Semi-analytic approximations for production of atmospheric muons and neutrinos

Simple approximations for fluxes of atmospheric muons and muon neutrinos are developed which display explicitly how the fluxes depend on primary cosmic ray energy and on features of pion production. For energies of approximately 10 GeV and above the results are sufficiently accurate to calculate response functions and to use for estimates of systematic uncertainties.Comment: 15 pages with 8 figure

Evaluating the Potential Efficacy of Invasive Lionfish (Pterois volitans) Removals

The lionfish, Pterois volitans (Linnaeus) and Pterois miles (Bennett), invasion of the Western Atlantic Ocean, Caribbean Sea and Gulf of Mexico has the potential to alter aquatic communities and represents a legitimate ecological concern. Several local removal programs have been initiated to control this invasion, but it is not known whether removal efforts can substantially reduce lionfish numbers to ameliorate these concerns. We used an age-structured population model to evaluate the potential efficacy of lionfish removal programs and identified critical data gaps for future studies. We used high and low estimates for uncertain parameters including: length at 50% vulnerability to harvest (Lvul), instantaneous natural mortality (M), and the Goodyear compensation ratio (CR). The model predicted an annual exploitation rate between 35 and 65% would be required to cause recruitment overfishing on lionfish populations for our baseline parameter estimates for M and CR (0.5 and 15). Lionfish quickly recovered from high removal rates, reaching 90% of unfished biomass six years after a 50-year simulated removal program. Quantifying lionfish natural mortality and the size-selective vulnerability to harvest are the most important knowledge gaps for future research. We suggest complete eradication of lionfish through fishing is unlikely, and substantial reduction of adult abundance will require a long-term commitment and may be feasible only in small, localized areas where annual exploitation can be intense over multiple consecutive years

Abundance and Sizes of Bay Scallops in Heterogeneous Habitats Along the Gulf Coast of Florida

Southern bay scallops (Argopecten irradians concentricus) form the basis of a recreational fishery along Florida\u27s Gulf Coast. Recent declines in scallop abundances have led to significant harvest restrictions. As a way to gain insight into influences on scallop abundances and size, surveys of bay scallops and coastal habitats were conducted in two relatively undisturbed, shallow estuaries along the north-central Gulf Coast of Florida. Scallop abundances did not vary significantly between years or between locations kilometers apart. Shell heights did vary significantly between years at locations kilometers apart; however, these differences were not consistently related to differences in chlorophyll concentrations in the water column or distributions of benthic habitat classes. At the 100-m scale within locations, scallops were not proportionally distributed across the major habitat classes (i.e., Syringodium filiforme, Thalassia testudinum, mixed seagrass assemblage, other seagrasses, and areas of no/low seagrass cover). In general, proportionately more scallops were observed in association with S. filiforme, T. testudinum, and mixed seagrass habitats. Bay scallops collected from S. filiforme and areas of no/low grass cover were consistently 1-3 mm larger than those collected from T. testudinum and mixed seagrass assemblages. These results suggest the importance of S. filiforme and T. testudinum as habitats for bay scallops. The results also point to the need for further investigation into possible functional differences among seagrass species that may influence the ecology of bay scallops at a small spatial scale and the need for closer examination of scallop movement that may allow for active habitat selection. The work presented here, plus further efforts to elucidate the drivers of small-scale differences in scallop abundances and sizes, will benefit managers who seek to enhance scallop fisheries or protect and restore coastal habitats

Variation in Seagrass-Associated Macroinvertebrate Communities Along the Gulf Coast of Peninsular Florida: An Exploration of Patterns and Ecological Consequences

