Addressing road-river infrastructure gaps using a model-based approach

The world's rivers are covered over and fragmented by road infrastructure. Road-river infrastructure result in many socio-environmental questions and documenting where different types occur is challenged by their sheer numbers. Equally, the United Nations has committed the next decade to ecosystem restoration, and decision makers across government, non-government, and private sectors require information about where different types of road-river infrastructure occur to guide management decisions that promote both transport and river system resilience. Field-based efforts alone cannot address data and information needs at relevant scales, such as across river basins, nations, or regions to guide road-river infrastructure remediation. As a first step toward overcoming these data needs in Great Britain, we constructed a georeferenced database of road-river infrastructure, validated a subset of locations, and used a Boosted Regression Tree model-based approach with environmental data to predict which infrastructure are bridges and culverts. We mapped 110,406 possible road-river infrastructure locations and were able to either validate or predict which of 110,194 locations were bridges (n=60,385) or culverts (n=49,809). Upstream drainage area had the greatest contribution to determining infrastructure type: when <10 km2 our model correctly predicted culverts 73% of the time but only 60% of the time for bridges. Road type and stream gradient also influenced model results. Our model-based approach is readily applied to other locations and contexts and can be used to inform decisions about management of smaller infrastructure that are frequently overlooked worldwide

A European eel (Anguilla anguilla) case study using structured elicitation to estimate instream infrastructure passability for freshwater fishes

Conservation efforts are hampered by limited understanding about how different types of instream infrastructure impact migration patterns and fish survival. We used a rapid, fully online IDEA protocol to elicit expert judgments for the passability of seven different in-stream infrastructures to elver European eels (Anguilla anguilla) in Great Britain. Nine experts provided judgments via our online survey, followed by a second elicitation via email for reflection and adjustment of initial estimates. We found that on average, bridges were judged the most passable (95% passability), followed by fords, nonperched culverts, weirs, sluices, dams, and perched culverts (7%). Results showed a high degree of agreement about how passable bridges and perched culverts are for elver eels, but less certainty about other infrastructure. Thirty-four distinct factors were identified that experts believed influence infrastructure passability for elver eels, including: the structure itself, hydraulics, elver characteristics, obstructions (e.g., debris accumulation), and vegetation (e.g., to aid climbing). We discuss how our rapid, online-only variation on the IDEA protocol compares with the more traditional protocol, and how the expert estimates generated in this study can be used in future scenario building and connectivity modeling, with a view to improving conservation to support species persistence

Fresh Waters and Fish Diversity: Distribution, Protection and Disturbance in Tropical Australia

Background: Given the globally poor protection of fresh waters for their intrinsic ecological values, assessments are needed to determine how well fresh waters and supported fish species are incidentally protected within existing terrestrial protected-area networks, and to identify their vulnerability to human-induced disturbances. To date, gaps in data have severely constrained any attempt to explore the representation of fresh waters in tropical regions.\ud \ud Methodology and Results: We determined the distribution of fresh waters and fish diversity in the Wet Tropics of Queensland, Australia. We then used distribution data of fresh waters, fish species, human-induced disturbances, and the terrestrial protected-area network to assess the effectiveness of terrestrial protected areas for fresh waters and fish species. We also identified human-induced disturbances likely to influence the effectiveness of freshwater protection and evaluated the vulnerability of fresh waters to these disturbances within and outside protected areas. The representation of fresh waters and fish species in the protected areas of the Wet Tropics is poor: 83% of stream types defined by order, 75% of wetland types, and 89% of fish species have less than 20% of their total Wet Tropics length, area or distribution completely within IUCN category II protected areas. Numerous disturbances affect fresh waters both within and outside of protected areas despite the high level of protection afforded to terrestrial areas in the Wet Tropics (>60% of the region). High-order streams and associated wetlands are influenced by the greatest number of human-induced disturbances and are also the least protected. Thirty-two percent of stream length upstream of protected areas has at least one human-induced disturbance present.\ud \ud Conclusions/Significance: We demonstrate the need for greater consideration of explicit protection and off-reserve management for fresh waters and supported biodiversity by showing that, even in a region where terrestrial protection is high, it does not adequately capture fresh waters

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil

Sixteen years of social and ecological dynamics reveal challenges and opportunities for adaptive management in sustaining the commons

Efforts to confront the challenges of environmental change and uncertainty include attempts to adaptively manage social–ecological systems. However, critical questions remain about whether adaptive management can lead to sustainable outcomes for both ecosystems and society. Here, we make a contribution to these efforts by presenting a 16-y analysis of ecological outcomes and perceived livelihood impacts from adaptive coral reef management in Papua New Guinea. The adaptive management system we studied was a customary rotational fisheries closure system (akin to fallow agriculture), which helped to increase the biomass of reef fish and make fish less wary (more catchable) relative to openly fished areas. However, over time the amount of fish in openly fished reefs slowly declined. We found that, overall, resource users tended to have positive perceptions about this system, but there were negative perceptions when fishing was being prohibited. We also highlight some of the key traits of this adaptive management system, including 1) strong social cohesion, whereby leaders played a critical role in knowledge exchange; 2) high levels of compliance, which was facilitated via a “carrot-and-stick” approach that publicly rewarded good behavior and punished deviant behavior; and 3) high levels of participation by community actors

Global Methylation in Exposure Biology and Translational Medical Science

Background: Many groups are actively investigating how the epigenetic state relates to environmental exposures and development of disease, including cancer. There are myriad choices for capturing and measuring the epigenetic state of a tissue, ranging from assessing the total methyl-CpG content to array-based platforms that simultaneously probe hundreds of thousands of CpG loci. There is an emerging literature that uses CpG methylation at repetitive sequences, including LINE-1 (long interspersed nuclear element-1) elements, to capture the epigenomic state

Knowledge sharing about deep-sea ecosystems to inform conservation and research decisions

The Marianas Trench Marine National Monument (MNM) currently extends policy-based protection to deep-sea ecosystems contained within it, but managers require better understanding of the current knowledge and knowledge gaps about these ecosystems to guide decision-making. To address this need, we present a case study of the Marianas Trench MNM using in-depth interviews to determine scientists’ (1) current understanding of anthropogenic drivers of change and system vulnerability in deep-sea ecosystems; and (2) perceptions of the least understood deep-sea ecosystems and processes in the Marianas Trench MNM, and which of these, if any, should be research priorities to fill knowledge gaps about these systems and the impacts from anthropogenic drivers of change. Interview respondents shared similar views on the current knowledge of deep-sea ecosystems and potential anthropogenic drivers of change in the Marianas Trench MNM. Respondents also identified trench and deep pelagic (bathyal, abyssal, and hadal zones) ecosystems as the least understood, and highlighted climate change, litter and waste, mining and fishing, and interactions between these drivers of change as critical knowledge gaps. To fill key knowledge gaps and inform conservation decision-making, respondents identified the need for monitoring networks and time-series data. Our approach demonstrates how in-depth interviews can be used to elicit knowledge to inform decision-making in data-limited situations