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USGS2012

A baseline analysis of the distribution, host-range, and severity of the rust Puccinia Psidii in the Hawaiian islands, 2005-2010

Puccinia psidii was first described by Winter (1884) on guava ( Psidium guajava L.) in Brazil. The rust is still a major pest of native guava in Brazil and is often referred to as “guava rust” internationally. It is unusual among rust fungi because of its broad and ever-expanding host-range within the Myrtaceae plant family (Simpson et al . 2006). The pathogen is regarded as a major threat to Eucalyptus plantations and other Myrtaceae worldwide (Coutinho et al . 1998, Grgurinovic et al . 2006, Glen et al . 2007). Infections of leaves and meristems are particularly severe on susceptible seedlings, cuttings, young trees, and coppice, causing plants to be stunted and multi-branched, inhibiting normal growth and development, and sometimes causing death to young seedlings (Booth et al . 2000, Rayachhetry et al . 2001). The fungus has expanded its host-range in Brazil, affecting both native and introduced Myrtaceae (Coutinho et al . 1998). Since its discovery in 1884, P. psidii has continually been discovered to have an expanding host-range within the Myrtaceae, affecting hosts throughout much of South and Central America and the Caribbean. Spreading out originally from Brazil in 1884, the fungus has been reported on hosts in the following countries (first record in parentheses): Paraguay (1884), Uruguay (1889), Ecuador (1891), Colombia (1913), Puerto Rico (1913), Cuba (1926), Dominican Republic (1933), Venezuela (1934), Jamaica (1936), Argentina (1946), Dominica (1948), Trinidad and Tobago (1951), Guatemala (1968), United States (Florida; 1977), Mexico (1981), El Salvador (1987), and Costa Rica (1998) (Simpson et al . 2006). It is possible that P. psidii was present in El Salvador and Costa Rica prior to 1980, but was not reported until 1987 and 1998, respectively. Until recently, Puccinia psidii was restricted to the Neotropics, Mexico, and the state of Florida in the United States. While the rust has been present in Florida for over 30 years, only recently has it spread westward. Although possibly present earlier, P. psidii was found in California in November 2005 in a nursery in San Diego County on Myrtus communis and documented by a report in a nursery newsletter (Mellano 2006). Puccinia psidii was first found in Hawai`i on a young plant of `ōhi`a ( Metrosideros polymorpha ) in April 2005, in a nursery on the island of O`ahu (Killgore and Heu 2005; Uchida et al . 2006). The fungus subsequently spread to most islands of the Hawaiian chain, infecting `ōhi`a and other myrtaceous hosts (Hauff 2006, Anderson et al . 2007). P. psidii was first found in Japan in May 2007 on cultivated `ōhi`a (Kawanishi et al . 2009). Most recently, a rust identified as Uredo rangelii was discovered in April 2010 in New South Wales, Australia (Carnegie et al . 2010). This rust is closely related to Puccinia psidii and is part of the guava rust complex described by Simpson et al . (2006). Although treated as a separate species by Simpson et al. (2006), many authors now consider U. rangelii a synonym for U. psidii , which is the anamorph (asexual stage) of P. psidii , and therefore, the same species (Glen et al . 2007, Carnegie et al . 2010). Because of the large diversity of native Myrtaceae present in Australia, the number of Myrtaceae hosts attacked by species of the guava rust complex will likely grow now that U. rangelii has arrived and is spreading in the country. As of this writing (June 2011), 94 species of Myrtaceae have been identified as hosts of U. rangelii in the states of New South Wales and Queensland. Damage is severe on nearly one-third of the species affected, and 16 of these species are threatened or endangered native species (Secretary of Australia, May 2011). The presence of Puccinia psidii in Hawai`i is particularly alarming for at least two reasons: (1) M. polymorpha is the dominant overstory tree of the native forest, and (2) P. psidii is now established in the Pacific region, where numerous Myrtaceae species are native. Native ecosystems in Hawai`i and the Pacific could be seriously affected by the spread of P. psidii , as both native and introduced Myrtaceae are significant components of many different plant communities throughout the region (Glen et al. 2007). Because the guava rust complex (i.e., P. psidii and U. rangelii ) now attacks well over 100 species of Myrtaceae worldwide, it is currently a priority for international quarantine and import restrictions in an effort to prevent further spread among Australasian and Pacific Myrtaceae. Several different studies have been done to determine what degree of genetic variation exists between isolates of Puccinia psidii from many different host plants and many different locations (Langrell et al . 2008, Kawanishi et al . 2009, Kadooka 2010, Graça et al . 2011). So far, all of these studies have shown that all of the Hawaiian samples tested so far have had the same genetic composition. Given that the P. psidii strain in Hawai`i has continually been shown for over five years to lack genetic variation at microsatellite marker sites (which are believed to undergo relatively rapid genetic change), a baseline evaluation of incidence and severity should be especially valuable to provide comparisons with future conditions. Worldwide, 23 Neotropical species in 11 genera and 59 Australasian and Pacific species in 13 genera had been recorded as hosts of Puccinia psidii before 2010 (Simpson et al . 2006, Anderson et al . 2007). Of those 82 species known to be hosts elsewhere, 42 are cultivated or naturalized in Hawai`i. Because of its wide host-range and aggressive pathogenicity, rust disease caused by P. psidii poses a considerable disease threat to many native and cultivated Myrtaceae throughout the world (Coutinho et al . 1998, Booth et al . 2000, Simpson et al . 2006). However, there are few reports comparing the severity of rust infection on native, introduced, and cultivated Myrtaceae (Rayachhetry et al . 2001, Perez et al . 2010). Since government agencies and the public are concerned about the extent of the rust movement within and to Hawai`i (Loope and La Rosa 2008, Loope 2010), there is a need to better understand the incidence, severity, and distribution of P. psidii in Hawai`i. To address that need, this research project was initiated to survey forests, surrounding plant communities, botanical gardens, and commercial nurseries to detect the presence and severity of P. psidii rust infections throughout Hawai`i on plants in the Myrtaceae family. This study provides a baseline on the host distribution and severity to compare current and future impacts of rust infections caused by P. psidii on native, naturalized, and cultivated Myrtaceae in Hawai`i.

