Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.

Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change

Modelling approaches for relating effects of change in river flow to populations of Atlantic salmon and brown trout

Modelling approaches for relating discharge to the biology of Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., growing in rivers are reviewed. Process-based and empirical models are set within a common framework of input of water flow and output of characteristics of fish, such as growth and survival, which relate directly to population dynamics. A continuum is envisaged incorporating various contributions of process and empirical structure as practical and appropriate to specific goals. This framework is compared with, and shown to differ from, approaches whose output is in the form of quantity and form of habitat (or usable area) based on its frequency of use by fish, which then is assumed to have some relationship with fish performance. A simple conceptual modeling approach is also developed to relate water flow to fish population characteristics to assess the likelihood of simple relationships between flow and usable area thresholds. Basic predictions of the model are tested against empirical data from a long-term individual-based study of juvenile S. salar and resident brook trout, Salvelinus fontinalis (Mitchell), in West Brook, Massachusetts. For this system, growth rates of both species increased linearly with flow during spring, summer and autumn months and bore no relation to Q95 or wetted-width discontinuities. Winter is identified as a season during which water might be abstracted most safely, but cautiously given sparse knowledge of wild salmonid fish at this time of year. These results, together with the fundamental conceptual problems inherent in usable area-based approaches, suggest that models that relate directly to fish performance outcomes may be more robust as a basis for flow prescriptions. However, this utility will depend strongly on our ability to generalize from a limited set of empirical studies and to use the results of these studies of management actions to inform and improve future models

Towards a life-history-based management framework for the effects of flow on juvenile salmonids in streams and rivers

Salmonid fishes have complex life cycles involving major changes in habitat requirements at different stages in their life history. Effects of changes in flow and flow regime on salmonids are therefore highly stage specific. Successful management requires consideration of stage-specific influences and integration of these effects over the entire life history to predict ultimate impacts on abundance and population viability. The state of science regarding stage-specific influences of flow regime on juvenile salmonids and their habitats, referring specifically to fundamental attributes of natural regimes and to characteristic alterations of these regimes associated with water management, is reviewed. It appears that a key consideration in integrating the stage-specific impacts of flow is the extent to which flow-related losses or gains early in ontogeny can be compensated by increased growth or survival later in juvenile life history. Further, fundamental interactions between flow and water temperature must be incorporated into the robust models ultimately required for science-based management. In the absence of such models and data, the current state of science may be sufficient to target specific aspects of flow regimes that are critical to multiple life-history stages, which can then serve as a basis for interim flow prescriptions and subsequent adaptive management

Modelling approaches for relating effects of change in river flow to populations of Atlantic salmon and brown trout

Modelling approaches for relating discharge to the biology of Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., growing in rivers are reviewed. Process-based and empirical models are set within a common framework of input of water flow and output of characteristics of fish, such as growth and survival, which relate directly to population dynamics. A continuum is envisaged incorporating various contributions of process and empirical structure as practical and appropriate to specific goals. This framework is compared with, and shown to differ from, approaches whose output is in the form of quantity and form of habitat (or usable area) based on its frequency of use by fish, which then is assumed to have some relationship with fish performance. A simple conceptual modeling approach is also developed to relate water flow to fish population characteristics to assess the likelihood of simple relationships between flow and usable area thresholds. Basic predictions of the model are tested against empirical data from a long-term individual-based study of juvenile S. salar and resident brook trout, Salvelinus fontinalis (Mitchell), in West Brook, Massachusetts. For this system, growth rates of both species increased linearly with flow during spring, summer and autumn months and bore no relation to Q95 or wetted-width discontinuities. Winter is identified as a season during which water might be abstracted most safely, but cautiously given sparse knowledge of wild salmonid fish at this time of year. These results, together with the fundamental conceptual problems inherent in usable area-based approaches, suggest that models that relate directly to fish performance outcomes may be more robust as a basis for flow prescriptions. However, this utility will depend strongly on our ability to generalize from a limited set of empirical studies and to use the results of these studies of management actions to inform and improve future models

Habitat-Mediated Foraging Limitations Drive Survival Bottlenecks for Juvenile Salmon

Realistic population models and effective conservation strategies require a thorough understanding of mechanisms driving stage-specific mortality. Mortality bottlenecks for many species occur in the juvenile stage and are thought to result from limitation on food or foraging habitat during a critical period for growth and survival. Without a way to account for maternal effects or to measure integrated consumption rates in the field, it has been virtually impossible to test these relationships directly. Hence uncertainties about mechanisms underlying such bottlenecks remain. In this study we randomize maternal effects across sites and apply a new method for measuring consumption integrated over weeks to months to test the hypothesis that food limitation drives early-season juvenile mortality bottlenecks in Atlantic salmon (Salmo salar). Using natural signatures of geologically derived cesium (133Cs), we estimated consumption rates of \u3e400 fry stocked into six streams. Two to four weeks after stocking, consumption was extremely low across sites (0.005 g x g(-1) x d(-1)) and was predicted to be below maintenance rations (i.e., yielding negative energy balances) for the majority of individuals from five of six sites. However, consumption during this time was positively correlated with growth rates and survival (measured at the end of the growing season). In contrast, consumption rates increased in mid- (0.030 g x g(-1) x d(-1)) and late (0.035 g x g(-1) x d(-1)) seasons, but juvenile survival and consumption were not correlated, and correlations between growth and consumption were weak. These findings are consistent with predictions of a habitat-based bioenergetic model constructed using the actual stream positions of the individual fish in the present study, which indicates that habitat-based models capture important environmental determinants of juvenile growth and survival. Hence, by combining approaches, reducing maternal effects and controlling initial conditions, we offer a general framework for linking foraging with juvenile survival and present the first direct consumption-based evidence for the early season bottleneck hypothesis

