OAR@UM Collection:

Global phylogeography and Mediterranean genetic structure of the endangered dusky grouper, Epinephelus marginatus (Teleostei: Serranidae), based on mitochondrial and microsatellite genetic markers

Sun, 01 Jan 2017 00:00:00 GMT

Title: Global phylogeography and Mediterranean genetic structure of the endangered dusky grouper, Epinephelus marginatus (Teleostei: Serranidae), based on mitochondrial and microsatellite genetic markers Abstract: The aim of this research is to describe the evolutionary relationship, demographic history and connectivity patterns of the endangered marine fish Epinephelus marginatus (Lowe, 1834) on a local, regional and global scale for the purpose of aiding in conservation management strategies. Assessment was based on an integrative approach to molecular population genetics using comparative phylogeography and coalescent based methodologies which has allowed for resolution of evolutionary processes, diversification of lineages, and phylogenetic species delimitation. The basis of molecular analyses were conducted using subsets from 377 E. marginatus samples collected from 17 localities and three continents throughout their global distribution in the Atlantic Ocean, SW Indian Ocean and Mediterranean Sea. Local and regional assessment pertaining to the central Mediterranean Maltese Fisheries Management Zone was based on 14 microsatellite genetic markers and describes a population decreasing in size (θH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, ρ < 0.001) with an estimated effective population size (Ne) of 130. Spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within the Fisheries Management Zone and resolved that they are regionally connected to a larger network within the Sicily Channel. Evaluation of global phylogeography was based on a 398 base pair catenated alignment of high density intraspecific variation spanning part of the tRNA proline gene and d-loop from the mitochondrial control region. Spatial Bayesian inference identified five explicit biogeographic populations throughout their global range in the Azores, Brazil, Senegal, South Africa and Mediterranean Sea. Molecular clock convergence analysis founded on within lineage mutation rate divergence surmised that E. marginatus has been present in the Azores since the Calabrian Age during the Pleistocene Epoch, however establishment of the remaining global populations began more recently during the Middle Pleistocene with colonisation of the nouveau Mediterranean lineage occurring around 150,000 years ago. Analysis conducted using a Bayesian model of random coalescence estimated that the global population of E. marginatus’ has grown roughly 25% over the last 100,000 years, mostly owing to expansion in west Africa, with a modern effective population size estimate (Nef) of around 4.4 million. Global AMOVA (ΦST = 0.44647, ρ < 0.001) and an exact test of population differentiation (ρ < 0.001) detected great and significant bifurcation between global populations. These findings are likely a reflection of strong biogeographic barriers to gene flow detected by Monmonier’s algorithm (bootstrap 92-100) leading to vicariance of global lineages. The high haplotype (h = 0.51-0.99) and low nucleotide (π = 0.019-0.037) diversity found is consistent with the hypothesis of itinerant peripatetic pelagic larval dispersal as the main mode of global spatial expansion. A haplotype network constructed with the TCS algorithm also revealed several substitutions between lineages suggesting once established each region has remained historically independent. Long-term estimates of asymmetrical immigration between global populations predicted using the Metropolis-Hastings sampler method of random coalescence were found to be low (ɣ̅ji = 1.73 individuals gen-1), reinforcing the notion of independent lineage trajectory following long-distance founder events. Whilst E. marginatus’ appear to display morphological cohesiveness throughout their global distribution, intraspecific genetic partitioning of lineages can be seen reflected in significant pairwise ΦST (0.31–0.69, ρ < 0.001) and Nei’s DXY (3.5–16.3, ρ < 0.001), where objective use of Nei’s D (DXY > 0.15), ΦST (ΦST > 0.25) and the Poisson Tree Process (bootstrap > 95) collectively identified the Azorean population as a separate phylogenetic unit. Mantel tests revealed genetic isolation by distance was not a fundamental factor influencing global population vicariance or lineage divergence. The process of vicariance leading to allopatric speciation is often gradual, where lineage divergence is representative of cryptic speciation on a continuum. In conclusion, evidence presented suggests that five Evolutionarily Significant Units should be assigned to each of the biogeographically discrete global populations and that assessment of species status and conservation management should be undertaken at a local level due to habitat fragmentation and population substructuring. Description: PH.D.