Hawai'i↗

USGS2024

Snake River Fall Chinook Salmon research and monitoring

In Chapter 1, we report on development and application of an integrated population model (IPM) for the natural-origin fall Chinook salmon population upstream of Lower Granite Dam. This year’s efforts represent the third update to the model. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model and estimating the effects of covariates on key demographic parameters. The goals of this year’s report are to 1) describe the modifications and advances made since the previous report, 2) to annually update and report the abundance estimates and other quantities used in the model, 3) to provide annual estimates of population parameters estimated by the IPM, and 4) to outline the next year’s tasks for advancing and/or applying the model. Since our last report on the life-cycle model, we have made a number of changes including: 1) incorporating jack abundance and age-structure data into the observation model, 2) changing smolt-to-adult survival (SAR) for subyearling and yearling to partial SARs that represent the joint probability surviving and entering the ocean at a given juvenile age, 3) combining age categories for rarely observed ages, 4) using scale data from unmarked fish to estimate age structure, and 5) generating composite life-cycle demographic parameters (cumulative capacity and productivity) from stage-specific parameters. We also generated juvenile abundance estimates, extended the model to include three additional brood years (1992– 2021), and ran the model to forecast returns to Lower Granite in 2022. For posterior medians of life stage-specific parameters, we estimated a mean productivity of 438 natural-origin juvenile recruits per female spawner, a capacity of 1.36 million juveniles, and a mean smolt-to-adult survival (SAR) of 1.2%. We detected strong density-dependent regulation, with juvenile recruits per spawner declining to about 50 juvenile recruits per female spawner at high spawner abundance. Across the entire life cycle, these stage-specific parameters resulted in a median cumulative intrinsic productivity of 1.93 adult female recruits per female spawner and a median equilibrium abundance of 2,851 female spawners (7,842 total spawners). Annual juvenile productivity varied from about 250–1,000 juveniles per spawner but displayed no temporal trends or patterns. For the three most recent brood years added to the model, recruits per spawner were higher than average but well within the range of uncertainty observed over the entire time series. In contrast to juvenile recruitment variability, SAR varied considerably among years and exhibited two periods of high survival (1996–2001 and 2007–2012) when SAR ranged from 2% to 6% and cumulative productivity ranged from 2 to 8 recruits per spawner. Partial SARs revealed that yearling outmigrants contributed substantially to the high SARs in the first high-survival period, but the second period was dominated by subyearlings. Yearlings contributed >30% to SAR in most years prior to 2007, and <30% since 2007. Our two-stage IPM provides a wealth of information about population dynamics affecting two key life-stage transitions (spawner to juvenile, and juvenile to spawner) centered on passage at Lower Granite Dam. By summarizing these stage-specific demographic parameters across the entire life cycle, this information will be useful for informing the recovery status of this threatened population. Whereas previous versions introduced hydrosystem and ocean covariates into the model, this phase of model development focused on solidifying the underlying model structure by introducing the concept of partial SARs and developing composite productivity and capacity as a function of underlying stage-specific parameters. Given this advancement, our next steps are to re-incorporate covariates into the model, specifically to understand how different factors affect partial SARs of subyearling and yearlings. Longer term model developments include:1) incorporating hatchery fish to explicitly estimate their survival as an alternative method for estimating natural-origin age composition, 2) expanding the model’s structure to include the three major spawning aggregates, 3) more explicitly modeling hydrosystem effects including transportation, and 4) using the model to assess retrospective and prospective management actions. In 2022, the U.S. Geological Survey (USGS) focused adult salmon survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use used a boat-mounted underwater video camera to count 99 deepwater redds at 16 of the 29 sites surveyed. Redd depths averaged 4.4 m. In conjunction with the Idaho Power Company, we collected genetic samples from 318 live fall Chinook salmon (Oncorhynchus tshawytscha) and 19 carcasses at 40 unique geographic locations that spanned 91 river kilometers. Eighty fish were collected at three sites (High Range [rkm 332.3], Dug Bar [rkm 315.4], and Three Creek [rkm 384.0]), which accounted for 23% of all collected fish in 2022. Most (333 fish) post-spawned salmon were collected from early to mid-November just after the peak of spawning. A summary of 2021 PBT results produced by the Idaho Power Company can be found in Appendix A.2. Beach seining and PIT tagging of subyearling fall Chinook salmon was conducted in Snake and Salmon rivers to obtain information on population metrics and growth as well as to provide data for ongoing life-cycle modeling. In the Snake River, we collected 7,496 subyearlings, tagged 4,139, and recaptured 502 (12.1%). Using 8-mm tags in 45–49-mm fish allowed us to represent an additional 25% of the juvenile population through PIT tagging beyond just using standard 9- and 12-mm tags. In the Salmon River, we captured 206 natural subyearlings with the majority (52%) of fish being captured at two sites: rkm 20 and 26. We tagged 145 subyearlings and recaptured 9 fish. Many of the subyearlings we tagged in the Snake River were detected passing Lower Granite Dam, but only 4 fish tagged in the Salmon River were detected. In total we detected 484 (11.3%) tagged fish at Lower Granite Dam, and detection rates varied by tag size and passage route. More subyearlings were detected passing via the removable spill weir (RSW) earlier in the season while more fish were detected passing through the juvenile fish bypass system (JBS) earlier in the season while more fish were detected passing via the removable spill weir (RSW) later in the season. In general, fish tagged with 12-mm PIT tags had higher detection rates than fish tagged with smaller tags. Survival to Lower Granite Dam was low and ranged from 0.22 to 0.36. Season-wide, growth of subyearlings was higher in the lower reach than in the upper reach of the Snake River.

