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At least 19 recordsLinked to original sources

Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data

The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus , and the Mexican, and central and northern South American Stenopelmatus . The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus , with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus . Based on our results, we propose the existence of four species-groups within the genus (the faulkneri , talpa , Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.

Invertebrate Systematics↗

The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema ) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina . Constraint tests supported monophyly of the genera Fusconaia and Pleurobema , including the subgenus P . ( Sintoxia ). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum , P. chattanoogaense and P. decisum , P. clava and P. oviforme , P. rubrum and P. sintoxia , F. askewi and F. lananensis , and F. cerina and F. flava . Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema ). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

Invertebrate Systematics↗

A meta-analysis of mercury biomagnification in freshwater predatory invertebrates: Community diversity and dietary exposure drive variability

Accurate estimates of methylmercury (MeHg) exposure are valuable to actionably assess risk and protect wildlife and human health. MeHg trophic transfer is a critical driver of risk: MeHg is generally biomagnified by a factor of 8.3 ± 7.5 from one trophic level to the next, averaged across freshwater communities (mean ± standard deviation). This variability can produce disparate risks even where basal MeHg concentrations are similar. Taxonomy may be one driver of this variability: physiologically diverse groups, like vertebrates and invertebrates, may assimilate MeHg differently. To determine whether taxonomy affects trophic transfer efficiency, we conducted a meta-analysis characterizing predatory invertebrate MeHg biomagnification. Our analyses estimated that freshwater predatory invertebrates biomagnify MeHg by factors of 2.1 ± 0.2 to 4.3 ± 0.3, with a 98.9 ± 0.4% posterior probability that factors are below 5 (mean ± standard error). When vertebrates or primary producers were included, a site’s trophic magnification factor was 18.6 ± 6.2 to 54.1 ± 7.7% higher than estimates for invertebrates alone. Biomagnification was inversely correlated to prey MeHg concentration and varied among systematic and functional groups. These data suggest that predatory invertebrates biomagnify MeHg less efficiently than vertebrates and that a community’s diversity and structure determine its biomagnification efficiency. Incorporating organismal variation in trophic transfer estimates may improve the assessment, communication, and management of MeHg risk.

Environmental Science & Technology↗

Biomedical and veterinary science can increase our understanding of coral disease

A balanced approach to coral disease investigation is critical for understanding the global decline of corals. Such an approach should involve the proper use of biomedical concepts, tools, and terminology to address confusion and promote clarity in the coral disease literature. Investigating disease in corals should follow a logical series of steps including identification of disease, systematic morphologic descriptions of lesions at the gross and cellular levels, measurement of health indices, and experiments to understand disease pathogenesis and the complex interactions between host, pathogen, and the environment. This model for disease investigation is widely accepted in the medical, veterinary and invertebrate pathology disciplines. We present standard biomedical rationale behind the detection, description, and naming of diseases and offer examples of the application of Koch's postulates to elucidate the etiology of some infectious diseases. Basic epidemiologic concepts are introduced to help investigators think systematically about the cause(s) of complex diseases. A major goal of disease investigation in corals and other organisms is to gather data that will enable the establishment of standardized case definitions to distinguish among diseases. Concepts and facts amassed from empirical studies over the centuries by medical and veterinary pathologists have standardized disease investigation and are invaluable to coral researchers because of the robust comparisons they enable; examples of these are given throughout this paper. Arguments over whether coral diseases are caused by primary versus opportunistic pathogens reflect the lack of data available to prove or refute such hypotheses and emphasize the need for coral disease investigations that focus on: characterizing the normal microbiota and physiology of the healthy host; defining ecological interactions within the microbial community associated with the host; and investigating host immunity, host-agent interactions, pathology, pathogenesis, and factors that promote the pathogenicity of the causative agent(s) of disease.

Journal of Experimental Marine Biology and Ecology↗

Space use of a dominant Arctic vertebrate: Effects of prey, sea ice, and land on Pacific walrus resource selection

