Genetic diversity and population structure of the sea lamprey (Petromyzon marinus L.) across its distributional range

Lampreys are a group of ancient vertebrates with 360 million years of existence. Throughout their evolution, they have acquired local adaptations to the colonized habitats, showing high plasticity and adaptive capacities. The sea lamprey (Petromyzon marinus L.) is a parasitic and anadromous species that occurs in both sides of the North Atlantic. The aims of this study were to analyse, using microsatellite markers, the genetic diversity and population structure of sea lamprey throughout its distributional range. Analyses demonstrated consistent signs of high population differentiation between European and North American samples (two-groups structure), most probably due to isolation by distance, but low differentiation among populations from the same coast. The apparent lack of homing in this species is in line with its high evolutive success, as homing may bring adults back to natal habitats that have changed, or that are intermittently unfavourable. Analyses also demonstrated higher levels of genetic diversity in North American samples; DIVERSIDADE GENÉTICA E ESTRUTURA POPULACIONAL DA LAMPREIA-MARINHA (PETROMYZON MARINUS L.) AO LONGO DA SUA ÁREA DE DISTRIBUIÇÃO Resumo: As lampreias são organismos ancestrais com cerca de 360 milhões de anos de existência. No decorrer da longa escala evolutiva têm vindo a adquirir adaptações aos locais que colonizaram, tendo uma forte capacidade evolutiva e adaptativa. A lampreia-marinha (Petromyzon marinus L.) é uma espécie parasita e anádroma que ocorre em ambas as costas do Atlântico Norte. Este estudo teve como principal objetivo estudar a diversidade genética e a estrutura populacional desta espécie ao longo da sua área de distribuição, através do uso de microssatélites. Os resultados demonstraram forte divergência entre populações das costas Este e Oeste do Atlântico Norte, provavelmente devido à elevada distância entre populações, mas pouca diferenciação entre populações da mesma costa. A ausência de homing nesta espécie terá contribuído para o seu sucesso evolutivo, uma vez que o homing pode levar indivíduos a reproduzirem-se em habitats que se tornaram desfavoráveis ou intermitentemente inapropriados. Os resultados demonstraram também uma maior variabilidade genética nas populações americanas.