Idaho, Oregon, Washington↗

USGS2015

Re-colonization by common eiders Somateria mollissima in the Aleutian Archipelago following removal of introduced arctic foxes Vulpes lagopus

Islands provide refuges for populations of many species where they find safety from predators, but the introduction of predators frequently results in elimination or dramatic reductions in island-dwelling organisms. When predators are removed, re-colonization for some species occurs naturally, and inter-island phylogeographic relationships and current movement patterns can illuminate processes of colonization. We studied a case of re-colonization of common eiders Somateria mollissima following removal of introduced arctic foxes Vulpes lagopus in the Aleutian Archipelago, Alaska. We expected common eiders to resume nesting on islands cleared of foxes and to re-colonize from nearby islets, islands, and island groups. We thus expected common eiders to show limited genetic structure indicative of extensive mixing among island populations. Satellite telemetry was used to record current movement patterns of female common eiders from six islands across three island groups. We collected genetic data from these and other nesting common eiders at 14 microsatellite loci and the mitochondrial DNA control region to examine population genetic structure, historical fluctuations in population demography, and gene flow. Our results suggest recent interchange among islands. Analysis of microsatellite data supports satellite telemetry data of increased dispersal of common eiders to nearby areas and little between island groups. Although evidence from mtDNA is suggestive of female dispersal among island groups, gene flow is insufficient to account for recolonization and rapid population growth. Instead, near-by remnant populations of common eiders contributed substantially to population expansion, without which re-colonization would have likely occurred at a much lower rate. Genetic and morphometric data of common eiders within one island group two and three decades after re-colonization suggests reduced movement of eiders among islands and little movement between island groups after populations were re-established. We predict that re-colonization of an island group where all common eiders are extirpated could take decades.

Alaska↗

USGS2014

Genomic characterization of H14 subtype influenza A viruses in New World waterfowl and experimental infectivity in mallards Anas platyrhynchos

Recent repeated isolation of H14 hemagglutinin subtype influenza A viruses (IAVs) in the New World waterfowl provides evidence to suggest that host and/or geographic ranges for viruses of this subtype may be expanding. In this study, we used genomic analyses to gain inference on the origin and evolution of H14 viruses in New World waterfowl and conducted an experimental challenge study in mallards ( Anas platyrhynchos ) to evaluate pathogenicity, viral replication, and transmissibility of a representative viral strain in a natural host species. Genomic characterization of H14 subtype IAVs isolated from New World waterfowl, including three isolates sequenced specifically for this study, revealed high nucleotide identity among individual gene segments (e.g. ≥95% shared identity among H14 HA gene segments). In contrast, lower shared identity was observed among internal gene segments. Furthermore, multiple neuraminidase subtypes were observed for H14 IAVs isolated in the New World. Gene segments of H14 viruses isolated after 2010 shared ancestral genetic lineages with IAVs isolated from wild birds throughout North America. Thus, genomic characterization provided evidence for viral evolution in New World waterfowl through genetic drift and genetic shift since purported introduction from Eurasia. In the challenge study, no clinical disease or lesions were observed among mallards experimentally inoculated with A/blue-winged teal/Texas/AI13-1028/2013(H14N5) or exposed via contact with infected birds. Titers of viral shedding for mallards challenged with the H14N5 IAV were highest at two days post-inoculation (DPI); however shedding was detected up to nine DPI using cloacal swabs. The distribution of viral antigen among mallards infected with H14N5 IAV was largely restricted to enterocytes lining the villi in the lower intestinal tract and in the epithelium of the bursa of Fabricius. Characterization of the infectivity of A/blue-winged teal/Texas/AI13-1028/2013(H14N5) in mallards provides support for similarities in viral replication and shedding as compared to previously described waterfowl-adapted, low pathogenic IAV strains in ducks.

