Cophylogenetic analysis of dated trees

Parasites and the associations they form with their hosts is an important area of research due to the associated health risks which parasites pose to the human population. The associations parasites form with their hosts are responsible for a number of the worst emerging diseases impacting global health today, including Ebola, HIV, and malaria. Macro-scale coevolutionary research aims to analyse these associations to provide further insights into these deadly diseases. This approach, first considered by Fahrenholz in 1913, has been applied to hundreds of coevolutionary systems and remains the most robust means to infer the underlying relationships which form between coevolving species. While reconciling the coevolutionary relationships between a pair of evolutionary systems is NP-Hard, it has been shown that if dating information exists there is a polynomial solution. These solutions however are computationally expensive, and are quickly becoming infeasible due to the rapid growth of phylogenetic data. If the rate of growth continues in line with the last three decades, the current means for analysing dated systems will become computationally infeasible. Within this thesis a collection of algorithms are introduced which aim to address this problem. This includes the introduction of the most efficient solution for analysing dated coevolutionary systems optimally, along with two linear time heuristics which may be applied where traditional algorithms are no longer feasible, while still offering a high degree of accuracy 91%. Finally, this work integrates these incremental results into a single model which is able to handle widespread parasitism, the case where parasites infect multiple hosts. This proposed model reconciles two competing theories of widespread parasitism, while also providing an accuracy improvement of 21%, one of the largest single improvements provided in this field to date. As such, the set of algorithms introduced within this thesis offers another step toward a unified coevolutionary analysis framework, consistent with Fahrenholz original coevolutionary analysis model

The WiggleZ Dark Energy Survey: Direct constraints on blue galaxy intrinsic alignments at intermediate redshifts

Correlations between the intrinsic shapes of galaxy pairs, and between the intrinsic shapes of galaxies and the large-scale density field, may be induced by tidal fields. These correlations, which have been detected at low redshifts (z<0.35) for bright red galaxies in the Sloan Digital Sky Survey (SDSS), and for which upper limits exist for blue galaxies at z~0.1, provide a window into galaxy formation and evolution, and are also an important contaminant for current and future weak lensing surveys. Measurements of these alignments at intermediate redshifts (z~0.6) that are more relevant for cosmic shear observations are very important for understanding the origin and redshift evolution of these alignments, and for minimising their impact on weak lensing measurements. We present the first such intermediate-redshift measurement for blue galaxies, using galaxy shape measurements from SDSS and spectroscopic redshifts from the WiggleZ Dark Energy Survey. Our null detection allows us to place upper limits on the contamination of weak lensing measurements by blue galaxy intrinsic alignments that, for the first time, do not require significant model-dependent extrapolation from the z~0.1 SDSS observations. Also, combining the SDSS and WiggleZ constraints gives us a long redshift baseline with which to constrain intrinsic alignment models and contamination of the cosmic shear power spectrum. Assuming that the alignments can be explained by linear alignment with the smoothed local density field, we find that a measurement of \sigma_8 in a blue-galaxy dominated, CFHTLS-like survey would be contaminated by at most +/-0.02 (95% confidence level, SDSS and WiggleZ) or +/-0.03 (WiggleZ alone) due to intrinsic alignments. [Abridged]Comment: 18 pages, 12 figures, accepted to MNRAS; v2 has correction to one author's name, NO other changes; v3 has minor changes in explanation and calculations, no significant difference in results or conclusions; v4 has an additional footnote about model interpretation, no changes to data/calculations/result

Identification of sea ice types in spaceborne synthetic aperture radar data

This paper presents a classification approach, its expected performance, the dependence of this performance on radar system performance, and expected ice scattering characteristics. Results using both aircraft and simulated ERS-1 SAR data are presented. The results are compared to limited field ice property measurements and coincident passive microwave imagery. An algorithm based on this experimental approach has been implemented in the geophysical processor system at the Alaska SAR Facility for classification of sea ice data in ERS-1 C band SAR data. The importance of an integrated postlaunch program for validation and improvement of this approach is discussed. -from Author

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measurements of the growth of structure and expansion rate at z=0.57 from anisotropic clustering