Seagrasses form vast meadows of structurally complex habitat that support faunal communities with greater numbers of species and individuals than nearby unstructured habitats. The Gulf coast of peninsular Florida represents a natural laboratory ideally suited to the study of processes that shape seagrass-associated invertebrate and fish communities within meadows of a single species of seagrass, Thalassia testudinum. This suitability arises from a pronounced structural and chemical gradient that exists over ecologically relevant spatial and temporal scales, as revealed by extensive monitoring of water quality and seagrass. We hypothesized that seagrass-associated invertebrate communities would vary across five estuarine systems spread along a spatial gradient in phosphorus concentration, an important driver of seagrass and phytoplankton growth in this region. The quantitative results based on data acquired at 25 stations (75 samples, 52,086 specimens, and 161 taxa) indicated that each of the five estuarine systems were distinct with regard to species composition and differences among systems were driven by abundant or relatively common species. In addition, we found evidence to indicate food webs in seagrass meadows along this gradient may differ, especially in the relative dominance of algal grazers and predatory invertebrates. These changes in species composition and trophic roles could be driven by phosphorus directly, through increases in rates of primary production with higher concentrations of phosphorus, or indirectly, through nutrient-mediated changes in the physical structure of the seagrass canopy. Our results suggest that differences in the habitat created by T. testudinum under differing phosphorus supplies lead to ecologically significant shifts in macroinvertebrate communities

Cuban Connection: Regional Role for Florida's Manatees

The status of the West Indian manatee [Trichechus manatus (Linnaeus, 1758)] remains enigmatic. The International Union for Conservation of Nature classifies the species as “Vulnerable” and the two subspecies [T. m. manatus (Linnaeus, 1758) and T. m. latirostris (Harlan, 1824)] as “Endangered.” The U.S. Fish and Wildlife Service now classifies West Indian manatees as “Threatened” primarily due to increased numbers of T. m. latirostris. Fully resolving the status of the species will require a better understanding of its population biology throughout the broader Caribbean region, especially the form and strength of genetic and demographic connections. Genetic studies indicate limited interbreeding among recent generations of groups of manatees separated by unsuitable coastal habitat or large expanses of open water, such as the Florida Straits. However, documentation of two, independent immigrations from Florida to Cuba within one generation raises the possibility of important demographic connections, especially if the number of manatees in Cuba is small. In addition, these events may foreshadow a change in the role that Florida's manatees play in effective conservation of T. manatus throughout its Caribbean range, with the potential for further connections as numbers of manatees in Florida increase and the availability of suitable habitat and food decreases

Causes of Mortality for Endangered Antillean Manatees in Cuba

The Antillean manatee is categorized as endangered by the International Union for the Conservation of Nature primarily due to its low abundance. Further declines in abundance are expected due to a group of human related threats that include illegal hunting, fatal interactions with fishing gear, increasing watercraft traffic, and pollution. The nature of current threats is not well described for every critical population of manatees. In particular, threats to manatees have not been documented or evaluated in a systematic manner in coastal waters surrounding Cuba, which is a major reason why plans specifically addressing conservation of manatees in Cuba have not been implemented. To address this lack of information, we assessed patterns in various threats by reviewing reports of stranded (alive or dead) and captured manatees, with some reports being historical and others consistently available since 2001. For 94% of the contemporary cases, carcasses of dead animals were reported; the remainder (6%) involved live manatees and subsequent efforts to rescue and rehabilitate them. Documented causes of mortality included poaching (38%), entanglement in fishing gear (10%), deaths of dependent calves (2.5%), and boat collisions (2.5%). The cause of death for the remaining 47% of reports could not be determined. Mortalities were highest in areas with intensive commercial fishing effort, and mortalities in marine protected areas indicated a need for improved management. These initial findings provide the first estimates of the magnitude of mortality of manatees in Cuba and yield valuable insights into the causes of deaths. The existence of intense and poorly regulated fishing in certain areas, including protected areas, represents a potentially significant threat to manatees. The effects and management of this activity, especially in habitats that are critical for manatees, merit further attention