Sea ice dominates marine ecosystems in the Arctic, and recent reductions in sea ice may alter food webs throughout the region. Sea ice loss may also stress Pacific walruses ( Odobenus rosmarus divergens ), which feed on benthic macroinvertebrates in the Bering and Chukchi seas. However, no studies have examined the effects of sea ice on foraging Pacific walrus space use patterns. We tested a series of hypotheses that examined walrus foraging resource selection as a function of proximity to resting substrates and prey biomass. We quantified walrus prey biomass with 17 benthic invertebrate families, which included bivalves, polychaetes, amphipods, tunicates, and sipunculids. We included covariates for distance to sea ice and distance to land, and systematically developed a series of candidate models to examine interactions among benthic prey biomass and resting substrates. We ranked candidate models with Bayesian Information Criterion and made inferences on walrus resource selection based on the top-ranked model. Based on the top model, biomass of the bivalve family Tellinidae, distance to ice, distance to land, and the interaction of distances to ice and land all positively influenced walrus foraging resource selection. Standardized model coefficients indicated that distance to ice explained the most variation in walrus foraging resource selection followed by Tellinidae biomass. Distance to land and the interaction of distances to ice and land accounted for similar levels of variation. Tellinidae biomass likely represented an index of overall bivalve biomass, indicating walruses focused foraging in areas with elevated levels of bivalve and tellinid biomass. Our results also emphasize the importance of sea ice to walruses. Projected sea ice loss will increase the duration of the open water season in the Chukchi Sea, altering the spatial distribution of resting sites relative to current foraging areas and possibly affecting the spatial structure of benthic communities.

Alaska↗

Changing patterns in coastal cutthroat trout (Oncorhynchus clarki clarki) diet and prey in a gradient of deciduous canopies

We examined the influence of riparian vegetation patterns on coastal cutthroat trout Oncorhynchus clarki clarki diet and prey from the summer of 2001 through the spring of 2002. Benthic and drifting invertebrates, allochthonous prey, and fish diet were collected from deciduous, conifer, and mixed sections of three Oregon coastal watersheds. The nine sites were best characterized as a continuum of deciduous cover, and shrub cover and proportion of deciduous canopy were positively correlated (r = 0.74). Most sources of prey (benthic invertebrate biomass, allochthonous invertebrate inputs, aquatic and total invertebrate drift) and aquatic prey ingested by coastal cutthroat trout were greater where shrub cover was more abundant. Only aquatic drift, total invertebrate drift, and allochthonous invertebrates were positively correlated with deciduous vegetation. Compared with coniferous sites, allochthonous invertebrates under deciduous and mixed canopies were almost 30% more abundant. Stream discharge likely influenced seasonal fluxes of aquatic invertebrate biomass in the benthos and drift. Aquatic insects dominated gut contents during this study; however, terrestrial prey were most common in the diet during the summer and fall. In the Pacific northwest, systematic removal of deciduous riparian vegetation to promote conifers may have unintended consequences on food resources of coastal cutthroat trout and aquatic food web interactions.

Oregon↗

Quantitative variation and the ecological role of vulpinic acid and atranorin in thallus of Letharia vulpina

High pressure liquid chromatography was used to determine concentrations of vulpinic acid and atranorin in the thaullus of Letharia vulpina . Vulpinic acid concentration is lowest in the old basal branches of the thallus and increases toward the young branch tips, whereas the reverse is true for atranorin. The suggested role of vulpinic acid as an anti-herbivore defense compound is supported by both this distribution of the compound and our observations that vulpinic acid acts as a feeding deterrent to certain invertebrates. No significant difference in the content of atranorin or vulpinic acid was found in lichens from microhabitats of different sunlight intensities.

Biochemical Systematics and Ecology↗

Sensitive ecological areas and species inventory of Actun Chapat Cave, Vaca Plateau, Belize

Cave ecosystems are considered one of the most poorly studied and fragile systems on Earth. Belize caves are no exception. This paper represents the first effort to synthesize information on both invertebrate and vertebrate observations from a Belize cave. Based on limited field research and a review of literature, we identified two ecologically sensitive areas, and developed a species inventory list containing 41 vertebrate and invertebrate morphospecies in Actun Chapat, Vaca Plateau, west-central Belize. Actun Chapat contains two ecologically sensitive areas: (1) a large multiple species bat roost, and (2) a subterranean pool containing troglobites and stygobites. The inventory list is a product of sporadic research conducted between 1973 and 2001. Ecological research in this cave system remains incomplete. An intensive systematic ecological survey of Actun Chapat with data collection over multiple seasons using a suite of survey techniques will provide a more complete inventory list. To minimize human disturbance to the ecologically sensitive areas, associated with ecotourism, we recommend limited to no access in the areas identified as "sensitive".

Journal of Cave and Karst Studies↗

Irrigation-induced contamination of water, sediment, and biota in the western United States-synthesis of data from the National Irrigation Water Quality Program

