores a need to rethink conservation strategies in light of the social-ecological system dynamics and potential future trajectories. Based on a structured narrative literature review process and iterative engagement with key regional stakeholders, we identify three interrelated factors critical to the system’s future outcomes that illustrate system complexity as well as trade-offs between urgent and deliberate action and unilateral and multilateral approaches to conservation: (1) influences of land management on biodiversity, (2) economic restructuring and shifting land use priorities, and (3) changing climate and disturbance regimes. We identify key gaps in the literature for each factor and across the factors—an effort that informs our call for research and practice agendas that address uncertainty and complexity at regional scales through more inclusive and future-oriented approaches.

Detecting shrub recovery in sagebrush steppe: Comparing Landsat-derived maps with field data on historical wildfires

Released February 19, 2021 07:02 EST

2021, Fire Ecology (17)

Cara Applestein, Matthew Germino


The need for basic information on spatial distribution and abundance of plant species for research and management in semiarid ecosystems is frequently unmet. This need is particularly acute in the large areas impacted by megafires in sagebrush steppe ecosystems, which require frequently updated information about increases in exotic annual invaders or recovery of desirable perennials. Remote sensing provides one avenue for obtaining this information. We considered how a vegetation model based on Landsat satellite imagery (30 m pixel resolution; annual images from 1985 to 2018) known as the National Land Cover Database (NLCD) “Back-in-Time” fractional component time-series, compared with field-based vegetation measurements. The comparisons focused on detection thresholds of post-fire emergence of fire-intolerant Artemisia L. species, primarily A. tridentata Nutt. (big sagebrush). Sagebrushes are scarce after fire and their paucity over vast burn areas creates challenges for detection by remote sensing. Measurements were made extensively across the Great Basin, USA, on eight burn scars encompassing ~500 000 ha with 80 plots sampled, and intensively on a single 113 000 ha burned area where we sampled 1454 plots.


Estimates of sagebrush cover from the NLCD were, as a mean, 6.5% greater than field-based estimates, and variance around this mean was high. The contrast between sagebrush cover measurements in field data and NLCD data in burned landscapes was considerable given that maximum cover values of sagebrush were ~35% in the field. It took approximately four to six years after the fire for NLCD to detect consistent, reliable signs of sagebrush recovery, and sagebrush cover estimated by NLCD ranged from 3 to 13% (equating to 0 to 7% in field estimates) at these times. The stabilization of cover and presence four to six years after fire contrasted with previous field-based studies that observed fluctuations over longer time periods.


While results of this study indicated that further improvement of remote sensing applications would be necessary to assess initial sagebrush recovery patterns, they also showed that Landsat satellite imagery detects the influence of burns and that the NLCD data tend to show faster rates of recovery relative to field observations.

Production of haploid gynogens to inform genomic resource development in the paleotetraploid pallid sturgeon (Scaphirhynchus albus)

Released February 19, 2021 06:37 EST

2021, Aquaculture (538)

Richard Flamio Jr., Kimberly Chojnacki, Aaron J. Delonay, Marlene J Dodson, Rachel M. Gocker, Jill Jenkins, Jeffrey Powell, Edward J. Heist

Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of osteichthyan fishes (>200 million years old) with most extant species at conservation risk. A relatively basal species, the pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this study was to produce pallid sturgeon gynogens that contain 100% homozygous DNA contributed by only the maternal parent and have enough DNA for future SNP marker development. When homozygous gynogens are sequenced, heterozygosity at a locus within an individual indicates the presence of incorrectly aligned sequences that contain PSVs; accurate identification of these multi-locus contigs can facilitate their exclusion when developing disomic markers. In this study, we attempted to produce two types of pallid sturgeon gynogens: a) haploid gynogens produced from the activation of pallid sturgeon eggs with ultraviolet-irradiated sperm from the distantly related paddlefish (Polyodon spathula), and b) doubled haploids produced from the activation of pallid sturgeon eggs with irradiated paddlefish milt followed by thermal shock to suppress the first mitotic division. Production of doubled haploids, gynogens with 100% homozygous DNA and double the genome content of haploid gynogens, was pursued because it was originally unknown if haploid gyongens would survive long enough to attain enough genetic material for SNP marker development. We performed flow cytometry and microsatellite genotyping on the specimens in order to confirm haploid and doubled haploid status. Our study was unable to successfully yield doubled haploids; however, we successfully produced haploid gynogens that contained enough nuclear DNA for our future SNP marker development study. Interestingly, this study also produced paddlefish × pallid sturgeon hybrids in the control groups in two separate years; this is the first study to report viable offspring between the paddlefish and a Scaphirhynchus sturgeon species and reflects on the malleability of the genomes of the species in this order.

Regionalization of surface-water statistics using multiple linear regression

Released February 18, 2021 15:40 EST

2019, Techniques and Methods 4-A12

William H. Farmer, Julie E. Kiang, Toby D. Feaster, Ken Eng

This report serves as a reference document in support of the regionalization of surface-water statistics using multiple linear regression. Streamflow statistics are quantitative characterizations of hydrology and are often derived from observed streamflow records. In the absence of observed streamflow records, as at unmonitored or ungaged locations, other techniques are required. Multiple linear regression is one tool that is widely used to regionalize or transfer information from gaged to ungaged locations. This report provides the background to support regression-based regionalization of streamflow statistics. This background includes tools for data assembly, exploratory data analysis, model estimation in a least-squares framework, and model evaluation.

Testing hypotheses on signatures of precipitation variability in the river and floodplain deposits of the Paleogene San Juan Basin, New Mexico, USA

Released February 18, 2021 13:16 EST

2020, Journal of Sedimentary Research (90) 1770-1801

Kristine L. Zellman, Piret Plink-Bjorklund, Henry Fricke

Much progress has been made in recent years towards a set of recognition criteria for river discharge variability in river channel deposits, and thus sedimentary proxies for precipitation variability. Despite this progress, there is currently no consensus on how different styles of discharge variability are reflected in river sedimentary records, and whether variable-discharge river records from different climate types can be distinguished. Herein, river discharge and precipitation variability in the Paleogene is investigated using associations between river channel and floodplain deposits across the Paleocene-Eocene boundary from the Paleocene upper Nacimiento Formation and the early Eocene San Jose Formation in the San Juan Basin, New Mexico, USA. The succession is identified as deposits of variable-discharge river systems based on shared channel-deposit characteristics with modern and ancient variable-discharge river systems and the proposed facies models, in addition to alternations of poorly drained and well-drained floodplain deposits and/or slickensides indicating alternating wet-dry cycles. A long-term stratigraphic trend toward increasingly well-drained floodplain deposits is also observed and hypothesized to indicate successively more arid conditions from the Paleocene into the early Eocene. Comparisons with modern rivers from various climate zones suggest a long-term shift from a monsoonal climate in the Paleocene, to a fluctuating subhumid climate, ultimately leading to semiarid to arid conditions in the early Eocene. These observations suggest that floodplain deposits may be a better indicator of ambient climate, whereas channel deposits are records for frequency and magnitude of high-intensity precipitation events. Therefore, the existing facies models for variable-discharge rivers that consider only channel facies may not capture critical information needed to make accurate interpretations of paleoclimatic conditions. This study also adds to a growing body of evidence from geologic records of mid-latitude Paleogene river systems suggesting increases in the magnitude or variability of river discharge coinciding with established climate perturbations.

Patterns of bubble bursting and weak explosive activity in an active lava lake—Halema‘uma‘u, Kīlauea, 2015

Released February 18, 2021 10:46 EST

2021, Professional Paper 1867-E

Bianca G. Mintz, Bruce F. Houghton, Edward W. Llewellin, Tim R. Orr, Jacopo Taddeucci, Rebecca J. Carey, Ulrich Kueppers, Damien Gaudin, Matthew R. Patrick, Michael Burton, Piergiorgio Scarlato, Alessandro La Spina

The rise of the Halemaʻumaʻu lava lake in 2013–2018 to depths commonly 40 meters or less below the rim of the vent was an excellent opportunity to study outgassing and the link to associated eruptive activity. We use videography to investigate the rise and bursting of bubbles through the free surface of the lake in 2015. We focus on low-energy explosive activity (spattering) in which the ascent and bursting of meter-sized, mechanically decoupled bubbles trigger the ejection of fluidal bombs to tens of meters above the free surface. A decay in initial pyroclast velocity with time follows the same functional form as that observed for ejecta at Stromboli (Italy), suggesting a similar bubble-burst mechanism. We also find that the upward velocity of the bubble crust as it bursts is around 2.5 times higher than the velocity of the bubble as it rises through the lake surface, indicating that the bubbles are over-pressurized. Prior to bursting, bubbles emerge at velocities of 4 to 14 meters per second, suggesting rise from depths of at least tens of meters but unaffected by the deeper circulation of the lava lake.

