749 research outputs found
The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology
Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events
First-year Sloan Digital Sky Survey-II (SDSS-II) supernova results: consistency and constraints with other intermediate-redshift datasets
We present an analysis of the luminosity distances of Type Ia Supernovae from
the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey in conjunction with
other intermediate redshift (z<0.4) cosmological measurements including
redshift-space distortions from the Two-degree Field Galaxy Redshift Survey
(2dFGRS), the Integrated Sachs-Wolfe (ISW) effect seen by the SDSS, and the
latest Baryon Acoustic Oscillation (BAO) distance scale from both the SDSS and
2dFGRS. We have analysed the SDSS-II SN data alone using a variety of
"model-independent" methods and find evidence for an accelerating universe at
>97% level from this single dataset. We find good agreement between the
supernova and BAO distance measurements, both consistent with a
Lambda-dominated CDM cosmology, as demonstrated through an analysis of the
distance duality relationship between the luminosity (d_L) and angular diameter
(d_A) distance measures. We then use these data to estimate w within this
restricted redshift range (z<0.4). Our most stringent result comes from the
combination of all our intermediate-redshift data (SDSS-II SNe, BAO, ISW and
redshift-space distortions), giving w = -0.81 +0.16 -0.18(stat) +/- 0.15(sys)
and Omega_M=0.22 +0.09 -0.08 assuming a flat universe. This value of w, and
associated errors, only change slightly if curvature is allowed to vary,
consistent with constraints from the Cosmic Microwave Background. We also
consider more limited combinations of the geometrical (SN, BAO) and dynamical
(ISW, redshift-space distortions) probes.Comment: 13 pages, 7 figures, accepted for publication in MNRA
Optical variability properties of high luminosity AGN classes
We present the results of a comparative study of the intra-night optical
variability (INOV) characteristics of radio-loud and radio-quiet quasars, which
involves a systematic intra-night optical monitoring of seven sets of high
luminosity AGNs covering the redshift range {\it z} to {\it z}
. The sample, matched in the optical luminosity -- redshift (M
-- z) plane, consists of seven radio-quiet quasars (RQQs), eight radio
lobe-dominated quasars (LDQs), six radio core-dominated quasars (CDQs) and five
BL Lac objects (BLs). Systematic CCD observations, aided by a careful data
analysis procedure, have allowed us to detect INOV with amplitudes as low as
1%. Present observations cover a total of 113 nights (720 hours) with only a
single quasar monitored as continuously as possible on a night. Considering
cases of only unambiguous detections of INOV we have estimated duty cycles
(DCs) of 17%, 12%, 20% and 72% respectively for RQQs, LDQs, CDQs, and BLs. The
low amplitude and low DC of INOV shown by RQQs compared to BLs can be
understood in terms of their having optical synchrotron jets which are modestly
misdirected from us. From our fairly extensive dataset, no unambiguous general
trend of a correlation between the INOV amplitude and the apparent optical
brightness of the quasar is noticed.Comment: 36 pages, 14 Figures, due to large size Fig. 5,6,11 and 12 are not
included. Intersted people contact to [email protected]. Submitted to
Journal of Astrophysics and Astronom
Reconciling Deep Calibration and Demographic History: Bayesian Inference of Post Glacial Colonization Patterns in Carcinus aestuarii (Nardo, 1847) and C. maenas (Linnaeus, 1758)
A precise inference of past demographic histories including dating of demographic events using Bayesian methods can only be achieved with the use of appropriate molecular rates and evolutionary models. Using a set of 596 mitochondrial cytochrome c oxidase I (COI) sequences of two sister species of European green crabs of the genus Carcinus (C. maenas and C. aestuarii), our study shows how chronologies of past evolutionary events change significantly with the application of revised molecular rates that incorporate biogeographic events for calibration and appropriate demographic priors. A clear signal of demographic expansion was found for both species, dated between 10,000 and 20,000 years ago, which places the expansions events in a time frame following the Last Glacial Maximum (LGM). In the case of C. aestuarii, a population expansion was only inferred for the Adriatic-Ionian, suggestive of a colonization event following the flooding of the Adriatic Sea (18,000 years ago). For C. maenas, the demographic expansion inferred for the continental populations of West and North Europe might result from a northward recolonization from a southern refugium when the ice sheet retreated after the LGM. Collectively, our results highlight the importance of using adequate calibrations and demographic priors in order to avoid considerable overestimates of evolutionary time scales
Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe
R-lineage mitochondrial DNA represents over 90% of the European population and is significantly present all around the planet (North Africa, Asia, Oceania, and America). This lineage played a major role in migration âout of Africaâ and colonization in Europe. In order to determine an accurate dating of the R lineage and its sublineages, we analyzed 1173 individuals and complete mtDNA sequences from Mitomap. This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario
A Proposal for a Three Detector Short-Baseline Neutrino Oscillation Program in the Fermilab Booster Neutrino Beam
A Short-Baseline Neutrino (SBN) physics program of three LAr-TPC detectors
located along the Booster Neutrino Beam (BNB) at Fermilab is presented. This
new SBN Program will deliver a rich and compelling physics opportunity,
including the ability to resolve a class of experimental anomalies in neutrino
physics and to perform the most sensitive search to date for sterile neutrinos
at the eV mass-scale through both appearance and disappearance oscillation
channels. Using data sets of 6.6e20 protons on target (P.O.T.) in the LAr1-ND
and ICARUS T600 detectors plus 13.2e20 P.O.T. in the MicroBooNE detector, we
estimate that a search for muon neutrino to electron neutrino appearance can be
performed with ~5 sigma sensitivity for the LSND allowed (99% C.L.) parameter
region. In this proposal for the SBN Program, we describe the physics analysis,
the conceptual design of the LAr1-ND detector, the design and refurbishment of
the T600 detector, the necessary infrastructure required to execute the
program, and a possible reconfiguration of the BNB target and horn system to
improve its performance for oscillation searches.Comment: 209 pages, 129 figure
BVRI Light Curves for 29 Type Ia Supernovae
BVRI light curves are presented for 27 Type Ia supernovae discovered during
the course of the Calan/Tololo Survey and for two other SNe Ia observed during
the same period. Estimates of the maximum light magnitudes in the B, V, and I
bands and the initial decline rate parameter m15(B) are also given.Comment: 17 pages, figures and tables are not included (contact first author
if needed), to appear in the Astronomical Journa
Updated Three-Stage Model for the Peopling of the Americas
Background: We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e.,40,000 years ago) expansion signal we had proposed for the proto-Amerind population. Methodology/Findings: Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World. Conclusions/Significance: The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of th
Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV
The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of âs = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pTâ„20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60â€pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2â€{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration
First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data
Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of
continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a
fully coherent search, based on matched filtering, which uses the position and rotational parameters
obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto-
noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch
between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have
been developed, allowing a fully coherent search for gravitational waves from known pulsars over a
fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of
11 pulsars using data from Advanced LIGOâs first observing run. Although we have found several initial
outliers, further studies show no significant evidence for the presence of a gravitational wave signal.
Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of
the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for
the first time. For an additional 3 targets, the median upper limit across the search bands is below the
spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried
out so far
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