In October 1985 the U.S. Department of the Interior (DOI), through the National Irrigation Water Quality Program (NIWQP), began a series of field investigations at 26 areas in the Western United States to determine whether irrigation drainage has had harmful effects on fish, wildlife, and humans or has reduced beneficial uses of water. In 1992 NIWQP initiated the Data Synthesis Project to evaluate data collected during the field investigations. Geologic, climatologic, and hydrologic data were evaluated and water, sediment, and biota from the 26 areas were analyzed to identify commonalities and dominant factors that result in irrigation-induced contamination of water and biota. Data collected for the 26 area investigations have been compiled and merged into a common data base. The structure of the data base is designed to enable assessment of relations between contaminant concentrations in water, sediment, and biota. The data base is available to the scientific community through the World Wide Web at URL http://www.usbr.gov/niwqp . Analysis of the data base for the Data Synthesis included use of summary statistics, factor analysis, and logistic regression. A Geographic Information System was used to store and analyze spatially oriented digital data such as land use, geology and evaporation rates. In the U.S. Department of the Interior (DOI) study areas, samples of water, bottom sediment, and biota were collected for trace-element and pesticide analysis. Contaminants most commonly associated with irrigation drainage were identified by comparing concentrations in water with established criteria. For surface water, the criteria used were typically chronic criteria for the protection of freshwater aquatic life. Because ground water can discharge to the surface where wildlife can be exposed to it, the criteria used for ground water were both the maximum contaminant levels (MCL's) for drinking water and the chronic criteria for the protection of freshwater aquatic life. Data collected by the NIWQP studies indicated that, in surface water, filtered and unfiltered samples had nearly the same concentrations of arsenic, boron, molybdenum, and selenium for concentrations greater than about 10 micrograms per liter. Therefore, in this concentration range, filtered concentrations can be directly compared to biological-effect levels developed for unfiltered samples. In the range of 1 to 10 micrograms per liter there may be a tendency for unfiltered arsenic concentrations to be greater than filtered concentrations. For selenium, however, the data suggest differences from equality in that range result from analytical imprecision and not a general tendency for unfiltered concentrations to be greater than filtered concentrations. This relation may not be true in lentic, nutrient-rich waters because in such settings algae can bioaccumulate large amounts of selenium and other trace elements. Selenium was the trace element in surface water that most commonly exceeded chronic criteria for the protection of freshwater aquatic life; more than 40 percent of the selenium concentrations in surface-water samples exceeded the U.S. Environmental Protection Agency (USEPA) aquatic-life chronic criterion (5 micrograms per liter). In 12 of the 26 areas at least 25 percent of the surface water-samples had selenium concentrations that either equaled or exceeded the chronic criterion (5 micrograms per liter). More than 28 percent of boron concentrations and almost 17 percent of the molybdenum concentrations exceeded the aquatic life criteria established by the State of California (550 and 19 micrograms per liter, respectively). In ground water, more than 22 percent of the arsenic concentrations and more than 35 percent of the selenium concentrations exceeded the MCL (10 and 50 micrograms per liter, respectively). Few samples of uranium in surface water exceeded a criterion for the protection of aquatic life (300 micrograms per liter), but 44 percent of the uranium concentrations in ground water exceeded the MCL (30 micrograms per liter). Molybdenum, selenium and uranium were the trace elements most commonly found in bottom-sediment samples that exceeded the upper limit of the 95th percentile expected range in soils of the Western United States. Selenium is the only trace element for which ecological sediment guidelines are used in this report. Selenium concentrations commonly exceeded the ecological sediment guideline of two micrograms per gram. DDT and its degradation products DDD and DDE were the most common pesticide residues found in surface water at concentrations exceeding criteria. However, almost all the samples exceeding the criteria were from a single study area, the Owyhee-Vale Reclamation Project areas in Oregon and Idaho. The organochlorine pesticide chlordane was detected in 30 percent of the bottom-sediment samples, and undegraded DDT was detected in 21 percent. DDT or its degradation products were detected in all 21 study areas where bottom-sediment samples were analyzed for organochlorine pesticides. A principal-components analysis indicated that elevated selenium concentrations in surface water are not associated with elevated boron, molybdenum, or arsenic concentrations. The occurrence of selenium is associated with sulfate and uranium. The association of boron and molybdenum with chloride suggests that evaporative processes control their concentrations. Arsenic is not associated with any other measured trace element and is associated negatively with selenium. This report focuses on selenium because it was the trace element most frequently found at concentrations exceeding criteria for the protection of aquatic life. Selenium concentrations in water are dynamic, and, at a given site, the selenium concentration can change by an order of magnitude during a year and from one year to another. In some areas, selenium contamination may not occur during normal or wet periods. However, during a drought, reduced water deliveries may result in selenium contamination by evaporative concentration. Marine sedimentary rocks, especially those of Late Cretaceous age, are likely to be seleniferous. Irrigation of soils derived from them can contribute large amounts of selenium to drainwater; shallow wells in and near irrigated areas contained hundreds to thousands of micrograms per liter of selenium. The median selenium concentration in surface-water samples from NIWQP sites associated with Upper Cretaceous marine sedimentary rocks is 7 micrograms per liter (range less than 1 to 8,300 micrograms per liter) and from sites not associated with such rocks is 0.4 micrograms per liter (range less than 1 to 390 micrograms per liter). Irrigation-induced selenium contamination has been observed only in arid or semiarid areas. In those NIWQP study areas having local geologic sources of selenium, typically more than 25 percent of the surface-water samples exceed the chronic criterion for selenium if the evaporation rate is 3.0 times greater than the annual precipitation. In terminal water bodies, selenium accumulates and is not flushed out. In both terminal and flow-through lakes and ponds, the median selenium concentrations in surface water for samples collected from June through August are nearly the same (1.0 and 0.8 micrograms per liter, respectively). However, the 75th-percentile selenium concentration for terminal water bodies (24 µg/L) is significantly higher than for flow-through systems (4 µg/L). Selenium concentrations in biota were compared with concentrations that have been demonstrated to have adverse effects on similar species (the effect level) or to have adverse effects on another species if consumed (the dietary effect level). Twenty-five percent of the plant samples had selenium concentrations exceeding the dietary effect level (3 micrograms per gram dry weight) whereas more than 57 percent of the invertebrate samples and 61 percent of the fish samples exceeded the dietary effect level. Of the more than 2,000 bird eggs collected, 