Fish species introductions provide novel insights into the patterns and drivers of phylogenetic structure in freshwaters.

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Fish species introductions provide novel insights into the patterns and drivers of phylogenetic structure in freshwaters.

Proc Biol Sci. 2014;281(1778):20133003

Authors: Strecker AL, Olden JD

Abstract
Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin’s naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species.

PMID: 24452027 [PubMed – in process]

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Gyrodactylid Ectoparasites in a Population of Rainbow Trout (Oncorhynchus mykiss).

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Gyrodactylid Ectoparasites in a Population of Rainbow Trout (Oncorhynchus mykiss).

J Am Assoc Lab Anim Sci. 2014;53(1):92-7

Authors: Garcia RL, Hansen AG, Chan MM, Sanders GE

Abstract
A colony of rainbow trout (Oncorhynchus mykiss) in a decentralized aquatic animal facility was noted to have an increase in morbidity and mortality (from 4 or 5 fish each month to 3 or 4 fish daily) approximately 2 wk after experimental procedures began. The primary clinical signs were erratic swimming behavior and ‘flashing’ of fish against surfaces within housing enclosures. Moribund and normal rainbow trout were presented alive for diagnostic evaluation; samples of water from housing enclosures were provided for water quality assessment. The trout were determined to be infected with gyrodactylids, a common monogenean ectoparasite of the skin and gills in both marine and freshwater fish. This case report describes the diagnosis, pathology, and treatment of gyrodactylids and husbandry modifications associated with the resolution of this clinical aquatic-animal case.

PMID: 24411786 [PubMed – in process]

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Opportunistic exploitation: an overlooked pathway to extinction.

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Opportunistic exploitation: an overlooked pathway to extinction.

Trends Ecol Evol. 2013 Jul;28(7):409-13

Authors: Branch TA, Lobo AS, Purcell SW

Abstract
How can species be exploited economically to extinction? Past single-species hypotheses examining the economic plausibility of exploiting rare species have argued that the escalating value of rarity allows extinction to be profitable. We describe an alternative pathway toward extinction in multispecies exploitation systems, termed ‘opportunistic exploitation’. In this mode, highly valued species that are targeted first by fishing, hunting, and logging become rare, but their populations can decline further through opportunistic exploitation while more common but less desirable species are targeted. Effectively, expanding exploitation to more species subsidizes the eventual extinction of valuable species at low densities. Managers need to recognize conditions that permit opportunistic depletion and pass regulations to protect highly desirable species when exploitation can expand to other species.

PMID: 23562732 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23562732?dopt=Abstract

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

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Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
Authors: Wesley A. Larson, Lisa W. Seeb, Meredith V. Everett, Ryan K. Waples, William D. Templin, James E. Seeb. All authors but William D. Templin are from SAFS.
Abstract
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment.
This work demonstrates the utility of genomic data to inform conservation in
highly exploited species with shallow population structure.

Species- and community-level responses combine to drive phenology of lake phytoplankton.

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Species- and community-level responses combine to drive phenology of lake phytoplankton.

Ecology. 2013 Oct;94(10):2188-94

Authors: Walters AW, González Sagrario Mde L, Schindler DE

Abstract
Global change is leading to shifts in the seasonal timing of growth and maturation for primary producers. Remote sensing is increasingly used to measure the timing of primary production in both aquatic and terrestrial ecosystems, but there is often a poor correlation between these results and direct observations of life-history responses of individual species. One explanation may be that, in addition to phenological shifts, global change is also causing shifts in community composition among species with different seasonal timing of growth and maturation. We quantified how shifts in species phenology and in community composition translated into phenological change in a diverse phytoplankton community from 1962 to 2000. During this time, the aggregate community spring-summer phytoplankton peak has shifted 63 days earlier. The mean taxon shift was only 3 days earlier, and shifts in taxa phenology explained only 40% of the observed community phenological shift. The remaining community shift was attributed to dominant early-season taxa increasing in abundance while a dominant late-season taxon decreased in abundance. In diverse producer communities experiencing multiple stressors, changes in species composition must be considered to fully understand and predict shifts in the seasonal timing of primary production.