We identify three styles of bubble bursting: (1) isolated, widely spaced, single bursts, (2) recurring clusters of discrete bubbles, and (3) prolonged episodes of overlapping bubble bursts along elongate narrow sources typically parallel to the margins of the lava lake. We call these styles of bursting isolated events, clusters, and prolonged episodes, respectively. The frequency of bubble bursting and the mass fluxes of gas and pyroclasts increase from styles 1 to 3. The intensity (mass eruption rate) for single bubble bursts ranges from 280 to 3,500 kilograms per second. The total erupted mass of pyroclasts for a single burst is <4,000 kilograms (kg) and for a single well-constrained prolonged episode is about 107 kg. These numbers place the observed spattering at the lowest end of basaltic explosivity in terms of erupted mass (that is, magnitude). Most ejecta fell back into the crater; only strands of Pele’s hair rose to heights where they could be advected downwind from the vent.

Collectively, the explosive activity accompanying the three styles of bubble bursting spans from impulsive, transient eruptive behaviors to sustained discharge; this shift represents progressively higher frequency and intensity of bubble bursting.

A structured approach to remediation site assessment: Lessons from 15 years of fish spawning habitat creation in the St. Clair‐Detroit River system

Released February 18, 2021 07:26 EST

2021, Restoration Ecology

J. Fischer, Edward F. Roseman, Christine Mayer, Todd Wills, Lynn Vaccaro, Jennifer Read, Bruce A. Manny, Gregory W. Kennedy, Roseanne Ellison, Richard Drouin, R. DeBruyne, Aline Cotel, Justin A. Chiotti, James C. Boase, David Bennion

Ideally, restoration re‐establishes natural processes in degraded habitats (e.g., flow and sediment regimes). However, in altered systems where process‐based restoration is not feasible, habitat construction is another approach to mitigate degradation. Because habitat construction does not directly focus on restoring processes that build and maintain desired habitats, projects must be developed and placed within the contemporary regulatory, ecological, and hydrogeomorphic context of a system, to maximize effectiveness. Here, we develop a framework for evaluating the regulatory, ecological, and hydrogeomorphic components using 15 years of fish spawning habitat construction in the St. Clair‐Detroit River System. The process began by identifying regulatory requirements at a coarse resolution to quickly focus on locations where ecological potential and hydrogeomorphic constraints could be assessed at finer resolutions. Next, ecological potential was assessed using a lithophilic fish spawning habitat suitability index. The suitability index identified five sites for habitat construction and Lake sturgeon spawning was documented at each site following construction. However, qualitative monitoring showed fine sediments accumulated at older sites. Thus, geomorphic assessments were incorporated to identify sediment sources and model flow within targeted areas. Since geomorphic assessments required the finest resolution and had the most uncertainty, they were conducted after broad‐scale regulatory considerations and ecological assessments narrowed focus to a few candidate sites. The order of operations identified in this case study evolved from the iterative approach of the restoration team, but in retrospect, it helped develop a framework that directed project development resources to aspects with more uncertainty, where learning is most critical.

Documentation of methods and inventory of irrigation information collected for the 2015 U.S. Geological Survey estimated use of water in the United States

Released February 17, 2021 13:00 EST

2021, Scientific Investigations Report 2020-5139

Jaime A. Painter, Justin T. Brandt, Rodney R. Caldwell, Jonathan V. Haynes, Amy L. Read

The U.S. Geological Survey (USGS) National Water-Use Science Project strives to report water-use estimates using the best available information for the period of the estimates. The information available on water used for irrigation activities varies from State to State and in some areas from county to county within a State, which results in many information sources and methods being used to estimate water withdrawals and consumption for the Nation. The variety of estimation methods makes it difficult to compare information across States and makes it difficult to understand how different methods or data sources bias irrigation water-use estimates and trends over time. The sources of information and methods used by USGS Water Science Centers to estimate irrigation water use (the number of irrigated acres by irrigation system type, withdrawal values by water source type, and consumed-water values) for 2015 are compiled and described herein to assist with interpreting the water-use estimates. State-level summaries of information sources and methods are compiled in appendix 1, and a dataset of calendar-year, county-level estimates of actual evapotranspiration for the conterminous United States and Hawaii is provided in an associated USGS data release.

Changes in rocky intertidal community structure during a marine heatwave in the northern Gulf of Alaska

Released February 17, 2021 07:45 EST

2021, Frontiers in Marine Science (8)

Ben Weitzman, Brenda Konar, Katrin Iken, Heather Coletti, Daniel Monson, Robert M Suryan, Thomas Dean, D. Hondolero, Mandy Lindeberg

Marine heatwaves are global phenomena that can have major impacts on the structure and function of coastal ecosystems. By mid-2014, the Pacific Marine Heatwave (PMH) was evident in intertidal waters of the northern Gulf of Alaska and persisted for multiple years. While offshore marine ecosystems are known to respond to these warmer waters, the response of rocky intertidal ecosystems to this warming is unclear. Intertidal communities link terrestrial and marine ecosystems and their resources are important to marine and terrestrial predators and to human communities for food and recreation, while simultaneously supporting a growing coastal tourism industry. Given that current climate change projections suggest increased frequency and duration of marine heatwaves, monitoring and understanding the impacts of heatwaves on intertidal habitats is important. As part of the Gulf Watch Alaska Long-Term Monitoring program, we examined rocky intertidal community structure at 21 sites across four regions spanning 1,200 km of coastline: Western Prince William Sound, Kenai Fjords National Park, Kachemak Bay, and Katmai National Park and Preserve. Sites were monitored annually from 2012 to 2019 at mid and low tidal strata. Before-PMH (2012–2014), community structure differed among regions. We found macroalgal foundation species declined during this period mirroring patterns observed elsewhere for subtidal habitat formers during heatwave events. The region-wide shift from an autotroph-macroalgal dominated rocky intertidal to a heterotroph-filter-feeder dominated state concurrent with the changing environmental conditions associated with a marine heatwave event suggests the PMH had Gulf-wide impacts to the structure of rocky intertidal communities. During/after-PMH (2015–2019), similarities in community structure increased across regions, leading to a greater homogenization of these communities, due to declines in macroalgal cover, driven mostly by a decline in the rockweed, Fucus distichus, and other fleshy red algae in 2015, followed by an increase in barnacle cover in 2016, and an increase in mussel cover in 2017. Strong, large-scale oceanographic events, like the PMH, may override local drivers to similarly influence patterns of intertidal community structure.

Drought stress and hurricane defoliation influence mountain clouds and moisture recycling in a tropical forest

Released February 16, 2021 13:48 EST

2021, PNAS (118)

Martha A. Scholl, Maoya Bassiouni, Angel J. Torres-Sanchez

Mountain ranges generate clouds, precipitation, and perennial streamflow for water supplies, but the role of forest cover in mountain hydrometeorology and cloud formation is not well understood. In the Luquillo Experimental Forest of Puerto Rico, mountains are immersed in clouds nightly, providing a steady precipitation source to support the tropical forest ecosystems and human uses. A severe drought in 2015 and the removal of forest canopy (defoliation) by Hurricane Maria in 2017 created natural experiments to examine interactions between the living forest and hydroclimatic processes. These unprecedented land-based observations over 4.5 y revealed that the orographic cloud system was highly responsive to local land-surface moisture and energy balances moderated by the forest. Cloud layer thickness and immersion frequency on the mountain slope correlated with antecedent rainfall, linking recycled terrestrial moisture to the formation of mountain clouds; and cloud-base altitude rose during drought stress and posthurricane defoliation. Changes in diurnal cycles of temperature and vapor-pressure deficit and an increase in sensible versus latent heat flux quantified local meteorological response to forest disturbances. Temperature and water vapor anomalies along the mountain slope persisted for at least 12 mo posthurricane, showing that understory recovery did not replace intact forest canopy function. In many similar settings around the world, prolonged drought, increasing temperatures, and deforestation could affect orographic cloud precipitation and the humans and ecosystems that depend on it.

Multilevel groundwater monitoring of hydraulic head, water temperature, and chemical constituents in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2014–18

Released February 16, 2021 13:00 EST

2021, Scientific Investigations Report 2021-5002

Brian V. Twining, Roy C. Bartholomay, Jason C. Fisher, Calvin Anderson

Radiochemical and chemical wastewater discharged to infiltration ponds and disposal wells since the early 1950s at the Idaho National Laboratory (INL), southeastern Idaho, has affected the water quality of the eastern Snake River Plain (ESRP) aquifer. In 2006, the U.S. Geological Survey (USGS), in cooperation with the U.S. Department of Energy, added a multilevel well-monitoring network to their ongoing monitoring program to begin describing the vertical movement and distribution of the chemical constituents in the ESRP aquifer.