44 percent had selenium concentrations exceeding 6 micrograms per gram, a threshold value for reduced hatchability. In 14 areas, selenium concentrations in eggs from some populations of birds exceeded 6 micrograms per gram. Selenium-caused deformities of bird embryos were found in four of the NIWQP study areas; however, most study areas were not systematically surveyed for such deformities. Eggs were sampled from 34 species of birds belonging to 10 orders. Nearly all the eggs collected come from aquatic species of birds, with American coots, mallards, and American avocets being the three species most frequently collected. Of the 34 species, at least one set of eggs from 16 species had a geometric-mean selenium concentration of at least 12.5 micrograms per gram, a high-risk threshold. All three species of grebes yielded at least one set of high risk eggs, as did four of five species of shorebirds and five of eleven species of waterfowl. Egg-set data were examined to determine if some feeding guilds are more at risk to selenium poisoning than others. Analysis of data for waterbird eggs from the study areas where the 75th percentile selenium concentration in surface water exceeded 5 µg/L suggests that herbivorous birds may bioaccumulate less selenium than insect- and fish-eating birds. For birds from these study areas, selenium concentrations for 39 percent of the egg sets from herbivorous birds fell in the normal range (less than 3 µg/g) while only 7 and 0 percent, respectively, of egg sets from insect- and fish-eating birds fall in the normal range. Although herbivorous birds may bioaccumulate less selenium, it does not appear that any waterbird feeding guilds are particularly well buffered from exposure to selenium contamination. Predictive tools were developed to aid managers in identifying specific land areas at risk for irrigation-induced selenium contamination. The tools range from identifying broad geographic regions where selenium contamination is likely, to assessing the probability that selenium concentrations in a specific stream or lake exceed the chronic criterion for selenium. A geographic information system was used to prepare a map that identifies land areas in the Western United States that are susceptible to selenium contamination if irrigated. On the basis of the 75th percentile, selenium concentration in surface water, 12 of the 26 NIWQP study areas were classified as contaminated, two as seleniferous, and 12 as uncontaminated. The map correctly identified both seleniferous areas and 10 of 12 selenium-contaminated areas as susceptible; 10 of 12 uncontaminated areas were correctly identified as not being susceptible. About 160,000 square miles are identified as being susceptible; of that area, about 4,100 square miles have been identified by satellite imagery as actively being irrigated. Principal-components analysis and pattern-recognition techniques indicate that major-ion chemistry of water samples alone can be used to identify selenium- and nonselenium-producing areas in the Western United States. Water samples composed of simple salts of sulfate typically have concentrations of selenium that exceed 3 µg/g, whereas samples composed of simple salts of chloride or carbonate typically have low selenium concentrations. Weathering of soils that contain reduced-sulfur minerals, such as pyrite, mobilizes sulfur and selenium because selenium commonly substitutes for sulfur in these minerals. In areas where the bedrock is composed of Upper Cretaceous marine sedimentary rocks, logistic regression of data from the NIWQP sites indicates that if the dissolved-solids concentration equals 1,000 milligrams per liter, the probability is about 69 percent that the selenium concentration will exceed 5 micrograms per liter, the U.S. Environmental Protection Agency chronic criterion. In areas where the bedrock is not composed of such rocks, the probability is only about 10 percent. The avian-egg data within the biotic data base were used to make a quantitative toxicological risk assessment. Of the 23 study areas where avian eggs were sampled, 14 areas yielded at least one egg containing 6 µg/g selenium, the threshold for embryotoxicity. However, only 6 of the study areas yielded eggs containing enough selenium to expect selenium-induced teratogenesis of duck embryos. Predicted probabilities of discovering embryo teratogenesis matched field observations in 13 of the 14 study areas reporting results of embryo assessments. Bird eggs were collected from 161 individual sampling sites and at 79 of those sites selenium concentrations in one or more eggs exceeded 6 µg/g. At the 79 sites where biological effects are expected on the basis of selenium concentrations in the eggs, the median rate was 3.9 percent of the hens losing at least one egg to selenium-induced embryotoxicity. This corresponds to about 1.2 percent selenium-induced egg inviability among otherwise viable eggs. Across all NIWQP study areas, the overall rate of hens projected to lose at least one egg to selenium-induced embryotoxicity is estimated to be 1.9 percent, which corresponds to about 0.3 percent selenium-induced egg inviability among otherwise viable eggs. After accounting for increased mortality of selenium poisoned-hatchlings due to other factors such as weather and predators, it was estimated that that increases of 0.3 and 1.2 percent in inviable eggs would cause approximately a 1.4 and 5.4 percent depression in nesting success. Regional surveys of nesting success among ducks revealed that duck populations commonly exist near their demographic break-even point. The vulnerable demographic condition of North American duck populations during the mid-1960's to mid-1980's was primarily due to noncontaminant factors, such as poor-quality nesting habitat and dry climatic cycles. Under such conditions, rates of 1.4- to 5.4-percent depression in nesting success caused by exposure to selenium from irrigation projects can be crucial for avian populations already close to their demographic break-even point. Even the worst-case levels of contaminant effects, however, could be tolerated by populations of ducks existing just modestly above demographic break-even points. This suggests the biotic risk to ducks could be addressed by reducing irrigation-induced water pollution but more effectively by restoring high-quality (more predator-safe) nesting habitat. An analysis at the nesting-site level was made of the relation between selenium content of water and bird eggs. Eggs from 93 bird populations were collected from nesting sites where the water sample collected during April-July contained less than 5 µg/L selenium. The average selenium concentration in egg sets was embryotoxic in 19 of the 93 populations. Of the populations collected at sites where the selenium in the water was less than 1 microgram per liter, only four of 54 populations contained embryotoxic concentrations. Eggs from 65 populations of birds were collected from nesting sites where selenium concentrations in water samples collected during April-July equaled or exceeded 5 µg/L, and 55 of those 65 populations contained embryotoxic concentrations of selenium in the eggs. An analysis at the study-area level was made of the relation between selenium contamination of water and selenium contamination of the food chain and egg loss due to selenium poisoning. Most food organisms, particularly aquatic invertebrates and fish, contained potentially harmful amounts of selenium in study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. The analysis also indicates that some hens are predicted to lose eggs to selenium poisoning in all study areas where selenium concentrations in more than 25 percent of the water samples exceed 5 µg/L. These results suggest that areas where selenium contamination of the food chain and loss of eggs to selenium poisoning is occurring may be identified using the same methods developed to identify areas where selenium contamination of water is likely to occur.

