Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.This work has been supported by Australian Research Council grants to MJP (DP07745015) and MB (FT0991741). The website for the funder is www.arc.gov.au. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The Mass Dependance of Satellite Quenching in Milky Way-like Halos

Using the Sloan Digital Sky Survey, we examine the quenching of satellite galaxies around isolated Milky Way-like hosts in the local Universe. We find that the efficiency of satellite quenching around isolated galaxies is low and roughly constant over two orders of magnitude in satellite stellar mass ($M_{*}$ = $10^{8.5}-10^{10.5} \, M_{\odot}$), with only $\sim~20\%$ of systems quenched as a result of environmental processes. While largely independent of satellite stellar mass, satellite quenching does exhibit clear dependence on the properties of the host. We show that satellites of passive hosts are substantially more likely to be quenched than those of star-forming hosts, and we present evidence that more massive halos quench their satellites more efficiently. These results extend trends seen previously in more massive host halos and for higher satellite masses. Taken together, it appears that galaxies with stellar masses larger than about $10^{8}~M_{\odot}$ are uniformly resistant to environmental quenching, with the relative harshness of the host environment likely serving as the primary driver of satellite quenching. At lower stellar masses ($< 10^{8}~M_{\odot}$), however, observations of the Local Group suggest that the vast majority of satellite galaxies are quenched, potentially pointing towards a characteristic satellite mass scale below which quenching efficiency increases dramatically.Comment: 14 pages, 8 figure

A Dichotomy in Satellite Quenching Around L* Galaxies

We examine the star formation properties of bright (~0.1 L*) satellites around isolated ~L* hosts in the local Universe using spectroscopically confirmed systems in the Sloan Digital Sky Survey DR7. Our selection method is carefully designed with the aid of N-body simulations to avoid groups and clusters. We find that satellites are significantly more likely to be quenched than a stellar mass-matched sample of isolated galaxies. Remarkably, this quenching occurs only for satellites of hosts that are themselves quenched: while star formation is unaffected in the satellites of star-forming hosts, satellites around quiescent hosts are more than twice as likely to be quenched than stellar-mass matched field samples. One implication of this is that whatever shuts down star formation in isolated, passive L* galaxies also plays at least an indirect role in quenching star formation in their bright satellites. The previously-reported tendency for "galactic conformity" in color/morphology may be a by-product of this host-specific quenching dichotomy. The S\'ersic indices of quenched satellites are statistically identical to those of field galaxies with the same specific star formation rates, suggesting that environmental and secular quenching give rise to the same morphological structure. By studying the distribution of pairwise velocities between the hosts and satellites, we find dynamical evidence that passive host galaxies reside in dark matter halos that are ~45% more massive than those of star-forming host galaxies of the same stellar mass. We emphasize that even around passive hosts, the mere fact that galaxies become satellites does not typically result in star formation quenching: we find that only ~30% of ~0.1 L* galaxies that fall in from the field are quenched around passive hosts, compared with ~0% around star forming hosts.Comment: 14 pages, 9 figure

Anitmicrobial Effects of Chemically Modified Essential Oils

Undergraduate Basi

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Impacts Of Changing Financial And International Market Conditions On Output For Colombia

Potential effects of financial stock values, world market demand, exchange rate fluctuations and other factors on output variations for Colombia are examined. An open macroeconomic model is developed to include the goods market, the monetary policy, and the formulation of inflation. The sample consists of quarterly data ranging from 1994.Q1 to 2007.Q2 with a total of 54 observations. A generalized least squares (GLS) method is employed in order to correct for both heteroskedasticity and autocorrelation simultaneously. The results indicate a higher stock market value, real appreciation of the peso, higher world market demand, a lower U.S. real interest rate, and a lower expected inflation rate would increase real output for Colombia. Increased deficit spending would not help raise real output, suggesting that fiscal prudence may be needed