The multilevel monitoring system (MLMS) at the INL has been ongoing since 2006, and this report summarizes data collected during 2014–18 from 11 multilevel monitoring wells. Hydraulic head (head) and groundwater temperature data were collected, including 177 measurements from hydraulically isolated depth intervals from 448.0 to 1,377.6 feet below land surface. One port (port 3) within well USGS 134 was not monitored owing to a valve failure.

Note: This is a partial abstract.

Spatial and temporal variability of nutrients and algae in the Republican River and Milford Lake, Kansas, June through November 2017 and May through November 2018

Released February 16, 2021 12:21 EST

2021, Scientific Investigations Report 2020-5135

Brianna M. Leiker, Justin R. Abel, Jennifer L. Graham, Guy M. Foster, Lindsey R. King, Tom C. Stiles, Riley P. Buley

Milford Lake has been listed as impaired and designated hypereutrophic because of excessive nutrient loading, specifically biologically available orthophosphate. It is the largest lake by surface area in Kansas and is a reservoir built for purposes including water supply and recreation. In 2015, the Kansas Department of Health and Environment (KDHE) divided the lake into three zones (Zones A, B, and C) for recreational monitoring of harmful algal blooms (HABs). Upstream Zone C has historically been more affected by HABs than Zones B and A, and Zone C has historically had the highest phosphorus concentrations.

The U.S. Geological Survey, in cooperation with the KDHE, completed a study in 2017–18 to assess the spatial and temporal variability of nutrients and algae in the Republican River (the primary inflow to Milford Lake) and Milford Lake using spatially and temporally dense data. During the study period, discrete water-quality samples were collected at 36 lake sites, 21 river sites, and 1 pond. All samples were analyzed for nutrients; some samples were also analyzed for chlorophyll, phycocyanin, microcystin, and (or) phytoplankton community composition and abundance. Results from this study provide perspective for understanding the potential role nutrient and algal conditions have in facilitating the formation of HABs and may inform future actions to prevent and mitigate HABs and their potential effects on human and environmental health.

In 2017, one low-flow floating synoptic on the Republican River into Zone C of Milford Lake and one 24-hour synoptic in Zone C of Milford Lake were completed. Results from the low-flow floating synoptic on July 17, 2017, at 21 river sites, 8 lake sites, and 1 pond site indicated that the Republican River was not contributing dissolved orthophosphate or total phosphorus concentrations higher than those in the main body of Milford Lake.

No patterns in nutrient or total microcystin concentrations were evident from the 24-hour synoptic at two sites on August 24–25, 2017. Total nitrogen was dominated by total Kjeldahl nitrogen (TKN) at both sites. Different oscillation activity in algal biomass and chlorophyll at the two sites demonstrated the variable nature of algal accumulations and their effects on nutrient and dissolved oxygen concentrations. Different patterns in chlorophyll and microcystin concentrations indicate that the relation between algal biomass and cyanotoxin concentrations were different at the two sites, possibly because of differences among algal communities present at each site.

Three whole-lake synoptics through Zones A, B, and C in Milford Lake were completed on July 10, August 9, and October 16–17, 2018, at 30 lake sites. Orthophosphate was consistently at least 77 percent of total phosphorus at all sites except the two most uplake sites. At the two most uplake sites, orthophosphate was between 52 and 72 percent of the total phosphorus present at the site.

Concentrations of TKN were not consistently increasing or decreasing during 2018. Total nitrogen was dominated by TKN in July and August. Very low concentrations of dissolved nitrate plus nitrite indicate that the nutrient was likely tied up in algal biomass. By October, total nitrogen was approximately one-half TKN and one-half dissolved nitrate plus nitrite. Higher concentrations of dissolved orthophosphate and dissolved nitrate plus nitrite in October than in July and August were likely caused by reduced biological activity (less uptake of nutrients) and lower air and water temperatures. Multiple inflow events (streamflow greater than median daily value) between August and October also may have moved nutrients through the lake.

Chlorophyll, phycocyanin, microcystin, and phytoplankton samples were collected at eight sites in 2018. Most sites had their highest chlorophyll concentrations in August. The three most uplake sites had their highest phycocyanin concentrations in July, whereas the other five sites had their highest phycocyanin concentrations in August. Two of 23 samples had detections of total microcystin (0.11 and 0.12 microgram per liter). Phytoplankton community composition mainly consisted of Bacillariophyta, Chlorophyta, Cryptophyta, and Cyanobacteria. Phytoplankton community composition and abundance data described broad seasonal patterns and did not capture the full range of possible conditions at each site.

The Mars 2020 Perseverance rover mast camera zoom (Mastcam-Z) multispectral, stereoscopic imaging investigation

Released February 15, 2021 11:15 EST

2021, Space Science Reviews (217)

J. F. Bell III, J. N. Maki, G. L. Mehall, M. A. Ravine, M. A. Caplinger, Z. J. Bailey, S. Brylow, J. A. Schaffner, K. M. Kinch, M. B. Madsen, A. Winhold, A. G. Hayes, P. Corlies, C. Tate, M. Barrington, E. Cisneros, E. Jensen, Katy L. Parise, Kelon Crawford, C. Rojas, L. Mehall, J. Joseph, J. B. Proton, N. Cluff, R. G. Deen, B. Betts, Edward A. Cloutis, A. J. Coates, Anthony Colaprete, K. S. Edgett, B. L. Ehlmann, Sarah A. Fagents, J. P. Grotzinger, C. Hardgrove, Kenneth E. Herkenhoff, Briony H. N. Horgan, R. Jaumann, J. R. Johnson, M. T. Lemmon, G. Paar, M Caballo-Perucha, S. Gupta, C Traxler, F. Preusker, M. S. Rice, M. S. Robinson, N. Schmitz, R. Sullivan, M. J. Wolff

Mastcam-Z is a multispectral, stereoscopic imaging investigation on the Mars 2020 mission’s Perseverance rover. Mastcam-Z consists of a pair of focusable, 4:1 zoomable cameras that provide broadband red/green/blue and narrowband 400-1000 nm color imaging with fields of view from 25.6° × 19.2° (26 mm focal length at 283 μrad/pixel) to 6.2° × 4.6° (110 mm focal length at 67.4 μrad/pixel). The cameras can resolve (≥ 5 pixels) ∼0.7 mm features at 2 m and ∼3.3 cm features at 100 m distance. Mastcam-Z shares significant heritage with the Mastcam instruments on the Mars Science Laboratory Curiosity rover. Each Mastcam-Z camera consists of zoom, focus, and filter wheel mechanisms and a 1648 × 1214 pixel charge-coupled device detector and electronics. The two Mastcam-Z cameras are mounted with a 24.4 cm stereo baseline and 2.3° total toe-in on a camera plate ∼2 m above the surface on the rover’s Remote Sensing Mast, which provides azimuth and elevation actuation. A separate digital electronics assembly inside the rover provides power, data processing and storage, and the interface to the rover computer. Primary and secondary Mastcam-Z calibration targets mounted on the rover top deck enable tactical reflectance calibration. Mastcam-Z multispectral, stereo, and panoramic images will be used to provide detailed morphology, topography, and geologic context along the rover’s traverse; constrain mineralogic, photometric, and physical properties of surface materials; monitor and characterize atmospheric and astronomical phenomena; and document the rover’s sample extraction and caching locations. Mastcam-Z images will also provide key engineering information to support sample selection and other rover driving and tool/instrument operations decisions.