western United States↗

2010-2015 Juvenile fish ecology in the Nisqually River Delta and Nisqually Reach Aquatic Reserve

The return of tidal inundation to over 750 acres of the U. S. Fish and Wildlife Service Billy Frank Jr. Nisqually National Wildlife Refuge (NNWR) in fall of 2009 was the crowning moment in the effort to protect and restore the Nisqually Delta. The Nisqually NWR project complemented three earlier restoration projects completed by the Nisqually Indian Tribe (Tribe) on tribal property to restore over 900 acres of the estuary, representing the largest estuary restoration project in the Pacific Northwest and one of the most significant advances to date towards the recovery of Puget Sound (USFWS 2005). In 2011 the Washington Department of Natural Resources (WADNR established the over 14000 acre Nisqually Reach Aquatic Reserve (Reserve), complementing the protection and restoration successes in the Nisqually Delta. The Reserve includes all state-owned aquatic lands around Anderson, Ketron and Eagle islands and part of McNeil Island (Figure 1, WDNR 2011). The Reserve also includes a diverse assemblage of nearshore and offshore habitats important to resident and migratory fish including federal endangered species act listed fish like Chinook salmon (Oncorynchus tshawytscha) and steelhead (O. mykiss). Studies in the Nisqually Estuary (Ellings and Hodgson 2007, David et al. 2014, Ellings et al. 2016) and South Puget Sound (Duffy 2003) have summarized fish use of the area. However, the fish ecology of the reserve had not been systematically surveyed. The Tribe, U.S. Geological Survey (USGS), NNWR, Nisqually River Foundation (NRF), and others are currently conducting a multi-year, interdisciplinary, hypothesis-based research and monitoring study investigating the impact of delta restoration on estuarine processes, habitat structures, and functions. Our interdisciplinary monitoring framework enables us to link key estuarine processes with habitat development and biological response at multiple scales across the restored footprint, reference marshes, and throughout the Nisqually Reach. Key research components include hydrology and sediment regime, channel and marsh topography and development, vegetation colonization, and invertebrate, bird, and fish abundance, habitat use, and foraging ecology. After the Reserve was established, the WDNR and the research partnership led by the Tribe expanded the existing delta fish ecology assessment to include sampling stations throughout the Reserve. The results of the Reserve fish ecology assessment provide a unique regional analysis of fish ecology from the Nisqually River to McNeil Island.

