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USGS2021

Opinion: A preferred approach for dealing with reproducibility and replicability in science

Science impacts our daily lives and guides national and international policies (1). Thus, results of scientific studies are of paramount importance; yet, there are concerns that many studies are not reproducible or replicable (2). To address these concerns, the National Research Council conducted a Consensus Study [NASEM 2019 (3)] that provides definitions of key concepts, discussions of problems, and recommendations for dealing with these problems. These recommendations are useful and well considered, but they do not go far enough in our opinion. The NASEM recommendations treat reproducibility and replicability as single-study issues, despite clear acknowledgement of the limitations of isolated studies and the need for research synthesis (3). We advocate a strategic approach to research, focusing on the accumulation of evidence via designed sequences of studies, as a means of dealing more effectively with reproducibility, replicability, and related problems. These sequences are designed to provide iterative tests based on comparison of data from empirical studies with predictions from competing hypotheses. Evidence is then formally accumulated based on the relative predictive abilities of the different hypotheses as the sequential studies proceed.

Proceedings of the National Academy of Sciences of↗
USGS1966

Monitoring wildlife for pesticide content

In May 1963, the President's Science Advisory Committee issued a report entitled Use of Pesticides . 17 the President already had requested the responsible federal agencies to implement the recommendations in the report. One of these recommendations was to provide for the development and coordination of a pesticide-monitoring program conducted on a continuing basis, by federal agencies to obtain timely systematic data on pesticide residues in the environment. Many people re engaged in research to learn the quantities of pesticide that may be hazardous. Yet there is concern that hazardous quantities may accumulate before the difficult task of evaluation can be completed. The President's report on environmental pollution 12 expresses the view that the soils and waters of the world cannot indefinitely provide a vast dumping ground to absorb and render harmless all human wastes. Chlorinated hydrocarbon pesticides are only one of these kinds of pollutants, yet they are particularly important because they persist long in the environment and accumulate in the tissues of animals.

National Academy of Sciences NRC Publication↗
USGS2015

Opinion: Endogenizing culture in sustainability science research and policy

Integrating the analysis of natural and social systems to achieve sustainability has been an international scientific goal for years ( 1 , 2 ). However, full integration has proven challenging, especially in regard to the role of culture ( 3 ), which is often missing from the complex sustainability equation. To enact policies and practices that can achieve sustainability, researchers and policymakers must do a better job of accounting for culture, difficult though this task may be. The concept of culture is complex, with hundreds of definitions that for years have generated disagreement among social scientists ( 4 ). Understood at the most basic level, culture constitutes shared values, beliefs, and norms through which people “see,” interpret, or give meaning to ideas, actions, and environments. Culture is often used synonymously with “worldviews” or “cosmologies” ( 5 , 6 ) to explain the patterned ways of assigning meanings and interpretations among individuals within groups. Used in this way, culture has been found to have only limited empirical support as an explanation of human risk perception ( 7 , 8 ) and environmentalism ( 9 ).

Proceedings of the National Academy of Sciences of↗
USGS2008

Humid tropical forest clearing from 2000 to 2005 quantified by using multitemporal and multiresolution remotely sensed data

Forest cover is an important input variable for assessing changes to carbon stocks, climate and hydrological systems, biodiversity richness, and other sustainability science disciplines. Despite incremental improvements in our ability to quantify rates of forest clearing, there is still no definitive understanding on global trends. Without timely and accurate forest monitoring methods, policy responses will be uninformed concerning the most basic facts of forest cover change. Results of a feasible and cost-effective monitoring strategy are presented that enable timely, precise, and internally consistent estimates of forest clearing within the humid tropics. A probability-based sampling approach that synergistically employs low and high spatial resolution satellite datasets was used to quantify humid tropical forest clearing from 2000 to 2005. Forest clearing is estimated to be 1.39% (SE 0.084%) of the total biome area. This translates to an estimated forest area cleared of 27.2 million hectares (SE 2.28 million hectares), and represents a 2.36% reduction in area of humid tropical forest. Fifty-five percent of total biome clearing occurs within only 6% of the biome area, emphasizing the presence of forest clearing “hotspots.” Forest loss in Brazil accounts for 47.8% of total biome clearing, nearly four times that of the next highest country, Indonesia, which accounts for 12.8%. Over three-fifths of clearing occurs in Latin America and over one-third in Asia. Africa contributes 5.4% to the estimated loss of humid tropical forest cover, reflecting the absence of current agro-industrial scale clearing in humid tropical Africa.