Geologic assessment of undiscovered oil and gas resources in the Cherokee Platform area of Kansas, Oklahoma, and Missouri

Released February 15, 2021 11:15 EST

2021, Scientific Investigations Report 2020-5110

Ronald M. Drake II, Joseph R. Hatch

In 2015, the U.S. Geological Survey completed a geology-based assessment to estimate the volumes of undiscovered, technically recoverable petroleum resources in the Cherokee Platform Province area of southeastern Kansas, northeastern Oklahoma, and southwestern Missouri. The U.S. Geological Survey identified four stratigraphic intervals that contain petroleum source rocks: (1) thin shales in the Middle to Upper Ordovician Simpson Group, (2) shales within the Upper Devonian to Lower Mississippian Woodford Shale and stratigraphically equivalent Chattanooga Shale, (3) coals and coal-associated shales and mudstones in the Middle Pennsylvanian (Desmoinesian) Cherokee and Marmaton Groups, and (4) thin marine shales within the Marmaton Group and the Upper Pennsylvanian (Missourian) Kansas City and Lansing Groups. Based on the nature of the petroleum accumulations, the characterization of the compositions and thermal maturity of the organic matter in the rocks, and the compositions of the produced petroleum, the U.S. Geological Survey identified three total petroleum systems (TPS) containing four assessment units (AU): the Paleozoic Composite TPS with the Paleozoic Conventional Assessment Unit (AU), the Woodford/Chattanooga TPS with the Woodford Shale Oil AU and the Woodford Biogenic Gas AU, and the Desmoinesian Coal TPS with the Desmoinesian Coalbed Gas AU. Assessment unit summaries follow

1. Three source rock intervals have contributed geochemically distinct oils to reservoirs within the Paleozoic Conventional AU. These intervals are the Simpson Group; the Woodford and Chattanooga Shales; and the Marmaton, Kansas City, and Lansing Groups. The major petroleum source rocks are the Woodford and Chattanooga Shales. The Paleozoic Conventional AU includes reservoirs that range in age from the Upper Cambrian Arbuckle Group to the lower Permian Chase Group. Most oil production in the province has been from Pennsylvanian sandstone reservoirs. Estimated undiscovered petroleum resources for this AU are a mean of 3 million barrels of oil (MMBO), 140 billion cubic feet of gas (BCFG), and 4 million barrels of natural gas liquids (MMBNGL).

2. The Woodford Shale Oil AU contains undiscovered continuous petroleum resources within the Woodford Shale and Chattanooga Shale. The geologic model for the AU assumes that petroleum resources remain trapped within the shale following petroleum migration. For most of the AU, organic matter within the Woodford Shale and Chattanooga Shale is thermally mature with respect to petroleum generation as shown by vitrinite reflectance values between 0.6 and 1 percent. Petroleum has been produced from the Woodford Shale and Chattanooga Shale. Estimated undiscovered petroleum resources for this AU are means of 460 MMBO, 640 BCFG, and 7 MMBNGL.

3. The Woodford Shale Biogenic Gas AU contains undiscovered continuous petroleum resources in the east-central portion of the Cherokee Platform Province near the Ozark uplift where the Woodford Shale and Chattanooga Shale are at depths of 1,250 ft or shallower. At those depths, methanogenesis and(or) biodegradation of thermogenic natural gases can be found where the shale may be more fractured and more susceptible to groundwater penetrations. The mean assessed volume of undiscovered gas for this assessment unit is 416 BCFG and 1 MMBNGL.

4. The Desmoinesian Coalbed Gas AU contains undiscovered continuous petroleum resources within the Middle Pennsylvanian coals and coal-associated shales and mudstones. The boundaries for the Desmoinesian Coalbed Gas AU are, in part, defined by the extent, depth, and thickness of the coals. Within the Desmoinesian Coalbed Gas AU, a sweet spot area was delineated based on a 10 foot or greater net coal thickness. Gas analytical data show that natural gas produced from the coals has a mixed biogenic and thermogenic origin and that there is significant migration of natural gas into the coals from adjacent conventional sandstone reservoirs. The estimated mean volume of undiscovered gas is 10.0 trillion cubic ft of gas (TCFG), and 23 MMBNGL.

For the three continuous (unconventional) assessment units and one conventional assessment unit in the Cherokee Platform Province, total mean volumes of undiscovered petroleum resources are estimated to be 463 MMBO, 11.2 TCFG and 35 MMBNGL.

SARS-CoV-2 exposure in escaped mink, Utah, USA

Released February 15, 2021 07:37 EST

2021, Emerging Infectious Diseases (27) 988-990

Susan A. Shriner, Jeremeny E. Ellis, J. Jeffrey Root, Annette Roug, Scott R. Stopak, Gerald W. Wiscomb, Jared R. Zierenberg, Hon S. Ip, Mia K. Torchetti, Thomas J. DeLiberto

In August 2020, outbreaks of coronavirus disease were confirmed on mink farms in Utah, USA. We surveyed mammals captured on and around farms for evidence of infection or exposure. Free-ranging mink, presumed domestic escapees, exhibited high antibody titers, suggesting a potential severe acute respiratory syndrome coronavirus 2 transmission pathway to native wildlife.

Electrical conductivity of the lithosphere-asthenosphere system

Released February 13, 2021 06:43 EST

2021, Physics of the Earth and Planetary Interiors (313)

Samer Naif, Kate Selway, Benjamin Scott Murphy, Gary D. Egbert, Anne Pommier

Electromagnetic geophysical methods image the electrical conductivity of the subsurface. Electrical conductivity is an intrinsic material property that is sensitive to temperature, composition, porosity, volatile and/or melt content, and other physical properties relevant to the solid Earth. Therefore, imaging the electrical structure of the crust and mantle yields valuable information on the physical and chemical state of the lithosphere-asthenosphere system.

Here we explore the viability of the passive magnetotelluric (MT) method for constraining upper mantle properties. We approach this problem in four successive steps: 1) review the electrical conductivity behavior of relevant materials; 2) predict the bulk electrical conductivity structure of oceanic and continental lithosphere for a suite of representative physical states; 3) generate synthetic MT data from the conductivity predictions; 4) compare and discuss the conductivity predictions and the synthetic data with select case studies from oceanic and continental settings. Our aim is to clarify the uncertainties associated with drawing inferences from electrical conductivity observations and ultimately to provide a basis for assigning confidence levels to interpretations.

Heatwave-induced synchrony within forage fish portfolio disrupts energy flow to top pelagic predators

Released February 12, 2021 11:01 EST

2021, Global Change Biology

Mayumi L. Arimitsu, John F. Piatt, Scott Hatch, Robert M. Suryan, Sonia Batten, Mary Anne Bishop, Rob W. Campbell, Heather Coletti, Dan Cushing, Kristen Gorman, Russell R. Hopcroft, Kathy J. Kuletz, Caitlin Elizabeth Marsteller, Caitlin McKinstry, David McGowan, John Moran, W. Scott Pegau, Anne Schaefer, Sarah K. Schoen, Jan Straley, Vanessa R. von Biela

During the Pacific marine heatwave of 2014–2016, abundance and quality of several key forage fish species in the Gulf of Alaska were simultaneously reduced throughout the system. Capelin (Mallotus catervarius), sand lance (Ammodytes personatus), and herring (Clupea pallasii) populations were at historically low levels, and within this community abrupt declines in portfolio effects identify trophic instability at the onset of the heatwave. Although compensatory changes in age‐structure, size, growth or energy content of forage fish were observed to varying degrees among all these forage fish, none were able to fully mitigate adverse impacts of the heatwave, which likely included both top‐down and bottom‐up forcing. Notably, changes to the demographic structure of forage fish suggested size‐selective removals typical of top‐down regulation. At the same time, zooplankton community structure may have driven bottom‐up regulation as copepod community structure shifted towards smaller, warm‐water species, and euphausiid biomass was reduced owing to the loss of cold‐water species. Mediated by these impacts on the forage fish community, an unprecedented disruption of the normal pelagic food web was signaled by higher trophic level disruptions during 2015–2016, when seabirds, marine mammals, and groundfish experienced shifts in distribution, mass mortalities, and reproductive failures. Unlike decadal‐scale variability underlying ecosystem regime shifts, the heatwave appeared to temporarily overwhelm the ability of the forage fish community to buffer against changes imposed by warm water anomalies, thereby eliminating any ecological advantages that may have accrued from having a suite of coexisting forage species with differing life history compensations.

Phylogeographic genetic diversity in the white sucker hepatitis B Virus across the Great Lakes Region and Alberta, Canada

Released February 12, 2021 10:40 EST

2021, Viruses (13)

Cynthia R Adams, Vicki S. Blazer, Jim Sherry, Robert S. Cornman, Luke R. Iwanowicz

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.