Salmon Recovery Program Technical Report↗

Data Delivery and Mapping Over the Web: National Water-Quality Assessment Data Warehouse

The U.S. Geological Survey began its National Water-Quality Assessment (NAWQA) Program in 1991, systematically collecting chemical, biological, and physical water-quality data from study units (basins) across the Nation. In 1999, the NAWQA Program developed a data warehouse to better facilitate national and regional analysis of data from 36 study units started in 1991 and 1994. Data from 15 study units started in 1997 were added to the warehouse in 2001. The warehouse currently contains and links the following data: -- Chemical concentrations in water, sediment, and aquatic-organism tissues and related quality-control data from the USGS National Water Information System (NWIS), -- Biological data for stream-habitat and ecological-community data on fish, algae, and benthic invertebrates, -- Site, well, and basin information associated with thousands of descriptive variables derived from spatial analysis, like land use, soil, and population density, and -- Daily streamflow and temperature information from NWIS for selected sampling sites.

Fact Sheet↗

Eelgrass (Zostera marina) and Seaweed Abundance along the Coast of Togiak National Wildlife Refuge, Alaska, 2008–10

We conducted a point-sampling survey to determine eelgrass ( Zostera marina ) and seaweed abundance in coastal waters adjacent to Togiak National Wildlife Refuge, Alaska, in July 2008–10. Eelgrass was known to be abundant in protected embayments of the southeastern Bering Sea and near the Togiak National Wildlife Refuge, but prior to this study, no systematic ground surveys had been conducted in these areas. We determined mean aboveground biomass of eelgrass to be highly variable among years observed, ranging from 32–72 grams dry weight per square meter (g/m 2 ) during successive years in Nanvak Bay and among the studied embayments in 2010: 47±4 g/m 2 in Nanvak Bay, 69±7 g/m 2 in Chagvan Bay, and 74±15 g/m 2 in Goodnews Bay. Seaweed density, abundance, and frequency scores were also highly variable among years and among embayments and were lower for seaweeds than for eelgrass in Nanvak and Chagvan bays, but not in Goodnews Bay. For all bays, mussels ( Mytilus spp.) and gastropods were the most common macro-invertebrates detected during surveys, whereas sea stars, crabs, and sponges were not observed in the embayments.

Alaska↗

Are hotspots of evolutionary potential adequately protected in southern California?

Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

Biological Conservation↗

Geospatial characteristics of Florida's coastal and offshore environments: Distribution of important habitats for coastal and offshore biological resources and offshore sand resources

The Geospatial Characteristics GeoPDF of Florida's Coastal and Offshore Environments is a comprehensive collection of geospatial data describing the political boundaries and natural resources of Florida. This interactive map provides spatial information on bathymetry, sand resources, and locations of important habitats (for example, Essential Fish Habitats (EFH), nesting areas, strandings) for marine invertebrates, fish, reptiles, birds, and marine mammals. The map should be useful to coastal resource managers and others interested in marine habitats and submerged obstructions of Florida's coastal region. In particular, as oil and gas explorations continue to expand, the map can be used to explore information regarding sensitive areas and resources in the State of Florida. Users of this geospatial database will have access to synthesized information in a variety of scientific disciplines concerning Florida's coastal zone. This powerful tool provides a one-stop assembly of data that can be tailored to fit the needs of many natural resource managers. The map was originally developed to assist the Bureau of Ocean Energy Management, Regulation, and Enforcement (BOEMRE) and coastal resources managers with planning beach restoration projects. The BOEMRE uses a systematic approach in planning the development of submerged lands of the Continental Shelf seaward of Florida's territorial waters. Such development could affect the environment. BOEMRE is required to ascertain the existing physical, biological, and socioeconomic conditions of the submerged lands and estimate the impact of developing these lands. Data sources included the National Oceanic and Atmospheric Administration, BOEMRE, Florida Department of Environmental Protection, Florida Geographic Data Library, Florida Fish and Wildlife Conservation Commission, Florida Natural Areas Inventory, and the State of Florida, Bureau of Archeological Research. Federal Geographic Data Committee (FGDC) compliant metadata are provided as attached xml files for all geographic information system (GIS) layers.

