Using molecular tools to differentiate closely related blackfly species of the genus Simulium
J. C. Day
- Biodiversity data are the foundation for conservation and managemet and taxonomy provides the reference system, skills and tools used to identify organisms. Species level data such as species richness, composition and diversity are common metrics. However, species level identification of organisms tends to be neglected within ecological work, especially within monitoring programmes, but also in conservation biology (Giangrande, 2003). This is because collection of species level data is time consuming, with identification of species-specific characteristics traditionally involving lengthy examination of samples using microscopy. In addition it is costly and species level data is almost impossible to collect if the taxa involved are species rich and difficult to identify (Báldi 1999). Other reasons why species level identification is neglected include the fact that sample collection can damage organisms, so diagnostic morphological features are lost, or that individuals may be in a life history stage or of a sex that does not have diagnostic morphological characteristics. Furthermore, the numbers of available expert taxonomists needed for species identification are in decline and have been for several decades. Species identification using molecular taxonomy where DNA is used as a marker is championed as a tool for resolving a range of morphological problems, such as the association of all life history stages, correlating male and female specimens to the same species and identifying partial specimens. Traditional taxonomy is built around morphological variations between species, with systematic inferences based upon shared physical characters. In molecular taxonomy on the other hand, proteins and genes are used to determine evolutionary relationships. ’DNA barcoding’ aims to provide an efficient method for species-level identification and it is thought that it will provide a powerful tool for taxonomic and biodiversity research (Hajibabaei et al. 2007). Cited strengths of a molecular based approach to species identification include the potential universality and objective nature of DNA data as taxonomic information, the usefulness of molecular data in animal groups characterized by morphological cryptic characters and the use of DNA sequence information to determine otherwise ‘unidentifiable’ biological material (such as incomplete specimens or immature specimens). Its aim is to increase the speed, precision and efficiency of field studies involving diverse and difficult to identify taxa and it has the potential to be automated to provide a rapid and consistently accurate supplementary identification system to traditional taxonomy. This project was a proof-of-concept study that investigated the feasibility of using DNA barcodes to differentiate closely related blackfly species of the genus Simulium. The longer term objective would be to apply such molecular approaches to organisms used in water quality monitoring and to biodiversity studies to provide a quick, robust but practical and cost effective tool for species identification. Great Britain is currently home to 33 morphospecies of blackfly many of which are morphologically close to other species and have been the cause of much systematic revision. In addition to evaluating the use of DNA barcodes in species identification, a non-destructive DNA extraction method was developed to preserve voucher pecimens that will allow a complete morphological classification to be carried after DNA extraction. Using molecular tools to differentiate closely related blackfly species of the genus Simulium v Finding an effective DNA barcode for an individual species involves accurate taxonomic identification and the retention of voucher specimens for future morphological studies. A rapid non-destructive method for DNA extraction from small insects was developed where no clean-up step was required prior to amplification and it was possible to extract DNA of sufficient quality in minutes retaining diagnostic morphological characteristics. For any molecular tool used for species discrimination, an important consideration is defining the specific genetic loci (e.g. the position of genes on a chromosome) to be monitored. All blackfly species in this study were successfully amplified with the standard barcoding coxI gene primer pair LCO1490 5'-GGT CAA CAA ATC ATA AAG ATA TTG G-3' and HCO2198 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3' (Folmer et al. 1994) and we did not need to optimise or redesign the primer sequence.
A guide to nestling development and aging in altricial passerines
Stephanie L. Jones
Geoffrey R. Geupel
Paula J. Gouse
- Nestling growth and development studies have been a topic of interest for a greater part of the last century (Sutton 1935, Walkinshaw 1948) and continue to be of interest today. This is not surprising since studies on nestling growth can provide a wealth of biological information that has larger implications for avian management and conservation. Despite this history of studying nestling development, basic information is still limited or absent for many species. Many questions remain unanswered, and contradictory conclusions are often found in the literature (Starck and Ricklefs 1998a). Therefore, much information on aging and development can still be gained from studying the development patterns of similar species and from comparative studies, across avian orders (Minea et al. 1982, Saunders and Hansen 1989, Carsson and Hörnfeldt 1993). Additionally, nestling growth studies can yield insight into the effects of different nesting strategies on productivity (O’Connor 1978), as well as the impacts of parental effort and environmental variables on fitness (Ross 1980, Ricklefs and Peters 1981, Magrath 1991). Since low reproductive success may play a significant role in the declines of many North American passerines (Sherry and Holmes 1992, Ballard et al. 2003), a better understanding of the factors that influence reproductive success is a vital component of avian conservation (Martin 1992). Data on nestling aging can be used to improve nest survival estimates (Dinsmore 2002, Nur et al. 2004), providing information that can be used to more precisely age nests (Pinkowski 1975, Podlesack and Blem 2002), (Jones and Geupel 2007). Indeed, the relatively short time period young spend developing in the nest is a critical part of a bird’s life cycle and a nestling’s developmental path can affect its survival to independence, its survival as an adult, and its future reproductive success.