特大地震激发地球自由振荡的数值模拟研究

Large earthquakes, such as the Chile earthquake in 1960 and the Sumatra-Andaman earthquake on Dec 26, 2004 in Indonesia, have generated the Earth’s free oscillations. The eigenfrequencies of the Earth’s free oscillations are closely related to the Earth’s internal structures. The conventional methods, which mainly focus on calculating the eigenfrequecies by analytical ways, and the analysis on observations can not easily study the whole processes from earthquake occurrence to the Earth’s free oscillation inspired. Therefore, we try to use numerical method incorporated with large-scale parallel computing to study on the Earth’s free oscillations excited by giant earthquakes. We first give a review of researches and developments of the Earth’s free oscillation, and basical theories under spherical coordinate system. We then give a review of the numerical simulation of seismic wave propagation and basical theories of spectral element method to simulate global seismic wave propagation. As a first step to study the Earth’s free oscillations, we use a finite element method to simulate the propagation of elastic waves and the generation of oscillations of the chime bell of Marquis Yi of Zeng, by striking different parts of the bell, which possesses the oval crosssection. The bronze chime bells of Marquis Yi of Zeng are precious cultural relics of China. The bells have a two-tone acoustic characteristic, i.e., striking different parts of the bell generates different tones. By analysis of the vibration in the bell and the spectrum analysis, we further help the understanding of the mechanism of two-tone acoustic characteristics of the chime bell of Marquis Yi of Zeng. The preliminary calculations have clearly shown that two different modes of oscillation can be generated by striking different parts of the bell, and indicate that finite element numerical simulation of the processes of wave propagation and two-tone generation of the chime bell of Marquis Yi of Zeng is feasible. These analyses provide a new quantitative and visual way to explain the mystery of the two-tone acoustic characteristics. The method suggested by this study can be applied to simulate free oscillations excited by great earthquakes with complex Earth structure. Taking into account of such large-scale structure of the Earth, small-scale low-precision numerical simulation can not simply meet the requirement. The increasing capacity in high-performance parallel computing and progress on fully numerical solutions for seismic wave fields in realistic three-dimensional spherical models, Spectral element method and high-performance parallel computing were incorporated to simulate the seismic wave propagation processes in the Earth’s interior, without the effects of the Earth’s gravitational potential. The numerical simulation shows that, the results of the toroidal modes of our calculation agree well with the theoretical values, although the accuracy of our results is much limited, the calculated peaks are little distorted due to three-dimensional effects. There exist much great differences between our calculated values of spheroidal modes and theoretical values, because we don’t consider the effect the Earth’ gravitation in numerical model, which leads our values are smaller than the theoretical values. When , is much smaller, the effect of the Earth’s gravitation make the periods of spheroidal modes become shorter. However, we now can not consider effects of the Earth’s gravitational potential into the numerical model to simulate the spheroidal oscillations, but those results still demonstrate that, the numerical simulation of the Earth’s free oscillation is very feasible. We make the numerical simulation on processes of the Earth’s free oscillations under spherically symmetric Earth model using different special source mechanisms. The results quantitatively show that Earth’s free oscillations excited by different earthquakes are different, and oscillations at different locations are different for free oscillation excited by the same earthquake. We also explore how the Earth’s medium attenuation will take effects on the Earth’s free oscillations, and take comparisons with the observations. The medium attenuation can make influences on the Earth’s free oscillations, though the effects on lower-frequency fundamental oscillations are weak. At last, taking 2008 Wenchuan earthquake for example, we employ spectral element method incorporated with large-scale parallel computing technology to investigate the characteristics of seismic wave propagation excited by Wenchuan earthquake. We calculate synthetic seismograms with one-point source model and three-point source model respectively. Full 3-D visualization of the numerical results displays the profile of the seismic wave propagation with respect to time. The three-point source, which was proposed by the latest investigations through field observation and reverse estimation, can better demonstrate the spatial and temporal characteristics of the source rupture processes than one-point source. Primary results show that those synthetic signals calculated from three-point source agree well with the observations. This can further reveal that the source rupturing process of Wenchuan earthquake is a multi-rupture process, which is composed by at least three or more stages of rupture processes. In conclusion, the numerical simulation can not only solve some problems concluding the Earth’s ellipticity and anisotropy, which can be easily solved by conventional methods, but also finally solve the problems concluding topography model and lateral heterogeneity. We will try to find a way to fully implement self-gravitation in spectral element method in future, and do our best to continue researching the Earth’s free oscillations using the numerical simulations to see how the Earth’ lateral heterogeneous will affect the Earth’s free oscillations. These will make it possible to bring modal spectral data increasingly to bear on furthering our understanding of the Earth’s three-dimensional structure.

An evaluation of the spatiotemporal structure of large-scale European drought within the HiGEM climate model

We compare the characteristics of synthetic European droughts generated by the HiGEM1 coupled climate model run with present day atmospheric composition with observed drought events extracted from the CRU TS3 data set. The results demonstrate consistency in both the rate of drought occurrence and the spatiotemporal structure of the events. Estimates of the probability density functions for event area, duration and severity are shown to be similar with confidence > 90%. Encouragingly, HiGEM is shown to replicate the extreme tails of the observed distributions and thus the most damaging European drought events. The soil moisture state is shown to play an important role in drought development. Once a large-scale drought has been initiated it is found to be 50% more likely to continue if the local soil moisture is below the 40th percentile. In response to increased concentrations of atmospheric CO2, the modelled droughts are found to increase in duration, area and severity. The drought response can be largely attributed to temperature driven changes in relative humidity. 1 HiGEM is based on the latest climate configuration of the Met Office Hadley Centre Unified Model (HadGEM1) with the horizontal resolution increased to 1.25 x 0.83 degrees in longitude and latitude in the atmosphere and 1/3 x 1/3 degrees in the ocean.