Florida↗

Nearshore energy subsidies support Lake Michigan fishes and invertebrates following major changes in food web structure

Aquatic food webs that incorporate multiple energy channels (e.g. nearshore benthic or pelagic) with varying productivity and turnover rates convey stability to biological communities by providing multiple independent energy sources. Within the Lake Michigan food web, invasive dreissenid mussels have caused rapid changes to food web structure and potentially altered the channels through which consumers acquire energy. We used stable C and N isotopes to determine how Lake Michigan food web structure has changed in the past decade, coincident with the expansion of dreissenid mussels, decreased pelagic phytoplankton production and increased nearshore benthic algal production. Fish and invertebrate samples collected from sites around Lake Michigan were analyzed to determine taxa-specific 13C:12C (delta 13C) and 15N:14N (delta 15N) ratios. Sampling took place during two distinct periods, 2002-2003 and 2010-2012, that spanned the period of dreissenid expansion, and included nearshore, pelagic and profundal fish and invertebrate taxa. Magnitude and direction of the 13C shift indicated significantly greater reliance upon nearshore benthic energy sources among nearly all fish taxa as well as profundal invertebrates. Although the mechanisms underlying this 13C shift likely varied among species, possible causes include the transport of benthic algal production to offshore waters and an increased reliance on nearshore prey items. Delta 15N shifts were more variable and of smaller magnitude across taxa although declines in delta 15N among some pelagic fishes may indicate a shift to alternative prey resources. Lake Michigan fishes and invertebrates appear to have responded to dreissenid induced changes in nutrient and energy pathways by switching from pelagic to alternative nearshore energy subsidies. Although large shifts in energy allocation (i.e. pelagic to nearshore benthic) resulting from invasive species appear to have affected total production at upper trophic levels, changes in trophic structure and utilization of novel energy pathways may help to stabilize food webs following species invasions.

Lake Michigan↗

Mass mortality of collector urchins Tripneustes gratilla in Hawai`i

As grazers, sea urchins are keystone species in tropical marine ecosystems, and their loss can have important ecological ramifications. Die-offs of urchins are frequently described, but their causes are often unclear, in part because systematic examinations of animal tissues at gross and microscopic level are not done. In some areas, urchins are being employed to control invasive marine algae. Here, we describe the pathology of a mortality event in Tripneustes gratilla in Hawai`i where urchins were translocated to control invasive algae. Although we did not determine the cause of the mortality event, our investigation indicates that animals died from inflammation of the test and epidermal ulceration, followed by inability to maintain coelomic fluid volume, colonization of coelomic fluid by opportunists (diatom, algae), and inappetence. Parasites, bacteria, fungi, and viruses were not evident as a primary cause of death. Pathology was suggestive of a toxin or other environmental cause such as lack of food, possibilities that could be pursued in future investigations. These findings highlight the need for caution and additional tools to better assess health when translocating marine invertebrates to ensure maximal biosecurity.

Hawaii↗

Cruise Report; RV Moana Wave cruise M1-01-GM; the bathymetry and acoustic backscatter of the mid shelf to upper slope off Panama City, Florida, northeastern Gulf of Mexico; September 3, through October 12, 2001, Panama City, FL to Panama City, FL