Patterns and processes of pathogen exposure in gray wolves across North America

Released February 12, 2021 10:23 EST

2021, Scientific Reports (11) 3722

E. E. Brandell, Paul Cross, Meggan E. Craft, Douglas W. Smith, E. J. Dubovi, Marie L. J. Gilbertson, Tyler Wheeldon, John A. Stephenson, Shannon Barber-Meyer, B. L. Borg, Mathew Sorum, Daniel R. Stahler, Allicia P Kelly, Morgan Anderson, H. D. Cluff, Daniel R. MacNulty, David L. Watts, G. Roffler, Helen M. Schwantje, Mark Hebblewhite, K. Beckman, P. J. Hudson

The presence of many pathogens varies in a predictable manner with latitude, with infections decreasing from the equator towards the poles. We investigated the geographic trends of pathogens infecting a widely distributed carnivore: the gray wolf (Canis lupus). Specifically, we investigated which variables best explain and predict geographic trends in seroprevalence across North American wolf populations and the implications of the underlying mechanisms. We compiled a large serological dataset of nearly 2000 wolves from 17 study areas, spanning 80° longitude and 50° latitude. Generalized linear mixed models were constructed to predict the probability of seropositivity of four important pathogens: canine adenovirus, herpesvirus, parvovirus, and distemper virus—and two parasites: Neospora caninum and Toxoplasma gondii. Canine adenovirus and herpesvirus were the most widely distributed pathogens, whereas N. caninum was relatively uncommon. Canine parvovirus and distemper had high annual variation, with western populations experiencing more frequent outbreaks than eastern populations. Seroprevalence of all infections increased as wolves aged, and denser wolf populations had a greater risk of exposure. Probability of exposure was positively correlated with human density, suggesting that dogs and synanthropic animals may be important pathogen reservoirs. Pathogen exposure did not appear to follow a latitudinal gradient, with the exception of N. caninum. Instead, clustered study areas were more similar: wolves from the Great Lakes region had lower odds of exposure to the viruses, but higher odds of exposure to N. caninum and T. gondii; the opposite was true for wolves from the central Rocky Mountains. Overall, mechanistic predictors were more informative of seroprevalence trends than latitude and longitude. Individual host characteristics as well as inherent features of ecosystems determined pathogen exposure risk on a large scale. This work emphasizes the importance of biogeographic wildlife surveillance, and we expound upon avenues of future research of cross-species transmission, spillover, and spatial variation in pathogen infection.

Airborne geophysical imaging of weak zones on Iliamna Volcano, Alaska: Implications for slope stability

Released February 12, 2021 07:44 EST

2021, Journal of Geophysical Research: Solid Earth (126)

Dana Elise Peterson, Carol A. Finn, Paul A. Bedrosian

Water‐saturated, hydrothermally altered rocks reduce the strength of volcanic edifices and increase the potential for sector collapses and far‐traveled mass flows of unconsolidated debris. Iliamna Volcano is an andesitic stratovolcano located on the western side of the Cook Inlet, ∼225 km southwest of Anchorage and is a source of repeated avalanches. The widespread snow and ice cover on Iliamna Volcano make surface alteration difficult to identify. However, intense hydrothermal alteration significantly reduces both the electrical resistivity and magnetization of volcanic rock and can therefore be identified with airborne geophysical measurements. We use airborne electromagnetic and magnetic data to map snow and ice thickness and identify underlying alteration zones at Iliamna Volcano, Alaska. Resistivities were calculated to an average depth of >300 m, and a 3‐D susceptibility model extends from the surface to the base of the volcano, about 3,000 m below the summit. Geophysical models image low resistivity (<30 ohm‐m) and low susceptibilities near the summit of Iliamna and below its older vent complex, with the low susceptibilities indicating alteration up to ∼800 m in thickness. Thin conductors (∼50–100 m thick) on the edifice slopes coincide with recorded locations of repeated debris avalanches over the past ∼60 years and are attributed to saturated zones at high elevation. Three‐dimensional slope stability models based upon the geophysically constrained alteration distribution suggest the edifice of Iliamna is unstable and could lead to collapse scars ∼400 m deep near the current and former vent complexes.

Nutrient concentrations, loads, and yields in the Middle Iowa River Basin, Iowa

Released February 11, 2021 17:37 EST

2021, Scientific Investigations Report 2020-5148

Jessica D. Garrett, Stephen J. Kalkhoff

Concentrations, loads, and yields of nitrate plus nitrite, total nitrogen, and total phosphorus were assessed in the Iowa River upstream from the Coralville Reservoir in east-central Iowa. The results of this study describe baseline nutrient transport during two historical reference periods, 1980–96 and 2006–10, that can be used to evaluate the progress of the implementation of reduction strategies in the Middle Iowa River Basin. Where available, nutrient data during the more recent period 2011–18 are also described. Data included nutrient concentrations and streamflow from multiple Federal, State, and Tribal agencies, and loads were computed using multiple techniques to provide valuable insights, which would otherwise not be possible.

Despite an upward trend for mean annual and base streamflow (the trend in high streamflow was not significant), average nutrient loads and yields in the Iowa River were smaller in the recent period (2011–18) than in either historical reference period. Notably smaller loads during the 2012 drought, however, caused pronounced skewed average loads for 2011–18. Comparisons among periods were difficult to make because of a short period of data upstream from Marshalltown, Iowa, at the upstream boundary of the study area and a lack of recent data near Marengo, Iowa, at the downstream boundary of the study area. Though spring and summer loads were a disproportionate part of annual loads, up to 90 percent, seasonal load comparisons to determine load reduction were more sensitive to one or the other historical period than was assessment of annual loads. Runoff-transport relations may provide an additional tool to assess load reduction.

Precipitation, peak streamflow, and inundation in the Bynum Run and Winters Run watersheds in Harford County, Maryland

Released February 11, 2021 16:10 EST

2021, Scientific Investigations Report 2021-5007

Christopher W. Nealen, Edward J. Doheny

The Harford County Department of Public Works and the U.S. Geological Survey have been working cooperatively to monitor continuous streamflow at several streamgages in Harford County, Maryland, including Bynum Run and Winters Run. A perceived recent uptick in the number of flooding events in the Bynum Run and Winters Run watersheds have led to questions about the relative frequency and magnitude of floods experienced by county residents. Precipitation, stage (water elevation), and peak flow analyses and trends were evaluated. Although there was no one contributor to point to for the perceived increase in flooding, it is most likely attributable to a combination of precipitation, stage, and peak flow. There have been numerous rainfall events with exceedingly long return intervals, but none were statistically out of the ordinary. The stages of the streams at higher flows are slightly higher (less than 0.5 feet) than historical stages, but likely are not great enough to cause a significant increase in flooding. The ratings (stage discharge relationship) for the streams have changed slightly. The latest ratings indicate erosion and deposition in the streambed over the years of observation, but again these alone do not result in more flooding. These factors taken together may point to an observational bias for incidental flooding. With the increase in land development, there may simply be more observations of flooding in the county.

Aeromagnetic map of Burney and the surrounding area, northeastern California

Released February 11, 2021 13:58 EST

2021, Open-File Report 2021-1006

Victoria E. Langenheim

An aeromagnetic survey was conducted to improve understanding of the geology and structure in the area around Burney, northeastern California. The new data are a substantial improvement over existing data and reveal a prominent north northwest-trending magnetic grain that allows extension of mapped faults, delineation of plutons within the Mesozoic basement in the northern Sierra Nevada, and linear anomalies that limit the amount of strike-slip offset along various faults in the area.

2020 drought in New England

Released February 11, 2021 13:00 EST

2020, Open-File Report 2020-1148

Pamela J. Lombard, Janet R. Barclay, Dee-Ann E. McCarthy

Below average and infrequent rainfall from May through September 2020 led to an extreme hydrologic drought across much of New England, with some areas experiencing a flash drought, reflecting its quick onset. The U.S. Geological Survey (USGS) recorded record-low streamflow and groundwater levels throughout the region. In September, the U.S. Department of Agriculture (2020) declared Aroostook County in Maine and Hillsborough and Merrimack Counties in New Hampshire as crop disaster areas. By the beginning of October, 166 community water systems and 5 municipalities in New Hampshire, more than 100 municipalities in Massachusetts, and several community water supplies in Connecticut, Maine, and Rhode Island had mandatory water restrictions in place.

Machine-learning predictions of redox conditions in groundwater in the Mississippi River Valley alluvial and Claiborne aquifers, south-central United States

Released February 10, 2021 14:57 EST

2021, Scientific Investigations Map 3468

Katherine J. Knierim, James A. Kingsbury, Connor J. Haugh

Machine-learning models developed by the U.S. Geological Survey were used to predict iron concentrations and the probability of dissolved oxygen (DO) concentrations exceeding a threshold of 1 milligram per liter (mg/L) in groundwater in aquifers of the Mississippi embayment physiographic region. DO and iron concentrations are driven by and reflect the oxidation-reduction (redox) conditions in groundwater. Predictions from boosted regression trees, a type of machine-learning model, of iron concentration and DO threshold probability were used to categorize redox zones in the Mississippi River Valley alluvial aquifer (MRVA), middle Claiborne aquifer (MCAQ), and lower Claiborne aquifer (LCAQ). Model predictions indicated that DO concentrations greater than 1 mg/L are uncommon across the MRVA. DO events (where the predicted probability was greater than 0.5) tended to occur on the margins of the MRVA and in upland areas where MCAQ and LCAQ units crop out at the surface or are at shallow depth. Predicted iron concentrations were higher in the MRVA than in the MCAQ and LCAQ. Uncer­tainty in predicted iron concentrations tended to be high in areas where measured concentrations were also high, result­ing in small areas (encompassing less than 1.5 percent of the areal extent of the MRVA) of predicted iron concentrations that exceeded 100,000 micrograms per liter. Despite the large magnitude of overpredicted iron concentrations, the general proportion and spatial distribution of predicted iron concen­trations reflected observed concentrations in groundwater wells. Where the probability of exceeding a DO concentration of 1 mg/L was 0.8 or more and the iron concentration was less than 1,000 micrograms per liter, aquifers were catego­rized as oxic. Oxic conditions were mostly in the uplands where MCAQ and LCAQ units crop out at the margins of the modeled area. The MRVA was mostly anoxic, which was controlled by DO threshold probabilities less than 0.1. The predictions and redox zones support conceptual models of redox conditions in the Mississippi embayment. The MRVA is predominantly anoxic with high iron concentrations. In the Claiborne aquifers (including the MCAQ and LCAQ), groundwater flows along regional flow paths toward the axis of the Mississippi embayment (the approximate location of the Mississippi River), the residence time in the aquifer increases, DO is consumed, and iron concentrations generally increase. Elevated concentrations of trace elements, such as manganese and arsenic, are often associated with reducing conditions in anoxic and mixed anoxic zones, but other factors such as sediment mineralogy affect the occurrence and distribution of these constituents.