Proceedings of the National Academy of Sciences of↗
USGS2004

Pacific and Atlantic Ocean influences on multidecadal drought frequency in the United States

More than half (52%) of the spatial and temporal variance in multidecadal drought frequency over the conterminous United States is attributable to the Pacific Decadal Oscillation (PDO) and the Atlantic Multidecadal Oscillation (AMO). An additional 22% of the variance in drought frequency is related to a complex spatial pattern of positive and negative trends in drought occurrence possibly related to increasing Northern Hemisphere temperatures or some other unidirectional climate trend. Recent droughts with broad impacts over the conterminous U.S. (1996, 1999-2002) were associated with North Atlantic warming (positive AMO) and north-eastern and tropical Pacific cooling (negative PDO). Much of the long-term predictability of drought frequency may reside in the multidecadal behavior of the North Atlantic Ocean. Should the current positive AMO (warm North Atlantic) conditions persist into the upcoming decade, we suggest two possible drought scenarios that resemble the continental-scale patterns of the 1930s (positive PDO) and 1950s (negative PDO) drought.

Proceedings of the National Academy of Sciences of↗
USGS2004

Environment, agriculture, and settlement patterns in a marginal Polynesian landscape

Beginning ca. A.D. 1400, Polynesian farmers established permanent settlements along the arid southern flank of Haleakala Volcano, Maui, Hawaiian Islands; peak population density (43-57 persons per km2) was achieved by A.D. 1700-1800, and it was followed by the devastating effects of European contact. This settlement, based on dryland agriculture with sweet potato as a main crop, is represented by >3,000 archaeological features investigated to date. Geological and environmental factors are the most important influence on Polynesian farming and settlement practices in an agriculturally marginal landscape. Interactions between lava flows, whose ages range from 3,000 to 226,000 years, and differences in rainfall create an environmental mosaic that constrained precontact Polynesian farming practices to a zone defined by aridity at low elevation and depleted soil nutrients at high elevation. Within this productive zone, however, large-scale agriculture was concentrated on older, tephra-blanketed lava flows; younger flows were reserved for residential sites, small ritual gardens, and agricultural temples.

Hawaii↗
USGS2004

Southern Peru desert shattered by the great 2001 earthquake: Implications for paleoseismic and paleo-El Nino-Southern Oscillation records

In the desert region around the coastal city of Ilo, the great southern Peru earthquake of June 23, 2001 (8.2-8.4 moment magnitude), produced intense and widespread ground-failure effects. These effects included abundant landslides, pervasive ground cracking, microfracturing of surficial hillslope materials, collapse of drainage banks over long stretches, widening of hillside rills, and lengthening of first-order tributary channels. We have coined the term "shattered landscape" to describe the severity of these effects. Long-term consequences of this landscape shattering are inferred to include increased runoff and sediment transport during postearthquake rainstorms. This inference was confirmed during the first minor postearthquake rainstorm there, which occurred in June and July of 2002. Greater amounts of rainfall in this desert region have historically been associated with El Nin??o events. Previous studies of an unusual paleoflood deposit in this region have concluded that it is the product of El Nin??o-generated precipitation falling on seismically disturbed landscapes. The effects of the 2001 earthquake and 2002 rainstorm support that conclusion.