An optimal estimator for the correlation of CMB anisotropies with Large Scale Structures and its application to WMAP-7year and NVSS

In the thesis we present the implementation of the quadratic maximum likelihood (QML) method, ideal to estimate the angular power spectrum of the cross-correlation between cosmic microwave background (CMB) and large scale structure (LSS) maps as well as their individual auto-spectra. Such a tool is an optimal method (unbiased and with minimum variance) in pixel space and goes beyond all the previous harmonic analysis present in the literature. We describe the implementation of the QML method in the {\it BolISW} code and demonstrate its accuracy on simulated maps throughout a Monte Carlo. We apply this optimal estimator to WMAP 7-year and NRAO VLA Sky Survey (NVSS) data and explore the robustness of the angular power spectrum estimates obtained by the QML method. Taking into account the shot noise and one of the systematics (declination correction) in NVSS, we can safely use most of the information contained in this survey. On the contrary we neglect the noise in temperature since WMAP is already cosmic variance dominated on the large scales. Because of a discrepancy in the galaxy auto spectrum between the estimates and the theoretical model, we use two different galaxy distributions: the first one with a constant bias $b$ and the second one with a redshift dependent bias $b(z)$. Finally, we make use of the angular power spectrum estimates obtained by the QML method to derive constraints on the dark energy critical density in a flat $\Lambda$CDM model by different likelihood prescriptions. When using just the cross-correlation between WMAP7 and NVSS maps with 1.8° resolution, we show that $\Omega_\Lambda$ is about the 70\% of the total energy density, disfavouring an Einstein-de Sitter Universe at more than 2 $\sigma$ CL (confidence level).

German Validation of the Conners Adult ADHD Rating Scale-Self-Report: Confirmation of Factor Structure in a Large Sample of Participants With ADHD

Objective: The Conners Adult ADHD Rating Scales (CAARS) assess symptoms specific to adults that are frequently used and have been translated into German. The current study tests the factor structure of the CAARS in a large sample of German adults with ADHD and compares the means of the CAARS subscales with those of healthy German controls. Method: CAARS were completed by 466 participants with ADHD and 851 healthy control participants. Confirmatory factor analysis was used to establish model fit with the American original. Comparisons between participants with ADHD and healthy controls and influences of gender, age, and degree of education were analyzed. Results: Confirmatory factor analysis showed a very good fit with the model for the American original. Differences between ADHD participants and healthy controls on all Conners Adult ADHD Rating Scales-Self-Report (CAARS-S) subscales were substantial and significant. Conclusion: The factor structure of the original American model was successfully replicated in this sample of adult German ADHD participants. (J. of Att. Dis. 2012; XX(X) 1-XX).

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the Saccharomyces cerevisiae (baker’s yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.

The Empirical Forcing Function as a tool for the diagnosis of large-scale atmospheric anomalies

The time-mean quasi-geostrophic potential vorticity equation of the atmospheric flow on isobaric surfaces can explicitly include an atmospheric (internal) forcing term of the stationary-eddy flow. In fact, neglecting some non-linear terms in this equation, this forcing can be mathematically expressed as a single function, called Empirical Forcing Function (EFF), which is equal to the material derivative of the time-mean potential vorticity. Furthermore, the EFF can be decomposed as a sum of seven components, each one representing a forcing mechanism of different nature. These mechanisms include diabatic components associated with the radiative forcing, latent heat release and frictional dissipation, and components related to transient eddy transports of heat and momentum. All these factors quantify the role of the transient eddies in forcing the atmospheric circulation. In order to assess the relevance of the EFF in diagnosing large-scale anomalies in the atmospheric circulation, the relationship between the EFF and the occurrence of strong North Atlantic ridges over the Eastern North Atlantic is analyzed, which are often precursors of severe droughts over Western Iberia. For such events, the EFF pattern depicts a clear dipolar structure over the North Atlantic; cyclonic (anticyclonic) forcing of potential vorticity is found upstream (downstream) of the anomalously strong ridges. Results also show that the most significant components are related to the diabatic processes. Lastly, these results highlight the relevance of the EFF in diagnosing large-scale anomalies, also providing some insight into their interaction with different physical mechanisms.

