QTL Analysis of Vernalisation Requirement and Heading Traits in \u3cem\u3eFestuca Pratensis\u3c/em\u3e Huds.

The transition from the vegetative phase to the reproductive phase occurs as a result of environmental and endogenous stimuli. In Festuca pratensis, low temperature and/or short days over a certain period (primary induction) followed by long days (secondary induction) will lead to heading and flowering (Heide, 1988). We present results from QTL mapping of vernalisation requirement and heading traits and mapping of the Vrn-1 ortholog in F. pratensis

The Unusually Luminous Extragalactic Nova SN 2010U

We present observations of the unusual optical transient SN 2010U, including spectra taken 1.03 days to 15.3 days after maximum light that identify it as a fast and luminous Fe II type nova. Our multi-band light curve traces the fast decline (t_2 = 3.5 days) from maximum light (M_V = -10.2 mag), placing SN 2010U in the top 0.5% of the most luminous novae ever observed. We find typical ejecta velocities of approximately 1100 km/s and that SN 2010U shares many spectral and photometric characteristics with two other fast and luminous Fe II type novae, including Nova LMC 1991 and M31N-2007-11d. For the extreme luminosity of this nova, the maximum magnitude vs. rate of decline relationship indicates a massive white dwarf progenitor with a low pre-outburst accretion rate. However, this prediction is in conflict with emerging theories of nova populations, which predict that luminous novae from massive white dwarfs should preferentially exhibit an alternate spectral type (He/N) near maximum light.Comment: 16 pages, 16 figures. Submitted to the Astrophysical Journa

Disease effects on reproduction can cause population cycles in seasonal environments

Recent studies of rodent populations have demonstrated that certain parasites can cause juveniles to delay maturation until the next reproductive season. Furthermore, a variety of parasites may share the same host, and evidence is beginning to accumulate showing nonindependent effects of different infections.We investigated the consequences for host population dynamics of a disease-induced period of no reproduction, and a chronic reduction in fecundity following recovery from infection (such as may be induced by secondary infections) using a modified SIR (susceptible, infected, recovered) model. We also included a seasonally varying birth rate as recent studies have demonstrated that seasonally varying parameters can have important effects on long-term host–parasite dynamics. We investigated the model predictions using parameters derived from five different cyclic rodent populations.Delayed and reduced fecundity following recovery from infection have no effect on the ability of the disease to regulate the host population in the model as they have no effect on the basic reproductive rate. However, these factors can influence the long-term dynamics including whether or not they exhibit multiyear cycles.The model predicts disease-induced multiyear cycles for a wide range of realistic parameter values. Host populations that recover relatively slowly following a disease-induced population crash are more likely to show multiyear cycles. Diseases for which the period of infection is brief, but full recovery of reproductive function is relatively slow, could generate large amplitude multiyear cycles of several years in length. Chronically reduced fecundity following recovery can also induce multiyear cycles, in support of previous theoretical studies.When parameterized for cowpox virus in the cyclic field vole populations (Microtus agrestis) of Kielder Forest (northern England), the model predicts that the disease must chronically reduce host fecundity by more than 70%, following recovery from infection, for it to induce multiyear cycles. When the model predicts quasi-periodic multiyear cycles it also predicts that seroprevalence and the effective date of onset of the reproductive season are delayed density-dependent, two phenomena that have been recorded in the field

The Langevin diffusion as a continuous-time model of animal movement and habitat selection

TM was supported by the Centre for Advanced Biological Modelling at the University of Sheffield, funded by the Leverhulme Trust, award number DS-2014-081.1. The utilisation distribution of an animal describes the relative probability of space use. It is natural to think of it as the long-term consequence of the animal's short-term movement decisions: it is the accumulation of small displacements which, over time, gives rise to global patterns of space use. However, many estimation methods for the utilisation distribution either assume the independence of observed locations and ignore the underlying movement (e.g. kernel density estimation), or are based on simple Brownian motion movement rules (e.g. Brownian bridges). 2. We introduce a new continuous-time model of animal movement, based on the Langevin diffusion. This stochastic process has an explicit stationary distribution, conceptually analogous to the idea of the utilisation distribution, and thus provides an intuitive framework to integrate movement and space use. We model the stationary (utilisation) distribution with a resource selection function to link the movement to spatial covariates, and allow inference about habitat preferences of animals. 3. Standard approximation techniques can be used to derive the pseudo-likelihood of the Langevin diffusion movement model, and to estimate habitat preference and movement parameters from tracking data. We investigate the performance of the method on simulated data, and discuss its sensitivity to the time scale of the sampling. We present an example of its application to tracking data of Steller sea lions (Eumetopias jubatus). 4. Due to its continuous-time formulation, this method can be applied to irregular telemetry data. The movement model is specified using a habitat-dependent utilisation distribution, and it provides a rigorous framework to estimate long-term habitat selection from correlated movement data. The Langevin movement model can be approximated by linear model, which allows for very fast inference. Standard tools such as residuals can be used for model checking.PostprintPeer reviewe

