First phylogenetic analyses of galaxy evolution

The Hubble tuning fork diagram, based on morphology, has always been the preferred scheme for classification of galaxies and is still the only one originally built from historical/evolutionary relationships. At the opposite, biologists have long taken into account the parenthood links of living entities for classification purposes. Assuming branching evolution of galaxies as a "descent with modification", we show that the concepts and tools of phylogenetic systematics widely used in biology can be heuristically transposed to the case of galaxies. This approach that we call "astrocladistics" has been first applied to Dwarf Galaxies of the Local Group and provides the first evolutionary galaxy tree. The cladogram is sufficiently solid to support the existence of a hierarchical organization in the diversity of galaxies, making it possible to track ancestral types of galaxies. We also find that morphology is a summary of more fundamental properties. Astrocladistics applied to cosmology simulated galaxies can, unsurprisingly, reconstruct the correct "genealogy". It reveals evolutionary lineages, divergences from common ancestors, character evolution behaviours and shows how mergers organize galaxy diversity. Application to real normal galaxies is in progress. Astrocladistics opens a new way to analyse galaxy evolution and a path towards a new systematics of galaxies

Galaxy Disks

The formation and evolution of galactic disks is particularly important for understanding how galaxies form and evolve, and the cause of the variety in which they appear to us. Ongoing large surveys, made possible by new instrumentation at wavelengths from the ultraviolet (GALEX), via optical (HST and large groundbased telescopes) and infrared (Spitzer) to the radio are providing much new information about disk galaxies over a wide range of redshift. Although progress has been made, the dynamics and structure of stellar disks, including their truncations, are still not well understood. We do now have plausible estimates of disk mass-to-light ratios, and estimates of Toomre's $Q$ parameter show that they are just locally stable. Disks are mostly very flat and sometimes very thin, and have a range in surface brightness from canonical disks with a central surface brightness of about 21.5 $B$-mag arcsec$^{-2}$ down to very low surface brightnesses. It appears that galaxy disks are not maximal, except possibly in the largest systems. Their HI layers display warps whenever HI can be detected beyond the stellar disk, with low-level star formation going on out to large radii. Stellar disks display abundance gradients which flatten at larger radii and sometimes even reverse. The existence of a well-defined baryonic Tully-Fisher relation hints at an approximately uniform baryonic to dark matter ratio. Thick disks are common in disk galaxies and their existence appears unrelated to the presence of a bulge component; they are old, but their formation is not yet understood. Disk formation was already advanced at redshifts of $\sim 2$, but at that epoch disks were not yet quiescent and in full rotational equilibrium. Downsizing is now well-established. The formation and history of star formation in S0s is still not fully understood.Comment: This review has been submitted for Annual Reviews of Astronomy & Astrophysics, vol. 49 (2011); the final printed version will have fewer figures and a somewhat shortened text. A pdf-version of this preprint with high-resolution figures is available from http://www.astro.rug.nl/~vdkruit/jea3/homepage/disks-ph.pdf. (table of contents added; 71 pages, 24 figures, 529 references

Cosmological Relativity: A General-Relativistic Theory for the Accelerating Expanding Universe

Recent observations of distant supernovae imply, in defiance of expectations, that the universe growth is accelerating, contrary to what has always been assumed that the expansion is slowing down due to gravity. In this paper a general-relativistic cosmological theory that gives a direct relationship between distances and redshifts in an expanding universe is presented. The theory is actually a generalization of Hubble's law taking gravity into account by means of Einstein's theory of general relativity. The theory predicts that the universe can have three phases of expansion, decelerating, constant and accelerating, but it is shown that at present the first two cases are excluded, although in the past it had experienced them. Our theory shows that the universe now is definitely in the stage of accelerating expansion, confirming the recent experimental results

Formation of Galaxy Clusters

In this review, we describe our current understanding of cluster formation: from the general picture of collapse from initial density fluctuations in an expanding Universe to detailed simulations of cluster formation including the effects of galaxy formation. We outline both the areas in which highly accurate predictions of theoretical models can be obtained and areas where predictions are uncertain due to uncertain physics of galaxy formation and feedback. The former includes the description of the structural properties of the dark matter halos hosting cluster, their mass function and clustering properties. Their study provides a foundation for cosmological applications of clusters and for testing the fundamental assumptions of the standard model of structure formation. The latter includes the description of the total gas and stellar fractions, the thermodynamical and non-thermal processes in the intracluster plasma. Their study serves as a testing ground for galaxy formation models and plasma physics. In this context, we identify a suitable radial range where the observed thermal properties of the intra-cluster plasma exhibit the most regular behavior and thus can be used to define robust observational proxies for the total cluster mass. We put particular emphasis on examining assumptions and limitations of the widely used self-similar model of clusters. Finally, we discuss the formation of clusters in non-standard cosmological models, such as non-Gaussian models for the initial density field and models with modified gravity, along with prospects for testing these alternative scenarios with large cluster surveys in the near future.Comment: 66 pages, 17 figures, review to be published in 2012 Annual Reviews of Astronomy & Astrophysic