PMID: 24358705 [PubMed – in process]

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Proposed changes to the nomenclature of Ichthyophonus sp. life stages and structures.

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Proposed changes to the nomenclature of Ichthyophonus sp. life stages and structures.

J Parasitol. 2013 Oct;99(5):906-9

Authors: Kocan RM

Abstract
Much of the terminology describing Ichthyophonus sp. life stages and structures can be traced to the mistaken classification of this organism as a fungus. This misidentification led early investigators to use mycological terms for the structures they observed; while some terminology is not so easily explained, it appears to have been co-opted from the fields of botany and bacteriology. The purpose of this exercise is to attempt to standardize the terminology associated with Ichthyophonus and to bring it into agreement with terminology currently used to define similar life stages of other protists. The proposed changes are (1) spore/macrospore/mother spore to “schizont,” (2) microspore/endospore to “merozoite,” and (3) pseudohyphae to “hyphae” or “germ tube.”

PMID: 23617800 [PubMed – in process]

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Isotopic evidence and consequences of the role of microbes in macroalgae detritus-based food webs

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Isotopic evidence and consequences of the role of microbes in macroalgae detritus-based food webs


Elizabeth A. Sosik, Charles A. Simenstad
School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195, USA

Vol. 494: 107–119, 2013
doi: 10.3354/meps10544

ABSTRACT
Deep subtidal coastal food webs are increasingly a focus among coastal researchers, largely due to the reliance of these systems on subsidies of organic detritus donated from allochthonous sources. To better understand the dynamics of these food webs, researchers have frequently employed multiple stable isotope (MSI; δ13C, δ15N, δ34S) analysis to gain insights into the relative importance and origins of various sources of detritus. However, the role of microbial decomposition in these detritus-based food webs has been poorly quantified and frequently overlooked in MSI food web mixing models. In this study, we explicitly examined the ecological and MSI methodological effects of microbial decomposition of algal detritus. We found a relationship
between δ15N enrichment and microbial abundance on decomposing kelp blades, and evidence that this pattern is influenced by the underlying biochemistry of the kelp. C:N ratios supported the hypothesis that microbial biofilms utilize nitrogen from kelp detritus, rather than augment the detrital nitrogen content. The results also showed that microbial effects can introduce a nonnegligible amount of error to MSI mixing models if left unquantified.

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.

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Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.

PeerJ. 2013;1:e215

Authors: Gavery MR, Roberts SB

Abstract
Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.

PMID: 24282674 [PubMed – as supplied by publisher]

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Diel horizontal migration in streams: juvenile fish exploit spatial heterogeneity in thermal and trophic resources.

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Diel horizontal migration in streams: juvenile fish exploit spatial heterogeneity in thermal and trophic resources.

Ecology. 2013 Sep;94(9):2066-75

Authors: Armstrong JB, Schindler DE, Ruff CP, Brooks GT, Bentley KE, Torgersen CE

Abstract
Vertical heterogeneity in the physical characteristics of lakes and oceans is ecologically salient and exploited by a wide range of taxa through diel vertical migration to enhance their growth and survival. Whether analogous behaviors exploit horizontal habitat heterogeneity in streams is largely unknown. We investigated fish movement behavior at daily timescales to explore how individuals integrated across spatial variation in food abundance and water temperature. Juvenile coho salmon made feeding forays into cold habitats with abundant food, and then moved long distances (350-1300 m) to warmer habitats that accelerated their metabolism and increased their assimilative capacity. This behavioral thermoregulation enabled fish to mitigate trade-offs between trophic and thermal resources by exploiting thermal heterogeneity. Fish that exploited thermal heterogeneity grew at substantially faster rates than did individuals that assumed other behaviors. Our results provide empirical support for the importance of thermal diversity in lotic systems, and emphasize the importance of considering interactions between animal behavior and habitat heterogeneity when managing and restoring ecosystems.

PMID: 24279277 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/24279277?dopt=Abstract