Evaluation of streamflow extent and hydraulic characteristics of a restored channel at Soldier Meadows, Black Rock Desert–High Rock Canyon Emigrant Trails National Conservation Area, Nevada

Released February 10, 2021 13:33 EST

2021, Scientific Investigations Report 2020-5143

Christopher M. Morris

The Soldier Meadows spring complex provides habitat for the desert dace, an endemic and threatened fish. The spring complex has been altered with the construction of irrigation ditches that remove water from natural stream channels. Irrigation ditches generally provide lower quality habitat for the desert dace. Land and wildlife management agencies are interested in increasing habitat extent and quality by filling in irrigation ditches and restoring streamflow to natural channels. The U.S. Geological Survey measured streamflow, surveyed topography, and combined light detection and ranging data to create a two-dimensional hydraulic model of the study area to understand how restoration would change streamflow extents and hydraulic characteristics. Streamflow measurements indicate that, except for a section of one irrigation ditch at the upstream end of the study area, the total volume of streamflow diverted into the irrigation ditches in the study area was minimal. Hydraulic modeling indicates filling in the irrigation ditch at the upper end of the study area would return streamflow to the natural channel, resulting in an increase in natural channel surface water extent, and a reduction of irrigation ditch surface water flow. The result would be a more heterogenous natural stream channel, ranging from shallow and slow to narrow and fast. 

Modeling water temperature response to dam operations and water management in Green Peter and Foster Lakes and the South Santiam River, Oregon

Released February 10, 2021 11:43 EST

2021, Scientific Investigations Report 2020-5145

Annett B. Sullivan, Stewart A. Rounds

Significant Findings

Green Peter and Foster Dams have altered natural seasonal temperature patterns in the South and Middle Santiam Rivers of the Willamette River Basin in northwestern Oregon. Cold-water releases from Green Peter Dam, upstream of Foster Lake, contribute to the cool-water conditions at Foster Dam. In summer, unseasonably cold water typically is discharged from Foster Dam into the Foster Dam fish ladder, which may be one factor contributing to the low numbers of upstream migrating Chinook salmon (Oncorhynchus tshawytscha) that enter the fish ladder. The U.S. Army Corps of Engineers is leading efforts to improve conditions for Chinook salmon upstream and downstream of these dams by considering structural alterations to Foster Dam and by exploring changes to the way the dams are operated.

The U.S. Geological Survey assisted the U.S. Army Corps of Engineers by using previously calibrated numerical models of flow and water quality for Green Peter and Foster Lakes and for the South Santiam River downstream of Foster Dam. These two-dimensional hydrodynamic and water-quality (CE-QUAL-W2) models were used to test scenarios of altered dam operations and alternate water-management strategies. Results of these scenarios provide information and insights into how the mixing and thermal characteristics of the lakes are affected by dam operations, how the mixing and timing of upstream source waters reaching Foster Dam are affected by dam operations, how river and fish-ladder temperature targets might be achieved, and how quickly (or slowly) such changes in the lakes and downstream river reaches occur, relative to typical unmodified operations at Green Peter and Foster Dams.

Aquatic toxicity of chemical road dust suppressants to freshwater organisms

Released February 10, 2021 10:11 EST

2021, Archives of Environmental Contamination and Toxicology

Bethany K. Kunz, Edward E. Little, Vincent L. Barandino

Unpaved roads make up at least 14 million kilometers of the worldwide road network. Although investigations of road runoff often are focused on paved roads, unpaved roads contribute large volumes of runoff to roadside aquatic habitats and introduce unique constituents to runoff, such as chemical dust suppressants. At least 200 products across five chemical categories are commercially available for road dust suppression and are typically applied at rates up to 4.5 L/m2. Many of these products are poorly described and are lacking basic information on environmental transport, fate, and potential toxicity to roadside organisms. We characterized the aquatic toxicity of 27 commercially available dust control products, including 13 biobased products from the U.S. Department of Agriculture BioPreferred catalog, using juvenile rainbow trout. Acute toxicity varied by more than 1000-fold among products, with 96-h LC50 values ranging from 1.7 to > 16,000 mg/L. Toxicity was not well-predicted by product category. Testing with selected products after simulated weathering under UV radiation did not provide evidence of photoenhanced toxicity. Additional tests with freshwater mussels, juvenile crayfish, pond snails, and amphibian larvae indicated that juvenile rainbow trout were reasonable surrogates for these organisms for a subset of products. This effort represents one of the first comparative studies of dust suppressant toxicity and provides important information for assessing risk to aquatic resources from a widely used but understudied class of contaminants in road runoff.

Sequestration of microfibers and other microplastics by green algae, Cladophora, in the US Great Lakes

Released February 10, 2021 08:13 EST

2021, Environmental Pollution (276)

Julie R. Peller, Meredith B. Nevers, Muruleedhara Byappanahalli, Cassie Nelson, Bharath Ganesh Babu, Mary Anne Evans, Eddie Kostelnik, Morgan Keller, Jenna Johnston, Sarah Shidler

Daunting amounts of microplastics are present in surface waters worldwide. A main category of microplastics is synthetic microfibers, which originate from textiles. These microplastics are generated and released in laundering and are discharged by wastewater treatment plants or enter surface waters from other sources. The polymers that constitute many common synthetic microfibers are mostly denser than water, and eventually settle out in aquatic environments. The interaction of these microfibers with submerged aquatic vegetation has not been thoroughly investigated but is potentially an important aquatic sink in surface waters. In the Laurentian Great Lakes, prolific growth of macrophytic Cladophora creates submerged biomass with a large amount of surface area and the potential to collect and concentrate microplastics. To determine the number of synthetic microfibers in Great Lakes Cladophora, samples were collected from Lakes Erie and Michigan at multiple depths in the spring and summer of 2018. After rinsing and processing the algae, associated synthetic microfibers were quantified. The average loads of synthetic microfibers determined from the Lake Erie and Lake Michigan samples were 32,000 per kg (dry weight (dw)) and 34,000 per kg (dw), respectively, 2–4 orders of magnitude greater than loads previously reported in water and sediment. To further explore this sequestration of microplastics, fresh and aged Cladophora were mixed with aqueous mixtures of microfibers or microplastic in the laboratory to simulate pollution events. Microscopic analyses indicated that fresh Cladophora algae readily interacted with microplastics via adsorptive forces and physical entanglement. These interactions mostly cease upon algal senescence, with an expected release of microplastics in benthic sediments. Collectively, these findings suggest that synthetic microfibers are widespread in Cladophora algae and the affinity between microplastics and Cladophora may offer insights for removing microplastic pollution.

Macroalgae in the Laurentian Great Lakes contain high loads of synthetic microfibers, both entangled and adsorbed, which likely account for an important fraction of microplastics in these surface waters.

