Hydrogeomorphic classification of Washington State rivers to support emerging environmental flow management strategies

Written by

Reidy Liermann, C.A. Olden, J.D., Beechie, T.J., Kennard, M.J., Skidmore, P.B., Konrad, C.P. and H. Imaki. 2012. Hydrogeomorphic classification of Washington State rivers to support emerging environmental flow management strategies. River Research and Applications28: 1340-1358.

As demand for fresh water increases in tandem with human population growth and a changing climate, the need to understand the ecological tradeoffs of flow regulation gains greater importance. Environmental classification is a first step towards quantifying these tradeoffs by creating the framework necessary for analysing the effects of flow variability on riverine biota. Our study presents a spatially explicit hydrogeomorphic classification of streams and rivers in Washington State, USA and investigates how projected climate change is likely to affect flow regimes in the future. We calculated 99 hydrologic metrics from 15 years of continuous daily discharge data for 64 gauges with negligible upstream impact, which were entered into a Bayesian mixture model to classify flow regimes into seven major classes described by their dominant flow source as follows: groundwater (GW), rainfall (RF), rain-with-snow (RS), snow-and-rain (SandR), snow-with-rain (SR), snowmelt (SM) and ultra-snowmelt (US). The largest class sizes were represented by the transitional RS and SandR classes (14 and 12 gauges, respectively), which are ubiquitous in temperate, mountainous landscapes found in Washington. We used a recursive partitioning algorithm and random forests to predict flow class based on a suite of environmental and climate variables. Overall classification success was 75%, and the model was used to predict normative flow classes at the reach scale for the entire state. Application of future climate change scenarios to the model inputs indicated shifts of varying magnitude from snow-dominated to rain-dominated flow classes. Lastly, a geomorphic classification was developed using a digital elevation model (DEM) and climatic data to assign stream segments as either dominantly able or unable to migrate, which was cross-tabulated with the flow types to produce a 14-tier hydrogeomorphic classification. The hydrogeomorphic classification provides a framework upon which empirical flow alteration–ecological response relationships can subsequently be developed using ecological information collected throughout the region.

Hydrologic classes of Washington State
Hydrologic classes of Washington State

Genomic resource development for shellfish of conservation concern.

Written by

Genomic resource development for shellfish of conservation concern.

Mol Ecol Resour. 2012 Dec 27;

Authors: Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ, Roberts SB

Abstract
Effective conservation of threatened species depends on the ability to assess organism physiology and population demography. To develop genomic resources to better understand the dynamics of two ecologically vulnerable species in the Pacific Northwest of the United States, larval transcriptomes were sequenced for the pinto abalone, Haliotis kamtschatkana kamtschatkana, and the Olympia oyster, Ostrea lurida. Based on comparative species analysis the Ostrea lurida transcriptome (41 136 contigs) is relatively complete. These transcriptomes represent the first significant contribution to genomic resources for both species. Genes are described based on biological function with particular attention to those associated with temperature change, oxidative stress and immune function. In addition, transcriptome-derived genetic markers are provided. Together, these resources provide valuable tools for future studies aimed at conservation of Haliotis kamtschatkana kamtschatkana, Ostrea lurida and related species.

PMID: 23280275 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23280275?dopt=Abstract

Characterization of genes involved in ceramide metabolism in the Pacific oyster

Written by

Characterization of genes involved in ceramide metabolism in the Pacific oyster, Crassostrea gigas

BMC Research Notes 2012, 5:502, DOI 10.1186/1756-0500-5-502

Authors: Timmins-Schiffman E, Roberts SB

Ceramide metabolism is an important part of the vertebrate response to a variety of environmental stressors.  Accumulation of ceramide, a lipid, can lead to stress-induced apoptosis.  We investigated the conservation of this pathway in invertebrates using the Pacific oyster as a model.  Using both in silico and in vivo methods, we identified multiple genes from the vertebrate ceramide metabolism pathway in the Pacific oyster and sequenced four of these genes.  We also measured the expression of these genes in response to a bacterial exposure to determine if ceramide metabolism may be part of the invertebrate stress response.  Genes involved in ceramide generation and break-down are present in the Pacific oyster.  The results from gene expression assays also suggested that ceramide metabolism may be a component of the invertebrate stress response, supporting that the form and function of this pathway are conserved in invertebrates.

Read Full Text….

Developing a broader scientific foundation for river restoration: Columbia River food webs.

Written by

Developing a broader scientific foundation for river restoration: Columbia River food webs.

Proc Natl Acad Sci U S A. 2012 Nov 28;

Authors: Naiman RJ, Alldredge JR, Beauchamp DA, Bisson PA, Congleton J, Henny CJ, Huntly N, Lamberson R, Levings C, Merrill EN, Pearcy WG, Rieman BE, Ruggerone GT, Scarnecchia D, Smouse PE, Wood CC

Abstract
Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure-without explicitly considering food webs-has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.

