Identifying Preservation and Restoration Priority Areas for Desert Fishes in an Increasingly Invaded World.

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Identifying Preservation and Restoration Priority Areas for Desert Fishes in an Increasingly Invaded World.

Environ Manage. 2013 Jan 26;

Authors: Pool TK, Strecker AL, Olden JD

Abstract
A commonly overlooked aspect of conservation planning assessments is that wildlife managers are increasingly focused on habitats that contain non-native species. We examine this management challenge in the Gila River basin (150,730 km(2)), and present a new planning strategy for fish conservation. By applying a hierarchical prioritization algorithm to >850,000 fish records in 27,181 sub-watersheds we first identified high priority areas (PAs) termed “preservation PAs” with high native fish richness and low non-native richness; these represent traditional conservation targets. Second, we identified “restoration PAs” with high native fish richness that also contained high numbers of non-native species; these represent less traditional conservation targets. The top 10 % of preservation and restoration PAs contained common native species (e.g., Catostomus clarkii, desert sucker; Catostomus insignis, Sonora sucker) in addition to native species with limited distributions (i.e., Xyrauchen texanus, razorback sucker; Oncorhynchus gilae apache, Apache trout). The top preservation and restoration PAs overlapped by 42 %, indicating areas with high native fish richness range from minimally to highly invaded. Areas exclusively identified as restoration PAs also encompassed a greater percentage of native species ranges than would be expected by the random addition of an equivalent basin area. Restoration PAs identified an additional 19.0 and 26.6 % of the total ranges of two federally endangered species-Meda fulgida (spikedace) and Gila intermedia (Gila chub), respectively, compared to top preservation PAs alone-despite adding only 5.8 % of basin area. We contend that in addition to preservation PAs, restoration PAs are well suited for complementary management activities benefiting native fishes.

PMID: 23354872 [PubMed – as supplied by publisher]

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Motion-guided attention promotes adaptive communications during social navigation.

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Motion-guided attention promotes adaptive communications during social navigation.

Proc Biol Sci. 2013;280(1754):20122003

Authors: Lemasson BH, Anderson JJ, Goodwin RA

Abstract
Animals are capable of enhanced decision making through cooperation, whereby accurate decisions can occur quickly through decentralized consensus. These interactions often depend upon reliable social cues, which can result in highly coordinated activities in uncertain environments. Yet information within a crowd may be lost in translation, generating confusion and enhancing individual risk. As quantitative data detailing animal social interactions accumulate, the mechanisms enabling individuals to rapidly and accurately process competing social cues remain unresolved. Here, we model how motion-guided attention influences the exchange of visual information during social navigation. We also compare the performance of this mechanism to the hypothesis that robust social coordination requires individuals to numerically limit their attention to a set of n-nearest neighbours. While we find that such numerically limited attention does not generate robust social navigation across ecological contexts, several notable qualities arise from selective attention to motion cues. First, individuals can instantly become a local information hub when startled into action, without requiring changes in neighbour attention level. Second, individuals can circumvent speed-accuracy trade-offs by tuning their motion thresholds. In turn, these properties enable groups to collectively dampen or amplify social information. Lastly, the minority required to sway a group’s short-term directional decisions can change substantially with social context. Our findings suggest that motion-guided attention is a fundamental and efficient mechanism underlying collaborative decision making during social navigation.

PMID: 23325772 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23325772?dopt=Abstract

Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries.

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Centennial-scale fluctuations and regional complexity characterize Pacific salmon population dynamics over the past five centuries.