The analysis of large scale data taken from the world groundnut (Arachis hypogaea L.) germplasm collection I. Two-way quantitative data

Data associated with germplasm collections are typically large and multivariate with a considerable number of descriptors measured on each of many accessions. Pattern analysis methods of clustering and ordination have been identified as techniques for statistically evaluating the available diversity in germplasm data. While used in many studies, the approaches have not dealt explicitly with the computational consequences of large data sets (i.e. greater than 5000 accessions). To consider the application of these techniques to germplasm evaluation data, 11328 accessions of groundnut (Arachis hypogaea L) from the International Research Institute for the Semi-Arid Tropics, Andhra Pradesh, India were examined. Data for nine quantitative descriptors measured in the rainy and post-rainy growing seasons were used. The ordination technique of principal component analysis was used to reduce the dimensionality of the germplasm data. The identification of phenotypically similar groups of accessions within large scale data via the computationally intensive hierarchical clustering techniques was not feasible and non-hierarchical techniques had to be used. Finite mixture models that maximise the likelihood of an accession belonging to a cluster were used to cluster the accessions in this collection. The patterns of response for the different growing seasons were found to be highly correlated. However, in relating the results to passport and other characterisation and evaluation descriptors, the observed patterns did not appear to be related to taxonomy or any other well known characteristics of groundnut.

Estimating the impact of reduced inertia on frequency stability due to large-scale wind penetration in Australian electricity network

Large-scale integration of non-inertial generators such as wind farms will create frequency stability issues due to reduced system inertia. Inertia based frequency stability study is important to predict the performance of power system with increased level of renewables. This paper focuses on the impact large-scale wind penetration on frequency stability of the Australian Power Network. MATLAB simulink is used to develop a frequency based dynamic model utilizing the network data from a simplified 14-generator Australian power system. The loss of generation is modeled as the active power disturbance and minimum inertia required to maintain the frequency stability is determined for five-area power system.

Meridional propagation of large-scale monsoon convective zones

Observational studies indicate that the convective activity of the monsoon systems undergo intraseasonal variations with multi-week time scales. The zone of maximum monsoon convection exhibits substantial transient behavior with successive propagating from the North Indian Ocean to the heated continent. Over South Asia the zone achieves its maximum intensity. These propagations may extend over 3000 km in latitude and perhaps twice the distance in longitude and remain as coherent entities for periods greater than 2-3 weeks. Attempts to explain this phenomena using simple ocean-atmosphere models of the monsoon system had concluded that the interactive ground hydrology so modifies the total heating of the atmosphere that a steady state solution is not possible, thus promoting lateral propagation. That is, the ground hydrology forces the total heating of the atmosphere and the vertical velocity to be slightly out of phase, causing a migration of the convection towards the region of maximum heating. Whereas the lateral scale of the variations produced by the Webster (1983) model were essentially correct, they occurred at twice the frequency of the observed events and were formed near the coastal margin, rather than over the ocean. Webster's (1983) model used to pose the theories was deficient in a number of aspects. Particularly, both the ground moisture content and the thermal inertia of the model were severely underestimated. At the same time, the sea surface temperatures produced by the model between the equator and the model's land-sea boundary were far too cool. Both the atmosphere and the ocean model were modified to include a better hydrological cycle and ocean structure. The convective events produced by the modified model possessed the observed frequency and were generated well south of the coastline. The improved simulation of monsoon variability allowed the hydrological cycle feedback to be generalized. It was found that monsoon variability was constrained to lie within the bounds of a positive gradient of a convective intensity potential (I). The function depends primarily on the surface temperature, the availability of moisture and the stability of the lower atmosphere which varies very slowly on the time scale of months. The oscillations of the monsoon perturb the mean convective intensity potential causing local enhancements of the gradient. These perturbations are caused by the hydrological feedbacks, discussed above, or by the modification of the air-sea fluxes caused by variations of the low level wind during convective events. The final result is the slow northward propagation of convection within an even slower convective regime. The ECMWF analyses show very similar behavior of the convective intensity potential. Although it is considered premature to use the model to conduct simulations of the African monsoon system, the ECMWF analysis indicates similar behavior in the convective intensity potential suggesting, at least, that the same processes control the low frequency structure of the African monsoon. The implications of the hypotheses on numerical weather prediction of monsoon phenomenon are discussed.