Proceedings of the National Academy of Sciences of↗
USGS2004

Emissions pathways, climate change, and impacts on California

The magnitude of future climate change depends substantially on the greenhouse gas emission pathways we choose. Here we explore the implications of the highest and lowest Intergovernmental Panel on Climate Change emissions pathways for climate change and associated impacts in California. Based on climate projections from two state-of-the-art climate models with low and medium sensitivity (Parallel Climate Model and Hadley Centre Climate Model, version 3, respectively), we find that annual temperature increases nearly double from the lower B1 to the higher A1fi emissions scenario before 2100. Three of four simulations also show greater increases in summer temperatures as compared with winter. Extreme heat and the associated impacts on a range of temperature-sensitive sectors are substantially greater under the higher emissions scenario, with some interscenario differences apparent before midcentury. By the end of the century under the B1 scenario, heatwaves and extreme heat in Los Angeles quadruple in frequency while heat-related mortality increases two to three times; alpine/subalpine forests are reduced by 50-75%; and Sierra snowpack is reduced 30-70%. Under A1fi, heatwaves in Los Angeles are six to eight times more frequent, with heat-related excess mortality increasing five to seven times; alpine/subalpine forests are reduced by 75-90%; and snowpack declines 73-90%, with cascading impacts on runoff and streamflow that, combined with projected modest declines in winter precipitation, could fundamentally disrupt California's water rights system. Although interscenario differences in climate impacts and costs of adaptation emerge mainly in the second half of the century, they are strongly dependent on emissions from preceding decades.

Proceedings of the National Academy of Sciences of↗
USGS2004

Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker

Sampling methods and results of a gene flow study are described that will be of interest to plant scientists, evolutionary biologists, ecologists, and stakeholders assessing the environmental safety of transgenic crops. This study documents gene flow on a landscape level from creeping bentgrass (Agrostis stolonifera L.), one of the first wind-pollinated, perennial, and highly outcrossing transgenic crops being developed for commercial use. Most of the gene flow occurred within 2 km in the direction of prevailing winds. The maximal gene flow distances observed were 21 km and 14 km in sentinel and resident plants, respectively, that were located in primarily nonagronomic habitats. The selectable marker used in these studies was the CP4 EPSPS gene derived from Agrobacterium spp. strain CP4 that encodes 5-enol-pyruvylshikimate-3-phosphate synthase and confers resistance to glyphosate herbicide. Evidence for gene flow to 75 of 138 sentinel plants of A. stolonifera and to 29 of 69 resident Agrostis plants was based on seedling progeny survival after spraying with glyphosate in greenhouse assays and positive TraitChek, PCR, and sequencing results. Additional studies are needed to determine whether introgression will occur and whether it will affect the ecological fitness of progeny or the structure of plant communities in which transgenic progeny may become established.

Proceedings of the National Academy of Sciences of↗
USGS2005

Host population persistence in the face of introduced vector-borne diseases: Hawaii amakihi and avian malaria

The past quarter century has seen an unprecedented increase in the number of new and emerging infectious diseases throughout the world, with serious implications for human and wildlife populations. We examined host persistence in the face of introduced vector-borne diseases in Hawaii, where introduced avian malaria and introduced vectors have had a negative impact on most populations of Hawaiian forest birds for nearly a century. We studied birds, parasites, and vectors in nine study areas from 0 to 1,800 m on Mauna Loa Volcano, Hawaii from January to October, 2002. Contrary to predictions of prior work, we found that Hawaii amakihi (Hemignathus virens), a native species susceptible to malaria, comprised from 24.5% to 51.9% of the avian community at three low-elevation forests (55-270 m). Amakihi were more abundant at low elevations than at disease-free high elevations, and were resident and breeding there. Infection rates were 24-40% by microscopy and 55-83% by serology, with most infected individuals experiencing low-intensity, chronic infections. Mosquito trapping and diagnostics provided strong evidence for year-round local transmission. Moreover, we present evidence that Hawaii amakihi have increased in low elevation habitats on south-eastern Hawaii Island over the past decade. The recent emergent phenomenon of recovering amakihi populations at low elevations, despite extremely high prevalence of avian malaria, suggests that ecological or evolutionary processes acting on hosts or parasites have allowed this species to recolonize low-elevation habitats. A better understanding of the mechanisms allowing coexistence of hosts and parasites may ultimately lead to tools for mitigating disease impacts on wildlife and human populations.

