Exotic pest insects: another perspective on coffee and conservation

Research on crop systems and biodiversity conservation in the tropics has mainly been concerned with how low to mid intensity agricultural systems can benefit from adjacent natural habitats by receiving ecosystem services from natural biodiversity. One intensively studied crop in this framework is coffee. Positive effects are relatively easy to quantify by comparing coffee yield and by recording native species diversity. However, a largely overlooked issue is how agricultural areas affect native organisms in adjacent natural habitats, for example through movement of pest species that could impose a risk of degrading these habitats. We give an example from Mauritius, where an introduced coffee pest severely reduces the reproductive success of a threatened endemic plant species. We argue that such effects may be more common than suggested by the literature, especially when crop and native plants are congeneric. In the long term, such negative effects may degrade natural habitats, thereby causing ecosystem services derived from these habitats to declin

Conserved defense responses between maize and sorghum to Exserohilum turcicum.

BACKGROUND:Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechanisms between the two plant species. To identify sorghum genes involved in the E. turcicum response, we conducted a genome-wide association study (GWAS). RESULTS:Using the sorghum conversion panel evaluated across three environments, we identified a total of 216 significant markers. Based on physical linkage with the significant markers, we detected a total of 113 unique candidate genes, some with known roles in plant defense. Also, we compared maize genes known to play a role in resistance to E. turcicum with the association mapping results and found evidence of genes conferring resistance in both crops, providing evidence of shared resistance between maize and sorghum. CONCLUSIONS:Using a genetics approach, we identified shared genetic regions conferring resistance to E. turcicum in both maize and sorghum. We identified several promising candidate genes for resistance to leaf blight in sorghum, including genes related to R-gene mediated resistance. We present significant advancements in the understanding of host resistance to E. turcicum, which is crucial to reduce losses due to this important pathogen

Seed Dispersal and Establishment of Endangered Plants on Oceanic Islands: The Janzen-Connell Model, and the Use of Ecological Analogues

BACKGROUND: The Janzen-Connell model states that plant-specific natural enemies may have a disproportionately large negative effect on progeny close to maternal trees. The majority of experimental and theoretical studies addressing the Janzen-Connell model have explored how it can explain existing patterns of species diversity in tropical mainland areas. Very few studies have investigated how the model's predictions apply to isolated oceanic islands, or to the conservation management of endangered plants. Here, we provide the first experimental investigation of the predictions of the Janzen-Connell model on an oceanic island, in a conservation context. In addition, we experimentally evaluate the use of ecological analogue animals to resurrect the functional component of extinct frugivores that could have dispersed seeds away from maternal trees. METHODOLOGY/PRINCIPAL FINDINGS: In Mauritius, we investigated seed germination and seedling survival patterns of the critically endangered endemic plant Syzygium mamillatum (Myrtaceae) in relation to proximity to maternal trees. We found strong negative effects of proximity to maternal trees on growth and survival of seedlings. We successfully used giant Aldabran tortoises as ecological analogues for extinct Mauritian frugivores. Effects of gut-passage were negative at the seed germination stage, but seedlings from gut-passed seeds grew taller, had more leaves, and suffered less damage from natural enemies than any of the other seedlings. CONCLUSIONS/SIGNIFICANCE: We provide the first experimental evidence of a distance-dependent Janzen-Connell effect on an oceanic island. Our results potentially have serious implications for the conservation management of rare plant species on oceanic islands, which harbour a disproportionately large fraction of the world's endemic and endangered plants. Furthermore, in contrast to recent controversy about the use of non-indigenous extant megafauna for re-wilding projects in North America and elsewhere, we argue that Mauritius and other oceanic islands are ideal study systems in which to empirically explore the use of ecological analogue species in restoration ecology

Two-photon transitions in primordial hydrogen recombination

The subject of cosmological hydrogen recombination has received much attention recently because of its importance to predictions for and cosmological constraints from CMB observations. While the central role of the two-photon decay 2s->1s has been recognized for many decades, high-precision calculations require us to consider two-photon decays from the higher states ns,nd->1s (n>=3). Simple attempts to include these processes in recombination calculations have suffered from physical problems associated with sequences of one-photon decays, e.g. 3d->2p->1s, that technically also produce two photons. These correspond to resonances in the two-photon spectrum that are optically thick, necessitating a radiative transfer calculation. We derive the appropriate equations, develop a numerical code to solve them, and verify the results by finding agreement with analytic approximations to the radiative transfer equation. The related processes of Raman scattering and two-photon recombination are included using similar machinery. Our results show that early in recombination the two-photon decays act to speed up recombination, reducing the free electron abundance by 1.3% relative to the standard calculation at z=1300. However we find that some photons between Ly-alpha and Ly-beta are produced, mainly by 3d->1s two-photon decay and 2s->1s Raman scattering. At later times these photons redshift down to Ly-alpha, excite hydrogen atoms, and act to slow recombination. Thus the free electron abundance is increased by 1.3% relative to the standard calculation at z=900. The implied correction to the CMB power spectrum is neligible for the recently released WMAP and ACBAR data, but at Fisher matrix level will be 7 sigma for Planck. [ABRIDGED]Comment: Matches PRD accepted version. 28 pages, 12 figure