The Hubble Constant

I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give $H_0$ values of around 72-74km/s/Mpc , with typical errors of 2-3km/s/Mpc. This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68km/s/Mpc and typical errors of 1-2km/s/Mpc. The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.Comment: Extensively revised and updated since the 2007 version: accepted by Living Reviews in Relativity as a major (2014) update of LRR 10, 4, 200

Large Scale Structure of the Universe

Galaxies are not uniformly distributed in space. On large scales the Universe displays coherent structure, with galaxies residing in groups and clusters on scales of ~1-3 Mpc/h, which lie at the intersections of long filaments of galaxies that are >10 Mpc/h in length. Vast regions of relatively empty space, known as voids, contain very few galaxies and span the volume in between these structures. This observed large scale structure depends both on cosmological parameters and on the formation and evolution of galaxies. Using the two-point correlation function, one can trace the dependence of large scale structure on galaxy properties such as luminosity, color, stellar mass, and track its evolution with redshift. Comparison of the observed galaxy clustering signatures with dark matter simulations allows one to model and understand the clustering of galaxies and their formation and evolution within their parent dark matter halos. Clustering measurements can determine the parent dark matter halo mass of a given galaxy population, connect observed galaxy populations at different epochs, and constrain cosmological parameters and galaxy evolution models. This chapter describes the methods used to measure the two-point correlation function in both redshift and real space, presents the current results of how the clustering amplitude depends on various galaxy properties, and discusses quantitative measurements of the structures of voids and filaments. The interpretation of these results with current theoretical models is also presented.Comment: Invited contribution to be published in Vol. 8 of book "Planets, Stars, and Stellar Systems", Springer, series editor T. D. Oswalt, volume editor W. C. Keel, v2 includes additional references, updated to match published versio

Constructing Biological Pathways by a Two-Step Counting Approach

Networks are widely used in biology to represent the relationships between genes and gene functions. In Boolean biological models, it is mainly assumed that there are two states to represent a gene: on-state and off-state. It is typically assumed that the relationship between two genes can be characterized by two kinds of pairwise relationships: similarity and prerequisite. Many approaches have been proposed in the literature to reconstruct biological relationships. In this article, we propose a two-step method to reconstruct the biological pathway when the binary array data have measurement error. For a pair of genes in a sample, the first step of this approach is to assign counting numbers for every relationship and select the relationship with counting number greater than a threshold. The second step is to calculate the asymptotic p-values for hypotheses of possible relationships and select relationships with a large p-value. This new method has the advantages of easy calculation for the counting numbers and simple closed forms for the p-value. The simulation study and real data example show that the two-step counting method can accurately reconstruct the biological pathway and outperform the existing methods. Compared with the other existing methods, this two-step method can provide a more accurate and efficient alternative approach for reconstructing the biological network

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201

Measuring our universe from galaxy redshift surveys

Galaxy redshift surveys have achieved significant progress over the last couple of decades. Those surveys tell us in the most straightforward way what our local universe looks like. While the galaxy distribution traces the bright side of the universe, detailed quantitative analyses of the data have even revealed the dark side of the universe dominated by non-baryonic dark matter as well as more mysterious dark energy (or Einstein's cosmological constant). We describe several methodologies of using galaxy redshift surveys as cosmological probes, and then summarize the recent results from the existing surveys. Finally we present our views on the future of redshift surveys in the era of Precision Cosmology.Comment: 82 pages, 31 figures, invited review article published in Living Reviews in Relativity, http://www.livingreviews.org/lrr-2004-

Fluids in cosmology

We review the role of fluids in cosmology by first introducing them in General Relativity and then by applying them to a FRW Universe's model. We describe how relativistic and non-relativistic components evolve in the background dynamics. We also introduce scalar fields to show that they are able to yield an inflationary dynamics at very early times (inflation) and late times (quintessence). Then, we proceed to study the thermodynamical properties of the fluids and, lastly, its perturbed kinematics. We make emphasis in the constrictions of parameters by recent cosmological probes.Comment: 34 pages, 4 figures, version accepted as invited review to the book "Computational and Experimental Fluid Mechanics with Applications to Physics, Engineering and the Environment". Version 2: typos corrected and references expande