Session A7- Research

Improperly designed road crossings act as barriers to movement of aquatic organisms and can depress local abundance and reduce local species richness, with potential impacts on population viability and biotic diversity. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population and community-level effects can be difficult to detect. In this study we tested the effects of barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, USA. Fishes were sampled using simple standard techniques above- and below- road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species, and that these variable effects on abundance would translate into lower species richness. Supporting these predictions, stream sections located above predicted impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In tum, these results suggest that when measured at appropriate scales (multiple streams within watersheds), with simple protocols amenable to use by management agencies, differences in local abundance and species richness may serve as indicators of the extent to which road crossings are barriers to fish movement, and help determine whether road crossing improvements have restored connectivity to stream fish populations and communities

Stage-Specific and Interactive Effects of Sedimentation and Trout on a Headwater Stream Salamander

In species with complex life cycles, stage-specific effects of environmental conditions combine with factors regulating stage-specific recruitment to determine population-level response to habitat disturbance. The abundance of the stream salamander Gyrinophilus porphyriticus(Plethodontidae) is negatively related to both logging-associated sedimentation and brook trout (Salvelinus fontinalis) in headwater streams throughout New Hampshire, USA. To understand the mechanisms underlying these patterns, we investigated stage-specific and interactive effects of sedimentation and brook trout on G. porphyriticus. We conducted quantitative surveys of salamanders, brook trout, and substrate embeddedness in 15 first-order streams and used a controlled experiment to test the direct and interactive effects of these factors on larval growth and survival. G. porphyriticus larvae and adults had opposite patterns of response to sediment and brook trout. Multiple regression analysis of our survey data indicated that abundance of larvae was negatively related to brook trout abundance, but unrelated to substrate embeddedness. In contrast, abundance of adults was primarily related to substrate embeddedness. Consistent with the field pattern of larval abundance, brook trout had a negative effect on growth and survival of larvae in the experiment. However, there was no effect of sediment and no interaction between brook trout and sediment. Larval and adult abundances were not significantly correlated in the study streams, indicative of the independent effects of sedimentation and brook trout on G. porphyriticus populations. These results suggest that adult resistance to fish may facilitate G. porphyriticus coexistence with brook trout, and that larval resistance to sedimentation can buffer populations from extinction in fishless streams impacted by logging. In streams with brook trout, where larval abundances are low, reductions in adult abundance caused by logging impacts may pose a risk to species persistence. Our findings underscore the value of information on species life history, demography, and community ecology in assessing sensitivity to anthropogenic perturbation

Do Low-Mercury Terrestrial Resources Subsidize Low-Mercury Growth of Stream Fish? Differences between Species along a Productivity Gradient

Low productivity in aquatic ecosystems is associated with reduced individual growth of fish and increased concentrations of methylmercury (MeHg) in fish and their prey. However, many stream-dwelling fish species can use terrestrially-derived food resources, potentially subsidizing growth at low-productivity sites, and, because terrestrial resources have lower MeHg concentrations than aquatic resources, preventing an increase in diet-borne MeHg accumulation. We used a large-scale field study to evaluate relationships among terrestrial subsidy use, growth, and MeHg concentrations in two stream-dwelling fish species across an in-stream productivity gradient. We sampled young-of-the-year brook trout ( Salvelinus fontinalis ) and Atlantic salmon ( Salmo salar ), potential competitors with similar foraging habits, from 20 study sites in streams in New Hampshire and Massachusetts that encompassed a wide range of aquatic prey biomass. Stable isotope analysis showed that brook trout used more terrestrial resources than Atlantic salmon. Over their first growing season, Atlantic salmon tended to grow larger than brook trout at sites with high aquatic prey biomass, but brook grew two-fold larger than Atlantic salmon at sites with low aquatic prey biomass. The MeHg concentrations of brook trout and Atlantic salmon were similar at sites with high aquatic prey biomass and the MeHg concentrations of both species increased at sites with low prey biomass and high MeHg in aquatic prey. However, brook trout had three-fold lower MeHg concentrations than Atlantic salmon at low- productivity, high-MeHg sites. These results suggest that differential use of terrestrial resource subsidies reversed the growth asymmetry between potential competitors across a productivity gradient and, for one species, moderated the effect of low in-stream productivity on MeHg accumulation

A comparative analysis of DNA barcode microarray feature size

<p>Abstract</p> <p>Background</p> <p>Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity.</p> <p>Results</p> <p>We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO) collection used for screens of pooled yeast (<it>Saccharomyces cerevisiae</it>) deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be <it>ALG7</it>.</p> <p>Conclusion</p> <p>We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.</p