Biological Invasions: Recommendations for U.S. Policy and Management

The Ecological Society of America has evaluated current U.S. national policies and practices on biological invasions in light of current scientific knowledge. Invasions by harmful nonnative species are increasing in number and area affected; the damages to ecosystems, economic activity, and human welfare are accumulating. Without improved strategies based on recent scientific advances and increased investments to counter invasions, harm from invasive species is likely to accelerate. Federal leadership, with the cooperation of state and local governments, is required to increase the effectiveness of prevention of invasions, detect and respond quickly to new potentially harmful invasions, control and slow the spread of existing invasions, and provide a national center to ensure that these efforts are coordinated and cost effective. Specifically, the Ecological Society of America recommends that the federal government take the following six actions: (1) Use new information and practices to better manage commercial and other pathways to reduce the transport and release of potentially harmful species; (2) Adopt more quantitative procedures for risk analysis and apply them to every species proposed for importation into the country; (3) Use new cost-effective diagnostic technologies to increase active surveillance and sharing of information about invasive species so that responses to new invasions can be more rapid and effective; (4) Create new legal authority and provide emergency funding to support rapid responses to emerging invasions; (5) Provide funding and incentives for cost-effective programs to slow the spread of existing invasive species in order to protect still uninvaded ecosystems, social and industrial infrastructure, and human welfare; and (6) Establish a National Center for Invasive Species Management (under the existing National Invasive Species Council) to coordinate and lead improvements in federal, state, and international policies on invasive species. Recent scientific and technical advances provide a sound basis for more cost-effective national responses to invasive species. Greater investments in improved technology and management practices would be more than repaid by reduced damages from current and future invasive species. The Ecological Society of America is committed to assist all levels of government and provide scientific advice to improve all aspects of invasive-species management

A Tale of Four “Carp”: Invasion Potential and Ecological Niche Modeling

. We assessed the geographic potential of four Eurasian cyprinid fishes (common carp, tench, grass carp, black carp) as invaders in North America via ecological niche modeling (ENM). These “carp” represent four stages of invasion of the continent (a long-established invader with a wide distribution, a long-established invader with a limited distribution, a spreading invader whose distribution is expanding, and a newly introduced potential invader that is not yet established), and as such illustrate the progressive reduction of distributional disequilibrium over the history of species' invasions.We used ENM to estimate the potential distributional area for each species in North America using models based on native range distribution data. Environmental data layers for native and introduced ranges were imported from state, national, and international climate and environmental databases. Models were evaluated using independent validation data on native and invaded areas. We calculated omission error for the independent validation data for each species: all native range tests were highly successful (all omission values <7%); invaded-range predictions were predictive for common and grass carp (omission values 8.8 and 19.8%, respectively). Model omission was high for introduced tench populations (54.7%), but the model correctly identified some areas where the species has been successful; distributional predictions for black carp show that large portions of eastern North America are at risk.ENMs predicted potential ranges of carp species accurately even in regions where the species have not been present until recently. ENM can forecast species' potential geographic ranges with reasonable precision and within the short screening time required by proposed U.S. invasive species legislation

Finding needles in haystacks:Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Natural Resources Research Institute Technical Report