Proceedings of the National Academy of Sciences of↗
USGS2001

Paleoclimate and Amerindians: Evidence from stable isotopes and atmospheric circulation

Two Amerindian demographic shifts are attributed to climate change in the northwest plains of North America: at ???11,000 calendar years before present (yr BP), Amerindian culture apparently split into foothills-mountains vs. plains biomes; and from 8,000-5,000 yr BP, scarce archaeological sites on the open plains suggest emigration during xeric "Altithermal" conditions. We reconstructed paleoclimates from stable isotopes in prehistoric bison bone and relations between weather and fractions of C4 plants in forage. Further, we developed a climate-change model that synthesized stable isotope, existing qualitative evidence (e.g., palynological, erosional), and global climate mechanisms affecting this midlatitude region. Our isotope data indicate significant warming from ???12,400 to 11,900 yr BP, supporting climate-driven cultural separation. However, isotope evidence of apparently wet, warm conditions at 7,300 yr BP refutes emigration to avoid xeric conditions. Scarcity of archaeological sites is best explained by rapid climate fluctuations after catastrophic draining of the Laurentide Lakes, which disrupted North Atlantic Deep Water production and subsequently altered monsoonal inputs to the open plains.

Proceedings of the National Academy of Sciences of↗
USGS2005

Degassing Lakes Nyos and Monoun: Defusing certain disaster

Since the catastrophic releases of CO 2 in the 1980s, Lakes Nyos and Monoun in Cameroon experienced CO 2 recharge at alarming rates of up to 80 mol/m 2 per yr. Total gas pressures reached 8.3 and 15.6 bar in Monoun (2003) and Nyos (2001), respectively, resulting in gas saturation levels up to 97%. These natural hazards are distinguished by the potential for mitigation to prevent future disasters. Controlled degassing was initiated at Nyos (2001) and Monoun (2003) amid speculation it could inadvertently destabilize the lakes and trigger another gas burst. Our measurements indicate that water column structure has not been compromised by the degassing and local stability is increasing in the zones of degassing. Furthermore, gas content has been reduced in the lakes ≈12-14%. However, as gas is removed, the pressure at pipe inlets is reduced, and the removal rate will decrease over time. Based on 12 years of limnological measurements we developed a model of future removal rates and gas inventory, which predicts that in Monoun the current pipe will remove ≈30% of the gas remaining before the natural gas recharge balances the removal rate. In Nyos the single pipe will remove ≈25% of the gas remaining by 2015; this slow removal extends the present risk to local populations. More pipes and continued vigilance are required to reduce the risk of repeat disasters. Our model indicates that 75-99% of the gas remaining would be removed by 2010 with two pipes in Monoun and five pipes in Nyos, substantially reducing the risks.

Lakes Nyos and Monoun↗
USGS2007

Whole-ecosystem study shows rapid fish-mercury response to changes in mercury deposition