PLoS ONE↗

USGS2003

Geochemistry of the furnace magnetite bed, Franklin, New Jersey, and the relationship between stratiform iron oxide ores and stratiform zinc oxide-silicate ores in the New Jersey highlands

The New Jersey Highlands terrace, which is an exposure of the Middle Proterozoic Grenville orogenic belt located in northeastern United States, contains stratiform zinc oxide-silicate deposits at Franklin and Sterling Hill and numerous massive magnetite deposits. The origins of the zinc and magnetite deposits have rarely been considered together, but a genetic link is suggested by the occurrence of the Furnace magnetite bed and small magnetite lenses immediately beneath the Franklin zinc deposit. The Furnace bed was metamorphosed and deformed along with its enclosing rocks during the Grenvillian orogeny, obscuring the original mineralogy and obliterating the original rock fabrics. The present mineralogy is manganiferous magnetite plus calcite. Trace hydrous silicates, some coexisting with fluorite, have fluorine contents that are among the highest ever observed in natural assemblages. Furnace bed calcite has ??13C values of -5 ?? 1 per mil relative to Peedee belemnite (PDB) and ??18O values of 11 to 20 per mil relative to Vienna-standard mean ocean water (VSMOW). The isotopic compositions do not vary as expected for an original siderite layer that decarbonated during metamorphism, but they are consistent with nearly isochemical metamorphism of an iron oxide + calcite protolith that is chemically and minerlogically similar to iron-rich sediments found near the Red Sea brine pools and isotopically similar to Superior-type banded iron formations. Other magniferous magnite + calcite bodies occur at approximately the same stratigraphic position as far 50 km from the zinc deposits. A model is presented in which the iron and zinc deposits formed along the western edge of a Middle Proterozoic marine basin. Zinc was transported by sulfate-stable brines and was precipitated under sulfate-stable conditions as zincian carbonates and Fe-Mn-Zn oxides and silicates. Whether the zincian assemblages settled from the water column or formed by replacement reactions in shallowly buried sediments is uncertain. The iron deposits formed at interfaces between anoxic and oxygenated waters. The Furnace magnetite bed resulted from seawater oxidation of hydrothermally transported iron near a brine conduit. Iron deposits also formed regionally on the basin floor at the interface betveen anoxic deep waters and oxygenated shallower waters. These deposits include not only manganiferous magnetite + calcite bodies similar to the Furnace magnetite bed but also silicate-facies deposits that formed by iron oxide accumulation where detrital sediment was abundant. A basin margin model can be extended to Grenvillian stratiform deposits in the northwest Adirondacks of New York and the Mont Laurier basin of Quebec. In these areas iron deposits (pyrite or magnetite) are found basinward of marble-hosted sphalerite deposits, such as those in the Balmat-Edwards district. Whether the iron and zinc precipitated as sulfide assemblages or carbonate-oxide-silicate assemblages depended on whether sufficient organic matter or other reductants were available in local sediments or bottom waters to stabilize H2S.

New Jersey↗

USGS2013

Geology, sequence stratigraphy, and oil and gas assessment of the Lewis Shale Total Petroleum System, San Juan Basin, New Mexico and Colorado: Chapter 5 in Total petroleum systems and geologic assessment of undiscovered oil and gas resources in the San Juan Basin Province, exclusive of Paleozoic rocks, New Mexico and Colorado

The Lewis Shale Total Petroleum System (TPS) in the San Juan Basin Province contains a continuous gas accumulation in three distinct stratigraphic units deposited in genetically related depositional environments: offshore-marine shales, mudstones, siltstones, and sandstones of the Lewis Shale, and marginal-marine shoreface sandstones and siltstones of both the La Ventana Tongue and the Chacra Tongue of the Cliff House Sandstone. The Lewis Shale was not a completion target in the San Juan Basin (SJB) in early drilling from about the 1950s through 1990. During that time, only 16 wells were completed in the Lewis from natural fracture systems encountered while drilling for deeper reservoir objectives. In 1991, existing wells that penetrated the Lewis Shale were re-entered by petroleum industry operators in order to fracture-stimulate the Lewis and to add Lewis gas production onto preexisting, and presumably often declining, Mesaverde Group production stratigraphically lower in the section. By 1997, approximately 101 Lewis completions had been made, both as re-entries into existing wells and as add-ons to Mesaverde production in new wells. Based on recent industry drilling and completion practices leading to successful gas production from the Lewis and because new geologic models indicate that the Lewis Shale contains both source rocks and reservoir rocks, the Lewis Shale TPS was defined and evaluated as part of this U.S. Geological Survey oil and gas assessment of the San Juan Basin. Gas in the Lewis Shale Total Petroleum System is produced from shoreface sandstones and siltstones in the La Ventana and Chacra Tongues and from distal facies of these prograding clastic units that extend into marine rocks of the Lewis Shale in the central part of the San Juan Basin. Reservoirs are in shoreface sandstone parasequences of the La Ventana and Chacra and their correlative distal parasequences in the Lewis Shale where both natural and artificially enhanced fractures produce gas. The Lewis Continuous Gas Assessment Unit (AU 50220261) is thought to be self-sourced from and self-sealed by marine shales and mudstones deposited within the Lewis Shale that enclose clastic parasequences in the La Ventana and Chacra Tongues. The gas resource is thought to be a continuous accumulation sourced from the Lewis Shale throughout the depositional basin. In the Lewis Continuous Gas Assessment Unit (AU 50220261), for continuous gas resources, there is an F95 of 8,315.22 billion cubic feet of gas (BCFG) and an F5 of 12,282.31 BCFG, with a mean value of 10,177.24 BCFG. There is an F95 of 18.08 million barrels of natural gas liquids (MMBNGL) and an F5 of 47.32 MMBNGL, with a mean of 30.53 MMBNGL.