Point spread function modelling and shear calibration for weak lensing surveys

Sun, 01 Jan 2017 00:00:00 GMT

Title: Point spread function modelling and shear calibration for weak lensing surveys Abstract: Gravitational lensing is a cosmological effect which causes the path of a light ray, emitted from a distant source such as galaxy, to be deflected as it travels towards an observer. Deflections occur because the gravitational field, caused by large concentrations of matter, acts like a lens. While gravitational lensing, is in itself an interesting cosmological effect to study, it is often used as a cosmological probe to further the understanding of the Universe and its evolution. When the deflections are small, changes to observed background galaxy shapes are very subtle, this regime is known as weak gravitational lensing. The effects of weak gravitational lensing cannot be directly measured from individual galaxies but rather through a statistical process on a population of galaxies. The benefit of weak gravitational lensing is that it can be used along any line of sight and therefore, is able to better constrain matter distributions on large cosmological scales. There are a number of ongoing weak lensing surveys such as the Kilo Degree Imaging Survey (KiDS) and the Dark Energy Survey (DES), which are currently producing large amounts of data. Larger datasets allow for higher precision on any inferred cosmological parameters. A crucial point, and the general motivation behind the work presented in this thesis, is that the improvement in precision must also be matched with a greater understanding of the systematics present in the measurement process. A suite of realistic image simulations based on KiDS data are presented. The simulations were used to derive an accurate correction function that was capable of constraining the systematic effects in the measurement process to the level of ~ 1%, as well as quantifying a number of improvements which were made to the shape measurement algorithm, lensfit. The subsequent work presented in this thesis is based on the upcoming Euclid mission, a space telescope which will produce the largest and most accurate weak lensing analysis of its time. For Euclid, the measurement errors caused by the systematics effects must be drastically reduced. The work presented is focused on the simulation and improvement of the measurement of the Point Spread Function (PSF). Uncertainties on the measurement of the PSF may have a major effect on the weak lensing analysis. A novel PSF modelling algorithm is presented and was specifically designed for use on Euclid. The algorithm can be configured to work for different types of observations which are expected to be taken across the mission lifetime. This includes calibration observations, observations where the focus of the telescope is varied as well as an algorithm to be used for the wide survey science observations. Additionally, a pipeline which is capable of simulating realistic Euclid-like broadband PSFs is also presented. A series of tests and results showed that the algorithm, in its many configurations, was generally able to recover a PSF model that satisfies Euclid's strict accuracy requirements. The thesis concludes with a proposed strategy for measuring Euclid's PSF from a number of observation types across the lifetime of the mission. Description: PH.D.

The ALICE High Momentum Particle IDentification (HMPID) apparatus and its deuteron detection capability

Sun, 01 Jan 2017 00:00:00 GMT

Title: The ALICE High Momentum Particle IDentification (HMPID) apparatus and its deuteron detection capability Abstract: The Particle IDentification (PID) capabilities of the High Momentum Particle IDentification detector (HMPID) was analyzed for a seven-year period. Installed on A Large Ion Collider Experiment (ALICE) on the Large Hadron Collider (LHC) at CERN, the HMPID has excellent PID performance for pions, 7f and kaons, Kin the transverse momentum range 1< PT <3 GeV /c and for protons, p up to 5 GeV /c. The detector is thus suited to measure (anti-) deuterons in the momentum interval 3-8 GeV /c. The HMPID uses seven Ring Imaging Cherenkov counters with 10.3m2 of active photosensitive area for the PID. The Cherenkov photon detection is achieved by CsI-coated, pad segmented photo-cathodes installed within a multi-wire proportional chamber (MWPC). The first objective was to establish the detector's stability during LHC Runl and part of Run2, in order to confirm and forecast its further operation and performance in future runs. The second objective was to analyze the PID capabilities in proton-proton and heavy ion collisions, whereby the particle mass spectrum produced with the HMPID is presented, with emphasis on the identification of (anti-) deuteron nuclei in the most central (0-103) Pb-Pb collisions. Description: B.SC.(HONS)MATHS&PHYSICS

Synchronisation of quantum systems

Sun, 01 Jan 2017 00:00:00 GMT

Title: Synchronisation of quantum systems Abstract: Synchronisation is a fundamental phenomenon which has been studied in different areas of science. The first few studies on synchronisation were observed and experimented by Christian Huygens in 1665, in fact we start by introducing his experiments and results. We then move to introduce mutual information as an order parameter for synchronisation, specifically for quantum systems. We introduce a model to analyse synchronisation of two qubits lying into two cavities, where one cavity is driven by a laser beam and the other one is populated by the photons that are leaking from the first cavity. The idea in the work that will be represented below is that the model composed of the two qubits, at particular expectation values should converge to a steady-state, if it is under the effect of synchronisation, where the two qubits will be phase-locked together, which means that there must be a constant phase-difference between them. Description: B.SC.(HONS)MATHS&PHYSICS