Proc Natl Acad Sci U S A. 2013 Jan 15;

Authors: Rogers LA, Schindler DE, Lisi PJ, Holtgrieve GW, Leavitt PR, Bunting L, Finney BP, Selbie DT, Chen G, Gregory-Eaves I, Lisac MJ, Walsh PB

Abstract
Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on interdecadal time scales (30- to 80-y cycles), centennial-scale variation, undetectable in modern-day catch records and survey data, has dominated salmon population dynamics over the past 500 y. Before 1900, variation in abundance was clearly not synchronous among stocks, and the only temporal signal common to lake sediment records from this region was the onset of commercial fishing in the late 1800s. Thus, historical changes in climate did not synchronize stock dynamics over centennial time scales, emphasizing that ecosystem complexity can produce a diversity of ecological responses to regional climate forcing. Our results show that marine fish populations may alternate between naturally driven periods of high and low abundance over time scales of decades to centuries and suggest that management models that assume time-invariant productivity or carrying capacity parameters may be poor representations of the biological reality in these systems.

PMID: 23322737 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23322737?dopt=Abstract

Frequency and intensity of productivity regime shifts in marine fish stocks.

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Frequency and intensity of productivity regime shifts in marine fish stocks.

Proc Natl Acad Sci U S A. 2013 Jan 15;

Authors: Vert-Pre KA, Amoroso RO, Jensen OP, Hilborn R

Abstract
Fish stocks fluctuate both in abundance and productivity (net population increase), and there are many examples demonstrating that productivity increased or decreased due to changes in abundance caused by fishing and, alternatively, where productivity shifted between low and high regimes, entirely unrelated to abundance. Although shifts in productivity regimes have been described, their frequency and intensity have not previously been assessed. We use a database of trends in harvest and abundance of 230 fish stocks to evaluate the proportion of fish stocks in which productivity is primarily related to abundance vs. those that appear to manifest regimes of high or low productivity. We evaluated the statistical support for four hypotheses: (i) the abundance hypothesis, where production is always related to population abundance; (ii) the regimes hypothesis, where production shifts irregularly between regimes that are unrelated to abundance; (iii) the mixed hypothesis, where even though production is related to population abundance, there are irregular changes in this relationship; and (iv) the random hypothesis, where production is random from year to year. We found that the abundance hypothesis best explains 18.3% of stocks, the regimes hypothesis 38.6%, the mixed hypothesis 30.5%, and the random hypothesis 12.6%. Fisheries management agencies need to recognize that irregular changes in productivity are common and that harvest regulation and management targets may need to be adjusted whenever productivity changes.

PMID: 23322735 [PubMed – as supplied by publisher]

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Pesticides in urban streams and early life stages of pacific coho salmon.

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Pesticides in urban streams and early life stages of pacific coho salmon.

Environ Toxicol Chem. 2013 Jan 7;

Authors: King KA, Grue CE, Grassley JM, Fisk RJ

Abstract
Pesticides are frequently detected in urban streams and are believed to be primarily the result of homeowner use. Although concentrations in most cases are low (<1 µg/L), there is concern that pesticide inputs threaten efforts to restore and enhance salmon habitat. The authors exposed early life stages of coho salmon (Oncorhynchus kisutch) to a pesticide mixture (“cocktail”) representative of those pesticides most frequently reported in urban streams in western Washington State, USA. Life stages were continuously exposed to pulses of the cocktail simulating those in urban streams in fall and winter when coho salmon eggs and sac fry are present. Nominal concentrations of eight herbicides, two insecticides, a fungicide, and a breakdown product were the maximum detected. Fertilization, hatching success, survival, deformities, and growth of fry were not significantly affected. A reduction in fertilization success (19-25%) was not reproducible even when gametes were exposed to 100 times the maximum concentrations detected. Based on the end points examined in the present study, the results suggest that direct exposure to the pesticides most frequently detected in urban streams in western Washington does not impair early life stages of coho salmon and is not a major factor governing the recovery of salmon populations. The extent to which pesticide exposure would affect smoltification, outmigration, and ocean survival needs to be determined. Environ. Toxicol. Chem. © 2013 SETAC.

PMID: 23297254 [PubMed – as supplied by publisher]

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Genomic resource development for shellfish of conservation concern.

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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

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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.

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

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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.

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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

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

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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