Methylmercury contamination of fisheries from centuries of industrial atmospheric emissions negatively impacts humans and wild-life worldwide. The response of fish methylmercury concentrations to changes in mercury deposition has been difficult to establish because sediments/soils contain large pools of historical contamination, and many factors in addition to deposition affect fish mercury. To test directly the response of fish contamination to changing mercury deposition, we conducted a whole-ecosystem experiment, increasing the mercury load to a lake and its watershed by the addition of enriched stable mercury isotopes. The isotopes allowed us to distinguish between experimentally applied mercury and mercury already present in the ecosystem and to examine bioaccumulation of mercury deposited to different parts of the watershed. Fish methylmercury concentrations responded rapidly to changes in mercury deposition over the first 3 years of study. Essentially all of the increase in fish methylmercury concentrations came from mercury deposited directly to the lake surface. In contrast, <1% of the mercury isotope deposited to the watershed was exported to the lake. Steady state was not reached within 3 years. Lake mercury isotope concentrations were still rising in lake biota, and watershed mercury isotope exports to the lake were increasing slowly. Therefore, we predict that mercury emissions reductions will yield rapid (years) reductions in fish methylmercury concentrations and will yield concomitant reductions in risk. However, a full response will be delayed by the gradual export of mercury stored in watersheds. The rate of response will vary among lakes depending on the relative surface areas of water and watershed.

Proceedings of the National Academy of Sciences of↗
USGS2007

A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay

Ecological observations sustained over decades often reveal abrupt changes in biological communities that signal altered ecosystem states. We report a large shift in the biological communities of San Francisco Bay, first detected as increasing phytoplankton biomass and occurrences of new seasonal blooms that began in 1999. This phytoplankton increase is paradoxical because it occurred in an era of decreasing wastewater nutrient inputs and reduced nitrogen and phosphorus concentrations, contrary to the guiding paradigm that algal biomass in estuaries increases in proportion to nutrient inputs from their watersheds. Coincidental changes included sharp declines in the abundance of bivalve mollusks, the key phytoplankton consumers in this estuary, and record high abundances of several bivalve predators: Bay shrimp, English sole, and Dungeness crab. The phytoplankton increase is consistent with a trophic cascade resulting from heightened predation on bivalves and suppression of their filtration control on phytoplankton growth. These community changes in San Francisco Bay across three trophic levels followed a state change in the California Current System characterized by increased upwelling intensity, amplified primary production, and strengthened southerly flows. These diagnostic features of the East Pacific "cold phase" lead to strong recruitment and immigration of juvenile flatfish and crustaceans into estuaries where they feed and develop. This study, built from three decades of observation, reveals a previously unrecognized mechanism of ocean-estuary connectivity. Interdecadal oceanic regime changes can propagate into estuaries, altering their community structure and efficiency of transforming land-derived nutrients into algal biomass.

California↗
USGS2008

Evaluation of the sustainability of deep groundwater as an arsenic-safe resource in the Bengal Basin

Tens of millions of people in the Bengal Basin region of Bangladesh and India drink groundwater containing unsafe concentrations of arsenic. This high-arsenic groundwater is produced from shallow (<100 m) depths by domestic and irrigation wells in the Bengal Basin aquifer system. The government of Bangladesh has begun to install wells to depths of >150 m where groundwater arsenic concentrations are nearly uniformly low, and many more wells are needed, however, the sustainability of deep, arsenic-safe groundwater has not been previously assessed. Deeper pumping could induce downward migration of dissolved arsenic, permanently destroying the deep resource. Here, it is shown, through quantitative, large-scale hydrogeologic analysis and simulation of the entire basin, that the deeper part of the aquifer system may provide a sustainable source of arsenic-safe water if its utilization is limited to domestic supply. Simulations provide two explanations for this result: deep domestic pumping only slightly perturbs the deep groundwater flow system, and substantial shallow pumping for irrigation forms a hydraulic barrier that protects deeper resources from shallow arsenic sources. Additional analysis indicates that this simple management approach could provide arsenic-safe drinking water to >90% of the arsenic-impacted region over a 1,000-year timescale. This insight may assist water-resources managers in alleviating one of the world's largest groundwater contamination problems.

Proceedings of the National Academy of Sciences of↗
USGS2008

Homage to Linnaeus: How many parasites? How many hosts?