Multi-scale interactions and predictability of the Indian summer monsoon

Following the seminal work of Charney and Shukla (198 1), the tropical climate is recognised to be more predictable than extra tropical climate as it is largely forced by 'external' slowly varying forcing and less sensitive to initial conditions. However, the Indian summer monsoon is an exception within the tropics where 'internal' low frequency (LF) oscillations seem to make significant contribution to its interannual variability (IAV) and makes it sensitive to initial conditions. Quantitative estimate of contribution of 'internal' dynamics to IAV of Indian monsoon is made using long experiments with an atmospheric general circulation model (AGCM) and through analysis of long daily observations. Both AGCM experiments and observations indicate that more than 50% of IAV of the monsoon is contributed by 'internal' dynamics making the predictable signal (external component) burried in unpredictable noise (internal component) of comparable amplitude. Better understanding of the nature of the 'internal' LF variability is crucial for any improvement in predicition of seasonal mean monsoon. Nature of 'internal' LF variability of the monsoon and mechanism responsible for it are investigated and shown that vigorous monsoon intraseasonal oscillations (ISO's) with time scale between 10-70 days are primarily responsible for generating the 'internal' IAV. The monsoon ISO's do this through scale interactions with synoptic disturbances (1-7 day time scale) on one hand and the annual cycle on the other. The spatial structure of the monsoon ISO's is similar to that of the seasonal mean. It is shown that frequency of occurance of strong (weak) phases of the ISO is different in different seasons giving rise to stronger (weaker) than normal monsoon. Change in the large scale circulation during strong (weak) phases of the ISO make it favourable (inhibiting) for cyclogenesis and gives rise to space time clustering of synoptic activity. This process leads to enhanced (reduced) rainfall in seasons of higher frequency of occurence strong (weak) phases of monsoon ISO.

Effects of large-scale deforestation on precipitation in the monsoon regions: Remote versus local effects

In this paper, using idealized climate model simulations, we investigate the biogeophysical effects of large-scale deforestation on monsoon regions. We find that the remote forcing from large-scale deforestation in the northern middle and high latitudes shifts the Intertropical Convergence Zone southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, and South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America, and Australia). The magnitude of the monsoonal precipitation changes depends on the location of deforestation, with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most, with 18% decline in precipitation over India. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation alongside the large local impacts on temperatures.

Response of Pacific Northwest vegetation to large-scale changes in climate during the last 100,000 years [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Paleoclimatic variations in western North America depend on a hierarchy of temporal and spatial controls that can be examined using a combination of modeling studies and data synthesis. ... The regional vegetation response to large-scale changes in the climate system of the last 21,000 years is used as a conceptual model to help explain earlier vegetation and climate at two localities.

Comparative analysis European wide marine ecosystem shifts - a large scale approach for developing the basis for ecosystem-based management

Abrupt and rapid ecosystem shifts (where major reorganizations of food-web and community structures occur), commonly termed regime shifts, are changes between contrasting and persisting states of ecosystem structure and function. These shifts have been increasingly reported for exploited marine ecosystems around the world from the North Pacific to the North Atlantic. Understanding the drivers and mechanisms leading to marine ecosystem shifts is crucial in developing adaptive management strategies to achieve sustainable exploitation of marine ecosystems. An international workshop on a comparative approach to analysing these marine ecosystem shifts was held at Hamburg University, Institute for Hydrobiology and Fisheries Science, Germany on 1-3 November 2010. Twenty-seven scientists from 14 countries attended the meeting, representing specialists from seven marine regions, including the Baltic Sea, the North Sea, the Barents Sea, the Black Sea, the Mediterranean Sea, the Bay of Biscay and the Scotian Shelf off the Canadian East coast. The goal of the workshop was to conduct the first large-scale comparison of marine ecosystem regime shifts across multiple regional areas, in order to support the development of ecosystem-based management strategies.

2-D R-matrix propagation: A large scale electron scattering simulation dominated by the multiplication of dynamically changing matrices

We examine the computational aspects of propagating a global R-matrix, R, across sub-regions in a 2-D plane. This problem originates in the large scale simulation of electron collisions with atoms and ions at intermediate energies. The propagation is dominated by matrix multiplications which are complicated because of the dynamic nature of R, which changes the designations of its rows and columns and grows in size as the propagation proceeds. The use of PBLAS to solve this problem on distributed memory HPC machines is the main focus of the paper.