Microbial pathogens and contaminants of emerging concern in groundwater at an urban subsurface stormwater infiltration site

Released February 10, 2021 07:14 EST

2021, Science of the Total Environment (775)

Jane R. de Lambert, James F. Walsh, Deanna P. Scher, Aaron Firnstahl, Mark A. Borchardt

Urban stormwater may contain a variety of pollutants, including viruses and other pathogens, and contaminants of emerging concern (pharmaceuticals, artificial sweeteners, and personal care products). In vulnerable geologic settings, the potential exists for these contaminants to reach underlying aquifers and contaminate drinking water wells. Viruses and other pathogens, as well as other contaminants of emerging concern, were measured in stormwater and groundwater at an urban site containing a stormwater cistern and related subsurface infiltration gallery, three shallow lysimeter wells, and a monitoring well. Five of 12 microbial targets were detected more than once across the eight rounds of sampling and at multiple sampling points, with human-specific Bacteroides detected most frequently. The microbial and chemical contaminants present in urban stormwater were much lower in the water table monitoring well than the vadose zone lysimeters. There may be numerous causes for these reductions, but they are most likely related to transit across fine-grained sediments that separate the water table from the vadose zone at this location. Precipitation amount prior to sample collection was significantly associated with microbial load. A significant relation between microbial load and chloride-bromide ratio was also observed. The reduction in number and concentrations of contaminants found in the monitoring well indicates that although geologically sensitive aquifers receiving urban stormwater effluent in the subsurface may be prone to contamination, those with a protective cap of fine-grained sediments are less vulnerable. These results can inform stormwater infiltration guidance relative to drinking water wells, with an emphasis on restricting infiltration near water supply wells finished in geologically sensitive aquifers to reduce public health risks.

Computational methodology to analyze the effect of mass transfer rate on attenuation of leaked carbon dioxide in shallow aquifers

Released February 10, 2021 07:11 EST

2021, Acta Polytechnica (61)

Radek Fucik, Jakub Solovsky, Michelle R. Plampin, Hao Wu, Jiri Mikyska, Tissa H. Illangasekare

Exsolution and re-dissolution of CO2 gas within heterogeneous porous media are investigated using experimental data and mathematical modeling. In a set of bench-scale experiments, water saturated with CO2 under a given pressure is injected into a 2-D water-saturated porous media system, causing CO2 gas to exsolve and migrate upwards. A layer of fine sand mimicking a heterogeneity within a shallow aquifer is present in the tank to study accumulation and trapping of exsolved CO2. Then, clean water is injected into the system and the accumulated CO2 dissolves back into the flowing water. Simulated exsolution and dissolution mass transfer processes are studied using both nearequilibrium and kinetic approaches and compared to experimental data under conditions that do and do not include lateral background water flow. The mathematical model is based on the mixed hybrid finite element method that allows for accurate simulation of both advection- and diffusion- dominated processes.

Multi-taxa database data dictionary

Released February 09, 2021 15:16 EST

2021, Techniques and Methods 16-B1

Elise Watson, Carlton J. Rochester, Chris W. Brown, Donn A. Holmes, Stacie A. Hathaway, Robert N. Fisher

The conservation of biological resources relies on the successful management of ecological and physiological research data. The Western Ecological Research Center of the U.S. Geological Survey is working with researchers, land managers, and decision makers from non-government organizations and city, county, state, and federal resource agencies to develop data management methods. Access to the most current and applicable research data available in making sound decisions to conserve species diversity is foundational. We sought to accomplish several goals in developing the data management strategy used in the Multi-Taxa database. Data persistence and availability are primary goals of well-developed databases. By documenting and sharing the structure and definitions of Multi-Taxa database, we hope to further the successful management of these crucial data. 

Environmental and anthropogenic drivers of contaminants in agricultural watersheds with implications for land management

Released February 09, 2021 13:33 EST

2021, Science of the Total Environment (774)

Kelly Smalling, Olivia H. Devereux, Stephanie Gordon, Patrick J. Phillips, Vicki S. Blazer, Michelle Hladik, Dana W. Kolpin, Michael T. Meyer, Adam Sperry, Tyler Wagner

If not managed properly, modern agricultural practices can alter surface and groundwater quality and drinking water resources resulting in potential negative effects on aquatic and terrestrial ecosystems. Exposure to agriculturally derived contaminant mixtures has the potential to alter habitat quality and negatively affect fish and other aquatic organisms. Implementation of conservation practices focused on improving water quality continues to increase particularly in agricultural landscapes throughout the United States. The goal of this study was to determine the consequences of land management actions on the primary drivers of contaminant mixtures in five agricultural watersheds in the Chesapeake Bay, the largest watershed of the Atlantic Seaboard in North America where fish health issues have been documented for two decades. Surface water was collected and analyzed for 301 organic contaminants to determine the benefits of implemented best management practices (BMPs) designed to reduce nutrients and sediment to streams in also reducing contaminants in surface waters. Of the contaminants measured, herbicides (atrazine, metolachlor), phytoestrogens (formononetin, genistein, equol), cholesterol and total estrogenicity (indicator of estrogenic response) were detected frequently enough to statistically compare to seasonal flow effects, landscape variables and BMP intensity. Contaminant concentrations were often positively correlated with seasonal stream flow, although the magnitude of this effect varied by contaminant across seasons and sites. Land-use and other less utilized landscape variables including biosolids, manure and pesticide application and percent phytoestrogen producing crops were inversely related with site-average contaminant concentrations. Increased BMP intensity was negatively related to contaminant concentrations indicating potential co-benefits of BMPs for contaminant reduction in the studied watersheds. The information gained from this study will help prioritize ecologically relevant contaminant mixtures for monitoring and contributes to understanding the benefits of BMPs on improving surface water quality to better manage living resources in agricultural landscapes inside and outside the Chesapeake Bay watershed.

3D Elevation Program—Federal best practices

Released February 09, 2021 10:50 EST

2021, Fact Sheet 2020-3062

Vicki Lukas, Vanessa Baez

The goal of the 3D Elevation Program (3DEP) is to complete nationwide data acquisition in 8 years, by 2023, to provide the first-ever national baseline of consistent high-resolution three-dimensional data—including bare earth elevations and three-dimensional point clouds—collected in a timeframe of less than a decade. Successful implementation of 3DEP depends on partnerships and the development and adoption of a unified Federal approach to acquiring data. The purpose of this document is to outline several best practices to aid the Federal 3DEP community in reaching a higher level of coordinated implementation, maximize Federal data investments, and reduce the number of years it will take to complete national coverage. The best practices are provided to Federal agencies as a checklist to assess the level of their participation and to inspire further adoption of Federal enterprise practices that will advance joint 3DEP coverage goals for the benefit of their missions and the Nation as a whole. It is anticipated that additional best practices will be defined and added as the effort matures.

Using high resolution satellite and telemetry data to track flooded habitats, their use by waterfowl, and evaluate effects of drought on waterfowl and shorebird bioenergetics in California

Released February 09, 2021 10:33 EST

2021, Open-File Report 2020-1102

Elliott L. Matchett, Matthew Reiter, Cory T. Overton, Dennis Jongsomjit, Michael L. Casazza

Wetland managers in the Central Valley of California, a dynamic hydrological landscape, require information regarding the amount and location of existing wetland habitat to make decisions on how to best use water resources to support multiple wildlife objectives, particularly during drought. Scientists from the U.S. Geological Survey Western Ecological Research Center (WERC), Point Blue Conservation Science (Point Blue), and the U.S. Fish and Wildlife Service (USFWS) partnered to learn how wetland and flooded agricultural habitats used by waterfowl and shorebirds change during the non-breeding season (July–April) particularly during drought. During extreme drought conditions, the ability to provide sufficient water for wildlife often depends on the timing of water deliveries to managed wetlands and winter-flooded crop fields and decisions on whether to fallow croplands. Waterfowl and shorebirds could be particularly affected by these decisions because they typically rest and feed in flooded habitats. Poor habitat conditions resulting from spatially or temporally suboptimal water deliveries (that is, mismatch between waterfowl habitat needs and timing and location of flooded habitats) could reduce waterfowl hunting opportunities and body condition. Point Blue scientists developed a system for near real-time tracking of habitats used by waterfowl, shorebirds, and some other wetland-dependent “waterbirds” ( and to assess the impacts of drought on habitat availability and on waterfowl and shorebird bioenergetics. The WERC researchers linked these data with near real-time tracking (telemetry) data of duck locations throughout the Valley. The team used these two datasets to relate duck locations to open-water characteristics and to learn how waterfowl use habitats under spatially and temporally changing conditions during drought and non-drought periods. We found that recent extreme drought (2013–15) significantly changed the timing and magnitude of flooding and consequently reduced the availability of habitats used by waterfowl and shorebirds more than other recent historic droughts 2000–11. Drought reduced irrigations of moist soil seed plants and thus there was lower food energy available for waterfowl. Analyses using bioenergetics models indicated that, overall, extreme drought increased food energy deficits (total number of deficit days) for shorebirds and waterfowl. Our analysis indicated a strong direct relationship between duck locations and classified habitat derived from open-water data during the wintering period (October–March). This result helps confirm the application of dynamic water data to identify flooded areas that provide waterfowl habitat. Presence of open water at a 1-hectare resolution can be used effectively to identify flooded landscape areas available as habitat for ducks. Our discoveries from evaluating use of space by ducks also indicated that nighttime feeding locations of ducks were concentrated nearby primary roosts and that foraging distances could depend on hydrologic dynamics of location (Suisun Marsh versus California excluding Suisun Marsh) and time of season (early, middle, late). Other results indicated that some areas on the California landscape with extremely reliable water supplies could receive consistent use by ducks year after year (in essence, almost drought proof). The Water Tracker is set up to automatically track wetland habitat and food availability each year and is making these data available to water and wetland managers. Results from this research are a significant step toward understanding how waterfowl and shorebird habitats can be optimally managed on the landscape to support desired populations of these migratory birds during extreme drought. 