Colorado;New Mexico↗

USGS1991

Heterosis and outbreeding depression: A multi-locus model and an application to salmon production

Both artificial propagation and efforts to preserve or augment natural populations sometimes involve, wittingly or unwittingly, the mixing of different gene pools. The advantages of such mixing vis-à-vis the alleviation of inbreeding depression are well known. Acknowledged, but less well understood, are the complications posed by outbreeding depression. This paper derives a simple model of outbreeding depression and demonstrates that it is reasonably possible to predict the generation-to-generation fitness course of hybrids derived from parents from different origins. Genetic difference, or distance between parental types, is defined by the drop in fitness experienced by one type reared at the site to which the other is locally adapted. For situations where decisions involving stock mixing must be made in the absence of complete information, a sensitivity analysis-based conflict resolution method (the Good-Bad-Ugly model) is described.

Fisheries Research↗

USGS2014

Trouble in the aquatic world: How wildlife professionals are battling amphibian declines

A parasitic fungus, similar to the one that caused the extinction of numerous tropical frog and toad species, is killing salamanders in Europe. Scientists first identified the fungus, Batrachochytrium salamandrivorans, in 2013 as the culprit behind the death of fire salamanders ( Salamandr a salamandra ) in the Netherlands ( Martel et al. 2013 ) and are now exploring its potential impact to other species. Although the fungus, which kills the amphibians by infecting their skin, has not yet spread to the United States, researchers believe it’s only a matter of time before it does and, when that happens, the impact on salamander populations could be devastating ( Martel et al. 2014 ). Reports of worldwide declines of amphibians began a quarter of a century ago ( Blaustein & Wake 1990 ). Globally, some amphibian population declines occurred in the late 1950s and early 1960s, and declining trends continued in North America ( Houlahan et al. 2000 ). In the earlier years, population declines were attributed primarily to overharvest due to unregulated supply of species such as the northern leopard frog ( Lithobate s pipiens ) for educational use ( Dodd 2013 ). In later years, however, causes of declines were less evident. In 1989, herpetologists at the First World Congress of Herpetology traded alarming stories of losses across continents and in seemingly protected landscapes, making it clear that amphibian population declines were a “global phenomenon.” In response to these reports, in 1991, the International Union for Conservation of Nature (IUCN) established the Declining Amphibian Populations Task Force to better understand the scale and scope of global amphibian declines. Unfortunately, the absence of long-term monitoring data and targeted studies made it difficult for the task force to compile information. Today, according to AmphibiaWeb.org, there are 7,342 amphibian species in the world — double the number since the first alerts of declines — making the situation appear deceptively less dire. In fact, our understanding of genetic diversity significantly raises the stakes, and we are at risk of losing far more species than we believed only a few years ago. According to the IUCN, amphibians now lead the list of vertebrate taxa affected by the larger “biodiversity crisis” and sixth major mass- extinction event on Earth ( Keith et al. 2014 , Wake and Vredenburg 2008 ).

The Wildlife Professional↗

USGS2013

Microbial source tracking as a tool for TMDL development, Little Blue River in Independence, Missouri

The Little Blue River in Jackson County, Missouri has been listed by the Missouri Department of Natural Resources as impaired by bacteria for the protection of aquatic life and contact recreation from urban point and nonpoint sources. The Clean Water Act requires that a total maximum daily load (TMDL) for Escherichia coli (E. coli) be developed. Over a 5-year period, 108 base-flow, 87 stormflow, 48 fecal source, and 12 sewage influent samples were collected and analyzed for E. coli and Bacteroides general and host-associated microbial source tracking (MST) genetic markers. Less than half of the main-stem base-flow samples exceeded the E. coli state standard, whereas, all of the stormflow samples exceeded the standard during the recreation season (April through October). Both E. coli and MST markers were detected more frequently and at higher concentrations in stormflow samples. Only 14 percent of samples with E. coli detections greater than the Missouri state standard of 206 colonies per 100 milliliters had the human-associated Bacteroides marker as the only identified marker; therefore, Little Blue River TMDL development may require a broader scope beyond the municipal separate storm sewer system if bacteria sources are to be identified and addressed. Fecal samples showed a greater specificity with the human-associated marker than the dog- or ruminant-associated Bacteroides markers; however, false positives were at least one order of magnitude lower than true positives. MST data may be a useful tool for identifying probable sources of contamination and directing TMDL strategies.

Missouri↗

USGS2012

The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022 - Advancing discovery and application through collaboration