Estimates of the total number of species that inhabit the Earth have increased significantly since Linnaeus's initial catalog of 20,000 species. The best recent estimates suggest that there are ≈6 million species. More emphasis has been placed on counts of free-living species than on parasitic species. We rectify this by quantifying the numbers and proportion of parasitic species. We estimate that there are between 75,000 and 300,000 helminth species parasitizing the vertebrates. We have no credible way of estimating how many parasitic protozoa, fungi, bacteria, and viruses exist. We estimate that between 3% and 5% of parasitic helminths are threatened with extinction in the next 50 to 100 years. Because patterns of parasite diversity do not clearly map onto patterns of host diversity, we can make very little prediction about geographical patterns of threat to parasites. If the threats reflect those experienced by avian hosts, then we expect climate change to be a major threat to the relatively small proportion of parasite diversity that lives in the polar and temperate regions, whereas habitat destruction will be the major threat to tropical parasite diversity. Recent studies of food webs suggest that ≈75% of the links in food webs involve a parasitic species; these links are vital for regulation of host abundance and potentially for reducing the impact of toxic pollutants. This implies that parasite extinctions may have unforeseen costs that impact the health and abundance of a large number of free-living species.

Proceedings of the National Academy of Sciences of↗
USGS2009

Prey choice and habitat use drive sea otter pathogen exposure in a resource-limited coastal system

The processes promoting disease in wild animal populations are highly complex, yet identifying these processes is critically important for conservation when disease is limiting a population. By combining field studies with epidemiologic tools, we evaluated the relationship between key factors impeding southern sea otter ( Enhydra lutris nereis ) population growth: disease and resource limitation. This threatened population has struggled to recover despite protection, so we followed radio-tagged sea otters and evaluated infection with 2 disease-causing protozoal pathogens, Toxoplasma gondii and Sarcocystis neurona , to reveal risks that increased the likelihood of pathogen exposure. We identified patterns of pathogen infection that are linked to individual animal behavior, prey choice, and habitat use. We detected a high-risk spatial cluster of S. neurona infections in otters with home ranges in southern Monterey Bay and a coastal segment near San Simeon and Cambria where otters had high levels of infection with T. gondii . We found that otters feeding on abalone, which is the preferred prey in a resource-abundant marine ecosystem, had a very low risk of infection with either pathogen, whereas otters consuming small marine snails were more likely to be infected with T. gondii . Individual dietary specialization in sea otters is an adaptive mechanism for coping with limited food resources along central coastal California. High levels of infection with protozoal pathogens may be an adverse consequence of dietary specialization in this threatened species, with both depleted resources and disease working synergistically to limit recovery.

California↗
USGS2009

Elevated CO 2 stimulates marsh elevation gain, counterbalancing sea-level rise

Tidal wetlands experiencing increased rates of sea-level rise (SLR) must increase rates of soil elevation gain to avoid permanent conversion to open water. The maximal rate of SLR that these ecosystems can tolerate depends partly on mineral sediment deposition, but the accumulation of organic matter is equally important for many wetlands. Plant productivity drives organic matter dynamics and is sensitive to global change factors, such as rising atmospheric CO 2 concentration. It remains unknown how global change will influence organic mechanisms that determine future tidal wetland viability. Here, we present experimental evidence that plant response to elevated atmospheric [CO 2 ] stimulates biogenic mechanisms of elevation gain in a brackish marsh. Elevated CO 2 (ambient + 340 ppm) accelerated soil elevation gain by 3.9 mm yr −1 in this 2-year field study, an effect mediated by stimulation of below-ground plant productivity. Further, a companion greenhouse experiment revealed that the CO 2 effect was enhanced under salinity and flooding conditions likely to accompany future SLR. Our results indicate that by stimulating biogenic contributions to marsh elevation, increases in the greenhouse gas, CO 2 , may paradoxically aid some coastal wetlands in counterbalancing rising seas.

Proceedings of the National Academy of Sciences↗