Optical and near-infrared observations of SN 2011dh - The first 100 days

We present optical and near-infrared (NIR) photometry and spectroscopy of the Type IIb supernova (SN) 2011dh for the first 100 days. We complement our extensive dataset with SWIFT ultra-violet (UV) and Spitzer mid-infrared (MIR) data to build a UV to MIR bolometric lightcurve using both photometric and spectroscopic data. Hydrodynamical modelling of the SN based on this bolometric lightcurve have been presented in Bersten (2012). We find that the absorption minimum for the hydrogen lines is never seen below ~11000 km/s but approaches this value as the lines get weaker. This suggests that the interface between the helium core and hydrogen rich envelope is located near this velocity in agreement with the Bersten et al. (2012) He4R270 ejecta model. Spectral modelling of the hydrogen lines using this ejecta model supports the conclusion and we find a hydrogen mass of 0.01-0.04 solar masses to be consistent with the observed spectral evolution. We estimate that the photosphere reaches the helium core at 5-7 days whereas the helium lines appear between ~10 and ~15 days, close to the photosphere and then move outward in velocity until ~40 days. This suggests that increasing non-thermal excitation due to decreasing optical depth for the gamma-rays is driving the early evolution of these lines. We also provide and discuss pre- and post-explosion observations of the SN site which shows a reduction by 75 percent in flux at the position of the yellow supergiant coincident with SN 2011dh. The B, V and r band decline rates of 0.0073, 0.0090 and 0.0053 mag/day respectively are consistent with the remaining flux being emitted by the SN. Hence we find that the star was indeed the progenitor of SN 2011dh as previously suggested by Maund et al. (2011) and which is also consistent with the results from the hydrodynamical modelling.Comment: 38 pages, 27 figures, 18 tables, accepted for publication by A&

Massive stars exploding in a He-rich circumstellar medium. IV. Transitional Type Ibn Supernovae

We present ultraviolet, optical and near-infrared data of the Type Ibn supernovae (SNe) 2010al and 2011hw. SN 2010al reaches an absolute magnitude at peak of M(R) = -18.86 +- 0.21. Its early light curve shows similarities with normal SNe Ib, with a rise to maximum slower than most SNe Ibn. The spectra are dominated by a blue continuum at early stages, with narrow P-Cygni He I lines indicating the presence of a slow-moving, He-rich circumstellar medium. At later epochs the spectra well match those of the prototypical SN Ibn 2006jc, although the broader lines suggest that a significant amount of He was still present in the stellar envelope at the time of the explosion. SN 2011hw is somewhat different. It was discovered after the first maximum, but the light curve shows a double-peak. The absolute magnitude at discovery is similar to that of the second peak (M(R) = -18.59 +- 0.25), and slightly fainter than the average of SNe Ibn. Though the spectra of SN 2011hw are similar to those of SN 2006jc, coronal lines and narrow Balmer lines are cleary detected. This indicates substantial interaction of the SN ejecta with He-rich, but not H-free, circumstellar material. The spectra of SN 2011hw suggest that it is a transitional SN Ibn/IIn event similar to SN 2005la. While for SN 2010al the spectro-photometric evolution favours a H-deprived Wolf-Rayet progenitor (of WN-type), we agree with the conclusion of Smith et al. (2012) that the precursor of SN 2011hw was likely in transition from a luminous blue variable to an early Wolf-Rayet (Ofpe/WN9) stage.Comment: 23 pages, 11 figures, 6 tables. Accepted by MNRA