PMID: 23197837 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23197837?dopt=Abstract

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

Written by

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

PLoS One. 2012;7(11):e49018

Authors: Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE

Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

PMID: 23185290 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23185290?dopt=Abstract

Please join the Alaska Salmon Program for our 2012 Science Symposium

Written by

Please join the Alaska Salmon Program for our 2012 Science Symposium

When: Friday, November 30, 2012, 1:30 ~ 5:30 pm
Where: Fishery Sciences Building (FSH) – 1122 NE Boat St.
Location: Room 102 (auditorium)

This annual symposium showcases the research of the UW School of Aquatic and Fishery Sciences’ Alaska Salmon Program undergraduate and graduate students, faculty, staff and visiting scientists.  Our program focuses on all aspects of the ecology of Pacific salmon in the North Pacific, Bering Sea, and watersheds of Southwest Alaska.  Participants will give brief talks sharing their research in both basic and applied ecology, as well as the biological and socioeconomic management of Alaskan fisheries. For a symposium schedule and general program information please go to: http://fish.washington.edu/research/alaska/.

Please feel free to come for whatever part of the afternoon you are available.  We hope to see you there!

Jackie Carter
jlcarter@uw.edu

An Energy Diet: Cut Back on Water, Pay More Attention to Fish

Written by

An Energy Diet: Cut Back on Water, Pay More Attention to Fish

The water-energy nexus is the subject of huge debate and research: How can the United States meet future energy demands while conserving precious water resources? The focus has mostly been on how various energy sources impact both water quantity and quality, with little attention paid to what this means for fish and other freshwater biodiversity.

A new report published in PLoS One from Nature Conservancy scientists and Julian Olden (University of Washington) fills that void by looking at how much water various energy technologies will consume in coming decades and how this could affect freshwater species. The findings show how U.S. energy choices could also save water resources—which will come under increasing pressure from population growth and climate change.

Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in a south-western Alaskan lake

Written by

Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in a south-western Alaskan lake

Journal of Evolutionary Biology, doi: 10.1111/jeb.12011

Authors: C. P. Gowell*†, T. P. Quinn† & E. B. Taylor‡
*Department of Biology, University of Puget Sound, Tacoma, WA, USA
†School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
‡Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada

Abstract
Ecologically, morphologically and genetically distinct populations within single taxa often coexist in postglacial lakes and have provided important model systems with which to investigate ecological and evolutionary processes such as niche partitioning and ecological speciation. Within the Salmonidae, these species complexes have been well studied, particularly within the Coregonus clupeaformis–C. laveratus (lake and European whitefish, respectively) group, but the phenomenon has been less well documented in the other whitefish genera, Prosopium and Stenodus. Here, we examined the morphology, feeding biology and genetic structure of three putative forms of the pygmy whitefish, Prosopium coulterii (Eigenmann & Eigenmann, 1892), first reported from Chignik Lake, south-western Alaska, over 40 years ago. Field collections and morphological analyses resolved a shallow water (< 5 m depth) low gill raker count form (< 15 first arch gill rakers), a deepwater (> 30 m), low gill raker form and a deepwater, high gill raker count (> 15 gill rakers) form. The two low gill raker count forms fed almost exclusively on benthic invertebrates (mostly chironomids), while the deepwater, high gill raker count form fed almost exclusively on zooplankton; differences in diet were also reflected in differences both in d13C and d15N stable isotopes. All three forms were characterized by the same major mitochondrial DNA clade that has been associated with persistence in, and postglacial dispersal from, a Beringian glacial refugium. Analysis of variation at nine microsatellite DNA loci indicated low, but significant differentiation among forms, especially between the two low gill raker count forms and the high gill raker count form. The extent of differentiation along phenotypic (considerable) and genetic (subtle) axes among the Chignik Lake forms is similar to that found among distinct taxa of Prosopium found in pre-glacial Bear Lake (Utah–Idaho, USA) which is probably at least ten times older than Chignik Lake. Our analyses illustrate the potential for the postglacial differentiation in traits subject to divergent natural selection across variable environments.

pp 2432 – 2448

Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

Written by

Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

Evol Appl. 2012 Nov;5(7):705-19

Authors: Seamons TR, Hauser L, Naish KA, Quinn TP

Abstract
TWO STRATEGIES HAVE BEEN PROPOSED TO AVOID NEGATIVE GENETIC EFFECTS OF ARTIFICIALLY PROPAGATED INDIVIDUALS ON WILD POPULATIONS: (i) integration of wild and captive populations to minimize domestication selection and (ii) segregation of released individuals from the wild population to minimize interbreeding. We tested the efficacy of the strategy of segregation by divergent life history in a steelhead trout, Oncorhynchus mykiss, system, where hatchery fish were selected to spawn months earlier than the indigenous wild population. The proportion of wild ancestry smolts and adults declined by 10-20% over the three generations since the hatchery program began. Up to 80% of the naturally produced steelhead in any given year were hatchery/wild hybrids. Regression model selection analysis showed that the proportion of hatchery ancestry smolts was lower in years when stream discharge was high, suggesting a negative effect of flow on reproductive success of early-spawning hatchery fish. Furthermore, proportions of hybrid smolts and adults were higher in years when the number of naturally spawning hatchery-produced adults was higher. Divergent life history failed to prevent interbreeding when physical isolation was ineffective, an inadequacy that is likely to prevail in many other situations.

PMID: 23144657 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23144657?dopt=Abstract