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

Simulating nutrient release from parental carcasses increases the growth, biomass and genetic diversity of juvenile Atlantic salmon

The net transport of nutrients by migratory fish from oceans to inland spawning areas has decreased due to population declines and migration barriers. Restoration of nutrients to increasingly oligotrophic upland streams (that were historically salmon spawning areas) have shown short‐term benefits for juvenile salmon, but the longer term consequences are little known. Here we simulated the deposition of a small number of adult Atlantic salmon Salmo salar carcasses at the end of the spawning period in five Scottish upland streams (‘high parental nutrient’ treatment), while leaving five reference streams without carcasses (‘low parental nutrient’ treatment). All streams received exactly the same number of salmon eggs (n = 3,000) drawn in equal number from the same 30 wild‐origin families, thereby controlling for initial egg density and genetic composition. We then monitored the resulting juvenile salmon and their macroinvertebrate prey, repeating the carcass addition treatment in the next spawning season. Macroinvertebrate biomass and abundance were five times higher in the high parental nutrient streams, even 1 year after the carcass addition, and led to faster growth of juvenile salmon over the next 2 years (but with no change in population density). This faster growth led to more fish exceeding the size threshold that would trigger emigration to sea at 2 rather than 3 years of age. There was also higher genetic diversity among surviving salmon in high parental nutrient streams; genotyping showed that these effects were not due to immigration but to differential survival. Synthesis and applications. This 2‐year field experiment shows that adding nutrients that simulate the presence of small numbers of adult salmon carcasses can have long‐term effects on the growth rate of juvenile salmon, likely increasing the number that will migrate to sea early and also increasing their genetic diversity. However, the feasibility of adding nutrients to spawning streams as a management tool to boost salmon populations will depend on whether the benefits at this stage are maintained over the entire life cycle

Simulating nutrient release from parental carcasses increases the growth, biomass and genetic diversity of juvenile Atlantic salmon

The net transport of nutrients by migratory fish from oceans to inland spawning areas has decreased due to population declines and migration barriers. Restoration of nutrients to increasingly oligotrophic upland streams (that were historically salmon spawning areas) have shown short‐term benefits for juvenile salmon, but the longer term consequences are little known. Here we simulated the deposition of a small number of adult Atlantic salmon Salmo salar carcasses at the end of the spawning period in five Scottish upland streams (‘high parental nutrient’ treatment), while leaving five reference streams without carcasses (‘low parental nutrient’ treatment). All streams received exactly the same number of salmon eggs (n = 3,000) drawn in equal number from the same 30 wild‐origin families, thereby controlling for initial egg density and genetic composition. We then monitored the resulting juvenile salmon and their macroinvertebrate prey, repeating the carcass addition treatment in the next spawning season. Macroinvertebrate biomass and abundance were five times higher in the high parental nutrient streams, even 1 year after the carcass addition, and led to faster growth of juvenile salmon over the next 2 years (but with no change in population density). This faster growth led to more fish exceeding the size threshold that would trigger emigration to sea at 2 rather than 3 years of age. There was also higher genetic diversity among surviving salmon in high parental nutrient streams; genotyping showed that these effects were not due to immigration but to differential survival. Synthesis and applications. This 2‐year field experiment shows that adding nutrients that simulate the presence of small numbers of adult salmon carcasses can have long‐term effects on the growth rate of juvenile salmon, likely increasing the number that will migrate to sea early and also increasing their genetic diversity. However, the feasibility of adding nutrients to spawning streams as a management tool to boost salmon populations will depend on whether the benefits at this stage are maintained over the entire life cycle

A ‘higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs

Protection of chromosome ends from DNA repair and degradation activities is mediated by specialized protein complexes bound to telomere repeats. Recently, it has become apparent that epigenetic regulation of the telomric chromatin template critically impacts on telomere function and telomere-length homeostasis from yeast to man. Across all species, telomeric repeats as well as the adjacent subtelomeric regions carry features of repressive chromatin. Disruption of this silent chromatin environment results in loss of telomere-length control and increased telomere recombination. In turn, progressive telomere loss reduces chromatin compaction at telomeric and subtelomeric domains. The recent discoveries of telomere chromatin regulation during early mammalian development, as well as during nuclear reprogramming, further highlights a central role of telomere chromatin changes in ontogenesis. In addition, telomeres were recently shown to generate long, non-coding RNAs that remain associated to telomeric chromatin and will provide new insights into the regulation of telomere length and telomere chromatin. In this review, we will discuss the epigenetic regulation of telomeres across species, with special emphasis on mammalian telomeres. We will also discuss the links between epigenetic alterations at mammalian telomeres and telomere-associated diseases

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Population Response to Habitat Fragmentation in a Stream-Dwelling Brook Trout Population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (∼45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tributary populations caused rapid (2–6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7–46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can ‘rescue’ isolated populations, particularly in one-dimensional stream networks where both natural and anthropogenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation

Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure

Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers) positions nucleosomes adjacent to the origin to promote replication origin function