Ecosystem science is critical to making informed decisions about natural resources that can sustain our Nation’s economic and environmental well-being. Resource managers and policy-makers are faced with countless decisions each year at local, state, tribal, territorial, and national levels on issues as diverse as renewable and non-renewable energy development, agriculture, forestry, water supply, and resource allocations at the urban-rural interface. The urgency for sound decision-making is increasing dramatically as the world is being transformed at an unprecedented pace and in uncertain directions. Environmental changes are associated with natural hazards, greenhouse gas emissions, and increasing demands for water, land, food, energy, mineral, and living resources. At risk is the Nation’s environmental capital, the goods and services provided by resilient ecosystems that are vital to the health and well-being of human societies. Ecosystem science—the study of systems of organisms interacting with their environment and the consequences of natural and human-induced change on these systems—is necessary to inform decision-makers as they develop policies to adapt to these changes. This Ecosystems Science Strategy is built on a framework that includes basic and applied science. It highlights the critical roles that USGS scientists and partners can play in building scientific understanding and providing timely information to decision-makers. The strategy underscores the connection between scientific discoveries and the application of new knowledge. The strategy integrates ecosystem science and decision-making, producing new scientific outcomes to assist resource managers and providing public benefits. The USGS is uniquely positioned to play an important role in ecosystem science. With its wide range of expertise, the agency can bring holistic, cross-scale, interdisciplinary capabilities to the design and conduct of monitoring, research, and modeling and to new technologies for data collection, management, and visualization. Collectively, these capabilities can be used to reveal ecological patterns and processes, explain how and why ecosystems change, and forecast change over different spatial and temporal scales. USGS science can provide managers with options and decision-support tools to use resources sustainably. The USGS has long-standing, collaborative relationships with the DOI and other partners in the natural sciences, in both conducting science and its application. The USGS engages these partners in cooperative investigations that otherwise would lack the necessary support or be too expensive for a single bureau to conduct. The heart of this strategy is a framework and vision for USGS ecosystems science that focuses on five long-term goals, which are seen as interconnected and reinforcing components: • Improve understanding of ecosystem structure, function, and processes. The focus for this goal is an understanding of how ecosystems work, including the dynamics of species, their populations, interactions, and genetics, and how they change across spatial and temporal scales. • Advance understanding of how drivers influence ecosystem change. The challenges here are explaining the drivers of ecosystem change, their spatio-temporal patterns, their uncertainties and interactions, and their influence on ecosystem processes and dynamics. • Improve understanding of the services that ecosystems provide to society. Here the emphasis is on the measurement of environmental capital and ecosystem services, and the identification of sources and patterns of change in space and time. • Develop tools, technologies, and capacities to inform decision-making about ecosystems. This includes developing new technologies and approaches for conducting applications-oriented ecosystem science. A principal challenge will be how to quantify uncertainty and incorporate it in decision analysis. • Apply science to enhance strategies for management, conservation, and restoration of ecosystems. These challenges include development of novel approaches to monitoring, assessment, and restoration of ecosystems; new methods to address species of concern and communities at risk; and innovations in decision analysis and support to address imminent ecosystem changes or those that are underway. Closely integrated with the five goals are four strategic approaches that provide the path forward for the USGS Ecosystems Mission Area. These approaches cross-cut all of the goals and are seen as essential to the implementation of this strategy: • Assess information needs for ecosystem science through enhanced partnerships. Work with the DOI and other agencies and institutions to identify, design, and implement priority decision-driven ecological research. • Promote the use of interdisciplinary ecosystem science. Design and conduct interdisciplinary process-oriented research in ecosystem science. • Enhance modeling and forecasting. Build models to forecast ecosystem change, assess future management scenarios, and reduce uncertainties through an adaptive learning process. • Support decision-making. Use quantitative approaches to assess the vulnerabilities of ecosystems, habitats, and species, and evaluate strategies for adaptation, restoration, and sustainable management. Following the strategic approaches are a set of proposed actions that represent a sampling of specific activities that align with this strategy and that address the Nation’s most pressing environmental needs. The strategy emphasizes coordination of activities across the USGS mission areas pursuant to these goals. Ecosystem science is inherently interdisciplinary and requires a broad perspective that incorporates the biological and physical sciences, climate science, information technology, and scientific capacity in mission areas across the Bureau. With its emphasis on coordination, this strategy can provide a critical underpinning for integrated science efforts with scientists from multiple mission areas of the USGS working together. Of course, the USGS will continue to conduct both discipline-specific and interdisciplinary investigations, and both will continue to be vital parts of the ecosystem science portfolio. Finally, the strategy stresses the importance of coordination with other Federal agencies and organizations in the natural resources community. The USGS collaborates with resource agencies in the DOI and other organizations throughout the world to meet societal needs for species and ecosystem management. Working with these agencies and organizations, the USGS will play a key role over the next decade in advancing the scientific foundation for sustaining the natural resources that diverse, productive, resilient ecosystems provide.

Open-File Report↗

USGS1989

Genetic differentiation among lake trout strains stocked into Lake Ontario

The lake trout Salvelinus namaycush is the focus of an international effort by fishery management agencies to restore this once‐native species to Lake Ontario. Evaluation of reproductive success and comparisons among stocked lake trout strains require genetic markers. We used allozyme variation to make genetic comparisons among strains of lake trout stocked into Lake Ontario. Forty‐two proteins presumed to be encoded by 102 loci were resolved electrophoretically; 18 loci were polymorphic. Among 16 samples from five principal origins (Finger Lakes, Great Lakes basin, northern New York–Adirondack, Manitoba, and mixed origins–Lake Ontario), the average observed heterozygosity was 0.029, and the proportion of polymorphic loci was 0.125. Significant differences occurred among the 16 samples at all 18 possible locus comparisons. The average F st value was 0.14. Hierarchical analysis indicated that the variation among samples within an origin was greatest within the Great Lakes basin, which included the greatest number of samples and represented the largest geographic area. Most variation observed among samples, however, occurred among origins. The 1983 and 1984 hatchery year classes produced from the 1978 Seneca brood stock did not differ significantly. The 1981 Seneca brood stock more closely resembled the sample of wild lake trout from Seneca Lake than progeny from the 1978 brood stock. The closer affinity of the 1981 brood stock to wild Seneca lake trout may be due to the larger number of wild adults from Seneca Lake used to found these fish than was used to establish the 1978 brood stock. Siscowet (“fat”) and “lean” lake trout from Lake Superior were significantly different from each other; however, the level of variation between them was not greater than that among samples from other origins, and thus did not support recognition of siscowet lake trout as a distinct subspecies. The Jenny Lake strain possessed a genetic affinity to the siscowet sample from Lake Superior. Historical reports about the origin of this strain suggest that siscowet lake trout from northern Lake Michigan may have been used to found this strain. Therefore, the Jenny Lake strain may serve as a gene source for the establishment of the siscowet lake trout in Lake Ontario. The substantial differentiation among lake trout strains reported here supports the feasibility of using allozyme markers to identify the parental sources of naturally produced young.