In partial fulfillment of the requirements under U.S. EPA Cooperative Agreement No. CR-817486. through the Environmental Research Laboratory-Duluth Project Officer Dr. P.M.' CookWe use the “solids concentration effect” in an attempt to measure the organic-carbon normalized sediment-water partition coefficient, Koc, for 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) using desorption from contaminated sediment from Lake Ontario. The sediment was collected from Station 208 (Onuska et al., J. Great Lakes Res. 9(2), 169-182, 1983); it contains 470 pg/g dry weight of dioxin and 2.37% of organic carbon. We prepared a series of sediment suspensions of decreasing solids concentration; after various periods of equilibration followed by separation of sediment solids and water by sedimentation, we analyzed the aqueous phase for dioxin and organic carbon. The ranges of solids concentration (Cs,w ), of total aqueous phase dioxin (Clc,w ), and of aqueous phase organic carbon (Coc,w) are 0.06-60 g/L, 2-1000 pg/L, and 0.23-65 mg/L respectively. For the measured partition coefficient, Kmoc , our data fit the functions, log Kmoc = a constant - log Cs,w, and log Kmoc = a constant - log Csorb,w; values of R2 range from 0.61 to 0.92. Csorb,w is related to the organic carbon content of the water by Csorb,w = Coc,w - 0.2 mg / L; the prime indicates that the aqueous organic carbon levels are corrected for blank contributions. The total aqueous phase dioxin concentration only depends strongly on the concentration of organic carbon when Coc,w > 0.2 mg / L. We think this is an example of the phenomenon described by the term “critical micelle concentration”, CMC, which is usually reserved for the description of surfactant solutions, but here we have evidence that it applies to natural organic carbon also. For the system here the CMC is about 0.2 mg/L. By spiking the apparatus with C13-labeled dioxin, we are able to judge the degree to which the system has reached equilibrium or steady state. We establish clearly thereby that the dioxin in the water is at steady state in four experiments. Another feature is the recovery of the settled sediment solids at the end of experiments, and we show that the dioxin concentration, on a dry weight basis, decreases; levels are in the range 230-380 pg/g. This begs the question: What is the organic-carbon normalized dioxin concentration in the sediment at the end of the experiment? With assumptions, mass balance shows that significant quantities of organic carbon are adsorbed on the walls of the apparatus, and it appears that equilibrium is reached when concentrations of dioxin on organic material in the sediment, in the water and on the walls of the apparatus are the same. When doing partitioning experiments at low solids in large apparatus, it is important to recover the settled solids, and determine the level of adsorbed chemical and the organic carbon content. Then, we can complete the mass balance and determine uniquely the quantities of material adsorbed to the walls of the apparatus. Work with less hydrophobic compounds than dioxin shows that Kmoc becomes independent of solids concentration as the solids concentration decreases, whence Koc = Kmoc. We did not reach a sufficiently small concentration of solids; however, we are able to conclude that for dioxin Koc > 7.1; this observation agrees with other partitioning work done with dioxin and its isomers

Natural Resources Research Institute Technical Report

Standard Operating Procedure of the TRACE ORGANIC ANALYTICAL LABORATORY (TOAL).The original version was written on 30 April 1996; minor revisions have been incorporated in this version, dated 01/04/99

Natural Resources Research Institute Technical Report

Progress Report of the Air Force Project; Covering the period 8/1/96 to 7/31//97; Agency No: DOD/F49620-94-1-0401; U of M No: 0756-5140 (1613-189-6090)In a large number of cases, we have to assess the risk of chemicals and predict the toxic potential of molecules in the face of limited experimental data. Structural criteria and functional criteria (if available) are routinely used to estimate the possible hazard posed by a chemical to the environment and ecosystem. Frequently, no biological or relevant physicochemical properties of the chemical species of interest are available to the risk assessor. In the proposed project, we will develop and implement a number of methods of quantifying molecular similarity of chemicals using techniques of computational and mathematical chemistry. Some of the methods are new and will be based on our own research on the theoretical development and implementation of molecular similarity methods. These techniques will be implemented in a user friendly computer environment of the Silicon Graphics workstation. The similarity methods will be used to select analogs of chemicals of interest to the Air Force, viz., QUADRICYCLANE, FLUOROCARBON ETHERS AND THEIR ANALOGS, from databases containing high quality physicochemical data and toxicity endpoints for large number of chemicals. The databases used in the project will come from three sources: a) public domain databases, b) our own in-house databases, and c) databases acquired from commercial vendors. The set of selected analogs, called probe-induced subsets, will be used to: a) develop structure-activity relationships (SAR), and b) carry out ranking of chemicals. Both of these methods will be used to estimate the hazard of the chemicals of interest. A set of chemicals (five to ten) will be chosen for experimental work with the purpose of evaluating and refining computer models. The set will include quadricyclane and fluorocarbon ethers of interest to the Air Force. It will also include a selection of analogs (probe-induced subset) that are readily available, suitable for experimentation, and for which data are lacking. Experiments will be performed to assess the biodegradability and photochemical degradability of the members of the set. Their toxicity will be tested by MicroTox and MutaTox. In cases where significant degradation is observed, the toxicity of the degradation products will also be tested. Direct measurement of the hydrophobicity (octanol-water partition coefficient) will be performed on the members of the set