UK Seabirds in 2005 : results from the UK Seabird Monitoring Programme
- Seabirds in the UK were generally more productive in 2005 than in 2004, when productivity for many species reached an all-time low. A presumed scarcity of sandeels in 2004, especially in the North Sea, led to widespread starvation of chicks in the Northern Isles and in many places along the east coast of Britain (there is also recent evidence that prey fish were of unusually low energy content in 2004 around SE Scotland). The likely knock-on effect for 2005 was that there were few larger sandeels present (those that hatched in 2004) and it is thought that feeding on these fish allow adults to attain breeding condition in spring. This food scarcity and a cold spring led to what was among the latest breeding seasons on record. However, a late appearance of young sandeels allowed some chicks to fledge, and alternative prey species (such as sprat and small haddock) were taken also. However, it is thought that some chicks starved in this late season, as sandeels become unavailable in late summer, when they settle on the seabed. Unusually, 2005 was a very poor breeding season for many species in NW Scotland, which was spared the food shortages of 2004 and previous years; preferred prey during chick rearing were scarce in this region in 2005.
Black Box Cryptanalysis of Hash Networks based on Multipermutations
Claus Peter Schnorr
- Black box cryptanalysis applies to hash algorithms consisting of many small boxes, connected by a known graph structure, so that the boxes can be evaluated forward and backwards by given oracles. We study attacks that work for any choice of the black boxes, i.e. we scrutinize the given graph structure. For example we analyze the graph of the fast Fourier transform (FFT). We present optimal black box inversions of FFT-compression functions and black box constructions of collisions. This determines the minimal depth of FFT-compression networks for collision-resistant hashing. We propose the concept of multipermutation, which is a pair of orthogonal latin squares, as a new cryptographic primitive that generalizes the boxes of the FFT. Our examples of multipermutations are based on the operations circular rotation, bitwise xor, addition and multiplication.
G-CSC Report 2010
- The present report gives a short summary of the research of the Goethe Center for Scientific Computing (G-CSC) of the Goethe University Frankfurt. G-CSC aims at developing and applying methods and tools for modelling and numerical simulation of problems from empirical science and technology. In particular, fast solvers for partial differential equations (i.e. pde) such as robust, parallel, and adaptive multigrid methods and numerical methods for stochastic differential equations are developed. These methods are highly adanvced and allow to solve complex problems..
The G-CSC is organised in departments and interdisciplinary research groups. Departments are localised directly at the G-CSC, while the task of interdisciplinary research groups is to bridge disciplines and to bring scientists form different departments together. Currently, G-CSC consists of the department Simulation and Modelling and the interdisciplinary research group Computational Finance.
A comparison of the Bering Sea, Gulf of Alaska, and Aleutian Islands large marine ecosystems through food web modeling / by K. Aydin ... [et al.]
Kerim Yunus Aydin
- Detailed mass balance food web models were constructed to compare ecosystem characteristics for three Alaska regions: the eastern Bering Sea (EBS), the Gulf of Alaska (GOA), and the Aleutian Islands (AI). This paper documents the methods and data used to construct the models and compares ecosystem structure and indicators across models. The common modeling framework, including biomass pool and fishery definitions, resulted in comparable food webs for the three ecosystems which showed that they all have the same apex predator—the Pacific halibut longline fishery. However, despite the similar methods used to construct the models, the data from each system included in the analysis clearly define differences in food web structure which may be important considerations for fishery management in Alaska ecosystems. The results showed that the EBS ecosystem has a much larger benthic influence in its food web than either the GOA or the AI. Conversely, the AI ecosystem has the strongest pelagic influence in its food web relative to the other two systems. The GOA ecosystem appears balanced between benthic and pelagic pathways, but is notable in having a smaller fisheries catch relative to the other two systems, and a high biomass of fish predators above trophic level (TL) 4, arrowtooth flounder and halibut. The patterns visible in aggregated food webs were confirmed in additional more detailed analyses of biomass and consumption in each ecosystem, using both the single species and whole ecosystem indicators developed here.