Lake Ontario↗

USGS2005

Vascular Plant and Vertebrate Inventory of Tumacacori National Historical Park

Executive Summary This report summarizes the results of the first comprehensive biological inventory of Tumacacori National Historical Park (NHP) in southern Arizona. These surveys were part of a larger effort to inventory vascular plants and vertebrates in eight National Park Service units in Arizona and New Mexico. From 2000 to 2003 we surveyed for vascular plants and vertebrates (fish, amphibians, reptiles, birds, and mammals) at Tumacacori NHP to document presence of species within the administrative boundaries of the park's three units. Because we used repeatable study designs and standardized field techniques, these inventories can serve as the first step in a long-term monitoring program. We recorded 591 species at Tumacacori NHP, significantly increasing the number of known species for the park (Table 1). Species of note in each taxonomic group include: * Plants: second record in Arizona of muster John Henry, a non-native species that is ranked a 'Class A noxious weed' in California; * Amphibian: Great Plains narrow-mouthed toad; * Reptiles: eastern fence lizard and Sonoran mud turtle; * Birds: yellow-billed cuckoo, green kingfisher, and one observation of the endangered southwestern willow flycatcher; * Fishes: four native species including an important population of the endangered Gila topminnow in the Tumacacori Channel; * Mammals: black bear and all four species of skunk known to occur in Arizona. We recorded 79 non-native species (Table E.S.1), many of which are of management concern, including: Bermudagrass, tamarisk, western mosquitofish, largemouth bass, bluegill, sunfish, American bullfrog, feral cats and dogs, and cattle. We also noted an abundance of crayfish (a non-native invertebrate). We review some of the important non-native species and make recommendations to remove them or to minimize their impacts on the native biota of the park. Based on the observed species richness, Tumacacori NHP possesses high biological diversity of plants, fish, and birds for a park of its size. This richness is due in part to the ecotone between ecological provinces (Madrean and Sonoran), the geographic distribution of the three units (23 km separates the most distant units), and their close proximity to the Santa Cruz River. The mesic life zone along the river, including rare cottonwood/willow forests and adjacent mesquite bosque at the Tumacacori unit, is representative of areas that have been destroyed or degraded in many other locations in the region. Additional elements such as the semi-desert grassland vegetation community are also related to high species richness for some taxonomic groups. This report includes lists of species recorded by us (or likely to be recorded with additional effort) and maps of study sites. We also suggest management implications and ways to maintain or enhance the unique biological resources of Tumacacori NHP: limit development adjacent to the park, exclude cattle and off-road vehicles, develop an eradication plan for non-native species, and hire a natural resource specialist. These recommendations are intended to assist park staff with addressing many of the goals set out in their most recent natural resources management plan. This study is the first step in a long-term process of compiling information on the biological resources of Tumacacori NHP and its surrounding areas, and our findings should not be viewed as the final authority on the plants and animals of the park. Therefore, we also recommend additional inventory and monitoring studies and identify components of our effort that could be improved upon, either through the application of new techniques (e.g., use of genetic markers) or by extending the temporal and/or spatial scope of our research.

Open-File Report↗

USGS2011

Swallows as a sentinel species for contaminant exposure and effect studies

Tree swallows are an important model species to study the effects of contaminants in wild bird populations and have been used extensively in studies across North America. The advantages of swallows compared to other avian species are detailed. Three case histories are provided where swallows have been successfully used in Natural Resource Damage and Ecological Risk Assessments. The final two sections of this chapter are for individuals who want more in-depth information and include a summary of the chemical classes for which there are swallow data, including effect levels when known. Information provided in this section can be used to put exposure to most classes of contaminants into context with other sites across North America. Finally, commonly used endpoints, ranging from population-level down to cellular and genetic endpoints, are discussed including considerations and pitfalls, and when further work is needed to more fully understand the role of environmental and biological variation in interpreting these endpoints.

Book chapter↗

USGS1993

Reconnaissance guidelines for gold exploration in Central Alaska

Distribution of more than 300 gold-bearing samples from the Livengood (Tolovana) and parts of the Fairbanks and Rampart mining districts in central Alaska, USA, indicate that the concentration of gold in placers is spatially related both to structural features and to Late Cretaceous and (or) Tertiary felsic plutons. The regional consistency of these spatial relationships is demonstrated by proximity analysis using a Geographic Information System (GIS), and suggests a genetic association between faults, felsic plutons, and gold occurrences. The local presence of gold within several of the plutons indicates that these are the source of some of the gold. In addition, some gold occurs proximal to faults where plutons are not present, suggesting that some of the gold was also derived from the country rock. We envision a model whereby weakly mineralized solutions, thermally driven by latent plutonic heat, were enriched by circulation through clastic units that may have had a naturally elevated gold background. The resultant enriched solutions were channeled and reconcentrated along or adjacent to large-scale fault systems. Future exploration to define individual target areas should be directed toward areas where Late Cretaceous and (or) Tertiary felsic plutons occur near major faults. ?? 1993.