SN 2009md: Another faint supernova from a low mass progenitor

We present adaptive optics imaging of the core collapse supernova (SN) 2009md, which we use together with archival \emph{Hubble Space Telescope} data to identify a coincident progenitor candidate. We find the progenitor to have an absolute magnitude of $V = -4.63^{+0.3}_{-0.4}$ mag and a colour of $V-I = 2.29^{+0.25}_{-0.39}$ mag, corresponding to a progenitor luminosity of log $L$/L$_{\odot}$ $\sim4.54\pm0.19$ dex. Using the stellar evolution code STARS, we find this to be consistent with a red supergiant progenitor with $M = 8.5_{-1.5}^{+6.5}$ M$_{\odot}$. The photometric and spectroscopic evolution of SN 2009md is similar to that of the class of sub-luminous Type IIP SNe; in this paper we compare the evolution of SN 2009md primarily to that of the sub-luminous SN 2005cs. We estimate the mass of $^{56}$Ni ejected in the explosion to be $(5.4\pm1.3) \times 10^{-3}$ M$_{\odot}$\ from the luminosity on the radioactive tail, which is in agreement with the low $^{56}$Ni masses estimated for other sub-luminous Type IIP SNe. From the lightcurve and spectra, we show the SN explosion had a lower energy and ejecta mass than the normal Type IIP SN 1999em. We discuss problems with stellar evolutionary models, and the discrepancy between low observed progenitor luminosities (log $L$/L$_{\odot}$ $\sim4.3-5$ dex) and model luminosities after the second-dredge-up for stars in this mass range, and consider an enhanced carbon burning rate as a possible solution. In conclusion, SN 2009md is a faint SN arising from the collapse of a progenitor close to the lower mass limit for core-collapse. This is now the third discovery of a low mass progenitor star producing a low energy explosion and low $^{56}$Ni ejected mass, which indicates that such events arise from the lowest end of the mass range that produces a core-collapse supernova (7-8 M$_{\odot}$).Comment: MNRAS accepted, revised version following referee's comment

SN 2009E: a faint clone of SN 1987A

In this paper we investigate the properties of SN 2009E, which exploded in a relatively nearby spiral galaxy (NGC 4141) and that is probably the faintest 1987A-like supernova discovered so far. Spectroscopic observations which started about 2 months after the supernova explosion, highlight significant differences between SN 2009E and the prototypical SN 1987A. Modelling the data of SN 2009E allows us to constrain the explosion parameters and the properties of the progenitor star, and compare the inferred estimates with those available for the similar SNe 1987A and 1998A. The light curve of SN 2009E is less luminous than that of SN 1987A and the other members of this class, and the maximum light curve peak is reached at a slightly later epoch than in SN 1987A. Late-time photometric observations suggest that SN 2009E ejected about 0.04 solar masses of 56Ni, which is the smallest 56Ni mass in our sample of 1987A-like events. Modelling the observations with a radiation hydrodynamics code, we infer for SN 2009E a kinetic plus thermal energy of about 0.6 foe, an initial radius of ~7 x 10^12 cm and an ejected mass of ~19 solar masses. The photospheric spectra show a number of narrow (v~1800 km/s) metal lines, with unusually strong Ba II lines. The nebular spectrum displays narrow emission lines of H, Na I, [Ca II] and [O I], with the [O I] feature being relatively strong compared to the [Ca II] doublet. The overall spectroscopic evolution is reminiscent of that of the faint 56Ni-poor type II-plateau supernovae. This suggests that SN 2009E belongs to the low-luminosity, low 56Ni mass, low-energy tail in the distribution of the 1987A-like objects in the same manner as SN 1997D and similar events represent the faint tail in the distribution of physical properties for normal type II-plateau supernovae.Comment: 19 pages, 9 figures (+7 in appendix); accepted for publication in A&A on 3 November 201

Observational and Physical Classification of Supernovae

This chapter describes the current classification scheme of supernovae (SNe). This scheme has evolved over many decades and now includes numerous SN Types and sub-types. Many of these are universally recognized, while there are controversies regarding the definitions, membership and even the names of some sub-classes; we will try to review here the commonly-used nomenclature, noting the main variants when possible. SN Types are defined according to observational properties; mostly visible-light spectra near maximum light, as well as according to their photometric properties. However, a long-term goal of SN classification is to associate observationally-defined classes with specific physical explosive phenomena. We show here that this aspiration is now finally coming to fruition, and we establish the SN classification scheme upon direct observational evidence connecting SN groups with specific progenitor stars. Observationally, the broad class of Type II SNe contains objects showing strong spectroscopic signatures of hydrogen, while objects lacking such signatures are of Type I, which is further divided to numerous subclasses. Recently a class of super-luminous SNe (SLSNe, typically 10 times more luminous than standard events) has been identified, and it is discussed. We end this chapter by briefly describing a proposed alternative classification scheme that is inspired by the stellar classification system. This system presents our emerging physical understanding of SN explosions, while clearly separating robust observational properties from physical inferences that can be debated. This new system is quantitative, and naturally deals with events distributed along a continuum, rather than being strictly divided into discrete classes. Thus, it may be more suitable to the coming era where SN numbers will quickly expand from a few thousands to millions of events.Comment: Extended final draft of a chapter in the "SN Handbook". Comments most welcom

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection