Cost-Effective Management of Snake River Chinook Salmon: Response to Wilson et al.

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73669/1/j.1523-1739.2009.01171.x.pd

Innovations in coastline management with natural and nature-based features (NNBF): lessons learned from three case studies

Coastal communities around the world are facing increased coastal flooding and shoreline erosion from factors such as sea-level rise and unsustainable development practices. Coastal engineers and managers often rely on gray infrastructure such as seawalls, levees and breakwaters, but are increasingly seeking to incorporate more sustainable natural and nature-based features (NNBF). While coastal restoration projects have been happening for decades, NNBF projects go above and beyond coastal restoration. They seek to provide communities with coastal protection from storms, erosion, and/or flooding while also providing some of the other natural benefits that restored habitats provide. Yet there remain many unknowns about how to design and implement these projects. This study examines three innovative coastal resilience projects that use NNBF approaches to improve coastal community resilience to flooding while providing a host of other benefits: 1) Living Breakwaters in New York Harbor; 2) the Coastal Texas Protection and Restoration Study; and 3) the South Bay Salt Pond Restoration Project in San Francisco Bay. We synthesize findings from these case studies to report areas of progress and illustrate remaining challenges. All three case studies began with innovative project funding and framing that enabled expansion beyond a sole focus on flood risk reduction to include multiple functions and benefits. Each project involved stakeholder engagement and incorporated feedback into the design process. In the Texas case study this dramatically shifted one part of the project design from a more traditional, gray approach to a more natural hybrid solution. We also identified common challenges related to permitting and funding, which often arise as a consequence of uncertainties in performance and long-term sustainability for diverse NNBF approaches. The Living Breakwaters project is helping to address these uncertainties by using detailed computational and physical modeling and a variety of experimental morphologies to help facilitate learning while monitoring future performance. This paper informs and improves future sustainable coastal resilience projects by learning from these past innovations, highlighting the need for integrated and robust monitoring plans for projects after implementation, and emphasizing the critical role of stakeholder engagement.Environmental Biolog

A cost-effectiveness analysis of Snake River salmon management activities

Master of ScienceNatural Resources and EnvironmentUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/114499/1/39015052046870.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/114499/2/39015052046870.pd

Cost-Effective Management of Snake River Chinook Salmon: Response to Wilson et al.

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73669/1/j.1523-1739.2009.01171.x.pd

Cost-Effective Management Alternatives for Snake River Chinook Salmon: a Biological-Economic Synthesis

The mandate to increase endangered salmon populations in the Columbia River Basin of North America has created a complex, controversial resource-management issue. We constructed an integrated assessment model as a tool for analyzing biological-economic trade-offs in recovery of Snake River spring- and summer-run chinook salmon ( Oncorhynchus tshawytscha ). We merged 3 frameworks: a salmon-passage model to predict migration and survival of smolts; an age-structured matrix model to predict long-term population growth rates of salmon stocks; and a cost-effectiveness analysis to determine a set of least-cost management alternatives for achieving particular population growth rates. We assessed 6 individual salmon-management measures and 76 management alternatives composed of one or more measures. To reflect uncertainty, results were derived for different assumptions of effectiveness of smolt transport around dams. Removal of an estuarine predator, the Caspian Tern ( Sterna caspia ), was cost-effective and generally increased long-term population growth rates regardless of transport effectiveness. Elimination of adult salmon harvest had a similar effect over a range of its cost estimates. The specific management alternatives in the cost-effective set depended on assumptions about transport effectiveness. On the basis of recent estimates of smolt transport effectiveness, alternatives that discontinued transportation or breached dams were prevalent in the cost-effective set, whereas alternatives that maximized transportation dominated if transport effectiveness was relatively high. More generally, the analysis eliminated 80–90% of management alternatives from the cost-effective set. Application of our results to salmon management is limited by data availability and model assumptions, but these limitations can help guide research that addresses critical uncertainties and information. Our results thus demonstrate that linking biology and economics through integrated models can provide valuable tools for science-based policy and management.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74238/1/j.1523-1739.2008.00913.x.pd

Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher’s Precision ID mtDNA Whole Genome Assay

The advent of massively parallel sequencing (MPS) in the past decade has opened the doors to mitochondrial whole-genome sequencing. Mitochondrial (mt) DNA is used in forensics due to its high copy number per cell and maternal mode of inheritance. Consequently, we have implemented the Thermo Fisher Precision ID mtDNA Whole Genome panel coupled with the Ion Chef™ and Ion S5™ for MPS analysis in the California Department of Justice, Missing Persons DNA Program. Thirty-one mostly challenging samples (degraded, inhibited, low template, or mixed) were evaluated for this study. The majority of these samples generated single source full or partial genome sequences with MPS, providing information in cases where previously there was none. The quantitative and sensitive nature of MPS analysis was beneficial, but also led to detection of low-level contaminants. In addition, we found Precision ID to be more susceptible to inhibition than our legacy Sanger assay. Overall, the success rate (full single source hypervariable regions I and II (HVI/HVII) for Sanger and control region for MPS result) for these challenging samples increased from 32.3% with Sanger sequencing to 74.2% with the Precision ID assay. Considering the increase in success rate, the simple workflow and the higher discriminating potential of whole genome data, the Precision ID platform is a significant improvement for the CA Department of Justice Missing Persons DNA Program