Journal of Geochemical Exploration↗

USGS2017

Climate change refugia and habitat connectivity promote species persistence

Background Climate change refugia, areas buffered from climate change relative to their surroundings, are of increasing interest as natural resource managers seek to prioritize climate adaptation actions. However, evidence that refugia buffer the effects of anthropogenic climate change is largely missing. Methods Focusing on the climate-sensitive Belding’s ground squirrel ( Urocitellus beldingi ), we predicted that highly connected Sierra Nevada meadows that had warmed less or shown less precipitation change over the last century would have greater population persistence, as measured by short-term occupancy, fewer extirpations over the twentieth century, and long-term persistence measured through genetic diversity. Results Across California, U. beldingi were more likely to persist over the last century in meadows with high connectivity that were defined as refugial based on a suite of temperature and precipitation factors. In Yosemite National Park, highly connected refugial meadows were more likely to be occupied by U. beldingi . More broadly, populations inhabiting Sierra Nevada meadows with colder mean winter temperatures had higher values of allelic richness at microsatellite loci, consistent with higher population persistence in temperature-buffered sites. Furthermore, both allelic richness and gene flow were higher in meadows that had higher landscape connectivity, indicating the importance of metapopulation processes. Conversely, anthropogenic refugia, sites where populations appeared to persist due to food or water supplementation, had lower connectivity, genetic diversity, and gene flow, and thus might act as ecological traps. This study provides evidence that validates the climate change refugia concept in a contemporary context and illustrates how to integrate field observations and genetic analyses to test the effectiveness of climate change refugia and connectivity. Conclusions Climate change refugia will be important for conserving populations as well as genetic diversity and evolutionary potential. Our study shows that in-depth modeling paired with rigorous fieldwork can identify functioning climate change refugia for conservation.

California↗

USGS2016

Science information to support Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis

The Missouri River Pallid Sturgeon Effects Analysis (EA) was commissioned by the U.S. Army Corps of Engineers to develop a foundation of understanding of how pallid sturgeon ( Scaphirhynchus albus ) population dynamics are linked to management actions in the Missouri River. The EA consists of several steps: (1) development of comprehensive, conceptual ecological models illustrating pallid sturgeon population dynamics and links to management actions and other drivers; (2) compilation and assessment of available scientific literature, databases, and models; (3) development of predictive, quantitative models to explore the system dynamics and population responses to management actions; and (4) analysis and assessment of effects of system operations and actions on species’ habitats and populations. This report addresses the second objective, compilation and assessment of relevant information. Scientific information on pallid sturgeon and its environment has grown substantially during the last decade. Presently available (2015) information indicates that stocked sturgeon are surviving and growing, and that wild and hatchery sturgeon are spawning in the wild. However, natural recruitment to age-1 and older has not been detected since systematic sampling began in 2005. Population models indicate the sensitivity of population growth to certain demographic variables, in particular early-life stage survival and perhaps adult fecundity. This report documents the existing population models for the pallid sturgeon, and the substantial quantities of information developed through the Pallid Sturgeon Population Assessment Program (PSPAP), the Habitat Assessment and Monitoring Program (HAMP), the Comprehensive Sturgeon Research Project (CSRP), range-wide genetics databases, and related research studies. The reference database compiled for the EA consists of over 190 peer-reviewed documents specifically related to pallid sturgeon and over 12,000 references on the Missouri River system and related species. Notwithstanding the large quantity of information available, the EA faces challenges in synthesizing the information into useful, quantitative models. In particular, critical demographic parameters for population models remain uncertain and the functional relationships between the two main categories of physical management action—changes in flow regime and reengineering channel form—and pallid sturgeon survival responses are obscure. In addition, there is an overarching uncertainty about how physical management actions interact with propagation management actions in view of evolving understanding of genetic structuring of the pallid sturgeon population. Synthesis efforts are also challenged by the fragmentation of information sources among projects and agencies; one objective of this report is to facilitate future assessments by providing documentation of what information is available and where.

Iowa, Kansas, Missouri, Montana, Nebraska, North D↗

USGS2008

Reverse Evolution of Armor Plates in the Threespine Stickleback

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not??only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution," [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime. ?? 2008 Elsevier Ltd. All rights reserved.

Current Biology↗

USGS2024

Differences in life history patterns of American shad, Alosa sapidissima, populations between ancestral, Atlantic coast, and non-native, Pacific coast rivers of North America

Organisms naturalized outside their native range can reveal new life history patterns in new environments. Here, we compare life history patterns of American shad, Alosa sapidissima, from five rivers along the U.S. Pacific coast (introduced range) with contemporary data from the Atlantic coast source populations. The Pacific coast fish grew slower, matured at a younger age, and were less often iteroparous than conspecifics from the Hudson River and Susquehanna River sources. Differences among the Pacific coast populations indicated that some combination of phenotypic plasticity and genetic adaptation has occurred since the transplants in the 1870s. Microchemical analysis of otoliths from returning adults demonstrated an immature, extended freshwater life history form, locally known as “mini-shad”. These fish remain in the river for at least 1 year or enter salt water briefly and then return to fresh water for several months prior to subsequent seaward migration and return as adults. This and other forms of variation (extent of estuary use and size at sea water entry) expand the understanding of Alosine migration and life history diversity.

Canadian Journal of Fisheries and Aquatic Sciences↗