A zone of deep-water reefs is thought to extend from the mid and outer shelf south of Mississippi and Alabama to at least the northwestern Florida shelf off Panama City, Florida (Figure 1, 67kb). The reefs off Mississippi and Alabama are found in water depths of 60 to 120 m (Ludwick and Walton, 1957; Gardner et al., in press) and were the focus of a multibeam echosounder (MBES) mapping survey by the U.S. Geological Survey (USGS) in 2000 (Gardner et al., 2000; in press). If this deep-water-reef trend does exist along the northwestern Florida shelf, then it is critical to determine the accurate geomorphology and type of the reefs that occur because of their importance as benthic habitats for fisheries. Precisely georeferenced high-resolution mapping of bathymetry is a fundamental first step in the study of areas suspected to be critical habitats. Morphology is thought to be critical to defining the distribution of dominant demersal plankton/planktivores communities. Fish faunas of shallow hermatypic reefs have been well studied, but those of deep ahermatypic reefs have been relatively ignored. The ecology of deep-water ahermatypic reefs is fundamentally different from hermatypic reefs because autochthonous intracellular symbiotic zooxanthellae (the carbon source for hermatypic corals) do not form the base of the trophic web in ahermatypic reefs. Instead, exogenous plankton, transported to the reef by currents, serves as the primary carbon source. Thus, one of the principle uses of the morphology data will be to identify whether any reefs found are hermatypic or ahermatypic in origin. Community structure and trophodynamics of demersal fishes of the outer continental of the northeastern Gulf of Mexico presently are the focus of a major USGS reseach project. A goal of the project is to answer questions concerning the relative roles played by morphology and surficial geology in controling biological differentiation. Deep-water reefs are important because they are fish havens, key spawning sites, and are critical early larval and juvenile habitats for economically important sport/food fishes. It is known that deep-water reefs function as a key source for re-population (via seasonal and ontogenetic migration) of heavily impacted inshore reefs. The deep-water reefs south of Mississippi and Alabama support a lush fauna of ahermatypic hard corals, soft corals, black corals, sessile crinoids and sponges, that together form a living habitat for a well-developed fish fauna. The fish fauna comprises typical Caribbean reef fishes and Carolinian shelf fishes, plus epipelagic fishes, and a few deep-sea fishes. The base of the megafaunal invertebrate food web is plankton, borne by essentially continuous semi-laminar currents generated by eddies, spawned off the Loop Current, that periodically travel across the shelf edge. A few, sidescan-sonar surveys have been made of areas locally identified as Destin Pinnacles, Steamboat Lumps Marine Reserve (Koenig et al., 2000; Scanlon, et al., 2000; 2001), Twin Ridges (Briere, et al., 2000; Scanlon, et al., 2000), and Madison-Swanson Marine Reserve (Koenig et al., 2000; Scanlon, et al., 2000; 2001). However, no quantitative and little qualitative information about the geomorphology and surficial geology can be gained from these data. Existing bathymetry along the northwestern Florida shelf suggests the existence of areas of possible isolated deep-water reefs. NOAA bathymetric maps NOS NH16-9 and NG16-12 show geomorphic expressions that hint of the presence of reefs in isolated areas rather than in a continuous zone. There has been no systematic, high-resolution bathymetry collected in this area, prior to this cruise. After the successful mapping of the deep-water reefs on the Mississippi and Alabama shelf (Gardner et al., 2000; in press), a partnership composed of the USGS, Minerals Management Service, and NOAA was formed to continue the deep-reef mapping to the northwest Florida mid shelf and upper slope. This cruise is the first fruit of that partnership.

Florida↗

Restoration of Rio Grande cutthroat trout Oncorhynchus clarkii virginalis to the Mescalero Apache Reservation

Rio Grande Cutthroat trout Oncorhynchus clarkii virginalis (RGCT) represents the most southern subspecies of cutthroat trout, endemic to Rio Grande, Canadian, and Pecos basins of New Mexico and southern Colorado. The subspecies currently occupies less than 12% of its historic range. The Mescalero Apache Tribe has partnered with U.S. Geological Survey-New Mexico Cooperative Fish and Wildlife Research Unit, New Mexico State University, U.S. Fish and Wildlife Service, and New Mexico Department of Game and Fish to meet mutually shared goals of restoring and maintaining a Pecos strain of RGCT to Tribal lands. The goal of this project was to assess the suitability of the Rio Ruidoso within the Mescalero Apache Reservation to support a self-sustaining RGCT population by conducting a systematic and comprehensive survey. We conducted three surveys (fall 2010, spring 2011 and 2012) to characterize water quality, macroinvertebrate assemblages, fish communities, and physical habitat (stream size, channel gradient, channel substrate, habitat complexity, riparian vegetation cover and structure, migration barriers to movement). Seven-100 m reaches throughout three major tributaries of the Rio Ruidoso within the Tribal lands were sampled during baseflow conditions October 2010, May 2011, and June 2012. Despite the onset of severe drought in 2011, water quality, physical habitat, and fish populations revealed that the Rio Ruidoso and its three tributaries would most likely support a self-sustaining RGCT population. Pools were abundant (mean, 8.9 pools/100 m), instream woody debris was present (range, 3.8-45.6 pieces/100 m), and instream dataloggers revealed daily maximum stream temperatures rarely exceeded criteria established in New Mexico for coldwater fishes, however, presence of frazil and anchor ice may limit fish distribution in the winter. Aquatic macroinvertebrate samples revealed a community of benthic invertebrates reflective of high quality cool to cold water. Overall densities of brown trout, rainbow trout and brook trout were high (overall mean, 0.23 fish/m2) and in relatively good condition (range of mean relative weight, 84-117). Should the Mescalero Apache Tribe decide to introduce RGCT, prior to chemical treatment, a barrier placed below the confluence of Middle and South forks of the Rio Ruidoso would create approximately 12 km of perennial flow and help protect against invasion of non-native fishes. The North Fork of the Rio Ruidoso is not a good candidate for reintroduction because of easy access by the public to reintroduce non-native fishes into the watershed. Lastly, an annual, long-term monitoring program of RGCT would help document that there was no subsequent incursion of non-native fishes.

Cooperator Science Series↗