Amnis Opes Institute

Corvallis, OR, United States

Amnis Opes Institute

Corvallis, OR, United States
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Omernik J.M.,U.S. Environmental Protection Agency | Griffith G.E.,U.S. Geological Survey | Hughes R.M.,Amnis Opes Institute | Weber M.H.,U.S. Environmental Protection Agency
Environmental Management | Year: 2017

Hydrologic units provide a convenient but problematic nationwide set of geographic polygons based on subjectively determined subdivisions of land surface areas at several hierarchical levels. The problem is that it is impossible to map watersheds, basins, or catchments of relatively equal size and cover the whole country. The hydrologic unit framework is in fact composed mostly of watersheds and pieces of watersheds. The pieces include units that drain to segments of streams, remnant areas, noncontributing areas, and coastal or frontal units that can include multiple watersheds draining to an ocean or large lake. Hence, half or more of the hydrologic units are not watersheds as the name of the framework “Watershed Boundary Dataset” implies. Nonetheless, hydrologic units and watersheds are commonly treated as synonymous, and this misapplication and misunderstanding can have some serious scientific and management consequences. We discuss some of the strengths and limitations of watersheds and hydrologic units as spatial frameworks. Using examples from the Northwest and Southeast United States, we explain how the misapplication of the hydrologic unit framework has altered the meaning of watersheds and can impair understanding associations between spatial geographic characteristics and surface water conditions. © 2017 Springer Science+Business Media New York (outside the USA)

Hughes R.M.,Amnis Opes Institute | Wagner E.J.,Utah Division of Wildlife Resources | Quinn T.P.,University of Washington | Griswold K.,Idaho State University
Fisheries | Year: 2010

Hardrock mining for metals has been, and is, an economically important land use in all western U.S. states. However, metals contamination associated with mining can be highly toxic to aquatic life, the composition of metalbearing rock often leads to acid mine drainage and increased concentrations of dissolved metals, and mine-related disruptions to soil and water often produce excess fine sediments and altered stream flows. Such environmental degradation leads to large numbers of perpetually polluted streams and impaired aquatic life and fisheries. The primary U.S. law governing mining, the General Mining Law of 1872, was passed during the pick-and-shovel era to encourage economic growth; however, modern mining processes are massive in extent, highly mechanized, and incorporate additional toxic chemicals for leaching metals from ores. We provide an overview of hardrock mining impacts to aquatic life, a set of mining case studies, and suggestions for amending U.S. mining law. Our hope is that this article will lead to improved management and rehabilitation of existing mine sites and sufficient protections for the aquatic life and fisheries likely to be disturbed by future mines.

Hughes R.M.,Oregon State University | Hughes R.M.,Amnis Opes Institute | Hughes R.M.,Federal University of Minas Gerais | Herlihy A.T.,Oregon State University | And 2 more authors.
Environmental Monitoring and Assessment | Year: 2012

The number of sites sampled must be considered when determining the effort necessary for adequately assessing taxa richness in an ecosystem for bioassessment purposes; however, there have been few studies concerning the number of sites necessary for bioassessment of large rivers. We evaluated the effect of sample size (i.e., number of sites) necessary to collect vertebrate (fish and aquatic amphibians), macroinverte-brate, and diatom taxa from seven large rivers in Oregon and Washington, USA during the summers of 2006-2008. We used Monte Carlo simulation to determine the number of sites needed to collect 90-95% of the taxa 75-95% of the time from 20 randomly located sites on each river. The river wetted widths varied from 27.8 to 126.0 m, mean substrate size varied from 1 to 10 cm, and mainstem distances sampled varied from 87 to 254 km. We sampled vertebrates at each site (i.e., 50 times the mean wetted channel width) by nearshore-raft electrofishing. We sampled benthic macroinvertebrates nearshore through the use of a 500-μm mesh kick net at 11 systematic stations. From each site composite sample, we identified a target of 500 macroinvertebrate individuals to the lowest possible taxon, usually genus. We sampled benthic diatoms nearshore at the same 11 stations from a 12-cm 2 area. At each station, we sucked diatoms from soft substrate into a 60-ml syringe or brushed them off a rock and rinsed them with river water into the same jar. We counted a minimum of 600 valves at 1,000× magnification for each site. We collected 120-211 diatom taxa, 98-128 macroinverte-brate taxa, and 14-33 vertebrate species per river. To collect 90-95% of the taxa 75-95% of the time that were collected at 20 sites, it was necessary to sample 11-16 randomly distributed sites for vertebrates, 13-17 sites for macroinvertebrates, and 16-18 sites for diatoms. We conclude that 12-16 randomly distributed sites are needed for cost-efficient sampling of vertebrate richness in the main stems of our study rivers, but 20 sites markedly underestimates the species richness of benthic macroinvertebrates and diatoms in those rivers. © Springer Science+Business Media B.V. 2011.