Observations of acrobat ants (Crematogaster sp.) preying on the eggs of the invasive giant applesnail (Pomacea maculata)

Released February 09, 2021 07:59 EST

2021, Southeastern Naturalist (1) N15-N18

Jacoby Carter, Jennifer Wilson, Susan Mopper

Herein we provide direct evidence for the consumption of Pomacea maculata (Giant Applesnail) eggs by ants in the genus Crematogaster. The observations were made during removal of snail egg masses at the Hudson Woods Unit of the Texas Mid-Coast National Wildlife Refuge, TX. We observed acrobat ants (Crematogaster sp.) removing snail eggs from an egg mass and carrying eggs back to their nest. While predation on Pomacea applesnail eggs has been reported elsewhere, to our knowledge this is the first time that it has been observed in North America.

Microbial and viral indicators of pathogens and human health risks from recreational exposure to waters impaired by fecal contamination

Released February 09, 2021 07:55 EST

2021, Journal of Sustainable Water in the Built Environment (7)

Anna M. McKee, Marcella A. Cruz

Fecal indicator bacteria (FIB) (e.g., fecal coliforms, Escherichia coli, and enterococci) have been used for decades to monitor for and protect the public from waterborne pathogens from fecal contamination. However, FIB may not perform well at predicting the presence of waterborne pathogens or human health outcomes from recreational exposure to fecal-contaminated surface waters. Numerous factors can influence the relationship between FIB and pathogens or human health outcomes, including the source(s) of contamination, the type of pathogen(s) present, differences in the survival and behavior of FIB and pathogens in the wastewater conveyance and treatment process, and varying environmental conditions. As a result, different indicators, such as source-specific microbial source tracking (MST) markers and viral fecal indicators, have been used as possible surrogates to better approximate pathogen abundance and human health risks in recreational waters. The performance of these alternative indicators has been mixed, with some promise of viral indicators better approximating viral pathogens than bacterial fecal indicators, and FIB generally more closely associated with bacterial and protozoal pathogen presence than human MST markers. Many of the assays to detect and quantify fecal indicators and pathogens are polymerase chain reaction-based assays, which detect and quantify nucleic acid [deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)] sequences specific to a target of interest. Recent advances in DNA and RNA sequencing technologies may push the field toward metabarcoding approaches, where multiple targets can be detected and quantified simultaneously. Metabarcoding is currently more applicable to bacterial and protozoal assessments than viral assessments based on a lack of universal metabarcoding markers for viruses. Innovative technologies, such as biosensors and nanotechnologies, may provide more sensitive and accurate tools to detect and quantify pathogens. When a specific pathogen is of concern for a recreational water body, a practical approach in estimating the likelihood of human health outcomes is the application of quantitative microbial risk assessments (QMRAs). Quantitative microbial risk assessments can be used to model the likelihood of pathogen-specific human health outcomes from recreational exposure as a function of a surrogate indicator. Inputs for QMRAs include the ratio between the indicator to be monitored and the pathogen of interest, the concentration of the indicator, the amount of water ingested, and the likelihood of the health outcome based on the estimated amount of pathogen consumed. There are numerous unknowns about the behavior and survival of fecal indicators and pathogens in environmental waters. Developing accurate models to predict pathogen concentrations from fecal indicators in recreational waters will require a better understanding of these unknowns. Current methods and technologies for detecting and quantifying fecal indicators and pathogens are limited due to the rare and patchy nature of pathogens. Technological advances may help improve sensitivity for detecting and quantifying pathogens.

Improving remotely sensed river bathymetry by image-averaging

Released February 09, 2021 07:50 EST

2021, Water Resources Research (57)

Carl J. Legleiter, Paul J. Kinzel

Basic data on river bathymetry is critical for numerous applications in river research and management and is increasingly obtained via remote sensing, but the noisy, pixelated appearance of image‐derived depth maps can compromise subsequent analyses. We hypothesized that this noise originates from reflectance from an irregular water surface and introduced a framework for mitigating these effects by Inferring Bathymetry from Averaged River Images (IBARI). This workflow produces time‐averaged images from video frames stabilized to account for platform motion and/or computes a spatial average from an ensemble simulated by randomly shifting images relative to themselves. We used field observations of water depth and helicopter‐based videos from a clear‐flowing river to assess the potential of this approach to improve depth retrieval. Our results indicated that depths inferred from averaged images were more accurate and precise than those inferred from single frames; observed versus predicted regression R2 increased from 0.80 to 0.88. In addition, IBARI significantly enhanced the texture of image‐derived depth maps, leading to smoother, more coherent representations of channel morphology. Depth retrieval improved with image sequence duration, but the number of images was more important than the length of time encompassed; shorter acquisitions at higher frame rates would economize data collection. We also demonstrated the potential to scale up the IBARI workflow by producing a mosaic of bathymetric maps derived from averaged images acquired at several hovering waypoints distributed along a 2.36 km reach. This approach is well‐suited to data collected from helicopters and small unmanned aircraft systems.

Estimation of suspended sediment at a discontinued streamgage on the lower Minnesota River at Fort Snelling State Park, Minnesota

Released February 08, 2021 18:20 EST

2021, Open-File Report 2021-1005

Joel T. Groten, Jon S. Hendrickson, Linda R. Loomis

In the spring of 2019, ice sheets transported down-stream during a large streamflow rise event in the lower Minnesota River destroyed an index-velocity streamgage at the Minnesota River at Fort Snelling State Park, Minnesota (U.S. Geological Survey station 05330920; hereafter referred to as “Ft. Snelling”). The streamgage previously used an acoustic Doppler velocity meter to provide instantaneous streamflow and suspended-sedimentation concentration (SSC) data in backwater conditions caused by the confluence with the Mississippi River. In response, the U.S. Geological Survey cooperated with the U.S. Army Corps of Engineers and Lower Minnesota River Watershed District to develop linear regression models that estimate SSCs and suspended-sand concentrations (sand) at the destroyed streamgage using streamflow data from an upstream site Minnesota River near Jordan, Minn. (U.S. Geological Survey station 05330000, hereafter referred to as “Jordan”).

Simple linear regression models were developed for selected positions on the streamflow hydrograph to estimate SSC and sand at Ft. Snelling from the streamflow at Jordan. Statistically significant models could not be developed for estimating SSC at low streamflows and sand at high streamflows. Models developed to estimate sand were more uncertain than models used to estimate SSC, and models using streamflow to predict SSC and sand were more uncertain than models using acoustic backscatter to predict SSC. Annual loads of SSC and sand estimated from these models show the dynamic nature of sediment transport and storage in this section of the lower Minnesota River. These models and the associated ancillary data can help with management decisions that are crucial in managing aquatic habitat, supporting power production, and commercial navigation.

Book review: Replacing GDP by 2030: Towards a common language for the well-being and sustainability community, Rutger Hoekstra, Cambridge University Press, Cambridge (2019)

Released February 08, 2021 09:39 EST

2021, Ecological Economics (183)

Kenneth J. Bagstad, Mairi-Jane Fox

Critiques of gross domestic product (GDP) as the economy's primary measuring stick have emanated from the feminist and ecological economics communities for decades (Kubiszewski et al., 2013) and have grown to include mainstream economists (Stiglitz, Sen, and Fitousi, 2009) and national accountants (Coyle, 2015). To the casual observer, such critiques seem to be growing almost as quickly as the number of proposed alternatives to GDP! Yet amidst the extensive literature on the topic, Rutger Hoekstra's “Replacing GDP by 2030: Towards a common language for the well-being and sustainability community” (Hoekstra, 2019) stands out for simultaneously diagnosing the failings of the “Beyond GDP” movement and proposing a roadmap towards the book's goal of developing data systems to underpin critically needed well-being and sustainability indicators at national and global scales.

Integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of pelagic seabirds

Released February 06, 2021 10:51 EST

2021, Systematic Biology

Joan Ferrer Obiol, Helen F. James, R. Terry Chesser, Vincent Bretagnolle, Jacob González-Solís, Julio Rozas, Marta Riutort, Andreanna J. Welch

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.