Algebraic values of Schwarz triangle functions
- We consider Schwarz maps for triangles whose angles are rather general rational multiples of pi. Under which conditions can they have algebraic values at algebraic arguments? The answer is based mainly on considerations of complex multiplication of certain Prym varieties in Jacobians of hypergeometric curves. The paper can serve as an introduction to transcendence techniques for hypergeometric functions, but contains also new results and examples.
Chemical and ecological health of white sucker (Catostomus commersoni) in Rock Creek Park, Washington, D.C., 2003-04 / by Cherie V. Miller ... [et al.] ; prepared in copoeration with the National Park Service
Cherie V. Miller
Holly S. Weyers
Vicki S. Blazer
Mary E. Freeman
- Several classes of chemicals that are known or suspected contaminants were found in bed sediment in Rock Creek, including polyaromatic hydrocarbons (PAHs), phthalate esters, organochlorine pesticides, dioxins and furans, trace metals and metalloids (mercury, arsenic, cadmium, chromium, cobalt, copper, lead, nickel, silver, and zinc), and polychlorinated biphenyls (total PCBs and selected aroclors). Concentrations of many of these chemicals consistently exceeded thresholdor chronic-effects guidelines for the protection of aquatic life and often exceeded probable effects levels (PELs). Exceedance of PELs was dependent on the amount of total organic carbon in the sediments. Concurrent with the collection of sediment-quality data, white sucker (Catostomus commersoni) were evaluated for gross-external and internal-organ anomalies, whole-body burdens of chemical contaminants, and gut contents to determine prey. The histopathology of internal tissues of white sucker was compared to contaminant levels in fish tissue and bed sediment. Gut contents were examined to determine preferential prey and thus potential pathways for the bioaccumulation of chemicals from bed sediments. Male and female fish were tested separately. Lesions and other necroses were observed in all fish collected during both years of sample collection, indicating that fish in Rock Creek have experienced some form of environmental stress. No direct cause and effect was determined for chemical exposure and compromised fish health, but a substantial weight of evidence indicates that white sucker, which are bottom-eeding fish and low-order consumers in Rock Creek, are experiencing some reduction in vitality, possibly due to immunosuppression. Abnormalities observed in gonads of both sexes of white sucker and observations of abnormal behavior during spawning indicated some interruption in reproductive success.
Max Horkheimer's voice goes digital
Economic impact of the spread of alien species in Germany : research report 20186211
- The European Strategy on Invasive Alien Species T-PWS(2002) 8 mandates intensified research by member nations on invasive species. This research will not be restricted solely to the biology and remediation of invasive species, but will also evaluate their adverse health effects and economic impact. Previous studies of these issues have only been carried out in the Unites States of America, or in a limited, regional manner. Consequently, 20 plant and animal species from various problem areas (species which pose a threat to public health; losses to agriculture, fisheries, and forestry; damage to public roads and waterways; costs associated with the protection of native species threatened by non-native species as mandated by Recommendation 77 of the Bern Convention were assessed in Germany nation-wide. The accruing costs were sorted into 3 categories: a) direct economic losses, such as those caused by destructive pest species; b) ecological costs, in the form of extra care and protection of native taxa, biotopes, or ecosystems threatened by invasive species; c) costs of measures to combat invasive species. Because of the nature of available data, as well as the different biology and ecology of the invasive species, each had to be treated individually, and the associated costs vary greatly from species to species. Moreover, not all of the species investigated cause economic losses. Accordingly, a nuanced approach to alien species is essential. Cost assessment of losses deriving from ecological damage was only possible in a few cases. Ongoing, multi-year studies incorporating cost/benefit analysis will be necessary to resolve remaining issues.