Ligeiro R.,Federal University of Minas Gerais | Ferreira W.,Federal University of Minas Gerais | Hughes R.M.,Federal University of Minas Gerais | Hughes R.M.,Amnis Opes Institute | And 2 more authors.
Environmental Monitoring and Assessment | Year: 2013

Subsampling has been widely applied in the laboratory to process freshwater macroinvertebrate samples. Currently, many governmental agencies and research groups apply the fixed-count approach, targeting a number of individuals per sample, and at the same time keeping track of the number of quadrats (fraction of the sample) processed. However, fixed-area methods are still in use. The objective of this paper was to evaluate the reliability of macroinvertebrate taxonomic richness estimates developed from processing a standard number of subsampling quadrats (i.e.; fixed-area approaches). We used a dataset from 18 tropical stream sites experiencing three different levels of human disturbance (most-, intermediate-, and least-disturbed). With 12 quadrats processed (half the sample), the collection curves started to stabilize, and for more than half of the sites studied, it was possible to sample at least 80 % of the total taxonomic richness of the sample. However, we observed that the minimum number of quadrats to achieve 80 % of taxonomic richness was strongly negatively correlated with the number of individuals collected in each site: the fewer the individuals in a sample, the greater the processed proportion of that sample needed to represent it properly. Thus our results indicate that for any given areal subsampling effort (any fixed fraction of the sample), samples with different numbers of individuals will be represented differently in terms of the proportion of the total number of taxa of the whole samples, those with greater numbers being overestimated and those with fewer numbers being underestimated. Therefore, we do not recommend the use of fixed-area subsampling methods alone if the main purpose is to measure and analyze taxonomic richness; instead, we encourage researchers to use fixed-count approaches for this purpose. © 2012 Springer Science+Business Media B.V.

Pan Y.,Portland State University | Hughes R.M.,Amnis Opes Institute | Hughes R.M.,Federal University of Lavras | Herlihy A.T.,U.S. Environmental Protection Agency | Kaufmann P.R.,U.S. Environmental Protection Agency
Hydrobiologia | Year: 2012

Current bioassessment efforts are focused on small wadeable streams, at least partly because assessing ecological conditions in non-wadeable large rivers poses many additional challenges. In this study, we sampled 20 sites in each of seven large rivers in the Pacific Northwest, USA, to characterize variation of benthic diatom assemblages among and within rivers relative to environmental conditions. Analysis of similarity (ANOSIM) indicated that diatom assemblages were significantly different among all the seven rivers draining different ecoregions. Longitudinal patterns in diatom assemblages showed river-specific features. Bray-Curtis dissimilarity index values did not increase as a function of spatial distance among the sampled reaches within any river but the Malheur. Standardized Mantel r of association between assemblage similarity and spatial distance among sites ranged from a high of 0.69 (Malheur) to a low of 0.18 (Chehalis). In the Malheur River, % monoraphids, nitrogen-tolerant taxa, and beta-mesosaprobous taxa all decreased longitudinally while % motile taxa, especially Nitzschia, showed an opposite trend, reflecting a strong in-stream water quality gradient. Similar longitudinal trends in water quality were observed in other rivers but benthic diatom assemblages showed either weak response patterns or no patterns. Our study indicated that benthic diatom assemblages can clearly reflect among-river factors. The relationships between benthic diatom assemblages and water quality within each river may depend on the strength of the water quality gradients, interactive effects of water quality and habitat conditions, and diatom sampling design. © 2012 Springer Science+Business Media B.V.

Nonnative or alien invasive species are commonly accorded threats to native biological assemblages; however, it is difficult to separate the effects of aliens from other covarying disturbances. We evaluated the effect of alien piscivorous fish on native prey species in seven Pacific Northwest rivers through the use of a spatially balanced random sample of 20 sites on each river. The rivers lacked large main-stem dams, and point sources, if any, met state and federal water quality standards. Individual sample sites were electrofished a distance equal to 50 times their mean wetted channel widths, and all fish were identified to species, measured, and returned to the rivers alive (except for museum voucher specimens). At nearly all sites in all seven rivers, we found that the catch per unit effort (CPUE) of native prey species varied inversely with the CPUE of alien piscivores. In the two rivers most dominated by alien piscivores, we collected native prey at only 20%-25% of the sites. We conclude that piscivorous alien fish are associated with reduced population sizes of native prey species, at least during the summer low-flow period, and are potential threats to prey species persistence.

Steel E.A.,National Oceanic and Atmospheric Administration | Steel E.A.,U.S. Department of Agriculture | Hughes R.M.,Oregon State University | Hughes R.M.,Amnis Opes Institute | And 8 more authors.
Living Reviews in Landscape Research | Year: 2010

Identifying and quantifying relationships among landscape patterns, anthropogenic disturbances, and aquatic ecosystems is a new and rapidly developing approach to riverine ecology. In this review, we begin by describing the policy and management drivers for landscape-scale riverine research and we synthesize the technological advances that have enabled dramatic progress in the field. We then describe the development of landscape-scale riverine research through a series of landmark theoretical and review papers. Focusing on landscape-fish relationships, we consider the degree to which past efforts have been successful at meeting three challenges: (1) Has new research effectively incorporated the strengths of new technologies or are we doing the same old thing with more expensive data? (2) Have we incorporated key concepts from landscape ecology to improve our understanding of how landscapes affect rivers? (3) Have we been able to use landscape analyses to address management and policy needs? We conclude with a review of opportunities for advancement in the field of landscape-scale riverine research. These include moving toward the development of mechanistic theories of how landscapes affect rivers across disparate regions; considering the spatio-temporal structure of human impacts to landscapes; harnessing new statistical tools; and carefully defining landscape and response metrics to capture specific features.

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