DEMAND AND SUPPLY ASSESSMENT FOR THE MICHIGAN FROZEN POTATO INDUSTRY

This report presents a general assessment of the demand and supply conditions affecting the Michigan frozen potato industry. The information has been drawn from various secondary sources and interviews with key industry informants. The report is one of the major outputs of an ongoing study being prepared for the Michigan Potato Industry Commission and funded by the Michigan Agricultural Experiment Station. This analysis was necessitated by the 80% reduction in Michigan frozen processing potato acreage by Simplot in 1997. This reduction of 5,000 acres for the Grand Rapids processing facility has created both short-term and long-term concerns for the Michigan potato industry. This assessment provides broad background information relevant to determining why this cutback occurred and its likely impact if continued in the future. The report begins with a consideration of demand conditions, including both domestic and international demand trends for consumption and consumer preferences. The report then discusses supply issues, including current North American production capacity, international sourcing trends, competition from Canadian imports, cost considerations, processing innovation, and industry consolidation. The report concludes with a section addressing key strategic issues suggested by the demand and supply trends. NOTE: This staff paper contains text only. For charts and graphs (exhibits 1-17b) which have been omitted, contact Christopher Peterson at ([email protected]).Crop Production/Industries,

Shear-driven size segregation of granular materials: modeling and experiment

Granular materials segregate by size under shear, and the ability to quantitatively predict the time required to achieve complete segregation is a key test of our understanding of the segregation process. In this paper, we apply the Gray-Thornton model of segregation (developed for linear shear profiles) to a granular flow with an exponential profile, and evaluate its ability to describe the observed segregation dynamics. Our experiment is conducted in an annular Couette cell with a moving lower boundary. The granular material is initially prepared in an unstable configuration with a layer of small particles above a layer of large particles. Under shear, the sample mixes and then re-segregates so that the large particles are located in the top half of the system in the final state. During this segregation process, we measure the velocity profile and use the resulting exponential fit as input parameters to the model. To make a direct comparison between the continuum model and the observed segregation dynamics, we locally map the measured height of the experimental sample (which indicates the degree of segregation) to the local packing density. We observe that the model successfully captures the presence of a fast mixing process and relatively slower re-segregation process, but the model predicts a finite re-segregation time, while in the experiment re-segregation occurs only exponentially in time

Successful Flash-Cooling of Xenon Derivatized Myoglobin Crystals

This paper demonstrates for the first time a method for preparing cryocooled xenon-derivatized protein crystals. The method is based upon the hypothesis and subsequent observation that the diffusion of a xenon atom from a tight binding site following depressurization occurs on a timescale of minutes. We have observed significant changes in diffraction intensities from myoglobin crystals for up to 5 min following depressurization from 1 MPa of xenon. In accordance with this observation, a xenon-derivatized myoglobin crystal was cryocooled at ~95 K within 20 s of complete depressurization. A crystallographic data set was then collected to 2.0 Å resolution and isomorphous and anomalous difference Patterson maps revealed the presence of a well ordered xenon site with an occupancy of approximately 0.5. Phasing statistics for this site were of good quality and demonstrate the practicality of this method. The ability to cryocool xenon-derivatized crystals will make this heavy-atom substitution method even more useful for single-isomorphous-replacement and multiple-isomorphous-replacement phasing of macromolecules

Managing Bison to Restore Biodiversity

Prior to their demise in the late 1800s, bison coexisted with and helped sustain a diverse and spectacular assemblage of animals and plant communities on the Great Plains. Bison, in concert with fire, exerted strong control on the structure of the vegetation by grazing, trampling, and wallowing. The changes in the vegetation induced changes in many animal populations. These impacts, coupled with the bison\u27s role as the major converter of grass to meat, so greatly affected other species that some have called bison a keystone species in the Great Plains ecosystem. The black-tailed prairie dog, dependent on bison grazing over a large part of the Great Plains, amplified the keystone influence of bison by its own grazing and burrowing activities and its utility as prey. Although modern bison-growing practices usually will preclude restoration of the large predators and scavengers that once were a part of the great faunal spectacle, other species can return, often even on small acreages. Maintenance of a habitat mosaic is the key to restoring some of the original biodiversity lost to the historic pursuit of single species pastoralism