We analyze the anisotropic clustering of massive galaxies from the Sloan Digital Sky Survey III Baryon Oscillation Spectroscopic Survey (BOSS) Data Release 9 (DR9) sample, which consists of 264,283 galaxies in the redshift range 0.43 < z < 0.7 spanning 3,275 square degrees. Both peculiar velocities and errors in the assumed redshift-distance relation ("Alcock-Paczynski effect") generate correlations between clustering amplitude and orientation with respect to the line-of-sight. Together with the sharp baryon acoustic oscillation (BAO) standard ruler, our measurements of the broadband shape of the monopole and quadrupole correlation functions simultaneously constrain the comoving angular diameter distance (2190 +/- 61 Mpc) to z=0.57, the Hubble expansion rate at z=0.57 (92.4 +/- 4.5 km/s/Mpc), and the growth rate of structure at that same redshift (d sigma8/d ln a = 0.43 +/- 0.069). Our analysis provides the best current direct determination of both DA and H in galaxy clustering data using this technique. If we further assume a LCDM expansion history, our growth constraint tightens to d sigma8/d ln a = 0.415 +/- 0.034. In combination with the cosmic microwave background, our measurements of DA, H, and growth all separately require dark energy at z > 0.57, and when combined imply \Omega_{\Lambda} = 0.74 +/- 0.016, independent of the Universe's evolution at z<0.57. In our companion paper (Samushia et al. prep), we explore further cosmological implications of these observations.Comment: 19 pages, 11 figures, submitted to MNRAS, comments welcom

Virgo's Intracluster Globular Clusters as Seen by the Advanced Camera for Surveys

We report the discovery of 4 candidate intracluster globular clusters (IGCs) in a single deep HST ACS field of the Virgo Cluster. We show that each cluster is roughly spherical, has a magnitude near the peak of the Virgo globular cluster luminosity function, has a radial profile that is best-fit by a King model, and is surrounded by an excess of point sources which have the colors and magnitudes of cluster red giant stars. Despite the fact that two of our IGC candidates have integrated colors redder than the mean of the M87 globular cluster system, we propose that all of the objects are metal-poor with [M/H] < -1. We show that the tidal radii of our intracluster globulars are all larger than the mean for Milky Way clusters, and suggest that the clusters have undergone less tidal stress than their Galactic counterparts. Finally, we normalize our globular cluster observations to the luminosity of intracluster stars, and derive a value of S_N ~ 6 for the specific frequency of Virgo intracluster globular clusters. We use these data to constrain the origins of Virgo's intracluster population, and suggest that globular clusters in our intracluster field have a different origin than globular clusters in the vicinity of M87. In particular, we argue that dwarf elliptical galaxies may be an important source of intracluster stars.Comment: 24 pages, 1 table, 5 figures, accepted for publication in Ap

Structure formation in cosmologies with oscillating dark energy

{abridged} We study the imprints on the formation and evolution of cosmic structures of dynamical dark energy models, characterized by an oscillating equation of state. The redshift evolution of the equation of state parameter w(z) for dark energy is characterized by two parameters, describing the amplitude and the frequency of the oscillations. We consider six different oscillating dark energy models, each characterized by a different set of parameter values. Under the common assumption that dark energy is not clustering on the scales of interest, we study different aspects of cosmic structure formation. In particular, we self-consistently solve the spherical collapse problem. We then estimate the behavior of several cosmological observables, such as the linear growth factor, the Integrated Sachs-Wolfe (ISW) effect, the number counts of massive structures, and the matter and cosmic shear power spectra. We show that, independently of the amplitude and the frequency of the dark energy oscillations, none of the aforementioned observables show an oscillating behavior as a function of redshift. This is a consequence of the said observables' being integrals over some functions of the expansion rate over cosmic history. We also notice that deviations with respect to the expectations for a fiducial LambdaCDM cosmology are generically small, and in the majority of the cases distinguishing an oscillating dark energy model would be difficult. Exceptions to this conclusion are provided by the cosmic shear power spectrum, which for some of the models shows a difference at the level of \sim 10% over a wide range of angular scales, and the abundance of galaxy clusters, which is modified at the $\sim 10-20$ level at $z \gtrsim 0.6$ for future wide weak lensing surveys.Comment: 18 pages, 15 figures, published on MNRA

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Global Ice and Land Climate Studies Using Scatterometer Image Data

Spaceborne scatterometers have provided continuous synoptic microwave coverage of the Earth for nearly a decade. Though these scatterometers were originally designed to measure oceanic surface winds, their data are also extremely useful in a broad range of ice and land applications, including the use of extensive scatterometer time series to determine seasonal and interannual variability and possible relationships to climate change. Under a NASA Earth Science Enterprise grant, the Scatterometer Climate Record Pathfinder (SCP) project has produced non-ocean scatterometer imagery and data products that are now publicly available for the first time (http://www.scp.byu.edu/)