The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation

Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. Drosophila Y chromosomes are composed entirely of silent heterochromatin, while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. Here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of Drosophila miranda. We show that the onset of heterochromatin formation on the neo-Y is triggered by an accumulation of repetitive DNA. The neo-X has evolved partial dosage compensation and we find that diverse mutational paths have been utilized to establish several dozen novel binding consensus motifs for the dosage compensation complex on the neo-X, including simple point mutations at pre-binding sites, insertion and deletion mutations, microsatellite expansions, or tandem amplification of weak binding sites. Spreading of these silencing or activating chromatin modifications to adjacent regions results in massive mis-expression of neo-sex linked genes, and little correspondence between functionality of genes and their silencing on the neo-Y or dosage compensation on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those becoming heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities along the ancestral chromosome that formed the sex chromosome to adopt active or repressive chromatin configurations. Our findings have broad implications for current models of sex chromosome evolution, and demonstrate how mechanistic constraints can limit evolutionary adaptations. Our study also highlights how evolution can follow predictable genetic trajectories, by repeatedly acquiring the same 21-bp consensus motif for recruitment of the dosage compensation complex, yet utilizing a diverse array of random mutational changes to attain the same phenotypic outcome

Shipwreck ecology:Understanding the function and processes from microbes to megafauna

An estimated three million shipwrecks exist worldwide and are recognized as cultural resources and foci of archaeological investigations. Shipwrecks also support ecological resources by providing underwater habitats that can be colonized by diverse organisms ranging from microbes to megafauna. In the present article, we review the emerging ecological subdiscipline of shipwreck ecology, which aims to understand ecological functions and processes that occur on shipwrecks. We synthesize how shipwrecks create habitat for biota across multiple trophic levels and then describe how fundamental ecological functions and processes, including succession, zonation, connectivity, energy flow, disturbance, and habitat degradation, manifest on shipwrecks. We highlight future directions in shipwreck ecology that are ripe for exploration, placing a particular emphasis on how shipwrecks may serve as experimental networks to address long-standing ecological questions.</p

Validation of Immersed Boundary Simulations of Heart Valve Hemodynamics against In Vitro 4D Flow MRI Data

The immersed boundary (IB) method is a mathematical framework for fluid-structure interaction problems (FSI) that was originally developed to simulate flows around heart valves. Validation of FSI simulations around heart valves against experimental data is challenging, however, due to the difficulty of performing robust and effective simulations, the complications of modeling a specific physical experiment, and the need to acquire experimental data that is directly comparable to simulation data. In this work, we performed physical experiments of flow through a pulmonary valve in an in vitro pulse duplicator, and measured the corresponding velocity field using 4D flow MRI (4-dimensional flow magnetic resonance imaging). We constructed a computer model of this pulmonary artery setup, including modeling valve geometry and material properties via a technique called design-based elasticity, and simulated flow through it with the IB method. The simulated flow fields showed excellent qualitative agreement with experiments, excellent agreement on integral metrics, and reasonable relative error in the entire flow domain and on slices of interest. These results validate our design-based valve model construction, the IB solvers used and the immersed boundary method for flows around heart valves

Weak lensing surveys and the intrinsic correlation of galaxy ellipticities

We explore the possibility that an intrinsic correlation between galaxy ellipticities arising during the galaxy formation process may account for part of the shear signal recently reported by several groups engaged in weak lensing surveys. Using high resolution N-body simulations we measure the projected ellipticities of dark matter halos and their correlations as a function of pair separation. With this simplifying, but not necessarily realistic assumption (halo shapes as a proxy for galaxy shapes), we find a positive detection of correlations up to scales of at least 20 h^-1mpc (limited by the box size). The signal is not strongly affected by variations in the halo finding technique, or by the resolution of the simulations. We translate our 3d results into angular measurements of ellipticity correlation functions and shear variance which can be directly compared to observations. We also measure similar results from simulated angular surveys made by projecting our simulation boxes onto the plane of the sky and applying a radial selection function. Interestingly, the shear variance we measure is a small, but not entirely negligible fraction (from ~10-20 %) of that seen by the observational groups, and the ellipticity correlation functions approximately mimic the functional form expected to be caused by weak lensing. The amplitude depends on the width in redshift of the galaxy distribution. If photometric redshifts are used to pick out a screen of background galaxies with a small width, then the intrinsic correlation may become comparable to the weak lensing signal. Although we are dealing with simulated dark matter halos, whether there is a signal from real galaxies could be checked with a nearby sample with known redshifts.Comment: 12 pages, 11 ps figures, emulateapj.sty, submitted to Ap

The GMRT EoR Experiment: Limits on Polarized Sky Brightness at 150 MHz

The GMRT reionization effort aims to map out the large scale structure of the Universe during the epoch of reionization (EoR). Removal of polarized Galactic emission is a difficult part of any 21 cm EoR program, and we present new upper limits to diffuse polarized foregrounds at 150 MHz. We find no high significance evidence of polarized emission in our observed field at mid galactic latitude (J2000 08h26m+26). We find an upper limit on the 2-dimensional angular power spectrum of diffuse polarized foregrounds of [l^2 C_l/(2 PI)]^{1/2}< 3K in frequency bins of width 1 MHz at 300<l<1000. The 3-dimensional power spectrum of polarized emission, which is most directly relevant to EoR observations, is [k^3 P_p(k)/(2 PI^2)]^{1/2} 0.03 h/Mpc, k < 0.1 h/Mpc. This can be compared to the expected EoR signal in total intensity of [k^3 P(k)/ (2 PI^2) ]^{1/2} ~ 10 mK. We find polarized structure is substantially weaker than suggested by extrapolation from higher frequency observations, so the new low upper limits reported here reduce the anticipated impact of these foregrounds on EoR experiments. We discuss Faraday beam and depth depolarization models and compare predictions of these models to our data. We report on a new technique for polarization calibration using pulsars, as well as a new technique to remove broadband radio frequency interference. Our data indicate that, on the edges of the main beam at GMRT, polarization squint creates ~ 3% leakage of unpolarized power into polarized maps at zero rotation measure. Ionospheric rotation was largely stable during these solar minimum night time observations.Comment: 17 pages, 6 figures, 2 tables; changed figures, added appendices. To appear in MNRA