Sussing merger trees: the Merger Trees Comparison Project

Merger trees follow the growth and merger of dark-matter haloes over cosmic history. As well as giving important insights into the growth of cosmic structure in their own right, they provide an essential backbone to semi-analytic models of galaxy formation. This paper is the first in a series to arise from the Sussing Merger Trees Workshop in which 10 different tree-building algorithms were applied to the same set of halo catalogues and their results compared. Although many of these codes were similar in nature, all algorithms produced distinct results. Our main conclusions are that a useful merger-tree code should possess the following features: (i) the use of particle IDs to match haloes between snapshots; (ii) the ability to skip at least one, and preferably more, snapshots in order to recover subhaloes that are temporarily lost during merging; (iii) the ability to cope with (and ideally smooth out) large, temporary fluctuations in halo mass. Finally, to enable different groups to communicate effectively, we defined a common terminology that we used when discussing merger trees and we encourage others to adopt the same language. We also specified a minimal output format to record the results

Sussing merger trees: stability and convergence

Merger trees are routinely used to follow the growth and merging history of dark matter haloes and subhaloes in simulations of cosmic structure formation. Srisawat et al. compared a wide range of merger-tree-building codes. Here we test the influence of output strategies and mass resolution on tree-building. We find that, somewhat surprisingly, building the tree from more snapshots does not generally produce more complete trees; instead, it tends to shorten them. Significant improvements are seen for patching schemes that attempt to bridge over occasional dropouts in the underlying halo catalogues or schemes that combine the halo-finding and tree-building steps seamlessly. The adopted output strategy does not affect the average number of branches (bushiness) of the resultant merger trees. However, mass resolution has an influence on both main branch length and the bushiness. As the resolution increases, a halo with the same mass can be traced back further in time and will encounter more small progenitors during its evolutionary history. Given these results, we recommend that, for simulations intended as precursors for galaxy formation models where of the order of 100 or more snapshots are analysed, the tree-building routine should be integrated with the halo finder, or at the very least be able to patch over multiple adjacent snapshots

Coping with the Lionfish Invasion: can targeted removals yield beneficial effects?

Invasive species generate significant environmental and economic costs, with maintenance management constituting a major expenditure. Such costs are generated by invasive Indo-Pacific lionfish (Pterois spp.) that further threaten already stressed coral reefs in the western Atlantic Ocean and Caribbean Sea. This brief review documents rapid range expansion and potential impacts of lionfish. In addition, preliminary experimental data from targeted removals contribute to debates about maintenance management. Removals at sites off Little Cayman Island shifted the size frequency distribution of remaining lionfish toward smaller individuals whose stomachs contained less prey and fewer fish. Fewer lionfish and decreased predation on threatened grouper, herbivores and other economically and ecologically important fishes represent key steps toward protecting reefs. However, complete evaluation of success requires long-term data detailing immigration and recruitment by lionfish, compensatory growth and reproduction of lionfish, reduced direct effects on prey assemblages, and reduced indirect effects mediated by competition for food. Preventing introductions is the best way to avoid impacts from invasive species and early detection linked to rapid response ranks second. Nevertheless, results from this case study suggest that targeted removals represent a viable option for shifting direct impacts of invasive lionfish away from highly vulnerable components of ecosystems

Circular DNA Intermediate in the Duplication of Nile Tilapia vasa Genes

vasa is a highly conserved RNA helicase involved in animal germ cell development. Among vertebrate species, it is typically present as a single copy per genome. Here we report the isolation and sequencing of BAC clones for Nile tilapia vasa genes. Contrary to a previous report that Nile tilapia have a single copy of the vasa gene, we find evidence for at least three vasa gene loci. The vasa gene locus was duplicated from the original site and integrated into two distant novel sites. For one of these insertions we find evidence that the duplication was mediated by a circular DNA intermediate. This mechanism of gene duplication may explain the origin of isolated gene duplicates during the evolution of fish genomes. These data provide a foundation for studying the role of multiple vasa genes in the development of tilapia gonads, and will contribute to investigations of the molecular mechanisms of sex determination and evolution in cichlid fishes